Lab & Research Group Publications

Looking for publications from a particular UC Santa Cruz Genomics Institute researcher or investigator?

  • Bibliographies for our individual faculty scholars may be found by visiting their Google Scholar profile.
  • Bibliographies from our labs and projects may be found by visiting their lab websites.

Complete Biography

Rice, Edward S; Kohno, Satomi; John, John St; Pham, Son; Howard, Jonathan; Lareau, Liana F; O’Connell, Brendan L; Hickey, Glenn; Armstrong, Joel; Deran, Alden; Superbubbles, ultrabubbles and cacti. Genome Research. 27-5. 686-696 (2017) Cold Spring Harbor Lab

Novak, Adam M; Hickey, Glenn; Garrison, Erik; Blum, Sean; Connelly, Abram; Dilthey, Alexander; Eizenga, Jordan; Elmohamed, MA Saleh; Guthrie, Sally; Kahles, André; Describing the Local Structure of Sequence Graphs. Genome Research. . 101378 (2017) Cold Spring Harbor Labs Journals

Paten, Benedict; Novak, Adam M; Garrison, Erik; Hickey, Glenn; Consistency of BRCA1 and BRCA2 Variant Classifications Among Clinical Diagnostic Laboratories. Genome Research. . 173-189 (2017) Springer, Cham

Haussler, David; Smuga-Otto, Maciej; Paten, Benedict; Novak, Adam M; Nikitin, Sergei; Zueva, Maria; Miagkov, Dmitrii; Nanopore sequencing and assembly of a human genome with ultra-long reads. Genome Research. . 34-49 (2017) Springer, Cham

Rosen, Yohei; Eizenga, Jordan; Paten, Benedict; Bayesian coalescent inference of past population dynamics from molecular sequences. Genome Research. . 101659 (2017) Cold Spring Harbor Labs Journals

Rand, Arthur C; Jain, Miten; Eizenga, Jordan M; Musselman-Brown, Audrey; Olsen, Hugh E; Akeson, Mark; Paten, Benedict; Rise and fall of the Beringian steppe bison. Genome Research. 14-4. 411-413 (2017) Nature Research

O’Connor, Brian D; Yuen, Denis; Chung, Vincent; Duncan, Andrew G; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent; Dynamics of Pleistocene population extinctions in Beringian brown bears. Genome Research. 6(2017) Faculty of 1000 Ltd

Paten, Benedict; Novak, Adam M; Eizenga, Jordan M; Garrison, Erik; Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Genome Research. 27-5. 665-676 (2017) Cold Spring Harbor Lab

Vivian, John; Rao, Arjun Arkal; Nothaft, Frank Austin; Ketchum, Christopher; Armstrong, Joel; Novak, Adam; Pfeil, Jacob; Narkizian, Jake; Deran, Alden D; Musselman-Brown, Audrey; Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Genome Research. 35-4. 314-316 (2017) Nature Research

Rosen, Yohei; Eizenga, Jordan; Paten, Benedict; Evidence for time dependency of molecular rate estimates. Genome Research. . 125542 (2017) Cold Spring Harbor Labs Journals

Lincoln, Stephen E; Yang, Shan; Cline, Melissa S; Kobayashi, Yuya; Zhang, Can; Topper, Scott; Haussler, David; Paten, Benedict; Nussbaum, Robert L; Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Genome Research. 1. 42745 (2017) American Society of Clinical Oncology

Jain, Miten; Koren, Sergey; Quick, Josh; Rand, Arthur C; Sasani, Thomas A; Tyson, John R; Beggs, Andrew D; Dilthey, Alexander T; Fiddes, Ian T; Malla, Sunir; Flight of the dodo. Genome Research. . 128835 (2017) Cold Spring Harbor Labs Journals

Barlow, Miriam; Crandall, Keith; de Meaux, Juliette; Di Rienzo, Anna; Dudley, Joel; Falush, Daniel; Gaut, Brandon; Ge, Song; Gojobori, Takashi; Gouy, Manolo; Gene structure-based splice variant deconvolution using a microarry platform. (2017)

Froese, Duane; Stiller, Mathias; Heintzman, Peter D; Reyes, Alberto V; Zazula, Grant D; Soares, Andr̩ ER; Meyer, Matthias; Hall, Elizabeth; Jensen, Britta JL; Arnold, Lee J; NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis. Genome Research. 114-13. 3457-3462 (2017) National Acad Sciences

Chang, Dan; Knapp, Michael; Enk, Jacob; Lippold, Sebastian; Kircher, Martin; Lister, Adrian; MacPhee, Ross DE; Widga, Christopher; Czechowski, Paul; Sommer, Robert; An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Research. 7. 44585 (2017) Nature Publishing Group

Schaefer, Nathan K; Shapiro, Beth; Green, Richard E; A knowledge-based clustering algorithm driven by gene ontology. Genome Research. 18-1. 203 (2017) BioMed Central

Shapiro, Beth; Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Genome Research. (2017) Plant and Animal Genome

Wang, Yue; Heintzman, Peter D; Newsom, Lee; Bigelow, Nancy H; Wooller, Matthew J; Shapiro, Beth; Williams, John W; GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Genome Research. (2017)

Gaut, Brandon; Ge, Song; Gojobori, Takashi; Gouy, Manolo; Hahn, Matthew; Hedges, S Blair; Henn, Brenna; Hernandez, Ryan D; Heyer, Evelyne; Innan, Hideki; Evaluation of local structure alphabets based on residue burial. (2017)

Vivian, John; Rao, Arjun Arkal; Nothaft, Frank Austin; Ketchum, Christopher; Armstrong, Joel; Novak, Adam; Pfeil, Jacob; Narkizian, Jake; Deran, Alden D; Musselman-Brown, Audrey; SCORE FUNCTIONS FOR ASSESSING CONSERVATION IN LOCALLY ALIGNED REGIONS OF DNA FROM TWO SPECIES UCSC TECH REPORT UCSC-CRL-02-30. Genome Research. 35-4. 314-316 (2017) Nature Research

Lincoln, Stephen E; Yang, Shan; Cline, Melissa S; Kobayashi, Yuya; Zhang, Can; Topper, Scott; Haussler, David; Paten, Benedict; Nussbaum, Robert L; Nucleic acids research Volume: 33 ISSN: 1362-4962 ISO Abbreviation: Nucleic Acids Res. Publication Date: 2005 Jan. Genome Research. 1. 42745 (2017) American Society of Clinical Oncology

Sanborn, John Zachary; Haussler, David; Bambam: parallel comparative analysis of high-throughput sequencing data. (2017) US Patent 9,646,134

Haussler, David; Smuga-Otto, Maciej; Paten, Benedict; Novak, Adam M; Nikitin, Sergei; Zueva, Maria; Miagkov, Dmitrii; A Flow Procedure for the Linearization of Genome Sequence Graphs. Genome Research. . 34-49 (2017) Springer, Cham

Novak, Adam M; Hickey, Glenn; Garrison, Erik; Blum, Sean; Connelly, Abram; Dilthey, Alexander; Eizenga, Jordan; Elmohamed, MA Saleh; Guthrie, Sally; Kahles, André; Genome Graphs. Genome Research. . 101378 (2017) Cold Spring Harbor Labs Journals

Vivian, John; Rao, Arjun Arkal; Nothaft, Frank Austin; Ketchum, Christopher; Armstrong, Joel; Novak, Adam; Pfeil, Jacob; Narkizian, Jake; Deran, Alden D; Musselman-Brown, Audrey; Toil enables reproducible, open source, big biomedical data analyses.. Genome Research. 35-4. 314 (2017)

Lincoln, Stephen E; Yang, Shan; Cline, Melissa S; Kobayashi, Yuya; Zhang, Can; Topper, Scott; Haussler, David; Paten, Benedict; Nussbaum, Robert L; Consistency of BRCA1 and BRCA2 variant classifications among clinical diagnostic laboratories. Genome Research. 1. 42745 (2017) American Society of Clinical Oncology

Morozova, Olena; Salama, Sofie R; Bjork, Isabel; Goldstein, Theodore C; Mueller, Sabine; Sender, Leonard S; Sweet-Cordero, Alejandro; Haussler, David; California Kids Cancer Comparison Team; Comparative genomic analysis for pediatric cancer patients evaluated in a California Initiative to Advance Precision Medicine Demonstration Project.. (2017) American Society of Clinical Oncology

Lawler, Mark; Haussler, David; Siu, Lillian L; Haendel, Melissa A; McMurry, Julie A; Knoppers, Bartha M; Chanock, Stephen J; Calvo, Fabien; The, Bin T.; Walia, Guneet; Sharing Clinical and Genomic Data on Cancer-The Need for Global Solutions. (2017) MASSACHUSETTS MEDICAL SOC WALTHAM WOODS CENTER, 860 WINTER ST,, WALTHAM, MA 02451-1413 USA

Goldman, Mary; Craft, Brian; Zhu, Jingchun; Haussler, David; The UCSC Xena system for cancer genomics data visualization and interpretation. (2017) American Association for Cancer Research

Beale, Holly; Lam, Du Linh; Vivian, John; Newton, Yulia; Shah, Avanthi Tayi; Bjork, Isabel; Goldstein, Ted; Brooks, Angela N; Stuart, Josh; Salama, Sofie; Identifying confidently measured genes in single pediatric cancer patient samples using RNA sequencing. (2017) American Association for Cancer Research

Rao, Arjun A; Toor, Jugmohit; Tripathi, Sarvind; Pfeil, Jacob; Sgourakis, Nikolaos; Salama, Sofie; Haussler, David; Identification of recurrent high-affinity MHC class I restricted neo-epitopes in neuroblastoma using ProTECT. (2017) American Association for Cancer Research

Learned, Katrina; Durbin, Ann; Currie, Robert; Beale, Holly; Lam, Du Linh; Goldstein, Theodore; Salama, Sofie R; Haussler, David; Morozova, Olena; Bjork, Isabel; Abstract LB-338: A critical evaluation of genomic data sharing: Barriers to accessing pediatric cancer genomic datasets: a Treehouse Childhood Cancer Initiative experience. (2017) American Association for Cancer Research

Morozova, Olena; Newton, Yulia; Shah, Avanthi Tayi; Beale, Holly; Lam, Du Linh; Vivian, John; Bjork, Isabel; Goldstein, Theodore; Stuart, Josh; Salama, Sofie; A pan-cancer analysis framework for incorporating gene expression information into clinical interpretation of pediatric cancer genomic data. (2017) American Association for Cancer Research

Barlow, Miriam; Crandall, Keith; de Meaux, Juliette; Di Rienzo, Anna; Dudley, Joel; Falush, Daniel; Gaut, Brandon; Ge, Song; Gojobori, Takashi; Gouy, Manolo; Molecul Biology Evolut. (2017)

Froese, Duane; Stiller, Mathias; Heintzman, Peter D; Reyes, Alberto V; Zazula, Grant D; Soares, Andr̩ ER; Meyer, Matthias; Hall, Elizabeth; Jensen, Britta JL; Arnold, Lee J; Fossil and genomic evidence constrains the timing of bison arrival in North America. Genome Research. 114-13. 3457-3462 (2017) National Acad Sciences

Chang, Dan; Knapp, Michael; Enk, Jacob; Lippold, Sebastian; Kircher, Martin; Lister, Adrian; MacPhee, Ross DE; Widga, Christopher; Czechowski, Paul; Sommer, Robert; The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis. Genome Research. 7. 44585 (2017) Nature Publishing Group

Schaefer, Nathan K; Shapiro, Beth; Green, Richard E; AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data. Genome Research. 18-1. 203 (2017) BioMed Central

Shapiro, Beth; Passenger Pigeon Genomics: Take III. Genome Research. (2017) Plant and Animal Genome

Wang, Yue; Heintzman, Peter D; Newsom, Lee; Bigelow, Nancy H; Wooller, Matthew J; Shapiro, Beth; Williams, John W; The southern coastal Beringian land bridge: cryptic refugium or pseudorefugium for woody plants during the Last Glacial Maximum?. Genome Research. (2017)

Gaut, Brandon; Ge, Song; Gojobori, Takashi; Gouy, Manolo; Hahn, Matthew; Hedges, S Blair; Henn, Brenna; Hernandez, Ryan D; Heyer, Evelyne; Innan, Hideki; Molecul Biology Evolut. (2017)

Rice, Edward S; Kohno, Satomi; John, John St; Pham, Son; Howard, Jonathan; Lareau, Liana F; O’Connell, Brendan L; Hickey, Glenn; Armstrong, Joel; Deran, Alden; Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Research. 27-5. 686-696 (2017) Cold Spring Harbor Lab

Paten, Benedict; Novak, Adam M; Garrison, Erik; Hickey, Glenn; Superbubbles, ultrabubbles and cacti. Genome Research. . 173-189 (2017) Springer, Cham

Rosen, Yohei; Eizenga, Jordan; Paten, Benedict; Modelling haplotypes with respect to reference cohort variation graphs. Genome Research. . 101659 (2017) Cold Spring Harbor Labs Journals

Rand, Arthur C; Jain, Miten; Eizenga, Jordan M; Musselman-Brown, Audrey; Olsen, Hugh E; Akeson, Mark; Paten, Benedict; Mapping DNA methylation with high-throughput nanopore sequencing. Genome Research. 14-4. 411-413 (2017) Nature Research

O’Connor, Brian D; Yuen, Denis; Chung, Vincent; Duncan, Andrew G; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent; The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. Genome Research. 6(2017) Faculty of 1000 Ltd

Paten, Benedict; Novak, Adam M; Eizenga, Jordan M; Garrison, Erik; Genome graphs and the evolution of genome inference. Genome Research. 27-5. 665-676 (2017) Cold Spring Harbor Lab

Vivian, John; Rao, Arjun Arkal; Nothaft, Frank Austin; Ketchum, Christopher; Armstrong, Joel; Novak, Adam; Pfeil, Jacob; Narkizian, Jake; Deran, Alden D; Musselman-Brown, Audrey; Toil enables reproducible, open source, big biomedical data analyses. Genome Research. 35-4. 314-316 (2017) Nature Research

Rosen, Yohei; Eizenga, Jordan; Paten, Benedict; Describing the Local Structure of Sequence Graphs. Genome Research. . 125542 (2017) Cold Spring Harbor Labs Journals

Lincoln, Stephen E; Yang, Shan; Cline, Melissa S; Kobayashi, Yuya; Zhang, Can; Topper, Scott; Haussler, David; Paten, Benedict; Nussbaum, Robert L; Consistency of BRCA1 and BRCA2 Variant Classifications Among Clinical Diagnostic Laboratories. Genome Research. 1. 42745 (2017) American Society of Clinical Oncology

Jain, Miten; Koren, Sergey; Quick, Josh; Rand, Arthur C; Sasani, Thomas A; Tyson, John R; Beggs, Andrew D; Dilthey, Alexander T; Fiddes, Ian T; Malla, Sunir; Nanopore sequencing and assembly of a human genome with ultra-long reads. Genome Research. . 128835 (2017) Cold Spring Harbor Labs Journals

Cancer Genome Atlas Research Network; Comprehensive molecular characterization of papillary renal-cell carcinoma. Genome Research. 2016-374. 135-145 (2016)

Campbell, Joshua D; Alexandrov, Anton; Kim, Jaegil; Wala, Jeremiah; Berger, Alice H; Pedamallu, Chandra Sekhar; Shukla, Sachet A; Guo, Guangwu; Brooks, Angela N; Murray, Bradley A; Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Genome Research. (2016) Nature Publishing Group

Berger, Alice H; Brooks, Angela N; Wu, Xiaoyun; Shrestha, Yashaswi; Chouinard, Candace; Piccioni, Federica; Bagul, Mukta; Kamburov, Atanas; Imielinski, Marcin; Hogstrom, Larson; High-throughput phenotyping of lung cancer somatic mutations. Genome Research. 30-2. 214-228 (2016) Cell Press

Wang, Lili; Brooks, Angela N; Fan, Jean; Wan, Youzhong; Gambe, Rutendo; Li, Shuqiang; Hergert, Sarah; Yin, Shanye; Freeman, Samuel S; Levin, Joshua Z; Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Genome Research. 30-5. 750-763 (2016) Cell Press

Speir, Matthew L; Zweig, Ann S; Rosenbloom, Kate R; Raney, Brian J; Paten, Benedict; Nejad, Parisa; Lee, Brian T; Learned, Katrina; Karolchik, Donna; Hinrichs, Angie S; The UCSC genome browser database: 2016 update. Genome Research. 44-D1. D717-D725 (2016) Oxford University Press

Hinrichs, Angie S; Raney, Brian J; Speir, Matthew L; Rhead, Brooke; Casper, Jonathan; Karolchik, Donna; Kuhn, Robert M; Rosenbloom, Kate R; Zweig, Ann S; Haussler, David; UCSC data integrator and variant annotation integrator. Genome Research. . btv766 (2016) Oxford University Press

Tyner, Cath; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Eisenhart, Christopher; Fischer, Clayton M; Gibson, David; Gonzalez, Jairo Navarro; Guruvadoo, Luvina; The UCSC Genome Browser database: 2017 update. Genome Research. . gkw1134 (2016) Oxford University Press

Speir, Matthew L; Zweig, Ann S; Rosenbloom, Kate R; Raney, Brian J; Paten, Benedict; Nejad, Parisa; Lee, Brian T; Learned, Katrina; Karolchik, Donna; Hinrichs, Angie S; Rapid and efficient analysis of 20,000 RNA-seq samples with Toil. Genome Research. 44-D1. D717-D725 (2016) Oxford University Press

Zerbino, Daniel R; Ballinger, Tracy; Paten, Benedict; Hickey, Glenn; Haussler, David; The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Research. 17-1. 400 (2016) BioMed Central

Computational Pan-Genomics Consortium; Data Sharing and reproducible Clinical genetic testing: successes and challenges. Genome Research. . bbw089 (2016) Oxford University Press

Gordon, David; Huddleston, John; Chaisson, Mark JP; Hill, Christopher M; Kronenberg, Zev N; Munson, Katherine M; Malig, Maika; Raja, Archana; Fiddes, Ian; Hillier, LaDeana W; What Have Public Databases Taught Us About Variant Classification? The Example of BRCA1 and BRCA2. Genome Research. 352-6281. aae0344 (2016) American Association for the Advancement of Science

Rand, Arthur C; Jain, Miten; Eizenga, Jordan; Musselman-Brown, Audrey; Olsen, Hugh E; Akeson, Mark; Paten, Benedict; Erratum to: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Research. . 47134 (2016) Cold Spring Harbor Labs Journals

Novak, Adam M; Garrison, Erik; Paten, Benedict; Nonhuman Genomics: Long-read sequence assembly of the gorilla genome. Genome Research. . 246-256 (2016) Springer International Publishing

Vivian, John; Rao, Arjun; Nothaft, Frank Austin; Ketchum, Christopher; Armstrong, Joel; Novak, Adam; Pfeil, Jacob; Narkizian, Jake; Deran, Alden D; Musselman-Brown, Audrey; Genome Graphs. Genome Research. . 62497 (2016) Cold Spring Harbor Labs Journals

Kolmogorov, Mikhail; Armstrong, Joel; Raney, Brian J; Streeter, Ian; Dunn, Matthew; Yang, Fengtang; Odom, Duncan; Flicek, Paul; Keane, Thomas; Thybert, David; A Flow Procedure for the Linearization of Genome Sequence Graphs. Genome Research. . 88435 (2016) Cold Spring Harbor Labs Journals

Jain, Miten; Olsen, Hugh E; Paten, Benedict; Akeson, Mark; Modelling haplotypes with respect to reference cohort variation graphs. Genome Research. 17-1. 239 (2016) BioMed Central

Yang, Shan; Cline, Melissa; Zhang, Can; Paten, Benedict; Mapping DNA methylation with high-throughput nanopore sequencing. Genome Research. 22. 166 (2016) NIH Public Access

Lincoln, S; Cline, M; Yang, S; Kobayashi, Y; Topper, S; Haussler, D; Paten, B; Nussbaum, R; The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. Genome Research. 18-6. 949-949 (2016) ELSEVIER SCIENCE INC 360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA

Jain, Miten; Olsen, Hugh E; Paten, Benedict; Akeson, Mark; Genome graphs and the evolution of genome inference. Genome Research. 17-1. 256 (2016) BioMed Central

Gordon, David; Huddleston, John; Chaisson, Mark JP; Hill, Christopher M; Kronenberg, Zev N; Munson, Katherine M; Malig, Maika; Raja, Archana; Fiddes, Ian; Hillier, Ladeana W; Toil enables reproducible, open source, big biomedical data analyses. Genome Research. 352-6281. 52 (2016)

Shapiro, Beth; Morphological and genetic identification and isotopic study of the hair of a cave lion (Panthera spelaea Goldfuss, 1810) from the Malyi Anyui River (Chukotka, Russia). Genome Research. (2016) Plant and Animal Genome

Shapiro, Beth; Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Genome Research. (2016) Plant and Animal Genome

Schaefer, Nathan K; Shapiro, Beth; Green, Richard E; Introduction to the Snowmastodon Project Special Volume The Snowmastodon Project. Genome Research. (2016)

Chang, Dan; Shapiro, Beth; Complex admixture preceded and followed the extinction of wisent in the wild. Genome Research. 12-2. 20150822 (2016) The Royal Society

Simpson, Joanna Paula; Penkman, Kirsty Elizabeth Helena; Demarchi, Beatrice; Koon, Hannah; Collins, Matthew James; Thomas-Oates, J; Shapiro, Beth; Stark, Meg; Wilson, J; Pathways to de‰Ûextinction: how close can we get to resurrection of an extinct species?. Genome Research. 69. 29-38 (2016) Academic Press

Cahill, James A; Heintzman, Peter; Teasdale, Matthew; Sores, Andre E Rodrigues; Knapp, Joshua; Edwards, Ceiridwen J; Stirling, Ian M; Bradley, Daniel G; Green, Richard E; Shapiro, Beth; Ancient DNA. Genome Research. 159(2016)

Barlow, Miriam; de Meaux, Juliette; Di Rienzo, Anna; Dudley, Joel; Falush, Daniel; Gaut, Brandon; Gojobori, Takashi; Gouy, Manolo; Gu, Xun; Hahn, Matthew; Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. (2016)

Enk, Jacob; Devault, Alison; Widga, Christopher; Saunders, Jeffrey; Szpak, Paul; Southon, John; Rouillard, Jean-Marie; Shapiro, Beth; Golding, G Brian; Zazula, Grant; Timing and causes of mid-Holocene mammoth extinction on St. Paul Island, Alaska. Genome Research. 4. 42 (2016) Frontiers

Chernova, OF; Kirillova, IV; Shapiro, B; Shidlovskiy, FK; Soares, AER; Levchenko, VA; Bertuch, F; Early cave art and ancient DNA record the origin of European bison. Genome Research. 142. 61-73 (2016) Pergamon

Heintzman, Peter D; Froese, Duane; Ives, John W; Soares, Andr̩ ER; Zazula, Grant D; Letts, Brandon; Andrews, Thomas D; Driver, Jonathan C; Hall, Elizabeth; Hare, P Gregory; Is amino acid racemization a useful tool for screening for. Genome Research. 113-29. 8057-8063 (2016) National Acad Sciences

Wۻcek, Karolina; Hartmann, Stefanie; Paijmans, Johanna LA; Taron, Ulrike; Xenikoudakis, Georgios; Cahill, James A; Heintzman, Peter D; Shapiro, Beth; Baryshnikov, Gennady; Bunevich, Aleksei N; The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis. Genome Research. . msw254 (2016) Oxford University Press

Barnett, Ross; Mendoza, Marie Zepeda; Soares, Andr̩ Rodrigues; Ho, Simon; Zazula, Grant; Yamaguchi, Nobuyuki; Shapiro, Beth; Kirillova, Irina; Larson, Greger; Gilbert, M; AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data. Genome Research. 2(2016) Ubiquity Press

Cahill, James A; Soares, Andr̩ ER; Green, Richard E; Shapiro, Beth; Passenger Pigeon Genomics: Take III. Genome Research. 371-1699. 20150138 (2016) The Royal Society

Shapiro, Beth; The southern coastal Beringian land bridge: cryptic refugium or pseudorefugium for woody plants during the Last Glacial Maximum?. Genome Research. (2016)

Cahill, James A; Fan, Zhenxin; Gronau, Ilan; Robinson, Jacqueline; Pollinger, John P; Shapiro, Beth; Wall, Jeff; Wayne, Robert K; NetAffx: Affymetrix probesets and annotations. Genome Research. 2-7. e1501714 (2016) American Association for the Advancement of Science

Graham, Russell W; Belmecheri, Soumaya; Choy, Kyungcheol; Culleton, Brendan J; Davies, Lauren J; Froese, Duane; Heintzman, Peter D; Hritz, Carrie; Kapp, Joshua D; Newsom, Lee A; Nova regulates brain-specific splicing to shape the synapse. Genome Research. . 201604903 (2016) National Acad Sciences

Soubrier, Julien; Gower, Graham; Chen, Kefei; Richards, Stephen M; Llamas, Bastien; Mitchell, Kieren J; Ho, Simon YW; Kosintsev, Pavel; Lee, Michael SY; Baryshnikov, Gennady; Unusual intron conservation near tissue-regulated exons found by splicing microarrays. Genome Research. 7(2016) Nature Publishing Group

Soares, Andr̩ ER; Novak, Ben J; Haile, James; Heupink, Tim H; Fjelds̴, Jon; Gilbert, M Thomas P; Poinar, Hendrik; Church, George M; Shapiro, Beth; Predicting protein structure using only sequence information. Genome Research. 16-1. 230 (2016) BioMed Central

Morozova, Olena; Newton, Yulia; Cline, Melissa; Yip, Stephen; Rao, Arjun; Stuart, Josh; Goldstein, Ted; Salama, Sofie; Deyell, Rebecca; Rassekh, S Rod; LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. (2016) American Association for Cancer Research

Vivian, John; Rao, Arjun; Nothaft, Frank Austin; Ketchum, Christopher; Armstrong, Joel; Novak, Adam; Pfeil, Jacob; Narkizian, Jake; Deran, Alden D; Musselman-Brown, Audrey; Global predictions and tests of erythroid regulatory regions. Genome Research. . 62497 (2016) Cold Spring Harbor Labs Journals

Goldman, Mary; Craft, Brian; Zhu, Jingchun; Swatloski, Teresa; Cline, Melissa; Haussler, David; Score functions for determining regional conservation in two-species local alignments. (2016) American Association for Cancer Research

Yang, Shan; Cline, Melissa; Zhang, Can; Paten, Benedict; The GENCODE human gene set. Genome Research. 22. 166 (2016) NIH Public Access

Lincoln, S; Cline, M; Yang, S; Kobayashi, Y; Topper, S; Haussler, D; Paten, B; Nussbaum, R; Fishing for Genes in the UCSC Browser A Tutorial. Genome Research. 18-6. 949-949 (2016) ELSEVIER SCIENCE INC 360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA

Lincoln, Stephen E; Cline, Melissa; Yang, Shan; Kobayashi, Yuya; Zhang, Molly; O’Leary, Erin; Topper, Scott; Paten, Benedict; Nussbaum, Robert; A Novel Method for Discovering Primate Gene Loss using the Ancestral Genome. (2016) American Society of Clinical Oncology

Speir, Matthew L; Zweig, Ann S; Rosenbloom, Kate R; Raney, Brian J; Paten, Benedict; Nejad, Parisa; Lee, Brian T; Learned, Katrina; Karolchik, Donna; Hinrichs, Angie S; Genome Research. 44-D1. D717-D725 (2016) Oxford University Press

Gordon, David; Huddleston, John; Chaisson, Mark JP; Hill, Christopher M; Kronenberg, Zev N; Munson, Katherine M; Malig, Maika; Raja, Archana; Fiddes, Ian; Hillier, LaDeana W; Genome Research. 352-6281. aae0344 (2016) American Association for the Advancement of Science

Tyner, Cath; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Eisenhart, Christopher; Fischer, Clayton M; Gibson, David; Gonzalez, Jairo Navarro; Guruvadoo, Luvina; Genome Research. . gkw1134 (2016) Oxford University Press

Gordon, David; Huddleston, John; Chaisson, Mark JP; Hill, Christopher M; Kronenberg, Zev N; Munson, Katherine M; Malig, Maika; Raja, Archana; Fiddes, Ian; Hillier, Ladeana W; Genome Research. 352-6281. 52 (2016)

Wiemann, Stefan; Pennacchio, Christa; Hu, Yanhui; Hunter, Preston; Harbers, Matthias; Amiet, Alexandra; Bethel, Graeme; Busse, Melanie; Carninci, Piero; Diekhans, Mark; Genome Research. 13-3. 191-192 (2016)

Morton, JJ; Bird, G; Keysar, SB; Astling, DP; Lyons, TR; Anderson, RT; Glogowska, MJ; Estes, P; Eagles, JR; Le, PN; Genome Research. 35-3. 290-300 (2016) Nature Publishing Group

Putnam, Nicholas H; O’Connell, Brendan L; Stites, Jonathan C; Rice, Brandon J; Blanchette, Marco; Calef, Robert; Troll, Christopher J; Fields, Andrew; Hartley, Paul D; Sugnet, Charles W; Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Research. 26-3. 342-350 (2016) Cold Spring Harbor Lab

Hinrichs, Angie S; Raney, Brian J; Speir, Matthew L; Rhead, Brooke; Casper, Jonathan; Karolchik, Donna; Kuhn, Robert M; Rosenbloom, Kate R; Zweig, Ann S; Haussler, David; UCSC data integrator and variant annotation integrator. Genome Research. 32-9. 1430-1432 (2016) Oxford University Press

Blau, C Anthony; Ramirez, Arturo B; Blau, Sibel; Pritchard, Colin C; Dorschner, Michael O; Schmechel, Stephen C; Martins, Timothy J; Mahen, Elisabeth M; Burton, Kimberly A; Komashko, Vitalina M; A distributed network for intensive longitudinal monitoring in metastatic triple-negative breast cancer. Genome Research. 14-1. 42964 (2016) Harborside Press, LLC

Zerbino, Daniel R; Ballinger, Tracy; Paten, Benedict; Hickey, Glenn; Haussler, David; Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. Genome Research. 17-1. 400 (2016) BioMed Central

Ceccarelli, Michele; Barthel, Floris P; Malta, Tathiane M; Sabedot, Thais S; Salama, Sofie R; Murray, Bradley A; Morozova, Olena; Newton, Yulia; Radenbaugh, Amie; Pagnotta, Stefano M; Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma. Genome Research. 164-3. 550-563 (2016) Cell Press

Gordon, David; Huddleston, John; Chaisson, Mark JP; Hill, Christopher M; Kronenberg, Zev N; Munson, Katherine M; Malig, Maika; Raja, Archana; Fiddes, Ian; Hillier, LaDeana W; Long-read sequence assembly of the gorilla genome. Genome Research. 352-6281. aae0344 (2016) American Association for the Advancement of Science

Siu, Lillian L; Lawler, Mark; Haussler, David; Knoppers, Bartha Maria; Lewin, Jeremy; Vis, Daniel J; Liao, Rachel G; Andre, Fabrice; Banks, Ian; Barrett, J Carl; Facilitating a culture of responsible and effective sharing of cancer genome data. Genome Research. 22-5. 464 (2016) NIH Public Access

Vivian, John; Rao, Arjun; Nothaft, Frank Austin; Ketchum, Christopher; Armstrong, Joel; Novak, Adam; Pfeil, Jacob; Narkizian, Jake; Deran, Alden D; Musselman-Brown, Audrey; Rapid and efficient analysis of 20,000 RNA-seq samples with Toil. Genome Research. . 62497 (2016) Cold Spring Harbor Labs Journals

Goldman, Mary; Craft, Brian; Zhu, Jingchun; Swatloski, Teresa; Cline, Melissa; Haussler, David; The UCSC Xena system for integrating and visualizing functional genomics. (2016) American Association for Cancer Research

Haussler, David; Odds for an enlightened rather than barren future. Genome Research. (2016)

Hiranuma, Nao; Liu, Jie; Song, Chaozhong; Goldsmith, Jacob; Dorschner, Michael; Pritchard, Colin; Burton, Kimberly; Mahen, Elisabeth; Blau, Sibel; Senecal, Francis; Cis-Compound Mutations are Prevalent in Triple Negative Breast Cancer and Can Drive Tumor Progression. Genome Research. . 85316 (2016) Cold Spring Harbor Labs Journals

Tyner, Cath; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Eisenhart, Christopher; Fischer, Clayton M; Gibson, David; Gonzalez, Jairo Navarro; Guruvadoo, Luvina; The UCSC Genome Browser database: 2017 update. Genome Research. 45-D1. D626-D634 (2016) Oxford University Press

Lincoln, S; Cline, M; Yang, S; Kobayashi, Y; Topper, S; Haussler, D; Paten, B; Nussbaum, R; What Have Public Databases Taught Us About Variant Classification? The Example of BRCA1 and BRCA2. Genome Research. 18-6. 949-949 (2016) ELSEVIER SCIENCE INC 360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA

Gordon, David; Huddleston, John; Chaisson, Mark JP; Hill, Christopher M; Kronenberg, Zev N; Munson, Katherine M; Malig, Maika; Raja, Archana; Fiddes, Ian; Hillier, Ladeana W; Nonhuman Genomics: Long-read sequence assembly of the gorilla genome. Genome Research. 352-6281. 52 (2016)

Sanborn, John Zachary; Haussler, David; Bambam: parallel comparative analysis of high-throughput sequencing data. (2016) US Patent App. 15/167,507

Kumar, Vinod; Westra, Harm Jan; Karjalainen, Juha; Zhernakova, Daria V; Esko, Tõnu; Hrdlickova, B; Almeida, R; Zhernakova, Alexandra; Reinmaa, Eva; Vosa, U; Genome-wide association study in asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. Genome Research. (2016) Nature Publishing Group

Qu, Kun; Garamszegi, Sara; Wu, Felix; Thorvaldsdottir, Helga; Liefeld, Ted; Ocana, Marco; Borges-Rivera, Diego; Pochet, Nathalie; Robinson, James T; Demchak, Barry; Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Genome Research. 13-3. 245-247 (2016) Nature Research

Shapiro, Beth; The curious case of the Dodo: Leveraging the Nicobar pigeon genome to resurrect this long-extinct bird. Genome Research. (2016) Plant and Animal Genome

Shapiro, Beth; Population Genomics of Passenger Pigeons. Genome Research. (2016) Plant and Animal Genome

Schaefer, Nathan K; Shapiro, Beth; Green, Richard E; Detecting hybridization using ancient DNA. Genome Research. (2016)

Chang, Dan; Shapiro, Beth; Using ancient DNA and coalescent-based methods to infer extinction. Genome Research. 12-2. 20150822 (2016) The Royal Society

Simpson, Joanna Paula; Penkman, Kirsty Elizabeth Helena; Demarchi, Beatrice; Koon, Hannah; Collins, Matthew James; Thomas-Oates, J; Shapiro, Beth; Stark, Meg; Wilson, J; The effects of demineralisation and sampling point variability on the measurement of glutamine deamidation in type I collagen extracted from bone. Genome Research. 69. 29-38 (2016) Academic Press

Cahill, James A; Heintzman, Peter; Teasdale, Matthew; Sores, Andre E Rodrigues; Knapp, Joshua; Edwards, Ceiridwen J; Stirling, Ian M; Bradley, Daniel G; Green, Richard E; Shapiro, Beth; Paleogenomics interpretation of admixture between polar bears and brown bears. Genome Research. 159(2016)

Barlow, Miriam; de Meaux, Juliette; Di Rienzo, Anna; Dudley, Joel; Falush, Daniel; Gaut, Brandon; Gojobori, Takashi; Gouy, Manolo; Gu, Xun; Hahn, Matthew; Molecul Biology Evolut. (2016)

Enk, Jacob; Devault, Alison; Widga, Christopher; Saunders, Jeffrey; Szpak, Paul; Southon, John; Rouillard, Jean-Marie; Shapiro, Beth; Golding, G Brian; Zazula, Grant; Mammuthus Population Dynamics in Late Pleistocene North America: Divergence, Phylogeography, and Introgression. Genome Research. 4. 42 (2016) Frontiers

Chernova, OF; Kirillova, IV; Shapiro, B; Shidlovskiy, FK; Soares, AER; Levchenko, VA; Bertuch, F; Morphological and genetic identification and isotopic study of the hair of a cave lion (Panthera spelaea Goldfuss, 1810) from the Malyi Anyui River (Chukotka, Russia). Genome Research. 142. 61-73 (2016) Pergamon

Heintzman, Peter D; Froese, Duane; Ives, John W; Soares, Andr̩ ER; Zazula, Grant D; Letts, Brandon; Andrews, Thomas D; Driver, Jonathan C; Hall, Elizabeth; Hare, P Gregory; Bison phylogeography constrains dispersal and viability of the Ice Free Corridor in western Canada. Genome Research. 113-29. 8057-8063 (2016) National Acad Sciences

W€Şcek, Karolina; Hartmann, Stefanie; Paijmans, Johanna LA; Taron, Ulrike; Xenikoudakis, Georgios; Cahill, James A; Heintzman, Peter D; Shapiro, Beth; Baryshnikov, Gennady; Bunevich, Aleksei N; Complex admixture preceded and followed the extinction of wisent in the wild. Genome Research. . msw254 (2016) Oxford University Press

Barnett, Ross; Mendoza, Marie Zepeda; Soares, Andr̩ Rodrigues; Ho, Simon; Zazula, Grant; Yamaguchi, Nobuyuki; Shapiro, Beth; Kirillova, Irina; Larson, Greger; Gilbert, M; Mitogenomics of the extinct cave lion, Panthera spelaea (Goldfuss, 1810), resolve its position within the Panthera cats. Genome Research. 2(2016) Ubiquity Press

Cahill, James A; Soares, Andr̩ ER; Green, Richard E; Shapiro, Beth; Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data. Genome Research. 371-1699. 20150138 (2016) The Royal Society

Shapiro, Beth; Pathways to de‰Ű�extinction: how close can we get to resurrection of an extinct species?. Genome Research. (2016)

Cahill, James A; Fan, Zhenxin; Gronau, Ilan; Robinson, Jacqueline; Pollinger, John P; Shapiro, Beth; Wall, Jeff; Wayne, Robert K; Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. Genome Research. 2-7. e1501714 (2016) American Association for the Advancement of Science

Graham, Russell W; Belmecheri, Soumaya; Choy, Kyungcheol; Culleton, Brendan J; Davies, Lauren J; Froese, Duane; Heintzman, Peter D; Hritz, Carrie; Kapp, Joshua D; Newsom, Lee A; Timing and causes of mid-Holocene mammoth extinction on St. Paul Island, Alaska. Genome Research. . 201604903 (2016) National Acad Sciences

Soubrier, Julien; Gower, Graham; Chen, Kefei; Richards, Stephen M; Llamas, Bastien; Mitchell, Kieren J; Ho, Simon YW; Kosintsev, Pavel; Lee, Michael SY; Baryshnikov, Gennady; Early cave art and ancient DNA record the origin of European bison. Genome Research. 7(2016) Nature Publishing Group

Soares, Andr̩ ER; Novak, Ben J; Haile, James; Heupink, Tim H; Fjelds̴, Jon; Gilbert, M Thomas P; Poinar, Hendrik; Church, George M; Shapiro, Beth; Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation. Genome Research. 16-1. 230 (2016) BioMed Central

Computational Pan-Genomics Consortium; Computational pan-genomics: status, promises and challenges. Genome Research. . bbw089 (2016) Oxford University Press

Rand, Arthur C; Jain, Miten; Eizenga, Jordan; Musselman-Brown, Audrey; Olsen, Hugh E; Akeson, Mark; Paten, Benedict; Cytosine Variant Calling with High-throughput Nanopore Sequencing. Genome Research. . 47134 (2016) Cold Spring Harbor Labs Journals

Novak, Adam M; Garrison, Erik; Paten, Benedict; A Graph Extension of the Positional Burrows-Wheeler Transform and its Applications. Genome Research. . 246-256 (2016) Springer International Publishing

Kolmogorov, Mikhail; Armstrong, Joel; Raney, Brian J; Streeter, Ian; Dunn, Matthew; Yang, Fengtang; Odom, Duncan; Flicek, Paul; Keane, Thomas; Thybert, David; Chromosome assembly of large and complex genomes using multiple references. Genome Research. . 88435 (2016) Cold Spring Harbor Labs Journals

Jain, Miten; Olsen, Hugh E; Paten, Benedict; Akeson, Mark; The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Research. 17-1. 239 (2016) BioMed Central

Yang, Shan; Cline, Melissa; Zhang, Can; Paten, Benedict; Data Sharing and reproducible Clinical genetic testing: successes and challenges. Genome Research. 22. 166 (2016) NIH Public Access

Jain, Miten; Olsen, Hugh E; Paten, Benedict; Akeson, Mark; Erratum to: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Research. 17-1. 256 (2016) BioMed Central

Brooks, Angela N; Duff, Michael O; May, Gemma; Yang, Li; Bolisetty, Mohan; Landolin, Jane; Wan, Ken; Sandler, Jeremy; Booth, Benjamin W; Celniker, Susan E; Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Research. 25-11. 1771-1780 (2015) Cold Spring Harbor Lab

Haeussler, Maximilian; Raney, Brian J; Hinrichs, Angie S; Clawson, Hiram; Zweig, Ann S; Karolchik, Donna; Casper, Jonathan; Speir, Matthew L; Haussler, David; Kent, W James; Navigating protected genomics data with UCSC Genome Browser in a Box. Genome Research. 31-5. 764-766 (2015) Oxford University Press

Rosenbloom, Kate R; Armstrong, Joel; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; The UCSC genome browser database: 2015 update. Genome Research. 43-D1. D670-D681 (2015) Oxford University Press

Rosenbloom, Kate R; Armstrong, Joel; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; The NIH BD2K center for big data in translational genomics. Genome Research. 43-D1. D670-D681 (2015) Oxford University Press

Novak, Adam M; Rosen, Yohei; Haussler, David; Paten, Benedict; Abstract B1-11: Application of the CN-AVG method to reconstruct the evolutionary history of glioblastoma multiforme. Genome Research. . btv435 (2015) Oxford University Press

Jain, Miten; Fiddes, Ian T; Miga, Karen H; Olsen, Hugh E; Paten, Benedict; Akeson, Mark; Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. Genome Research. 12-4. 351-356 (2015) Nature Research

Koepfli, Klaus-Peter; Paten, Benedict; O’Brien, Stephen J; Computational pan-genomics: status, promises and challenges. Genome Research. 3-1. 57-111 (2015) Annual Reviews

Nguyen, Ngan; Hickey, Glenn; Zerbino, Daniel R; Raney, Brian; Earl, Dent; Armstrong, Joel; Kent, W James; Haussler, David; Paten, Benedict; Long-read sequence assembly of the gorilla genome. Genome Research. 22-5. 387-401 (2015) Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA

Paten, Benedict; Diekhans, Mark; Druker, Brian J; Friend, Stephen; Guinney, Justin; Gassner, Nadine; Guttman, Mitchell; Kent, W James; Mantey, Patrick; Margolin, Adam A; Cytosine Variant Calling with High-throughput Nanopore Sequencing. Genome Research. 22-6. 1143-1147 (2015) The Oxford University Press

Philippakis, Anthony A; Azzariti, Danielle R; Beltran, Sergi; Brookes, Anthony J; Brownstein, Catherine A; Brudno, Michael; Brunner, Han G; Buske, Orion J; Carey, Knox; Doll, Cassie; A Graph Extension of the Positional Burrows-Wheeler Transform and its Applications. Genome Research. 36-10. 915-921 (2015)

Ip, Camilla LC; Loose, Matthew; Tyson, John R; de Cesare, Mariateresa; Brown, Bonnie L; Jain, Miten; Leggett, Richard M; Eccles, David A; Zalunin, Vadim; Urban, John M; Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Research. 4(2015) Faculty of 1000 Ltd

Ballinger, Tracy J; Zerbino, Daniel; Paten, Benedict; Haussler, David; Chromosome assembly of large and complex genomes using multiple references. (2015) American Association for Cancer Research

Molak, Martyna; Suchard, Marc A; Ho, Simon YW; Beilman, David W; Shapiro, Beth; Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100. Genome Research. 15-1. 81-86 (2015)

Shapiro, Beth; Graham, Russell W; Letts, Brandon; Post-glacial dispersal patterns of Northern pike inferred from an 8800 year old pike (Esox cf. lucius) skull from interior Alaska. Genome Research. 44-1. 14-23 (2015)

Shapiro, Beth; Genomic data from extinct North American Camelops revise camel evolutionary history. (2015) Princeton University Press

Cahill, James A; Stirling, Ian; Kistler, Logan; Salamzade, Rauf; Ersmark, Erik; Fulton, Tara L; Stiller, Mathias; Green, Richard E; Shapiro, Beth; Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns. Genome Research. 24-6. 1205-1217 (2015)

Shapiro, Beth; Genome-wide evidence reveals that African and Eurasian golden jackals are distinct species. Genome Research. (2015) Plant and Animal Genome

Shapiro, Beth; Genetic relatedness in two-tiered plains zebra societies suggests that females choose to associate with kin. Genome Research. (2015) Plant and Animal Genome

Shapiro, Beth; Mammoth 2.0: will genome engineering resurrect extinct species?. Genome Research. (2015) Plant and Animal Genome

Alter, S Elizabeth; Meyer, Matthias; Post, Klaas; Czechowski, Paul; Gravlund, Peter; Gaines, Cork; Rosenbaum, Howard C; Kaschner, Kristin; Turvey, Samuel T; Plicht, Johannes; Life and extinction of megafauna in the ice-age Arctic. Genome Research. 24-7. 1510-1522 (2015)

Wooller, Matthew J; Gaglioti, Benjamin; Fulton, Tara L; Lopez, Andres; Shapiro, Beth; A method for positive forensic identification of samples from extremely low-coverage sequence data. Genome Research. 120. 118-125 (2015) Pergamon

Heintzman, Peter D; Zazula, Grant D; Cahill, James A; Reyes, Alberto V; MacPhee, Ross DE; Shapiro, Beth; The curious case of the Dodo: Leveraging the Nicobar pigeon genome to resurrect this long-extinct bird. Genome Research. 32-9. 2433-2440 (2015) Oxford University Press

Seguin-Orlando, Andaine; Hoover, Cindi A; Vasiliev, Sergei K; Ovodov, Nikolai D; Shapiro, Beth; Cooper, Alan; Rubin, Edward M; Willerslev, Eske; Orlando, Ludovic; Population Genomics of Passenger Pigeons. Genome Research. 1-1. 42744 (2015) Routledge

Kirillova, Irina V; Zanina, Oksana G; Chernova, Olga F; Lapteva, Elena G; Trofimova, Svetlana S; Lebedev, Vladimir S; Tiunov, Alexei V; Soares, Andre ER; Shidlovskiy, Fedor K; Shapiro, Beth; Detecting hybridization using ancient DNA. Genome Research. 84-2. 232-245 (2015) Academic Press

Seguin-Orlando, Andaine; Gamba, Cristina; Der Sarkissian, Clio; Ermini, Luca; Louvel, Guillaume; Boulygina, Eugenia; Sokolov, Alexey; Nedoluzhko, Artem; Lorenzen, Eline D; Lopez, Patricio; Using ancient DNA and coalescent-based methods to infer extinction. Genome Research. 5(2015) Nature Publishing Group

Koepfli, Klaus-Peter; Pollinger, John; Godinho, Raquel; Robinson, Jacqueline; Lea, Amanda; Hendricks, Sarah; Schweizer, Rena M; Thalmann, Olaf; Silva, Pedro; Fan, Zhenxin; A review of the dodo and its ecosystem: insights from a vertebrate concentration LagerstÌ_tte in Mauritius. Genome Research. 25-16. 2158-2165 (2015) Cell Press

Tong, Wenfei; Shapiro, Beth; Rubenstein, Daniel I; History, Philosophy & Ethics Return of the Crazy Bird: The Sad, Strange Tale of the Dodo. By Clara Pinto‰ÛCorreia. Copernicus Books. New York: Springer‰ÛVerlag. $27.50. xv+ 216 p; ill.; index. ISBN: 0‰ÛÒ387‰ÛÒ98876‰ÛÒ9. 2003.. Genome Research. 152-15. 2059-2078 (2015) Brill

Shapiro, Beth; The effects of demineralisation and sampling point variability on the measurement of glutamine deamidation in type I collagen extracted from bone. Genome Research. 16-1. 228 (2015) BioMed Central

Mann, Daniel H; Groves, Pamela; Reanier, Richard E; Gaglioti, Benjamin V; Kunz, Michael L; Shapiro, Beth; Paleogenomics interpretation of admixture between polar bears and brown bears. Genome Research. 112-46. 14301-14306 (2015) National Acad Sciences

Rambaut, Andrew; Shapiro, Beth; Drummond, Alexei J; Taveira, Nuno; Kosakovsky Pond, Sergei L; Pybus, Oliver G; Lemey, Philippe; Barroso, Helena; Molecul Biology Evolut. (2015) PUBLIC LIBRARY SCIENCE

Vohr, Samuel H; Najar, Carlos Fernando Buen Abad; Shapiro, Beth; Green, Richard E; Mammuthus Population Dynamics in Late Pleistocene North America: Divergence, Phylogeography, and Introgression. Genome Research. 16-1. 1034 (2015) BioMed Central

Ho, Simon YW; DuchÌ»ne, SebastiÌÁn; Molak, Martyna; Shapiro, Beth; Using DNA to investigate the human past. Genome Research. 24-24. 6007-6012 (2015)

Heintzman, Peter D; Soares, AndrÌ© ER; Chang, Dan; Shapiro, Beth; Bison phylogeography constrains dispersal and viability of the Ice Free Corridor in western Canada. Genome Research. (2015) Wiley‰ÛVCH Verlag GmbH & Co. KGaA

Rijsdijk, Kenneth F; Hume, Julian P; Louw, Perry GB De; Meijer, Hanneke JM; Janoo, Anwar; De Boer, Erik J; Steel, Lorna; De Vos, John; Van Der Sluis, Laura G; Hooghiemstra, Henry; Mitogenomics of the extinct cave lion, Panthera spelaea (Goldfuss, 1810), resolve its position within the Panthera cats. Genome Research. 35-sup1. 42814 (2015) Taylor & Francis

Barlow, Miriam; de Meaux, Juliette; Di Rienzo, Anna; Dudley, Joel; Falush, Daniel; Gaut, Brandon; Gojobori, Takashi; Gouy, Manolo; Gu, Xun; Hahn, Matthew; ENCODE whole-genome data in the UCSC Genome Browser: update 2012. (2015)

Karchin, Rachel; Cline, Melissa S; Comparative genomics search for losses of long-established genes on the human lineage. Genome Research. 134-5. 455 (2015) NIH Public Access

Morozova, Olena; Newton, Yulia; Cline, Melissa; Zhu, Jingchun; Learned, Katrina; Stuart, Josh; Salama, Sofie; Arceci, Robert; Haussler, David; Sequence analysis with the Kestrel SIMD parallel processor. (2015) American Association for Cancer Research

Zhu, Jingchun; Craft, Brian; Goldman, Mary; Cline, Melissa; Diekhans, Mark; Haussler, David; Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. (2015) American Association for Cancer Research

Rosenbloom, Kate R; Armstrong, Joel; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; Genome Research. 43-D1. D670-D681 (2015) Oxford University Press

Paten, Benedict; Diekhans, Mark; Druker, Brian J; Friend, Stephen; Guinney, Justin; Gassner, Nadine; Guttman, Mitchell; Kent, W James; Mantey, Patrick; Margolin, Adam A; Genome Research. 22-6. 1143-1147 (2015) The Oxford University Press

Zhu, Jingchun; Craft, Brian; Goldman, Mary; Cline, Melissa; Diekhans, Mark; Haussler, David; (2015) American Association for Cancer Research

Dobrynin, Pavel; Liu, Shiping; Tamazian, Gaik; Xiong, Zijun; Yurchenko, Andrey A; Krasheninnikova, Ksenia; Kliver, Sergey; Schmidt-Küntzel, Anne; Koepfli, Klaus-Peter; Johnson, Warren; Genome Research. 16-1. 277 (2015) BioMed Central

Ballinger, Tracy; Ewing, Adam D; Haussler, David; Retrotransposon mobilization in cancer genomes. Genome Research. (2015)

Novak, Adam M; Rosen, Yohei; Haussler, David; Paten, Benedict; Canonical, stable, general mapping using context schemes. Genome Research. 31-22. 3569-3576 (2015) Oxford University Press

Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Kheradpour, Pouya; Zhang, Zhizhuo; Heravi-Moussavi, Alireza; Liu, Yaping; Amin, Viren; Integrative analysis of 111 reference human epigenomes. Genome Research. 518-7539. 317 (2015) NIH Public Access

Ewing, Adam D; Houlahan, Kathleen E; Hu, Yin; Ellrott, Kyle; Caloian, Cristian; Yamaguchi, Takafumi N; Bare, J Christopher; P’ng, Christine; Waggott, Daryl; Sabelnykova, Veronica Y; Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Genome Research. 12-7. 623-630 (2015) Nature Research

Nguyen, Ngan; Hickey, Glenn; Zerbino, Daniel R; Raney, Brian; Earl, Dent; Armstrong, Joel; Kent, W James; Haussler, David; Paten, Benedict; Building a pan-genome reference for a population. Genome Research. 22-5. 387-401 (2015) Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA

Paten, Benedict; Diekhans, Mark; Druker, Brian J; Friend, Stephen; Guinney, Justin; Gassner, Nadine; Guttman, Mitchell; James Kent, W; Mantey, Patrick; Margolin, Adam A; The NIH BD2K center for big data in translational genomics. Genome Research. 22-6. 1143-1147 (2015) Oxford University Press

Speir, Matthew L; Zweig, Ann S; Rosenbloom, Kate R; Raney, Brian J; Paten, Benedict; Nejad, Parisa; Lee, Brian T; Learned, Katrina; Karolchik, Donna; Hinrichs, Angie S; The UCSC genome browser database: 2016 update. Genome Research. 44-D1. D717-D725 (2015) Oxford University Press

Cancer Genome Atlas Research Network; Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas. Genome Research. 2015-372. 2481-2498 (2015)

Radenbaugh, Amie J; The identification and characterization of alterations to DNA and RNA in cancer using next-generation sequencing data. (2015) University of California, Santa Cruz

Molak, Martyna; Suchard, Marc A; Ho, Simon YW; Beilman, David W; Shapiro, Beth; Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon‰Ű�date and calibration error into Bayesian phylogenetic analyses of ancient DNA. Genome Research. 15-1. 81-86 (2015)

Shapiro, Beth; Graham, Russell W; Letts, Brandon; A revised evolutionary history of armadillos (Dasypus) in North America based on ancient mitochondrial DNA. Genome Research. 44-1. 14-23 (2015)

Shapiro, Beth; How to clone a mammoth: the science of de-extinction. (2015) Princeton University Press

Cahill, James A; Stirling, Ian; Kistler, Logan; Salamzade, Rauf; Ersmark, Erik; Fulton, Tara L; Stiller, Mathias; Green, Richard E; Shapiro, Beth; Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Genome Research. 24-6. 1205-1217 (2015)

Shapiro, Beth; Paleogenomics. Genome Research. (2015) Plant and Animal Genome

Shapiro, Beth; The evolutionary consequences of interspecies hybridization: insights from ancient and modern bear genomes. Genome Research. (2015) Plant and Animal Genome

Shapiro, Beth; The Rise and Fall of the Passenger Pigeon. Genome Research. (2015) Plant and Animal Genome

Alter, S Elizabeth; Meyer, Matthias; Post, Klaas; Czechowski, Paul; Gravlund, Peter; Gaines, Cork; Rosenbaum, Howard C; Kaschner, Kristin; Turvey, Samuel T; Plicht, Johannes; Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100. Genome Research. 24-7. 1510-1522 (2015)

Wooller, Matthew J; Gaglioti, Benjamin; Fulton, Tara L; Lopez, Andres; Shapiro, Beth; Post-glacial dispersal patterns of Northern pike inferred from an 8800 year old pike (Esox cf. lucius) skull from interior Alaska. Genome Research. 120. 118-125 (2015) Pergamon

Heintzman, Peter D; Zazula, Grant D; Cahill, James A; Reyes, Alberto V; MacPhee, Ross DE; Shapiro, Beth; Genomic data from extinct North American Camelops revise camel evolutionary history. Genome Research. 32-9. 2433-2440 (2015) Oxford University Press

Seguin-Orlando, Andaine; Hoover, Cindi A; Vasiliev, Sergei K; Ovodov, Nikolai D; Shapiro, Beth; Cooper, Alan; Rubin, Edward M; Willerslev, Eske; Orlando, Ludovic; Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns. Genome Research. 1-1. 42744 (2015) Routledge

Kirillova, Irina V; Zanina, Oksana G; Chernova, Olga F; Lapteva, Elena G; Trofimova, Svetlana S; Lebedev, Vladimir S; Tiunov, Alexei V; Soares, Andre ER; Shidlovskiy, Fedor K; Shapiro, Beth; An ancient bison from the mouth of the Rauchua River (Chukotka, Russia). Genome Research. 84-2. 232-245 (2015) Academic Press

Seguin-Orlando, Andaine; Gamba, Cristina; Der Sarkissian, Clio; Ermini, Luca; Louvel, Guillaume; Boulygina, Eugenia; Sokolov, Alexey; Nedoluzhko, Artem; Lorenzen, Eline D; Lopez, Patricio; Pros and cons of methylation-based enrichment methods for ancient DNA. Genome Research. 5(2015) Nature Publishing Group

Koepfli, Klaus-Peter; Pollinger, John; Godinho, Raquel; Robinson, Jacqueline; Lea, Amanda; Hendricks, Sarah; Schweizer, Rena M; Thalmann, Olaf; Silva, Pedro; Fan, Zhenxin; Genome-wide evidence reveals that African and Eurasian golden jackals are distinct species. Genome Research. 25-16. 2158-2165 (2015) Cell Press

Tong, Wenfei; Shapiro, Beth; Rubenstein, Daniel I; Genetic relatedness in two-tiered plains zebra societies suggests that females choose to associate with kin. Genome Research. 152-15. 2059-2078 (2015) Brill

Shapiro, Beth; Mammoth 2.0: will genome engineering resurrect extinct species?. Genome Research. 16-1. 228 (2015) BioMed Central

Mann, Daniel H; Groves, Pamela; Reanier, Richard E; Gaglioti, Benjamin V; Kunz, Michael L; Shapiro, Beth; Life and extinction of megafauna in the ice-age Arctic. Genome Research. 112-46. 14301-14306 (2015) National Acad Sciences

Rambaut, Andrew; Shapiro, Beth; Drummond, Alexei J; Taveira, Nuno; Kosakovsky Pond, Sergei L; Pybus, Oliver G; Lemey, Philippe; Barroso, Helena; Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. (2015) PUBLIC LIBRARY SCIENCE

Vohr, Samuel H; Najar, Carlos Fernando Buen Abad; Shapiro, Beth; Green, Richard E; A method for positive forensic identification of samples from extremely low-coverage sequence data. Genome Research. 16-1. 1034 (2015) BioMed Central

Ho, Simon YW; DuchĚ»ne, SebastiĚÁn; Molak, Martyna; Shapiro, Beth; Time‰Ű�dependent estimates of molecular evolutionary rates: evidence and causes. Genome Research. 24-24. 6007-6012 (2015)

Heintzman, Peter D; Soares, AndrĚ© ER; Chang, Dan; Shapiro, Beth; Paleogenomics. Genome Research. (2015) Wiley‰Ű�VCH Verlag GmbH & Co. KGaA

Rijsdijk, Kenneth F; Hume, Julian P; Louw, Perry GB De; Meijer, Hanneke JM; Janoo, Anwar; De Boer, Erik J; Steel, Lorna; De Vos, John; Van Der Sluis, Laura G; Hooghiemstra, Henry; A review of the dodo and its ecosystem: insights from a vertebrate concentration LagerstĚ_tte in Mauritius. Genome Research. 35-sup1. 42814 (2015) Taylor & Francis

Barlow, Miriam; de Meaux, Juliette; Di Rienzo, Anna; Dudley, Joel; Falush, Daniel; Gaut, Brandon; Gojobori, Takashi; Gouy, Manolo; Gu, Xun; Hahn, Matthew; Molecul Biology Evolut. (2015)

Novak, Adam M; Rosen, Yohei; Haussler, David; Paten, Benedict; Canonical, stable, general mapping using context schemes. Genome Research. . btv435 (2015) Oxford University Press

Jain, Miten; Fiddes, Ian T; Miga, Karen H; Olsen, Hugh E; Paten, Benedict; Akeson, Mark; Improved data analysis for the MinION nanopore sequencer. Genome Research. 12-4. 351-356 (2015) Nature Research

Koepfli, Klaus-Peter; Paten, Benedict; O’Brien, Stephen J; The Genome 10K Project: a way forward. Genome Research. 3-1. 57-111 (2015) Annual Reviews

Paten, Benedict; Diekhans, Mark; Druker, Brian J; Friend, Stephen; Guinney, Justin; Gassner, Nadine; Guttman, Mitchell; Kent, W James; Mantey, Patrick; Margolin, Adam A; The NIH BD2K center for big data in translational genomics. Genome Research. 22-6. 1143-1147 (2015) The Oxford University Press

Philippakis, Anthony A; Azzariti, Danielle R; Beltran, Sergi; Brookes, Anthony J; Brownstein, Catherine A; Brudno, Michael; Brunner, Han G; Buske, Orion J; Carey, Knox; Doll, Cassie; The Matchmaker Exchange: a platform for rare disease gene discovery. Genome Research. 36-10. 915-921 (2015)

Ip, Camilla LC; Loose, Matthew; Tyson, John R; de Cesare, Mariateresa; Brown, Bonnie L; Jain, Miten; Leggett, Richard M; Eccles, David A; Zalunin, Vadim; Urban, John M; MinION Analysis and Reference Consortium: Phase 1 data release and analysis. Genome Research. 4(2015) Faculty of 1000 Ltd

Ballinger, Tracy J; Zerbino, Daniel; Paten, Benedict; Haussler, David; Abstract B1-11: Application of the CN-AVG method to reconstruct the evolutionary history of glioblastoma multiforme. (2015) American Association for Cancer Research

Brooks, Angela N; Choi, Peter S; de Waal, Luc; Sharifnia, Tanaz; Imielinski, Marcin; Saksena, Gordon; Pedamallu, Chandra Sekhar; Sivachenko, Andrey; Rosenberg, Mara; Chmielecki, Juliann; A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events. Genome Research. 9-1. e87361 (2014) Public Library of Science

Watanabe, Hideo; Ma, Qiuping; Peng, Shouyong; Adelmant, Guillaume; Swain, Danielle; Song, Wenyu; Fox, Cameron; Francis, Joshua M; Pedamallu, Chandra Sekhar; DeLuca, David S; SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas. Genome Research. 124-4. 1636-1645 (2014) American Society for Clinical Investigation

Cancer Genome Atlas Research Network; Comprehensive molecular profiling of lung adenocarcinoma. Genome Research. 511-7511. 543-550 (2014) Nature Research

Collisson, EA; Campbell, J; Brooks, A; Berger, A; Lee, William; Chmielecki, Juliann; Beer, D; Cope, Leslie; Creighton, C; Danilova, Ludmila; Comprehensive molecular profiling of lung adenocarcinoma: The cancer genome atlas research network. Genome Research. 511-7511. 543-550 (2014) Nature Publishing Group

Nguyen, Ngan; Hickey, Glenn; Raney, Brian J; Armstrong, Joel; Clawson, Hiram; Zweig, Ann; Karolchik, Donna; Kent, William James; Haussler, David; Paten, Benedict; Comparative assembly hubs: web-accessible browsers for comparative genomics. Genome Research. 30-23. 3293-3301 (2014) Oxford University Press

Raney, Brian J; Dreszer, Timothy R; Barber, Galt P; Clawson, Hiram; Fujita, Pauline A; Wang, Ting; Nguyen, Ngan; Paten, Benedict; Zweig, Ann S; Karolchik, Donna; Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Genome Research. 30-7. 1003-1005 (2014) Oxford University Press

Haeussler, Maximilian; Karolchik, Donna; Clawson, Hiram; Raney, Brian J; Rosenbloom, Kate R; Fujita, Pauline A; Hinrichs, Angie S; Speir, Matthew L; Eisenhart, Chris; Zweig, Ann S; The UCSC Ebola genome portal. Genome Research. (2014) Public Library of Science

Karolchik, Donna; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Cline, Melissa S; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; The UCSC genome browser database: 2014 update. Genome Research. 42-D1. D764-D770 (2014) Oxford University Press

Paten, Benedict; Zerbino, Daniel R; Hickey, Glenn; Haussler, David; An algebraic framework to sample the rearrangement histories of a cancer metagenome with double cut and join, duplication and deletion events.. Genome Research. 15-1. 206 (2014) BioMed Central

Nguyen, Ngan; Hickey, Glenn; Raney, Brian J; Armstrong, Joel; Clawson, Hiram; Zweig, Ann; Karolchik, Donna; Kent, William James; Haussler, David; Paten, Benedict; Ragout—a reference-assisted assembly tool for bacterial genomes. Genome Research. 30-23. 3293-3301 (2014) Oxford University Press

Raney, Brian J; Dreszer, Timothy R; Barber, Galt P; Clawson, Hiram; Fujita, Pauline A; Wang, Ting; Nguyen, Ngan; Paten, Benedict; Zweig, Ann S; Karolchik, Donna; Large-scale multiple alignment and transcriptionally-associated pattern discovery in vertebrate genomes. Genome Research. 30-7. 1003-1005 (2014) Oxford University Press

Nguyen, Ngan; Hickey, Glenn; Zerbino, Daniel R; Raney, Brian; Earl, Dent; Armstrong, Joel; Haussler, David; Paten, Benedict; An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Genome Research. . 207-221 (2014) Springer International Publishing

Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Harris, Robert S; Fitzgerald, Stephen; Beal, Kathryn; Seledtsov, Igor; Molodtsov, Vladimir; Raney, Brian J; Clawson, Hiram; Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Genome Research. 24-12. 2077-2089 (2014) Cold Spring Harbor Lab

Paten, Benedict; Novak, Adam; Haussler, David; Canonical, stable, general mapping using context schemes. Genome Research. (2014)

Kolmogorov, Mikhail; Raney, Brian; Paten, Benedict; Pham, Son; Improved data analysis for the MinION nanopore sequencer. Genome Research. 30-12. i302-i309 (2014) Oxford University Press

Jacobs, Frank MJ; Greenberg, David; Nguyen, Ngan; Haeussler, Maximilian; Ewing, Adam D; Katzman, Sol; Paten, Benedict; Salama, Sofie R; Haussler, David; Building a pan-genome reference for a population. Genome Research. 516-7530. 242-245 (2014) Nature Research

Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; John, John A St; Capella-Gutiérrez, Salvador; Castoe, Todd A; The Matchmaker Exchange: a platform for rare disease gene discovery. Genome Research. 346-6215. 1254449 (2014) American Association for the Advancement of Science

Shapiro, Beth; A genetic algorithm approach to study the evolution of female preference based on male age. Genome Research. (2014) Plant and Animal Genome

Shapiro, B; Hofreiter, Michael; Rainfall and parasitic wasp (Hymenoptera: Ichneumonoidea) activity in successional forest stages at Barro Colorado Nature Monument, Panama, and La Selva Biological Station, Costa Rica. Genome Research. 343-6169. 1236573 (2014) American Association for the Advancement of Science

Shapiro, Beth; Ho, Simon YW; Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon‰Ûdate and calibration error into Bayesian phylogenetic analyses of ancient DNA. Genome Research. 23-3. 499-501 (2014)

Sarkissian, C; Ermini, Luca; JÌ_nsson, HÌÁkon; Alekseev, AN; Crubezy, E; Shapiro, B; Orlando, L; Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Genome Research. 23-7. 1780-1798 (2014)

Kistler, Logan; Montenegro, ́lvaro; Smith, Bruce D; Gifford, John A; Green, Richard E; Newsom, Lee A; Shapiro, Beth; How to clone a mammoth: the science of de-extinction. Genome Research. 111-8. 2937-2941 (2014) National Acad Sciences

Horn, Susanne; Prost, Stefan; Stiller, Mathias; Makowiecki, Daniel; Kuznetsova, Tatiana; Benecke, Norbert; Pucher, Erich; Hufthammer, Anne K; Schouwenburg, Charles; Shapiro, Beth; Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Genome Research. 23-7. 1717-1729 (2014)

Harington, C Richard; Cournoyer, Mario; Chartier, Michel; Fulton, Tara Lynn; Shapiro, Beth; Whole-genome analyses resolve early branches in the tree of life of modern birds. Genome Research. 51-5. 527-535 (2014) NRC Research Press

Barnett, Ross; Yamaguchi, Nobuyuki; Shapiro, Beth; Ho, Simon YW; Barnes, Ian; Sabin, Richard; Werdelin, Lars; Cuisin, Jacques; Larson, Greger; Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Genome Research. 14-1. 70 (2014) BioMed Central

Ng, Terry Fei Fan; Chen, Li-Fang; Zhou, Yanchen; Shapiro, Beth; Stiller, Mathias; Heintzman, Peter D; Varsani, Arvind; Kondov, Nikola O; Wong, Walt; Deng, Xutao; Phylogeography of lions (Panthera leo) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Genome Research. 111-47. 16842-16847 (2014) National Acad Sciences

Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon YW; Faircloth, Brant C; Nabholz, Benoit; Howard, Jason T; An ancient bison from the mouth of the Rauchua River (Chukotka, Russia). Genome Research. 346-6215. 1320-1331 (2014) American Association for the Advancement of Science

Schubert, Mikkel; JÌ_nsson, HÌÁkon; Chang, Dan; Der Sarkissian, Clio; Ermini, Luca; Ginolhac, AurÌ©lien; Albrechtsen, Anders; Dupanloup, Isabelle; Foucal, Adrien; Petersen, Bent; Pros and cons of methylation-based enrichment methods for ancient DNA. Genome Research. 111-52. E5661-E5669 (2014) National Acad Sciences

Johnson, Kirk R; Miller, Ian M; Pigati, Jeffrey S; Fossil and genomic evidence constrains the timing of bison arrival in North America. Genome Research. 82-3. 473-476 (2014) Cambridge University Press

Paz, Inbal; Kosti, Idit; Ares, Manuel; Cline, Melissa; Mandel-Gutfreund, Yael; The UCSC genome browser. Genome Research. . gku406 (2014) Oxford Univ Press

Cline, Melissa; Morozova, Olena; Swatloski, Teresa; Craft, Brian; Goldman, Mary; Haussler, David; Zhu, Jingchun; Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. (2014) American Association for Cancer Research

Wilks, Christopher; Cline, Melissa S; Weiler, Erich; Diehkans, Mark; Craft, Brian; Martin, Christy; Murphy, Daniel; Pierce, Howdy; Black, John; Nelson, Donavan; The share of human genomic DNA under selection estimated from human–mouse genomic alignments. Genome Research. 2014. bau093 (2014) Oxford University Press

Yue, Feng; Cheng, Yong; Breschi, Alessandra; Vierstra, Jeff; Wu, Weisheng; Ryba, Tyrone; Sandstrom, Richard; Ma, Zhihai; Davis, Carrie; Pope, Benjamin D; The UCSC proteome browser. Genome Research. 515-7527. 355-364 (2014) Nature Research

Goldman, Mary; Craft, Brian; Swatloski, Teresa; Cline, Melissa; Morozova, Olena; Diekhans, Mark; Haussler, David; Zhu, Jingchun; The UCSC Kestrel parallel processor. Genome Research. . gku1073 (2014) Oxford University Press

Karolchik, Donna; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Cline, Melissa S; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome. Genome Research. 42-D1. D764-D770 (2014) Oxford University Press

Farrell, Catherine M; O’Leary, Nuala A; Harte, Rachel A; Loveland, Jane E; Wilming, Laurens G; Wallin, Craig; Diekhans, Mark; Barrell, Daniel; Searle, Stephen MJ; Aken, Bronwen; Genome Research. 42-D1. D865-D872 (2014) Oxford University Press

Ezkurdia, Iakes; Juan, David; Rodriguez, Jose Manuel; Frankish, Adam; Deikhans, Mark; Harrow, Jennifer L; Vazquez, Jesus; Valencia, Alfonso; Tress, Michael; Genome Research. . 1909 (2014) Cold Spring Harbor Labs Journals

Ezkurdia, Iakes; Juan, David; Rodriguez, Jose Manuel; Frankish, Adam; Diekhans, Mark; Harrow, Jennifer; Vazquez, Jesus; Valencia, Alfonso; Tress, Michael L; Genome Research. 23-22. 5866-5878 (2014) Oxford University Press

Sisu, Cristina; Pei, Baikang; Leng, Jing; Frankish, Adam; Zhang, Yan; Balasubramanian, Suganthi; Harte, Rachel; Wang, Daifeng; Rutenberg-Schoenberg, Michael; Clark, Wyatt; Genome Research. 111-37. 13361-13366 (2014) National Acad Sciences

Goldman, Mary; Craft, Brian; Swatloski, Teresa; Cline, Melissa; Morozova, Olena; Diekhans, Mark; Haussler, David; Zhu, Jingchun; Genome Research. . gku1073 (2014) Oxford University Press

Karolchik, Donna; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Cline, Melissa S; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; Genome Research. 42-D1. D764-D770 (2014) Oxford University Press

Paten, Benedict; Zerbino, Daniel R; Hickey, Glenn; Haussler, David; A unifying model of genome evolution under parsimony. Genome Research. 15-1. 206 (2014) BioMed Central

Radenbaugh, Amie J; Ma, Singer; Ewing, Adam; Stuart, Joshua M; Collisson, Eric A; Zhu, Jingchun; Haussler, David; RADIA: RNA and DNA integrated analysis for somatic mutation detection. Genome Research. 9-11. e111516 (2014) Public Library of Science

Nguyen, Ngan; Hickey, Glenn; Zerbino, Daniel R; Raney, Brian J; Earl, Dent; Armstrong, Joel; Haussler, David; Paten, Benedict; Building a Pangenome Reference for a Population.. Genome Research. . 207-221 (2014)

Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Harris, Robert S; Fitzgerald, Stephen; Beal, Kathryn; Seledtsov, Igor; Molodtsov, Vladimir; Raney, Brian J; Clawson, Hiram; Alignathon: a competitive assessment of whole-genome alignment methods. Genome Research. 24-12. 2077-2089 (2014) Cold Spring Harbor Lab

Paten, Benedict; Novak, Adam; Haussler, David; Mapping to a reference genome structure. Genome Research. (2014)

Cancer Genome Atlas Research Network; Comprehensive molecular profiling of lung adenocarcinoma. Genome Research. 511-7511. 543 (2014) NIH Public Access

Wilks, Christopher; Cline, Melissa S; Weiler, Erich; Diehkans, Mark; Craft, Brian; Martin, Christy; Murphy, Daniel; Pierce, Howdy; Black, John; Nelson, Donavan; The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Genome Research. 2014(2014) Oxford University Press

Jacobs, Frank MJ; Greenberg, David; Nguyen, Ngan; Haeussler, Maximilian; Ewing, Adam D; Katzman, Sol; Paten, Benedict; Salama, Sofie R; Haussler, David; An evolutionary arms race between KRAB zinc finger genes 91/93 and SVA/L1 retrotransposons. Genome Research. 516-7530. 242 (2014) NIH Public Access

Haeussler, Maximilian; Raney, Brian J; Hinrichs, Angie S; Clawson, Hiram; Zweig, Ann S; Karolchik, Donna; Casper, Jonathan; Speir, Matthew L; Haussler, David; Kent, W James; Navigating protected genomics data with UCSC Genome Browser in a Box. Genome Research. 31-5. 764-766 (2014) Oxford University Press

Lowe, Craig B; Clarke, Julia A; Baker, Allan J; Haussler, David; Edwards, Scott V; Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Genome Research. 32-1. 23-28 (2014) Oxford University Press

Rosenbloom, Kate R; Armstrong, Joel; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; The UCSC genome browser database: 2015 update. Genome Research. 43-D1. D670-D681 (2014) Oxford University Press

Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; John, John A St; Capella-Gutiérrez, Salvador; Castoe, Todd A; Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Genome Research. 346-6215. 1254449 (2014) American Association for the Advancement of Science

OBrien, Stephen J; Haussler, David; Ryder, Oliver; The birds of Genome10K. Genome Research. 3-1. 32 (2014) BioMed Central

Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M; Lee, Chul; Storz, Jay F; Antunes, Agostinho; Greenwold, Matthew J; Meredith, Robert W; Comparative genomics reveals insights into avian genome evolution and adaptation. Genome Research. 346-6215. 1311-1320 (2014) American Association for the Advancement of Science

Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon YW; Faircloth, Brant C; Nabholz, Benoit; Howard, Jason T; Whole-genome analyses resolve early branches in the tree of life of modern birds. Genome Research. 346-6215. 1320-1331 (2014) American Association for the Advancement of Science

Goldman, Mary; Craft, Brian; Swatloski, Teresa; Cline, Melissa; Morozova, Olena; Diekhans, Mark; Haussler, David; Zhu, Jingchun; The UCSC cancer genomics browser: update 2015. Genome Research. 43-D1. D812-D817 (2014) Oxford University Press

Haeussler, Maximilian; Karolchik, Donna; Clawson, Hiram; Raney, Brian J; Rosenbloom, Kate R; Fujita, Pauline A; Hinrichs, Angie S; Speir, Matthew L; Eisenhart, Chris; Zweig, Ann S; The UCSC Ebola genome portal. Genome Research. 6(2014) Public Library of Science

Cancer Genome Atlas Research Network; Comprehensive molecular characterization of urothelial bladder carcinoma. Genome Research. 507-7492. 315 (2014) NIH Public Access

Duhig, Edwina; Clarke, Belinda; Yang, Ian A; Fong, Kwun M; Hunter, Lindy; Windsor, Morgan; Bowman, Rayleen V; Cancer Genome Atlas Research Network; Comprehensive molecular profiling of lung adenocarcinoma: the cancer genome atlas research network. Genome Research. 511-7511. 543-550 (2014) Nature Publishing Group

Bass, Adam J; Thorsson, Vesteinn; Shmulevich, Ilya; Reynolds, Sheila M; Miller, Michael; Bernard, Brady; Hinoue, Toshinori; Laird, Peter W; Curtis, Christina; Shen, Hui; Comprehensive molecular characterization of gastric adenocarcinoma. Genome Research. 513-7517. 202 (2014) NIH Public Access

Mangan, Mary E; Williams, Jennifer M; Kuhn, Robert M; Lathe, Warren C; The UCSC genome browser: what every molecular biologist should know. Genome Research. . 19.9. 1-19.9. 36 (2014) John Wiley & Sons, Inc.

Shapiro, Beth; Detecting Barriers to Gene Flow Among Extinct Populations. Genome Research. (2014) Plant and Animal Genome

Shapiro, B; Hofreiter, Michael; A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Genome Research. 343-6169. 1236573 (2014) American Association for the Advancement of Science

Shapiro, Beth; Ho, Simon YW; Ancient hyaenas highlight the old problem of estimating evolutionary rates. Genome Research. 23-3. 499-501 (2014)

Sarkissian, C; Ermini, Luca; JĚ_nsson, HĚÁkon; Alekseev, AN; Crubezy, E; Shapiro, B; Orlando, L; Shotgun microbial profiling of fossil remains. Genome Research. 23-7. 1780-1798 (2014)

Kistler, Logan; Montenegro, �lvaro; Smith, Bruce D; Gifford, John A; Green, Richard E; Newsom, Lee A; Shapiro, Beth; Transoceanic drift and the domestication of African bottle gourds in the Americas. Genome Research. 111-8. 2937-2941 (2014) National Acad Sciences

Horn, Susanne; Prost, Stefan; Stiller, Mathias; Makowiecki, Daniel; Kuznetsova, Tatiana; Benecke, Norbert; Pucher, Erich; Hufthammer, Anne K; Schouwenburg, Charles; Shapiro, Beth; Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe. Genome Research. 23-7. 1717-1729 (2014)

Harington, C Richard; Cournoyer, Mario; Chartier, Michel; Fulton, Tara Lynn; Shapiro, Beth; Brown bear (Ursus arctos)(9880ĺ±35 BP) from late-glacial Champlain Sea deposits at Saint-Nicolas, Quebec, Canada, and the dispersal history of brown bears. Genome Research. 51-5. 527-535 (2014) NRC Research Press

Barnett, Ross; Yamaguchi, Nobuyuki; Shapiro, Beth; Ho, Simon YW; Barnes, Ian; Sabin, Richard; Werdelin, Lars; Cuisin, Jacques; Larson, Greger; Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. Genome Research. 14-1. 70 (2014) BioMed Central

Ng, Terry Fei Fan; Chen, Li-Fang; Zhou, Yanchen; Shapiro, Beth; Stiller, Mathias; Heintzman, Peter D; Varsani, Arvind; Kondov, Nikola O; Wong, Walt; Deng, Xutao; Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Genome Research. 111-47. 16842-16847 (2014) National Acad Sciences

Schubert, Mikkel; JĚ_nsson, HĚÁkon; Chang, Dan; Der Sarkissian, Clio; Ermini, Luca; Ginolhac, AurĚ©lien; Albrechtsen, Anders; Dupanloup, Isabelle; Foucal, Adrien; Petersen, Bent; Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Genome Research. 111-52. E5661-E5669 (2014) National Acad Sciences

Johnson, Kirk R; Miller, Ian M; Pigati, Jeffrey S; Introduction to the Snowmastodon Project Special Volume The Snowmastodon Project. Genome Research. 82-3. 473-476 (2014) Cambridge University Press

Nguyen, Ngan; Hickey, Glenn; Zerbino, Daniel R; Raney, Brian; Earl, Dent; Armstrong, Joel; Haussler, David; Paten, Benedict; Building a pangenome reference for a population. Genome Research. . 207-221 (2014) Springer International Publishing

Kolmogorov, Mikhail; Raney, Brian; Paten, Benedict; Pham, Son; Ragout—a reference-assisted assembly tool for bacterial genomes. Genome Research. 30-12. i302-i309 (2014) Oxford University Press

Jacobs, Frank MJ; Greenberg, David; Nguyen, Ngan; Haeussler, Maximilian; Ewing, Adam D; Katzman, Sol; Paten, Benedict; Salama, Sofie R; Haussler, David; An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Genome Research. 516-7530. 242-245 (2014) Nature Research

Weinstein, John N; Collisson, Eric A; Mills, Gordon B; Shaw, Kenna R Mills; Ozenberger, Brad A; Ellrott, Kyle; Shmulevich, Ilya; Sander, Chris; Stuart, Joshua M; Cancer Genome Atlas Research Network; The cancer genome atlas pan-cancer analysis project. Genome Research. 45-10. 1113-1120 (2013) Nature Publishing Group

Meyer, Laurence R; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Kuhn, Robert M; Wong, Matthew; Sloan, Cricket A; Rosenbloom, Kate R; Roe, Greg; Rhead, Brooke; The UCSC Genome Browser database: extensions and updates 2013. Genome Research. 41-D1. D64-D69 (2013) Oxford University Press

Rosenbloom, Kate R; Sloan, Cricket A; Malladi, Venkat S; Dreszer, Timothy R; Learned, Katrina; Kirkup, Vanessa M; Wong, Matthew C; Maddren, Morgan; Fang, Ruihua; Heitner, Steven G; ENCODE data in the UCSC Genome Browser: year 5 update. Genome Research. 41-D1. D56-D63 (2013) Oxford University Press

Bradnam, Keith R; Fass, Joseph N; Alexandrov, Anton; Baranay, Paul; Bechner, Michael; Birol, Inanç; Boisvert, Sébastien; Chapman, Jarrod A; Chapuis, Guillaume; Chikhi, Rayan; A million cancer genome warehouse. Genome Research. 2-1. 10 (2013) BioMed Central

Hickey, Glenn; Paten, Benedict; Earl, Dent; Zerbino, Daniel; Haussler, David; Building a pangenome reference for a population. Genome Research. . btt128 (2013) Oxford University Press

Zerbino, Daniel R; Paten, Benedict; Hickey, Glenn; Haussler, David; Mapping to a reference genome structure. Genome Research. (2013)

Molak, Martyna; Lorenzen, Eline D; Shapiro, Beth; Ho, Simon YW; Human evolution: Turning back the clock. Genome Research. 30-2. 253-262 (2013) Oxford University Press

Gill, Mandev S; Lemey, Philippe; Faria, Nuno R; Rambaut, Andrew; Shapiro, Beth; Suchard, Marc A; Identifying deeper taxonomic relationships among RNA viruses. Genome Research. 30-3. 713-724 (2013) Oxford University Press

Vilstrup, Julia T; Seguin-Orlando, Andaine; Stiller, Mathias; Ginolhac, Aurelien; Raghavan, Maanasa; Nielsen, Sandra CA; Weinstock, Jacobo; Froese, Duane; Vasiliev, Sergei K; Ovodov, Nikolai D; Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Genome Research. 8-2. e55950 (2013) Public Library of Science

Cahill, James A; Green, Richard E; Fulton, Tara L; Stiller, Mathias; Jay, Flora; Ovsyanikov, Nikita; Salamzade, Rauf; John, John St; Stirling, Ian; Slatkin, Montgomery; Detecting Barriers to Gene Flow Among Extinct Populations. Genome Research. 9-3. e1003345 (2013) Public Library of Science

Fulton, Tara L; Norris, Ryan W; Graham, Russell W; Semken, Holmes A; Shapiro, Beth; A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Genome Research. 22-9. 2540-2548 (2013)

Green, Richard E; Shapiro, Beth; Shotgun microbial profiling of fossil remains. Genome Research. 23-7. R286-R288 (2013) Cell Press

Orlando, Ludovic; Ginolhac, AurÌ©lien; Zhang, Guojie; Froese, Duane; Albrechtsen, Anders; Stiller, Mathias; Schubert, Mikkel; Cappellini, Enrico; Petersen, Bent; Moltke, Ida; Brown bear (Ursus arctos)(9880å±35 BP) from late-glacial Champlain Sea deposits at Saint-Nicolas, Quebec, Canada, and the dispersal history of brown bears. Genome Research. 499-7456. 74-78 (2013) Nature Research

Thalmann, Olaf; Shapiro, Beth; Cui, Pin; Schuenemann, Verena J; Sawyer, Susanna K; Greenfield, DL; GermonprÌ©, MB; Sablin, MV; LÌ_pez-GirÌÁldez, F; Domingo-Roura, X; Buried Middle Pleistocene ice wedge systems and longterm survival of ancient Yedoma carbon. Genome Research. 342-6160. 871-874 (2013) American Association for the Advancement of Science

Farhat, Maha R; Shapiro, B Jesse; Kieser, Karen J; Sultana, Razvan; Jacobson, Karen R; Victor, Thomas C; Warren, Robin M; Streicher, Elizabeth M; Calver, Alistair; Sloutsky, Alex; Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation. Genome Research. 45-10. 1183-1189 (2013) Nature Publishing Group

Shapiro, Beth; Integration of biological networks and gene expression data using Cytoscape. Genome Research. . 475-481 (2013) Princeton University Press

Shapiro, Beth; Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy. Genome Research. . 475-481 (2013)

Shapiro, Beth; Predicting reliable regions in protein sequence alignments. Genome Research. . 475-481 (2013)

Shapiro, Beth; Hofreiter, Michael; Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy. Genome Research. . 475-481 (2013)

Meyer, Laurence R; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Kuhn, Robert M; Wong, Matthew; Sloan, Cricket A; Rosenbloom, Kate R; Roe, Greg; Rhead, Brooke; Exploring biological networks with Cytoscape software. Genome Research. 41-D1. D64-D69 (2013) Oxford Univ Press

Goldman, Mary; Craft, Brian; Swatloski, Teresa; Ellrott, Kyle; Cline, Melissa; Diekhans, Mark; Ma, Singer; Wilks, Chris; Stuart, Josh; Haussler, David; Abstract A33: Exploring pediatric cancer genomics with the UCSC Cancer Genomics Browser. Genome Research. 41-D1. D949-D954 (2013) Oxford Univ Press

Cline, Melissa S; Craft, Brian; Swatloski, Teresa; Goldman, Mary; Ma, Singer; Haussler, David; Zhu, Jingchun; A comparative encyclopedia of DNA elements in the mouse genome. Genome Research. 3. 2652 (2013) Nature Publishing Group

Hall, Megan P; Nagel, Roland J; Fagg, W Samuel; Shiue, Lily; Cline, Melissa S; Perriman, Rhonda J; Donohue, John Paul; Ares, Manuel; The UCSC cancer genomics browser: update 2015. Genome Research. 19-5. 627-638 (2013) Cold Spring Harbor Lab

Pistoni, Mariaelena; Shiue, Lily; Cline, Melissa S; Bortolanza, Sergia; Neguembor, Maria Victoria; Xynos, Alexandros; Ares Jr, Manuel; Gabellini, Davide; Human genetics special issue on computational molecular medicine. Genome Research. 9-1. e1003186 (2013) Public Library of Science

Nakamori, Masayuki; Sobczak, Krzysztof; Puwanant, Araya; Welle, Steve; Eichinger, Katy; Pandya, Shree; Dekdebrun, Jeannne; Heatwole, Chad R; McDermott, Michael P; Chen, Tian; Abstract LB-212: Treehouse Childhood Cancer Project: a resource for sharing and multiple cohort analysis of pediatric cancer genomics data. Genome Research. 74-6. 862-872 (2013) Wiley Online Library

Lopez-Bigas, Nuria; Cline, Melissa; Broom, Bradley; Margolin, Adam; Omberg, Larsson; Weinstein, John; Axton, Myles; A discriminative framework for detecting remote protein homologies. Genome Research. (2013) Nature Research

Pistoni, Mariaelena; Shiue, Lily; Cline, Melissa S; Bortolanza, Sergia; Neguembor, Maria Victoria; Xynos, Alexandros; Ares Jr, Manuel; Gabellini, Davide; Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species. Genome Research. 9-1. e1003186 (2013) Public Library of Science

Karolchik, D; Barber, GP; Casper, J; Clawson, H; Cline, MS; Diekhans, M; Dreszer, TR; Fujita, PA; Guruvadoo, L; Haeussler, M; CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Genome Research. (2013)

Diekhans, Mark; Team, UCSC CGHub; (2013)

Goldman, Mary; Craft, Brian; Swatloski, Teresa; Ellrott, Kyle; Cline, Melissa; Diekhans, Mark; Ma, Singer; Wilks, Chris; Stuart, Josh; Haussler, David; Genome Research. 41-D1. D949-D954 (2013) Oxford University Press

Meyer, Laurence R; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Kuhn, Robert M; Wong, Matthew; Sloan, Cricket A; Rosenbloom, Kate R; Roe, Greg; Rhead, Brooke; Genome Research. 41-D1. D64-D69 (2013) Oxford University Press

Rosenbloom, Kate R; Sloan, Cricket A; Malladi, Venkat S; Dreszer, Timothy R; Learned, Katrina; Kirkup, Vanessa M; Wong, Matthew C; Maddren, Morgan; Fang, Ruihua; Heitner, Steven G; Genome Research. 41-D1. D56-D63 (2013) Oxford University Press

Douville, Christopher; Carter, Hannah; Kim, Rick; Niknafs, Noushin; Diekhans, Mark; Stenson, Peter D; Cooper, David N; Ryan, Michael; Karchin, Rachel; Genome Research. . btt017 (2013) Oxford University Press

Niknafs, Noushin; Kim, Dewey; Kim, RyangGuk; Diekhans, Mark; Ryan, Michael; Stenson, Peter D; Cooper, David N; Karchin, Rachel; Genome Research. 132-11. 1235-1243 (2013) Springer Berlin Heidelberg

Wilks, Christopher; Maltbie, Dan; Diekhans, Mark; Haussler, David; Genome Research. 35. 42748 (2013)

Ezkurdia, Iakes; Juan, David; Rodriguez, Jose Manuel; Frankish, Adam; Diekhans, Mark; Harrow, Jennifer; Vazquez, Jesus; Valencia, Alfonso; Tress, Michael L; Genome Research. (2013)

Karolchik, D; Barber, GP; Casper, J; Clawson, H; Cline, MS; Diekhans, M; Dreszer, TR; Fujita, PA; Guruvadoo, L; Haeussler, M; Genome Research. (2013)

Cancer Genome Atlas Research Network; Integrated genomic characterization of endometrial carcinoma. Genome Research. 497-7447. 67 (2013) NIH Public Access

Bradnam, Keith R; Fass, Joseph N; Alexandrov, Anton; Baranay, Paul; Bechner, Michael; Birol, Inanç; Boisvert, Sébastien; Chapman, Jarrod A; Chapuis, Guillaume; Chikhi, Rayan; Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Genome Research. 2-1. 10 (2013) BioMed Central

Brennan, Cameron W; Verhaak, Roel GW; McKenna, Aaron; Campos, Benito; Noushmehr, Houtan; Salama, Sofie R; Zheng, Siyuan; Chakravarty, Debyani; Sanborn, J Zachary; Berman, Samuel H; The somatic genomic landscape of glioblastoma. Genome Research. 155-2. 462-477 (2013) Cell Press

Sanborn, J Zachary; Salama, Sofie R; Grifford, Mia; Brennan, Cameron W; Mikkelsen, Tom; Jhanwar, Suresh; Katzman, Sol; Chin, Lynda; Haussler, David; Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Genome Research. 73-19. 6036-6045 (2013) AACR

Hickey, Glenn; Paten, Benedict; Earl, Dent; Zerbino, Daniel; Haussler, David; HAL: a hierarchical format for storing and analyzing multiple genome alignments. Genome Research. 29-10. 1341-1342 (2013) Oxford University Press

Cline, Melissa S; Craft, Brian; Swatloski, Teresa; Goldman, Mary; Ma, Singer; Haussler, David; Zhu, Jingchun; Exploring TCGA pan-cancer data at the UCSC cancer genomics browser. Genome Research. 3(2013) Nature Publishing Group

Wong, Christopher K; Vaske, Charles J; Ng, Sam; Sanborn, J Zachary; Benz, Stephen C; Haussler, David; Stuart, Joshua M; The UCSC Interaction Browser: multidimensional data views in pathway context. Genome Research. 41-W1. W218-W224 (2013) Oxford University Press

Farrell, Catherine M; O’Leary, Nuala A; Harte, Rachel A; Loveland, Jane E; Wilming, Laurens G; Wallin, Craig; Diekhans, Mark; Barrell, Daniel; Searle, Stephen MJ; Aken, Bronwen; Current status and new features of the Consensus Coding Sequence database. Genome Research. 42-D1. D865-D872 (2013) Oxford University Press

Ewing, Adam D; Ballinger, Tracy J; Earl, Dent; Harris, Christopher C; Ding, Li; Wilson, Richard K; Haussler, David; Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Research. 14-3. R22 (2013) BioMed Central

Paull, Evan O; Carlin, Daniel E; Niepel, Mario; Sorger, Peter K; Haussler, David; Stuart, Joshua M; Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Genome Research. 29-21. 2757-2764 (2013) Oxford University Press

Wilks, Christopher; Maltbie, Dan; Diekhans, Mark; Haussler, David; Cghub: Kick-starting the worldwide genome web. Genome Research. 35. 42748 (2013)

Weinstein, John N; Collisson, Eric A; Mills, Gordon B; Shaw, Kenna R Mills; Ozenberger, Brad A; Ellrott, Kyle; Shmulevich, Ilya; Sander, Chris; Stuart, Joshua M; Cancer Genome Atlas Research Network; The cancer genome atlas pan-cancer analysis project. Genome Research. 45-10. 1113-1120 (2013) Nature Research

Karolchik, Donna; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Cline, Melissa S; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; The UCSC genome browser database: 2014 update. Genome Research. 42-D1. D764-D770 (2013) Oxford University Press

Khurana, Ekta; Fu, Yao; Colonna, Vincenza; Mu, Xinmeng Jasmine; Kang, Hyun Min; Lappalainen, Tuuli; Sboner, Andrea; Lochovsky, Lucas; Chen, Jieming; Harmanci, Arif; Integrative annotation of variants from 1092 humans: application to cancer genomics. Genome Research. 342-6154. 1235587 (2013) American Association for the Advancement of Science

Haussler, David; Large-scale comparative genomics for cancer research. (2013) Banff International Research Station for Mathematical Innovation and Discovery

Molak, Martyna; Lorenzen, Eline D; Shapiro, Beth; Ho, Simon YW; Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages. Genome Research. 30-2. 253-262 (2013) Oxford University Press

Gill, Mandev S; Lemey, Philippe; Faria, Nuno R; Rambaut, Andrew; Shapiro, Beth; Suchard, Marc A; Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Genome Research. 30-3. 713-724 (2013) Oxford University Press

Vilstrup, Julia T; Seguin-Orlando, Andaine; Stiller, Mathias; Ginolhac, Aurelien; Raghavan, Maanasa; Nielsen, Sandra CA; Weinstock, Jacobo; Froese, Duane; Vasiliev, Sergei K; Ovodov, Nikolai D; Mitochondrial phylogenomics of modern and ancient equids. Genome Research. 8-2. e55950 (2013) Public Library of Science

Cahill, James A; Green, Richard E; Fulton, Tara L; Stiller, Mathias; Jay, Flora; Ovsyanikov, Nikita; Salamzade, Rauf; John, John St; Stirling, Ian; Slatkin, Montgomery; Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. Genome Research. 9-3. e1003345 (2013) Public Library of Science

Fulton, Tara L; Norris, Ryan W; Graham, Russell W; Semken, Holmes A; Shapiro, Beth; Ancient DNA supports southern survival of Richardson’s collared lemming (Dicrostonyx richardsoni) during the last glacial maximum. Genome Research. 22-9. 2540-2548 (2013)

Green, Richard E; Shapiro, Beth; Human evolution: Turning back the clock. Genome Research. 23-7. R286-R288 (2013) Cell Press

Orlando, Ludovic; Ginolhac, Aur̩lien; Zhang, Guojie; Froese, Duane; Albrechtsen, Anders; Stiller, Mathias; Schubert, Mikkel; Cappellini, Enrico; Petersen, Bent; Moltke, Ida; Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Genome Research. 499-7456. 74-78 (2013) Nature Research

Thalmann, Olaf; Shapiro, Beth; Cui, Pin; Schuenemann, Verena J; Sawyer, Susanna K; Greenfield, DL; GermonprĚ©, MB; Sablin, MV; LĚ_pez-GirĚÁldez, F; Domingo-Roura, X; Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Genome Research. 342-6160. 871-874 (2013) American Association for the Advancement of Science

Farhat, Maha R; Shapiro, B Jesse; Kieser, Karen J; Sultana, Razvan; Jacobson, Karen R; Victor, Thomas C; Warren, Robin M; Streicher, Elizabeth M; Calver, Alistair; Sloutsky, Alex; Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Genome Research. 45-10. 1183-1189 (2013) Nature Publishing Group

Shapiro, Beth; Ancient DNA. Genome Research. . 475-481 (2013) Princeton University Press

Shapiro, Beth; Ancient DNA. Genome Research. . 475-481 (2013)

Shapiro, Beth; Hofreiter, Michael; Ancient DNA. Genome Research. . 475-481 (2013)

Hickey, Glenn; Paten, Benedict; Earl, Dent; Zerbino, Daniel; Haussler, David; HAL: a hierarchical format for storing and analyzing multiple genome alignments. Genome Research. . btt128 (2013) Oxford University Press

Zerbino, Daniel R; Paten, Benedict; Hickey, Glenn; Haussler, David; An algebraic framework to sample the rearrangement histories of a cancer metagenome with double cut and join, duplication and deletion events.. Genome Research. (2013)

Imielinski, Marcin; Berger, Alice H; Hammerman, Peter S; Hernandez, Bryan; Pugh, Trevor J; Hodis, Eran; Cho, Jeonghee; Suh, James; Capelletti, Marzia; Sivachenko, Andrey; Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Genome Research. 150-6. 1107-1120 (2012) Cell Press

Dreszer, Timothy R; Karolchik, Donna; Zweig, Ann S; Hinrichs, Angie S; Raney, Brian J; Kuhn, Robert M; Meyer, Laurence R; Wong, Mathew; Sloan, Cricket A; Rosenbloom, Kate R; The UCSC Genome Browser database: extensions and updates 2011. Genome Research. 40-D1. D918-D923 (2012) Oxford University Press

Westesson, Oscar; Lunter, Gerton; Paten, Benedict; Holmes, Ian; Phylogenetic automata, pruning, and multiple alignment. Genome Research. 7-4. e34572 (2012) Public Library of Science

Zerbino, DR; Paten, B; Haussler, D; Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Genome Research. 336-6078. 179-182 (2012) American Association for the Advancement of Science

Haussler, David; Patterson, David A; Diekhans, Mark; Fox, Armando; Jordan, Michael; Joseph, Anthony D; Ma, Singer; Paten, Benedict; Shenker, Scott; Sittler, Taylor; Alignathon: a competitive assessment of whole-genome alignment methods. (2012) CALIFORNIA UNIV BERKELEY DEPT OF ELECTRICAL ENGINEERING AND COMPUTER SCIENCE

Fulton, Tara L; Wagner, Stephen M; Fisher, Clemency; Shapiro, Beth; Multiple losses of flight and recent speciation in steamer ducks. Genome Research. 194-1. 52-57 (2012) Urban & Fischer

Letts, Brandon; Shapiro, Beth; Homotherium serum and Cervalces from the Great Lakes Region, USA: geochronology, morphology and ancient DNA. Genome Research. . 87-92 (2012) Humana Press

Fulton, Tara L; Wagner, Stephen M; Shapiro, Beth; Is the endangered Grevy’s zebra threatened by hybridization?. Genome Research. . 29-35 (2012) Humana Press

Fulton, Tara L; Letts, Brandon; Shapiro, Beth; Grevy’s zebra conservation: overcoming threats of isolation, genetic hybridization and demographic instability. Genome Research. . rspb20112599 (2012) The Royal Society

DalÌ©n, Love; Orlando, Ludovic; Shapiro, Beth; Brandstr̦m-Durling, Mikael; Quam, Rolf; Gilbert, M Thomas P; FernÌÁndez-Lomana, J Carlos DÌ_ez; Willerslev, Eske; Arsuaga, Juan Luis; G̦therstr̦m, Anders; Ancient hybridization and an Irish origin for the modern polar bear matriline. Genome Research. 29-8. 1893-1897 (2012) Oxford University Press

Fischer, Anne; Shapiro, Beth; Muriuki, Cecilia; Heller, Martin; Schnee, Christiane; Bongcam-Rudloff, Erik; Vilei, Edy M; Frey, Joachim; Jores, Joerg; Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages. Genome Research. 7-4. e36150 (2012) Public Library of Science

Ginolhac, Aurelien; Vilstrup, Julia; Stenderup, Jesper; Rasmussen, Morten; Stiller, Mathias; Shapiro, Beth; Zazula, Grant; Froese, Duane; Steinmann, Kathleen E; Thompson, John F; Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Genome Research. 13-1. 177 (2012) BioMed Central

Letts, Brandon; Fulton, Tara L; Stiller, Mathias; Andrews, Thomas D; MacKAY, GLEN; Popko, Richard; Shapiro, Beth; Understanding the adenine richness of the HIV genome through the estimation of misincorporation rates in viv. Genome Research. . 80-94 (2012) The Arctic Institute of North America

MacDonald, GM; Beilman, DW; Kuzmin, YV; Orlova, LA; Kremenetski, KV; Shapiro, B; Wayne, RK; Van Valkenburgh, B; Population genomic analysis of within-host HIV diversity. Genome Research. 3. 893 (2012) Nature Publishing Group

Widga, Chris; Fulton, Tara L; Martin, Larry D; Shapiro, Beth; Mitochondrial phylogenomics of modern and ancient equids. Genome Research. 41-4. 546-556 (2012)

Shapiro, Beth; Hofreiter, Michael; Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. (2012) Springer

Froese, DG; Jensen, BJ; Reyes, A; Poinar, H; Shapiro, B; Zazula, G; Calmels, F; Paleogenomics. Genome Research. 1. 408 (2012)

Dreszer, Timothy R; Karolchik, Donna; Zweig, Ann S; Hinrichs, Angie S; Raney, Brian J; Kuhn, Robert M; Meyer, Laurence R; Wong, Mathew; Sloan, Cricket A; Rosenbloom, Kate R; The effects of alternative splicing on transmembrane proteins in the mouse genome.. Genome Research. 40-D1. D918-D923 (2012) Oxford Univ Press

Stamatoyannopoulos, John A; Snyder, Michael; Hardison, Ross; Ren, Bing; Gingeras, Thomas; Gilbert, David M; Groudine, Mark; Bender, Michael; Kaul, Rajinder; Canfield, Theresa; Affy exon tissues: exon levels in normal tissues in human, mouse and rat. Genome Research. 13-8. 418 (2012) BioMed Central

Charizanis, Konstantinos; Lee, Kuang-Yung; Batra, Ranjan; Goodwin, Marianne; Zhang, Chaolin; Yuan, Yuan; Shiue, Lily; Cline, Melissa; Scotti, Marina M; Xia, Guangbin; Thread 4: Data discovery, transparency and visualization. Genome Research. 75-3. 437-450 (2012) Cell Press

Dreszer, Timothy R; Karolchik, Donna; Zweig, Ann S; Hinrichs, Angie S; Raney, Brian J; Kuhn, Robert M; Meyer, Laurence R; Wong, Mathew; Sloan, Cricket A; Rosenbloom, Kate R; Genome Research. 40-D1. D918-D923 (2012) Oxford University Press

Harte, Rachel A; Farrell, Catherine M; Loveland, Jane E; Suner, Marie-Marthe; Wilming, Laurens; Aken, Bronwen; Barrell, Daniel; Frankish, Adam; Wallin, Craig; Searle, Steve; Genome Research. 2012. bas008 (2012) Oxford University Press

Pei, Baikang; Sisu, Cristina; Frankish, Adam; Howald, Cédric; Habegger, Lukas; Mu, Xinmeng Jasmine; Harte, Rachel; Balasubramanian, Suganthi; Tanzer, Andrea; Diekhans, Mark; Genome Research. 13-9. R51 (2012) BioMed Central

Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen L; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen; Genome Research. 22-9. 1760-1774 (2012) Cold Spring Harbor Lab

Haussler, David; Patterson, David A; Diekhans, Mark; Fox, Armando; Jordan, Michael; Joseph, Anthony D; Ma, Singer; Paten, Benedict; Shenker, Scott; Sittler, Taylor; (2012) CALIFORNIA UNIV BERKELEY DEPT OF ELECTRICAL ENGINEERING AND COMPUTER SCIENCE

Cancer Genome Atlas Network; Comprehensive molecular characterization of human colon and rectal cancer. Genome Research. 487-7407. 330 (2012) NIH Public Access

Cancer Genome Atlas Research Network; Comprehensive genomic characterization of squamous cell lung cancers. Genome Research. 489-7417. 519 (2012) NIH Public Access

Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen L; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen; GENCODE: the reference human genome annotation for The ENCODE Project. Genome Research. 22-9. 1760-1774 (2012) Cold Spring Harbor Lab

Meyer, Laurence R; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Kuhn, Robert M; Wong, Matthew; Sloan, Cricket A; Rosenbloom, Kate R; Roe, Greg; Rhead, Brooke; The UCSC Genome Browser database: extensions and updates 2013. Genome Research. 41-D1. D64-D69 (2012) Oxford University Press

Heiser, Laura M; Sadanandam, Anguraj; Kuo, Wen-Lin; Benz, Stephen C; Goldstein, Theodore C; Ng, Sam; Gibb, William J; Wang, Nicholas J; Ziyad, Safiyyah; Tong, Frances; Subtype and pathway specific responses to anticancer compounds in breast cancer. Genome Research. 109-8. 2724-2729 (2012) National Acad Sciences

Rosenbloom, Kate R; Sloan, Cricket A; Malladi, Venkat S; Dreszer, Timothy R; Learned, Katrina; Kirkup, Vanessa M; Wong, Matthew C; Maddren, Morgan; Fang, Ruihua; Heitner, Steven G; ENCODE data in the UCSC Genome Browser: year 5 update. Genome Research. 41-D1. D56-D63 (2012) Oxford University Press

Kristensen, Vessela N; Vaske, Charles J; Ursini-Siegel, Josie; Van Loo, Peter; Nordgard, Silje H; Sachidanandam, Ravi; Sørlie, Therese; Wärnberg, Fredrik; Haakensen, Vilde D; Helland, Åslaug; Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Genome Research. 109-8. 2802-2807 (2012) National Acad Sciences

Kuhn, Robert M; Haussler, David; Kent, W James; The UCSC genome browser and associated tools. Genome Research. 14-2. 144-161 (2012) Oxford University Press

Raab, Jesse R; Chiu, Jonathan; Zhu, Jingchun; Katzman, Sol; Kurukuti, Sreenivasulu; Wade, Paul A; Haussler, David; Kamakaka, Rohinton T; Human tRNA genes function as chromatin insulators. Genome Research. 31-2. 330-350 (2012) EMBO Press

Goldman, Mary; Craft, Brian; Swatloski, Teresa; Ellrott, Kyle; Cline, Melissa; Diekhans, Mark; Ma, Singer; Wilks, Chris; Stuart, Josh; Haussler, David; The UCSC cancer genomics browser: update 2013. Genome Research. 41-D1. D949-D954 (2012) Oxford University Press

Zerbino, DR; Paten, B; Haussler, D; Integrating genomes. Genome Research. 336-6078. 179-182 (2012) American Association for the Advancement of Science

Ng, Sam; Collisson, Eric A; Sokolov, Artem; Goldstein, Theodore; Gonzalez-Perez, Abel; Lopez-Bigas, Nuria; Benz, Christopher; Haussler, David; Stuart, Joshua M; PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Genome Research. 28-18. i640-i646 (2012) Oxford University Press

Lowe, Craig B; Haussler, David; 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. Genome Research. 7-8. e43128 (2012) Public Library of Science

Wong, Pamela BY; Wiley, Edward O; Johnson, Warren E; Ryder, Oliver A; O’Brien, Stephen J; Haussler, David; Koepfli, Klaus-Peter; Houck, Marlys L; Perelman, Polina; Mastromonaco, Gabriela; Tissue sampling methods and standards for vertebrate genomics. Genome Research. 1-1. 8 (2012) BioMed Central

Bernardi, Giacomo; Wiley, Edward O; Mansour, Hicham; Miller, Michael R; Orti, Guillermo; Haussler, David; O’Brien, Stephen J; Ryder, Oliver A; Venkatesh, Byrappa; The fishes of Genome 10K. Genome Research. 7. 42800 (2012) Elsevier

Onodera, Courtney S; Underwood, Jason G; Katzman, Sol; Jacobs, Frank; Greenberg, David; Salama, Sofie R; Haussler, David; Gene isoform specificity through enhancer-associated antisense transcription. Genome Research. 7-8. e43511 (2012) Public Library of Science

Haussler, David; Patterson, David A; Diekhans, Mark; Fox, Armando; Jordan, Michael; Joseph, Anthony D; Ma, Singer; Paten, Benedict; Shenker, Scott; Sittler, Taylor; A million cancer genome warehouse. (2012) CALIFORNIA UNIV BERKELEY DEPT OF ELECTRICAL ENGINEERING AND COMPUTER SCIENCE

Cancer Genome Atlas Network; Comprehensive molecular portraits of human breast tumors. Genome Research. 490-7418. 61 (2012) NIH Public Access

ENCODE Project Consortium; An integrated encyclopedia of DNA elements in the human genome. Genome Research. 489-7414. 57 (2012) NIH Public Access

Riggs, ER; Church, DM; Hanson, K; Horner, VL; Kaminsky, EB; Kuhn, RM; Wain, KE; Williams, ES; Aradhya, S; Kearney, HM; Towards an evidence?based process for the clinical interpretation of copy number variation. Genome Research. 81-5. 403-412 (2012) Wiley Online Library

de Leeuw, Nicole; Dijkhuizen, Trijnie; Hehir?Kwa, Jayne Y; Carter, Nigel P; Feuk, Lars; Firth, Helen V; Kuhn, Robert M; Ledbetter, David H; Martin, Christa Lese; van Ravenswaaij?Arts, Conny; Diagnostic interpretation of array data using public databases and internet sources. Genome Research. 33-6. 930-940 (2012) Wiley Online Library

Riggs, ER; Kaminsky, EB; Patel, V; Faucett, WA; Thorland, E; Church, D; Paschall, J; Jackson, L; Aradhya, S; Kuhn, R; Towards a Universal Database of Human Genomic Variation: Lessons Learned from the ISCA Consortium. Genome Research. 136-4. 333-333 (2012) KARGER ALLSCHWILERSTRASSE 10, CH-4009 BASEL, SWITZERLAND

Laura Clarke, Xiangqun Zheng-Bradley, Richard Smith, Eugene Kulesha, Chunlin Xiao, Iliana Toneva, Brendan Vaughan, Don Preuss, Rasko Leinonen, Martin Shumway, Stephen Sherry, Paul Flicek & The 1000 Genomes Project Consortium; The 1000 Genomes Project: data management and community access. Genome Research. 9. 459-462 (2012) Nature

Fulton, Tara L; Wagner, Stephen M; Fisher, Clemency; Shapiro, Beth; Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons. Genome Research. 194-1. 52-57 (2012) Urban & Fischer

Letts, Brandon; Shapiro, Beth; Case study: ancient DNA recovered from Pleistocene-age remains of a Florida armadillo. Genome Research. . 87-92 (2012) Humana Press

Fulton, Tara L; Wagner, Stephen M; Shapiro, Beth; Case study: recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon. Genome Research. . 29-35 (2012) Humana Press

Fulton, Tara L; Letts, Brandon; Shapiro, Beth; Multiple losses of flight and recent speciation in steamer ducks. Genome Research. . rspb20112599 (2012) The Royal Society

DalĚ©n, Love; Orlando, Ludovic; Shapiro, Beth; Brandstr̦m-Durling, Mikael; Quam, Rolf; Gilbert, M Thomas P; FernĚÁndez-Lomana, J Carlos DĚ_ez; Willerslev, Eske; Arsuaga, Juan Luis; G̦therstr̦m, Anders; Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. Genome Research. 29-8. 1893-1897 (2012) Oxford University Press

Fischer, Anne; Shapiro, Beth; Muriuki, Cecilia; Heller, Martin; Schnee, Christiane; Bongcam-Rudloff, Erik; Vilei, Edy M; Frey, Joachim; Jores, Joerg; The origin of the ‰Ű÷Mycoplasma mycoides cluster‰ŰŞcoincides with domestication of ruminants. Genome Research. 7-4. e36150 (2012) Public Library of Science

Ginolhac, Aurelien; Vilstrup, Julia; Stenderup, Jesper; Rasmussen, Morten; Stiller, Mathias; Shapiro, Beth; Zazula, Grant; Froese, Duane; Steinmann, Kathleen E; Thompson, John F; Improving the performance of true single molecule sequencing for ancient DNA. Genome Research. 13-1. 177 (2012) BioMed Central

Letts, Brandon; Fulton, Tara L; Stiller, Mathias; Andrews, Thomas D; MacKAY, GLEN; Popko, Richard; Shapiro, Beth; Ancient DNA reveals genetic continuity in mountain woodland caribou of the Mackenzie and Selwyn Mountains, Northwest Territories, Canada. Genome Research. . 80-94 (2012) The Arctic Institute of North America

MacDonald, GM; Beilman, DW; Kuzmin, YV; Orlova, LA; Kremenetski, KV; Shapiro, B; Wayne, RK; Van Valkenburgh, B; Pattern of extinction of the woolly mammoth in Beringia. Genome Research. 3. 893 (2012) Nature Publishing Group

Widga, Chris; Fulton, Tara L; Martin, Larry D; Shapiro, Beth; Homotherium serum and Cervalces from the Great Lakes Region, USA: geochronology, morphology and ancient DNA. Genome Research. 41-4. 546-556 (2012)

Shapiro, Beth; Hofreiter, Michael; Ancient DNA: Methods and Protocols. (2012) Springer

Froese, DG; Jensen, BJ; Reyes, A; Poinar, H; Shapiro, B; Zazula, G; Calmels, F; Buried Middle Pleistocene ice wedge systems and longterm survival of ancient Yedoma carbon. Genome Research. 1. 408 (2012)

Westesson, Oscar; Lunter, Gerton; Paten, Benedict; Holmes, Ian; Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. Genome Research. 7-4. e34572 (2012) Public Library of Science

Graveley, Brenton R; Brooks, Angela N; Carlson, Joseph W; Duff, Michael O; Landolin, Jane M; Yang, Li; Artieri, Carlo G; van Baren, Marijke J; Boley, Nathan; Booth, Benjamin W; The developmental transcriptome of Drosophila melanogaster. Genome Research. 471-7339. 473-479 (2011) Nature Research

Brooks, Angela N; Yang, Li; Duff, Michael O; Hansen, Kasper D; Park, Jung W; Dudoit, Sandrine; Brenner, Steven E; Graveley, Brenton R; Conservation of an RNA regulatory map between Drosophila and mammals. Genome Research. 21-2. 193-202 (2011) Cold Spring Harbor Lab

Brooks, Angela N; Aspden, Julie L; Podgornaia, Anna I; Rio, Donald C; Brenner, Steven E; Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. Genome Research. 17-10. 1884-1894 (2011) Cold Spring Harbor Lab

Paten, Benedict; Diekhans, Mark; Earl, Dent; John, John St; Ma, Jian; Suh, Bernard; Haussler, David; Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 18-3. 469-481 (2011) Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA

Paten, Benedict; Earl, Dent; Nguyen, Ngan; Diekhans, Mark; Zerbino, Daniel; Haussler, David; An alignment-free generalization to indels of Felsenstein’s phylogenetic pruning algorithm. Genome Research. 21-9. 1512-1528 (2011) Cold Spring Harbor Lab

Earl, Dent; Bradnam, Keith; John, John St; Darling, Aaron; Lin, Dawei; Fass, Joseph; Yu, Hung On Ken; Buffalo, Vince; Zerbino, Daniel R; Diekhans, Mark; Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization. Genome Research. 21-12. 2224-2241 (2011) Cold Spring Harbor Lab

Westesson, Oscar; Lunter, Gerton; Paten, Benedict; Holmes, Ian; Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. Genome Research. 11034347(2011)

Roskin, Krishna M; Paten, Benedict; Haussler, David; Integrating genomes. Genome Research. 12-1. 144 (2011) BioMed Central

ENCODE Project Consortium; A unifying model of genome evolution under parsimony. Genome Research. 9-4. e1001046 (2011)

Westesson, Oscar; Lunter, Gerton; Paten, Benedict; Holmes, Ian; HAL: a hierarchical format for storing and analyzing multiple genome alignments. Genome Research. (2011)

Ho, Simon YW; Shapiro, Beth; Ancient DNA typing of archaeological pig remains corroborates historical records. Genome Research. 11-3. 423-434 (2011) Blackwell Publishing Ltd

Ho, Simon YW; Lanfear, Robert; Phillips, Matthew J; Barnes, Ian; Thomas, Jessica A; Kolokotronis, Sergios-Orestis; Shapiro, Beth; Recovery of DNA from footprints in the snow. Genome Research. 60-3. 366-375 (2011) Oxford University Press

Shapiro, Beth; Ho, Simon YW; Drummond, Alexei J; Suchard, Marc A; Pybus, Oliver G; Rambaut, Andrew; Discovery of lost diversity of paternal horse lineages using ancient DNA. Genome Research. 28-2. 879-887 (2011) Oxford University Press

Harrison, Abby; Lemey, Philippe; Hurles, Matthew; Moyes, Chris; Horn, Susanne; Pryor, Jan; Malani, Joji; Supuri, Mathias; Masta, Andrew; Teriboriki, Burentau; Ancient DNA confirms a local origin of domesticated chenopod in eastern North America. Genome Research. 3-2. 83-101 (2011) Molecular Diversity Preservation International

Orlando, Ludovic; Ginolhac, Aurelien; Raghavan, Maanasa; Vilstrup, Julia; Rasmussen, Morten; Magnussen, Kim; Steinmann, Kathleen E; Kapranov, Philipp; Thompson, John F; Zazula, Grant; Population-level genotyping of coat colour polymorphism in woolly mammoth (Mammuthus primigenius). Genome Research. 21-10. 1705-1719 (2011) Cold Spring Harbor Lab

Lippold, Sebastian; Knapp, Michael; Kuznetsova, Tatyana; Leonard, Jennifer A; Benecke, Norbert; Ludwig, Arne; Rasmussen, Morten; Cooper, Alan; Weinstock, Jaco; Willerslev, Eske; Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. Genome Research. 2. 450 (2011) Nature Research

Kistler, Logan; Shapiro, Beth; The origin of the ‰Û÷Mycoplasma mycoides cluster‰Ûªcoincides with domestication of ruminants. Genome Research. 38-12. 3549-3554 (2011) Academic Press

Lorenzen, Eline D; Nogu̩s-Bravo, David; Orlando, Ludovic; Weinstock, Jaco; Binladen, Jonas; Marske, Katharine A; Ugan, Andrew; Borregaard, Michael K; Gilbert, M Thomas P; Nielsen, Rasmus; Improving the performance of true single molecule sequencing for ancient DNA. Genome Research. 479-7373. 359-364 (2011) Nature Publishing Group

Workman, Claire; Dalen, Love; Vartanyan, Sergey; Shapiro, Beth; Kosintsev, Pavel; Sher, Andrei; Gotherstrom, Anders; Barnes, Ian; Ancient DNA reveals genetic continuity in mountain woodland caribou of the Mackenzie and Selwyn Mountains, Northwest Territories, Canada. Genome Research. 30-17. 2304-2308 (2011) Pergamon

Higham, Tom; Compton, Tim; Stringer, Chris; Jacobi, Roger; Shapiro, Beth; Trinkaus, Erik; Chandler, Barry; Gr̦ning, Flora; Collins, Chris; Hillson, Simon; Pattern of extinction of the woolly mammoth in Beringia. Genome Research. 479-7374. 521-524 (2011) Nature Publishing Group

Edwards, Ceiridwen J; Suchard, Marc A; Lemey, Philippe; Welch, John J; Barnes, Ian; Fulton, Tara L; Barnett, Ross; O’Connell, Tamsin C; Coxon, Peter; Monaghan, Nigel; Protocols for sampling viral sequences to study epidemic dynamics. Genome Research. 21-15. 1251-1258 (2011) Cell Press

Barnett, Ross; Shapiro, B; Barnes, I; Ho, S; Burger, J; Yamaguchi, Nobuyuki; Time‰Ûdependent estimates of molecular evolutionary rates: evidence and causes. Genome Research. 2011-1. 2733 (2011) Bloomsbury Qatar Foundation Journals

Rosenbloom, Kate R; Dreszer, Timothy R; Long, Jeffrey C; Malladi, Venkat S; Sloan, Cricket A; Raney, Brian J; Cline, Melissa S; Karolchik, Donna; Barber, Galt P; Clawson, Hiram; Protein sequence alignment reliability: prediction and measurement. Genome Research. . gkr1012 (2011) Oxford University Press

Cline, Melissa S; Karchin, Rachel; The consequences of alternative splicing on biological pathways. Genome Research. 27-4. 441-448 (2011) Oxford University Press

Earl, Dent; Bradnam, Keith; John, John St; Darling, Aaron; Lin, Dawei; Fass, Joseph; Yu, Hung On Ken; Buffalo, Vince; Zerbino, Daniel R; Diekhans, Mark; Genome Research. 21-12. 2224-2241 (2011) Cold Spring Harbor Lab

Paten, Benedict; Diekhans, Mark; Earl, Dent; John, John St; Ma, Jian; Suh, Bernard; Haussler, David; Genome Research. 18-3. 469-481 (2011) Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA

Paten, Benedict; Earl, Dent; Nguyen, Ngan; Diekhans, Mark; Zerbino, Daniel; Haussler, David; Genome Research. 21-9. 1512-1528 (2011) Cold Spring Harbor Lab

Wong, Wing Chung; Kim, Dewey; Carter, Hannah; Diekhans, Mark; Ryan, Michael C; Karchin, Rachel; Genome Research. 27-15. 2147-2148 (2011) Oxford Univ Press

Rosenbloom, Kate R; Dreszer, Timothy R; Long, Jeffrey C; Malladi, Venkat S; Sloan, Cricket A; Raney, Brian J; Cline, Melissa S; Karolchik, Donna; Barber, Galt P; Clawson, Hiram; Genome Research. . gkr1012 (2011) Oxford University Press

Cancer Genome Atlas Research Network; Integrated genomic analyses of ovarian carcinoma. Genome Research. 474-7353. 609 (2011) NIH Public Access

Dreszer, Timothy R; Karolchik, Donna; Zweig, Ann S; Hinrichs, Angie S; Raney, Brian J; Kuhn, Robert M; Meyer, Laurence R; Wong, Mathew; Sloan, Cricket A; Rosenbloom, Kate R; The UCSC Genome Browser database: extensions and updates 2011. Genome Research. 40-D1. D918-D923 (2011) Oxford University Press

Lindblad-Toh, Kerstin; Garber, Manuel; Zuk, Or; Lin, Michael F; Parker, Brian J; Washietl, Stefan; Kheradpour, Pouya; Ernst, Jason; Jordan, Gregory; Mauceli, Evan; A high-resolution map of human evolutionary constraint using 29 mammals. Genome Research. 478-7370. 476 (2011) NIH Public Access

Locke, Devin P; Hillier, LaDeana W; Warren, Wesley C; Worley, Kim C; Nazareth, Lynne V; Muzny, Donna M; Yang, Shiaw-Pyng; Wang, Zhengyuan; Chinwalla, Asif T; Minx, Pat; Comparative and demographic analysis of orangutan genomes. Genome Research. 469-7331. 529 (2011) NIH Public Access

Earl, Dent; Bradnam, Keith; John, John St; Darling, Aaron; Lin, Dawei; Fass, Joseph; Yu, Hung On Ken; Buffalo, Vince; Zerbino, Daniel R; Diekhans, Mark; Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21-12. 2224-2241 (2011) Cold Spring Harbor Lab

Alföldi, Jessica; Di Palma, Federica; Grabherr, Manfred; Williams, Christina; Kong, Lesheng; Mauceli, Evan; Russell, Pamela; Lowe, Craig B; Glor, Richard; Jaffe, Jacob D; The genome of the green anole lizard and a comparative analysis with birds and mammals. Genome Research. 477-7366. 587 (2011) NIH Public Access

Rosenbloom, Kate R; Dreszer, Timothy R; Long, Jeffrey C; Malladi, Venkat S; Sloan, Cricket A; Raney, Brian J; Cline, Melissa S; Karolchik, Donna; Barber, Galt P; Clawson, Hiram; ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Genome Research. 40-D1. D912-D917 (2011) Oxford University Press

Wang, Nicholas J; Sanborn, Zachary; Arnett, Kelly L; Bayston, Laura J; Liao, Wilson; Proby, Charlotte M; Leigh, Irene M; Collisson, Eric A; Gordon, Patricia B; Jakkula, Lakshmi; Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma. Genome Research. 108-43. 17761-17766 (2011) National Acad Sciences

Lowe, Craig B; Kellis, Manolis; Siepel, Adam; Raney, Brian J; Clamp, Michele; Salama, Sofie R; Kingsley, David M; Lindblad-Toh, Kerstin; Haussler, David; Three periods of regulatory innovation during vertebrate evolution. Genome Research. 333-6045. 1019-1024 (2011) American Association for the Advancement of Science

Zhou, Xin; Maricque, Brett; Xie, Mingchao; Li, Daofeng; Sundaram, Vasavi; Martin, Eric A; Koebbe, Brian C; Nielsen, Cydney; Hirst, Martin; Farnham, Peggy; The human epigenome browser at Washington University. Genome Research. 8-12. 989-990 (2011) Nature Research

Katzman, Sol; Capra, John A; Haussler, David; Pollard, Katherine S; Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Research. 3. 614-626 (2011) Oxford University Press

Paten, Benedict; Earl, Dent; Nguyen, Ngan; Diekhans, Mark; Zerbino, Daniel; Haussler, David; Cactus: Algorithms for genome multiple sequence alignment. Genome Research. 21-9. 1512-1528 (2011) Cold Spring Harbor Lab

Paten, Benedict; Diekhans, Mark; Earl, Dent; John, John St; Ma, Jian; Suh, Bernard; Haussler, David; Cactus graphs for genome comparisons. Genome Research. 18-3. 469-481 (2011) Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA

Roskin, Krishna M; Paten, Benedict; Haussler, David; Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization. Genome Research. 12-1. 144 (2011) BioMed Central

Vaske, Charles J; Benz, Stephen C; Stuart, Joshua M; Haussler, David; Pathway recognition algorithm using data integration on genomic models (PARADIGM). (2011) US Patent App. 13/068,002

Haussler, David; Cancer genomics. Genome Research. . 42798 (2011) ACM

Haussler, David; David Haussler.. Genome Research. 29-3. 243 (2011)

Ho, Simon YW; Shapiro, Beth; Skyline‰Ű�plot methods for estimating demographic history from nucleotide sequences. Genome Research. 11-3. 423-434 (2011) Blackwell Publishing Ltd

Ho, Simon YW; Lanfear, Robert; Phillips, Matthew J; Barnes, Ian; Thomas, Jessica A; Kolokotronis, Sergios-Orestis; Shapiro, Beth; Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Genome Research. 60-3. 366-375 (2011) Oxford University Press

Shapiro, Beth; Ho, Simon YW; Drummond, Alexei J; Suchard, Marc A; Pybus, Oliver G; Rambaut, Andrew; A Bayesian phylogenetic method to estimate unknown sequence ages. Genome Research. 28-2. 879-887 (2011) Oxford University Press

Harrison, Abby; Lemey, Philippe; Hurles, Matthew; Moyes, Chris; Horn, Susanne; Pryor, Jan; Malani, Joji; Supuri, Mathias; Masta, Andrew; Teriboriki, Burentau; Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation. Genome Research. 3-2. 83-101 (2011) Molecular Diversity Preservation International

Orlando, Ludovic; Ginolhac, Aurelien; Raghavan, Maanasa; Vilstrup, Julia; Rasmussen, Morten; Magnussen, Kim; Steinmann, Kathleen E; Kapranov, Philipp; Thompson, John F; Zazula, Grant; True single-molecule DNA sequencing of a pleistocene horse bone. Genome Research. 21-10. 1705-1719 (2011) Cold Spring Harbor Lab

Lippold, Sebastian; Knapp, Michael; Kuznetsova, Tatyana; Leonard, Jennifer A; Benecke, Norbert; Ludwig, Arne; Rasmussen, Morten; Cooper, Alan; Weinstock, Jaco; Willerslev, Eske; Discovery of lost diversity of paternal horse lineages using ancient DNA. Genome Research. 2. 450 (2011) Nature Research

Kistler, Logan; Shapiro, Beth; Ancient DNA confirms a local origin of domesticated chenopod in eastern North America. Genome Research. 38-12. 3549-3554 (2011) Academic Press

Lorenzen, Eline D; Nogu̩s-Bravo, David; Orlando, Ludovic; Weinstock, Jaco; Binladen, Jonas; Marske, Katharine A; Ugan, Andrew; Borregaard, Michael K; Gilbert, M Thomas P; Nielsen, Rasmus; Species-specific responses of Late Quaternary megafauna to climate and humans. Genome Research. 479-7373. 359-364 (2011) Nature Publishing Group

Workman, Claire; Dalen, Love; Vartanyan, Sergey; Shapiro, Beth; Kosintsev, Pavel; Sher, Andrei; Gotherstrom, Anders; Barnes, Ian; Population-level genotyping of coat colour polymorphism in woolly mammoth (Mammuthus primigenius). Genome Research. 30-17. 2304-2308 (2011) Pergamon

Higham, Tom; Compton, Tim; Stringer, Chris; Jacobi, Roger; Shapiro, Beth; Trinkaus, Erik; Chandler, Barry; Gr̦ning, Flora; Collins, Chris; Hillson, Simon; The earliest evidence for anatomically modern humans in northwestern Europe. Genome Research. 479-7374. 521-524 (2011) Nature Publishing Group

Edwards, Ceiridwen J; Suchard, Marc A; Lemey, Philippe; Welch, John J; Barnes, Ian; Fulton, Tara L; Barnett, Ross; O’Connell, Tamsin C; Coxon, Peter; Monaghan, Nigel; Ancient hybridization and an Irish origin for the modern polar bear matriline. Genome Research. 21-15. 1251-1258 (2011) Cell Press

Barnett, Ross; Shapiro, B; Barnes, I; Ho, S; Burger, J; Yamaguchi, Nobuyuki; Phylogeography of lions (Panthera leo) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Genome Research. 2011-1. 2733 (2011) Bloomsbury Qatar Foundation Journals

Westesson, Oscar; Lunter, Gerton; Paten, Benedict; Holmes, Ian; An alignment-free generalization to indels of Felsenstein’s phylogenetic pruning algorithm. Genome Research. 11034347(2011)

ENCODE Project Consortium; A user’s guide to the encyclopedia of DNA elements (ENCODE). Genome Research. 9-4. e1001046 (2011)

Westesson, Oscar; Lunter, Gerton; Paten, Benedict; Holmes, Ian; Phylogenetic automata, pruning, and multiple alignment. Genome Research. (2011)

Roy, Sushmita; Ernst, Jason; Kharchenko, Peter V; Kheradpour, Pouya; Negre, Nicolas; Eaton, Matthew L; Landolin, Jane M; Bristow, Christopher A; Ma, Lijia; Lin, Michael F; Identification of functional elements and regulatory circuits by Drosophila modENCODE. Genome Research. 330-6012. 1787-1797 (2010) American Association for the Advancement of Science

Fujita, Pauline A; Rhead, Brooke; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Cline, Melissa S; Goldman, Mary; Barber, Galt P; Clawson, Hiram; Coelho, Antonio; The UCSC genome browser database: update 2011. Genome Research. . gkq963 (2010) Oxford University Press

Rosenbloom, Kate R; Dreszer, Timothy R; Pheasant, Michael; Barber, Galt P; Meyer, Laurence R; Pohl, Andy; Raney, Brian J; Wang, Ting; Hinrichs, Angie S; Zweig, Ann S; ENCODE whole-genome data in the UCSC Genome Browser. Genome Research. 38-suppl 1. D620-D625 (2010) Oxford Univ Press

Raney, Brian J; Cline, Melissa S; Rosenbloom, Kate R; Dreszer, Timothy R; Learned, Katrina; Barber, Galt P; Meyer, Laurence R; Sloan, Cricket A; Malladi, Venkat S; Roskin, Krishna M; ENCODE whole-genome data in the UCSC genome browser (2011 update). Genome Research. . gkq1017 (2010) Oxford University Press

Kent, W James; Zweig, Ann S; Barber, G; Hinrichs, Angie S; Karolchik, Donna; BigWig and BigBed: enabling browsing of large distributed datasets. Genome Research. 26-17. 2204-2207 (2010) Oxford University Press

Haudry, Yannick; Ramialison, Mirana; Paten, Benedict; Wittbrodt, Joachim; Ettwiller, Laurence; Cactus: Algorithms for genome multiple sequence alignment. Genome Research. 5-2. 323-334 (2010) Nature Publishing Group

Paten, Benedict; Diekhans, Mark; Earl, Dent; John, John St; Ma, Jian; Suh, Bernard; Haussler, David; A user’s guide to the encyclopedia of DNA elements (ENCODE). Genome Research. . 410-425 (2010) Springer Berlin Heidelberg

Campos, Paula F; Willerslev, Eske; Sher, Andrei; Orlando, Ludovic; Axelsson, Erik; Tikhonov, Alexei; Aaris-SÌürensen, Kim; Greenwood, Alex D; Kahlke, Ralf-Dietrich; Kosintsev, Pavel; A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius). Genome Research. 107-12. 5675-5680 (2010) National Acad Sciences

Firth, Cadhla; Kitchen, Andrew; Shapiro, Beth; Suchard, Marc A; Holmes, Edward C; Rambaut, Andrew; Engineered polymerases amplify the potential of ancient DNA. Genome Research. 27-9. 2038-2051 (2010) SMBE

Edwards, Ceiridwen J; Magee, David A; Park, Stephen DE; McGettigan, Paul A; Lohan, Amanda J; Murphy, Alison; Finlay, Emma K; Shapiro, Beth; Chamberlain, Andrew T; Richards, Martin B; Skyline‰Ûplot methods for estimating demographic history from nucleotide sequences. Genome Research. 5-2. e9255 (2010) Public Library of Science

Shapiro, Beth; Hofreiter, Michael; Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation. Genome Research. 32-5. 388-391 (2010) WILEY‰ÛVCH Verlag

Kuhn, Tyler S; McFarlane, Keri A; Groves, Pamela; Mooers, Arne Ì÷; Shapiro, Beth; Inferring evolutionary history and processes using ancient DNA. Genome Research. 19-7. 1312-1323 (2010) Blackwell Publishing Ltd

Haile, James; Larson, Greger; Owens, Kimberley; Dobney, Keith; Shapiro, Beth; Species-specific responses of Late Quaternary megafauna to climate and humans. Genome Research. 37-1. 174-177 (2010) Elsevier

Stack, J Conrad; Welch, J David; Ferrari, Matt J; Shapiro, Beth U; Grenfell, Bryan T; Ancient hyaenas highlight the old problem of estimating evolutionary rates. Genome Research. 7-48. 1119-1127 (2010) The Royal Society

Fujita, Pauline A; Rhead, Brooke; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Cline, Melissa S; Goldman, Mary; Barber, Galt P; Clawson, Hiram; Coelho, Antonio; ANOSVA: a statistical method for detecting splice variation from expression data. Genome Research. . gkq963 (2010) Oxford Univ Press

Du, Hongqing; Cline, Melissa S; Osborne, Robert J; Tuttle, Daniel L; Clark, Tyson A; Donohue, John Paul; Hall, Megan P; Shiue, Lily; Swanson, Maurice S; Thornton, Charles A; Exploring alternative transcript structure in the human genome using blocks and InterPro. Genome Research. 17-2. 187-193 (2010) Nature Research

Raney, Brian J; Cline, Melissa S; Rosenbloom, Kate R; Dreszer, Timothy R; Learned, Katrina; Barber, Galt P; Meyer, Laurence R; Sloan, Cricket A; Malladi, Venkat S; Roskin, Krishna M; Integrating expression data with domain interaction networks. Genome Research. . gkq1017 (2010) Oxford Univ Press

Salomonis, Nathan; Schlieve, Christopher R; Pereira, Laura; Wahlquist, Christine; Colas, Alexandre; Zambon, Alexander C; Vranizan, Karen; Spindler, Matthew J; Pico, Alexander R; Cline, Melissa S; An empirical study of the branch coverage of different fault classes. Genome Research. 107-23. 10514-10519 (2010) National Acad Sciences

Fujita, Pauline A; Rhead, Brooke; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Cline, Melissa S; Goldman, Mary; Barber, Galt P; Clawson, Hiram; Coelho, Antonio; Cghub: Kick-starting the worldwide genome web. Genome Research. . gkq963 (2010) Oxford University Press

Searle, S; Frankish, A; Bignell, A; Aken, B; Derrien, T; Diekhans, M; Harte, R; Howald, C; Kokocinski, F; Lin, M; Genome Research. 11-S1. P36 (2010) BioMed Central

Paten, Benedict; Diekhans, Mark; Earl, Dent; John, John St; Ma, Jian; Suh, Bernard; Haussler, David; Genome Research. . 410-425 (2010) Springer Berlin Heidelberg

1000 Genomes Project Consortium; A map of human genome variation from population scale sequencing. Genome Research. 467-7319. 1061 (2010) Europe PMC Funders

Fujita, Pauline A; Rhead, Brooke; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Cline, Melissa S; Goldman, Mary; Barber, Galt P; Clawson, Hiram; Coelho, Antonio; The UCSC genome browser database: update 2011. Genome Research. 39-suppl_1. D876-D882 (2010) Oxford University Press

International Cancer Genome Consortium; International network of cancer genome projects. Genome Research. 464-7291. 993 (2010) NIH Public Access

Maunakea, Alika K; Nagarajan, Raman P; Bilenky, Mikhail; Ballinger, Tracy J; D’Souza, Cletus; Fouse, Shaun D; Johnson, Brett E; Hong, Chibo; Nielsen, Cydney; Zhao, Yongjun; Conserved role of intragenic DNA methylation in regulating alternative promoters. Genome Research. 466-7303. 253 (2010) NIH Public Access

Harris, R Alan; Wang, Ting; Coarfa, Cristian; Nagarajan, Raman P; Hong, Chibo; Downey, Sara L; Johnson, Brett E; Fouse, Shaun D; Delaney, Allen; Zhao, Yongjun; Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Genome Research. 28-10. 1097-1105 (2010) Nature Research

Vaske, Charles J; Benz, Stephen C; Sanborn, J Zachary; Earl, Dent; Szeto, Christopher; Zhu, Jingchun; Haussler, David; Stuart, Joshua M; Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Genome Research. 26-12. i237-i245 (2010) Oxford University Press

Raney, Brian J; Cline, Melissa S; Rosenbloom, Kate R; Dreszer, Timothy R; Learned, Katrina; Barber, Galt P; Meyer, Laurence R; Sloan, Cricket A; Malladi, Venkat S; Roskin, Krishna M; ENCODE whole-genome data in the UCSC genome browser (2011 update). Genome Research. 39-suppl_1. D871-D875 (2010) Oxford University Press

Underwood, Jason G; Uzilov, Andrew V; Katzman, Sol; Onodera, Courtney S; Mainzer, Jacob E; Mathews, David H; Lowe, Todd M; Salama, Sofie R; Haussler, David; FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Genome Research. 7-12. 995-1001 (2010) Nature Research

Sanborn, J Zachary; Benz, Stephen C; Craft, Brian; Szeto, Christopher; Kober, Kord M; Meyer, Laurence; Vaske, Charles J; Goldman, Mary; Smith, Kayla E; Kuhn, Robert M; The UCSC cancer genomics browser: update 2011. Genome Research. 39-suppl_1. D951-D959 (2010) Oxford University Press

Katzman, Sol; Kern, Andrew D; Pollard, Katherine S; Salama, Sofie R; Haussler, David; GC-biased evolution near human accelerated regions. Genome Research. 6-5. e1000960 (2010) Public Library of Science

Kern, Andrew D; Haussler, David; A population genetic hidden Markov model for detecting genomic regions under selection. Genome Research. 27-7. 1673-1685 (2010) Oxford University Press

Lowe, Craig B; Bejerano, Gill; Salama, Sofie R; Haussler, David; Endangered species hold clues to human evolution. Genome Research. 101-4. 437-447 (2010) Oxford University Press

Paten, Benedict; Diekhans, Mark; Earl, Dent; John, John St; Ma, Jian; Suh, Bernard B; Haussler, David; Cactus Graphs for Genome Comparisons.. Genome Research. . 410-425 (2010)

Harte, Rachel A; Karolchik, Donna; Kuhn, Robert M; Kent, W James; Haussler, David; Databases and Genome Browsers. Genome Research. . 905-921 (2010) Springer Berlin Heidelberg

Miller, David T; Adam, Margaret P; Aradhya, Swaroop; Biesecker, Leslie G; Brothman, Arthur R; Carter, Nigel P; Church, Deanna M; Crolla, John A; Eichler, Evan E; Epstein, Charles J; Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Genome Research. 86-5. 749-764 (2010) Elsevier

Zhou, Xin; Maricque, Brett; Xie, Mingchao; Li, Daofeng; Sundaram, Vasavi; Martin, Eric A; Koebbe, Brian C; Nielsen, Cydney; Hirst, Martin; Farnham, Peggy; Nature America, Inc. All rights reserv. Genome Research. 201. 1 (2010)

Harte, Rachel A; Karolchik, Donna; Kuhn, Robert M; Kent, W James; Haussler, David; Databases and Genome Browsers. Genome Research. . 905-921 (2010) Springer

Consortium, 1000 Genomes Project; A map of human genome variation from population-scale sequencing. Genome Research. 467-7319. 1061-1073 (2010) Nature

Consortium, The 1000 Genomes Project; A map of human genome variation from population-scale sequencing. Genome Research. 467. 1061-1073 (2010) Nature

Campos, Paula F; Willerslev, Eske; Sher, Andrei; Orlando, Ludovic; Axelsson, Erik; Tikhonov, Alexei; Aaris-SĚürensen, Kim; Greenwood, Alex D; Kahlke, Ralf-Dietrich; Kosintsev, Pavel; Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Genome Research. 107-12. 5675-5680 (2010) National Acad Sciences

Firth, Cadhla; Kitchen, Andrew; Shapiro, Beth; Suchard, Marc A; Holmes, Edward C; Rambaut, Andrew; Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Genome Research. 27-9. 2038-2051 (2010) SMBE

Edwards, Ceiridwen J; Magee, David A; Park, Stephen DE; McGettigan, Paul A; Lohan, Amanda J; Murphy, Alison; Finlay, Emma K; Shapiro, Beth; Chamberlain, Andrew T; Richards, Martin B; A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius). Genome Research. 5-2. e9255 (2010) Public Library of Science

Shapiro, Beth; Hofreiter, Michael; Analysis of ancient human genomes. Genome Research. 32-5. 388-391 (2010) WILEY‰Ű�VCH Verlag

Kuhn, Tyler S; McFarlane, Keri A; Groves, Pamela; Mooers, Arne Ě÷; Shapiro, Beth; Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon. Genome Research. 19-7. 1312-1323 (2010) Blackwell Publishing Ltd

Haile, James; Larson, Greger; Owens, Kimberley; Dobney, Keith; Shapiro, Beth; Ancient DNA typing of archaeological pig remains corroborates historical records. Genome Research. 37-1. 174-177 (2010) Elsevier

Stack, J Conrad; Welch, J David; Ferrari, Matt J; Shapiro, Beth U; Grenfell, Bryan T; Protocols for sampling viral sequences to study epidemic dynamics. Genome Research. 7-48. 1119-1127 (2010) The Royal Society

Haudry, Yannick; Ramialison, Mirana; Paten, Benedict; Wittbrodt, Joachim; Ettwiller, Laurence; Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation. Genome Research. 5-2. 323-334 (2010) Nature Publishing Group

Paten, Benedict; Diekhans, Mark; Earl, Dent; John, John St; Ma, Jian; Suh, Bernard; Haussler, David; Cactus graphs for genome comparisons. Genome Research. . 410-425 (2010) Springer Berlin Heidelberg

Blanchette, Marco; Green, Richard E; MacArthur, Stewart; Brooks, Angela N; Brenner, Steven E; Eisen, Michael B; Rio, Donald C; Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Genome Research. 33-4. 438-449 (2009) Cell Press

Rhead, Brooke; Karolchik, Donna; Kuhn, Robert M; Hinrichs, Angie S; Zweig, Ann S; Fujita, Pauline A; Diekhans, Mark; Smith, Kayla E; Rosenbloom, Kate R; Raney, Brian J; The UCSC genome browser database: update 2010. Genome Research. . gkp939 (2009) Oxford University Press

Kuhn, Robert M; Karolchik, Donna; Zweig, Ann S; Wang, Ting; Smith, Kayla E; Rosenbloom, Kate R; Rhead, B; Raney, Brian J; Pohl, Andy; Pheasant, Michael; The UCSC genome browser database: update 2009. Genome Research. 37-suppl 1. D755-D761 (2009) Oxford University Press

Paten, Benedict; Herrero, Javier; Beal, Kathryn; Birney, Ewan; Cactus graphs for genome comparisons. Genome Research. 25-3. 295-301 (2009) Oxford University Press

Barnett, Ross; Shapiro, Beth; Barnes, IAN; Ho, Simon YW; Burger, Joachim; Yamaguchi, Nobuyuki; Higham, Thomas FG; Wheeler, H; Rosendahl, Wilfried; Sher, Andrei V; Molecular phylogeny and evolution of the extinct bovid Myotragus balearicus. Genome Research. 18-8. 1668-1677 (2009) Blackwell Publishing Ltd

Magiorkinis, Gkikas; Magiorkinis, Emmanouil; Paraskevis, Dimitrios; Ho, Simon YW; Shapiro, Beth; Pybus, Oliver G; Allain, Jean-Pierre; Hatzakis, Angelos; Beringia as an Ice Age genetic museum. Genome Research. 6-12. e1000198 (2009) Public Library of Science

Bunce, Michael; Worthy, Trevor H; Phillips, Matthew J; Holdaway, RN; Willerslev, Eske; Haile, James; Shapiro, Beth; Scofield, RP; Drummond, A; Kamp, Peter JJ; Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Genome Research. 106-49. 20646-20651 (2009) National Acad Sciences

Firth, Cadhla; Charleston, Michael A; Duffy, Siobain; Shapiro, Beth; Holmes, Edward C; Late Pleistocene northward-dispersing Bison antiquus from the Bighill Creek Formation, Gallelli gravel pit, Alberta, Canada, and the fate of Bison occidentalis. Genome Research. 83-24. 12813-12821 (2009) American Society for Microbiology

Rambaut, Andrew; Ho, Simon YW; Drummond, Alexei J; Shapiro, Beth; A late Pleistocene steppe bison (Bison priscus) partial carcass from Tsiigehtchic, Northwest Territories, Canada. Genome Research. 26-2. 245-248 (2009) Oxford University Press

Collins, Matthew J; Penkman, Kirsty EH; Rohland, Nadin; Shapiro, Beth; Dobberstein, Reimer C; Ritz-Timme, Stefanie; Hofreiter, Michael; Analysis of ancient human genomes. Genome Research. . rspb20090563 (2009) The Royal Society

Zazula, Grant D; MacKay, Glen; Andrews, Thomas D; Shapiro, Beth; Letts, Brandon; Brock, Fiona; Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon. Genome Research. 28-25. 2734-2742 (2009) Pergamon

Weinstock, Jaco; Shapiro, Beth; Prieto, Alfredo; MarÌ_n, Juan Carlos; Gonzalez, Benito A; Gilbert, M Thomas P; Willerslev, Eske; True single-molecule DNA sequencing of a pleistocene horse bone. Genome Research. 28-15. 1369-1373 (2009) Pergamon

Rijsdijk, Kenneth F; Hume, Julian P; Bunnik, Frans; Florens, FB Vincent; Baider, Claudia; Shapiro, Beth; van der Plicht, Johannes; Janoo, Anwar; Griffiths, Owen; van den Hoek Ostende, Lars W; Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Genome Research. 28-1. 14-24 (2009) Pergamon

Cordingley, JE; Sundaresan, SR; Fischhoff, IR; Shapiro, B; Ruskey, J; Rubenstein, DI; Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. Genome Research. 12-6. 505-513 (2009) Blackwell Publishing Ltd

Cordingley, JE; Sundaresan, SR; Larison, BJ; Shapiro, B; Rubenstein, DI; Ancient DNA supports southern survival of Richardson’s collared lemming (Dicrostonyx richardsoni) during the last glacial maximum. Genome Research. 12-6. 520-521 (2009) Blackwell Publishing Ltd

Saumtally, Salem; Bholah, Assenjee; De Louw, Perry GB; Vernimmen, Tamara; Cremer, Holger; Hoek Ostende, Lars W; Griffiths, Owen; Janoo, Anwar; Plicht, Johannes van der; Shapiro, Beth; Ancient DNA analysis indicates the first English lions originated from North Africa. (2009)

Cline, Melissa S; Kent, W James; Covariation of mutations: A computational approach for determination of function and structure from sequence. Genome Research. 27-2. 153 (2009) Nature Publishing Group

Pohl, Andrew A; Sugnet, Charles W; Clark, Tyson A; Smith, Kayla; Fujita, Pauline A; Cline, Melissa S; Multiple endocrine adenoma syndrome: report of a case of diabetes mellitus following subtotal pancreatectomy. Genome Research. 25-18. 2442-2443 (2009) Oxford Univ Press

Karolchik, Donna; Hinrichs, Angie S; Kent, W James; Tracking and coordinating an international curation effort for the CCDS Project. Genome Research. . 1.4. 1-1.4. 33 (2009) John Wiley & Sons, Inc.

Rhead, Brooke; Karolchik, Donna; Kuhn, Robert M; Hinrichs, Angie S; Zweig, Ann S; Fujita, Pauline A; Diekhans, Mark; Smith, Kayla E; Rosenbloom, Kate R; Raney, Brian J; 1SA, UK 2University of California, 1156 High Street, Santa Cruz, CA 95064, USA 3Massachusetts Institute of Technology, 77 Massachusetts Avenue 750, Cambridge, MA 02139, USA 4Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland. Genome Research. . gkp939 (2009) Oxford University Press

Kuhn, Robert M; Karolchik, Donna; Zweig, Ann S; Wang, Ting; Smith, Kayla E; Rosenbloom, Kate R; Rhead, B; Raney, Brian J; Pohl, Andy; Pheasant, Michael; Lessons from the alignment of human and mouse genomes: Finding candidate functional sequences despite variation in conservation.. Genome Research. 37-suppl 1. D755-D761 (2009) Oxford University Press

Pruitt, Kim D; Harrow, Jennifer; Harte, Rachel A; Wallin, Craig; Diekhans, Mark; Maglott, Donna R; Searle, Steve; Farrell, Catherine M; Loveland, Jane E; Ruef, Barbara J; Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Research. 19-7. 1316-1323 (2009) Cold Spring Harbor Lab

Haussler, David; O’Brien, Stephen J; Ryder, Oliver A; Barker, F Keith; Clamp, Michele; Crawford, Andrew J; Hanner, Robert; Hanotte, Olivier; Johnson, Warren E; McGuire, Jimmy A; XactMice: humanizing mouse bone marrow enables microenvironment reconstitution in a patient-derived xenograft model of head and neck cancer. Genome Research. 100-6. 659-674 (2009)

Ryan, Michael; Diekhans, Mark; Lien, Stephanie; Liu, Yun; Karchin, Rachel; Genome Research. 25-11. 1431-1432 (2009) Oxford University Press

Temple, Gary; Gerhard, Daniela S; Rasooly, Rebekah; Feingold, Elise A; Good, Peter J; Robinson, Cristen; Mandich, Allison; Derge, Jeffrey G; Lewis, Jeanne; Shoaf, Debonny; Genome Research. 19-12. 2324-2333 (2009) Cold Spring Harbor Lab

Bignell, A; Frankish, A; Aken, B; Diekhans, M; Kokocinski, F; Lin, M; Tress, M; Van Baren, J; Barnes, I; Hunt, T; (2009)

Pruitt, Kim D; Harrow, Jennifer; Harte, Rachel A; Wallin, Craig; Diekhans, Mark; Maglott, Donna R; Searle, Steve; Farrell, Catherine M; Loveland, Jane E; Ruef, Barbara J; Genome Research. 19-8. 1506-1506 (2009) COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2924 USA

Rhead, Brooke; Karolchik, Donna; Kuhn, Robert M; Hinrichs, Angie S; Zweig, Ann S; Fujita, Pauline A; Diekhans, Mark; Smith, Kayla E; Rosenbloom, Kate R; Raney, Brian J; The UCSC genome browser database: update 2010. Genome Research. 38-suppl_1. D613-D619 (2009) Oxford University Press

Pruitt, Kim D; Harrow, Jennifer; Harte, Rachel A; Wallin, Craig; Diekhans, Mark; Maglott, Donna R; Searle, Steve; Farrell, Catherine M; Loveland, Jane E; Ruef, Barbara J; The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Research. 19-7. 1316-1323 (2009) Cold Spring Harbor Lab

Han, Jinju; Pedersen, Jakob S; Kwon, S Chul; Belair, Cassandra D; Kim, Young-Kook; Yeom, Kyu-Hyeon; Yang, Woo-Young; Haussler, David; Blelloch, Robert; Kim, V Narry; Posttranscriptional crossregulation between Drosha and DGCR8. Genome Research. 136-1. 75-84 (2009) Elsevier

Rosenbloom, Kate R; Dreszer, Timothy R; Pheasant, Michael; Barber, Galt P; Meyer, Laurence R; Pohl, Andy; Raney, Brian J; Wang, Ting; Hinrichs, Angie S; Zweig, Ann S; ENCODE whole-genome data in the UCSC Genome Browser. Genome Research. 38-suppl_1. D620-D625 (2009) Oxford University Press

Haussler, David; O’Brien, Stephen J; Ryder, Oliver A; Barker, F Keith; Clamp, Michele; Crawford, Andrew J; Hanner, Robert; Hanotte, Olivier; Johnson, Warren E; McGuire, Jimmy A; Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species. (2009)

Zhu, Jingchun; Sanborn, J Zachary; Benz, Stephen; Szeto, Christopher; Hsu, Fan; Kuhn, Robert M; Karolchik, Donna; Archie, John; Lenburg, Marc E; Esserman, Laura J; The UCSC cancer genomics browser. Genome Research. 6-4. 239-240 (2009) Nature Publishing Group

Temple, Gary; Gerhard, Daniela S; Rasooly, Rebekah; Feingold, Elise A; Good, Peter J; Robinson, Cristen; Mandich, Allison; Derge, Jeffrey G; Lewis, Jeanne; Shoaf, Debonny; The completion of the mammalian gene collection (MGC). Genome Research. 19-12. 2324-2333 (2009) Cold Spring Harbor Lab

Wang, Ting; Szeto, Christopher; Zhu, Jingchu; Sanborn, J Zachary; Benz, Stephen; Haussler, David; Identification of distinct global Copy Number Alteration signatures in different human cancer types and mouse models with the UCSC Cancer Genomics Browser. Genome Research. 69(2009) AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA 19106-4404 USA

Pruitt, Kim D; Harrow, Jennifer; Harte, Rachel A; Wallin, Craig; Diekhans, Mark; Maglott, Donna R; Searle, Steve; Farrell, Catherine M; Loveland, Jane E; Ruef, Barbara J; The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes (vol 19, pg 1316, 2009). Genome Research. 19-8. 1506-1506 (2009) COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2924 USA

Kulp, DC; Wang, H; Haussler, D; Hubbell, E; Hu, Js; Mei, G; Cline, M; Lu, G; Clark, T; Siani-Rose, MA; Gene structure-based splice variant deconvolution using a microarry platform.. Genome Research. 19(2009)

Mangan, Mary E; Williams, Jennifer M; Kuhn, Robert M; Lathe, Warren C; The UCSC genome browser: what every molecular biologist should know. Genome Research. . 19.9. 1-19.9. 28 (2009) Wiley Online Library

Zhu, Jingchun; Sanborn, J; Benz, Stephen; Hsu, Fan; Szeto, Christopher; Kuhn, Robert; Karolchik, Donna; Archie, John; Lenburg, Marc; Esserman, Laura; Abstract# 2469: UCSC cancer genomics browser. (2009) AACR

Barnett, Ross; Shapiro, Beth; Barnes, IAN; Ho, Simon YW; Burger, Joachim; Yamaguchi, Nobuyuki; Higham, Thomas FG; Wheeler, H; Rosendahl, Wilfried; Sher, Andrei V; Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Genome Research. 18-8. 1668-1677 (2009) Blackwell Publishing Ltd

Magiorkinis, Gkikas; Magiorkinis, Emmanouil; Paraskevis, Dimitrios; Ho, Simon YW; Shapiro, Beth; Pybus, Oliver G; Allain, Jean-Pierre; Hatzakis, Angelos; The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis. Genome Research. 6-12. e1000198 (2009) Public Library of Science

Bunce, Michael; Worthy, Trevor H; Phillips, Matthew J; Holdaway, RN; Willerslev, Eske; Haile, James; Shapiro, Beth; Scofield, RP; Drummond, A; Kamp, Peter JJ; The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Genome Research. 106-49. 20646-20651 (2009) National Acad Sciences

Firth, Cadhla; Charleston, Michael A; Duffy, Siobain; Shapiro, Beth; Holmes, Edward C; Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2. Genome Research. 83-24. 12813-12821 (2009) American Society for Microbiology

Rambaut, Andrew; Ho, Simon YW; Drummond, Alexei J; Shapiro, Beth; Accommodating the effect of ancient DNA damage on inferences of demographic histories. Genome Research. 26-2. 245-248 (2009) Oxford University Press

Collins, Matthew J; Penkman, Kirsty EH; Rohland, Nadin; Shapiro, Beth; Dobberstein, Reimer C; Ritz-Timme, Stefanie; Hofreiter, Michael; Is amino acid racemization a useful tool for screening for ancient DNA in bone?. Genome Research. . rspb20090563 (2009) The Royal Society

Zazula, Grant D; MacKay, Glen; Andrews, Thomas D; Shapiro, Beth; Letts, Brandon; Brock, Fiona; A late Pleistocene steppe bison (Bison priscus) partial carcass from Tsiigehtchic, Northwest Territories, Canada. Genome Research. 28-25. 2734-2742 (2009) Pergamon

Weinstock, Jaco; Shapiro, Beth; Prieto, Alfredo; MarĚ_n, Juan Carlos; Gonzalez, Benito A; Gilbert, M Thomas P; Willerslev, Eske; The Late Pleistocene distribution of vicu̱as (Vicugna vicugna) and the ‰ŰĎextinction‰Űť of the gracile llama (‰ŰĎLama gracilis‰Űť): New molecular data. Genome Research. 28-15. 1369-1373 (2009) Pergamon

Rijsdijk, Kenneth F; Hume, Julian P; Bunnik, Frans; Florens, FB Vincent; Baider, Claudia; Shapiro, Beth; van der Plicht, Johannes; Janoo, Anwar; Griffiths, Owen; van den Hoek Ostende, Lars W; Mid-Holocene vertebrate bone Concentration-LagerstĚ_tte on oceanic island Mauritius provides a window into the ecosystem of the dodo (Raphus cucullatus). Genome Research. 28-1. 14-24 (2009) Pergamon

Cordingley, JE; Sundaresan, SR; Fischhoff, IR; Shapiro, B; Ruskey, J; Rubenstein, DI; Is the endangered Grevy’s zebra threatened by hybridization?. Genome Research. 12-6. 505-513 (2009) Blackwell Publishing Ltd

Cordingley, JE; Sundaresan, SR; Larison, BJ; Shapiro, B; Rubenstein, DI; Grevy’s zebra conservation: overcoming threats of isolation, genetic hybridization and demographic instability. Genome Research. 12-6. 520-521 (2009) Blackwell Publishing Ltd

Saumtally, Salem; Bholah, Assenjee; De Louw, Perry GB; Vernimmen, Tamara; Cremer, Holger; Hoek Ostende, Lars W; Griffiths, Owen; Janoo, Anwar; Plicht, Johannes van der; Shapiro, Beth; Mid-Holocene vertebrate bone Concentration-LagerstĚ_tte on oceanic island Mauritius provides a window into the ecosystem of the dodo (Raphus cucullatus). (2009)

Paten, Benedict; Herrero, Javier; Beal, Kathryn; Birney, Ewan; Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Genome Research. 25-3. 295-301 (2009) Oxford University Press

Karolchik, Donna; Kuhn, Robert M; Baertsch, Robert; Barber, Galt P; Clawson, Hiram; Diekhans, Mark; Giardine, Belinda; Harte, Rachel A; Hinrichs, Angela S; Hsu, Fan; The UCSC genome browser database: 2008 update. Genome Research. 36-suppl 1. D773-D779 (2008) Oxford University Press

Zweig, Ann S; Karolchik, Donna; Kuhn, Robert M; Haussler, David; Kent, W James; UCSC genome browser tutorial. Genome Research. 92-2. 75-84 (2008) Academic Press

Karolchik, Donna; Bejerano, Gill; Hinrichs, Angie S; Kuhn, Robert M; Miller, Webb; Rosenbloom, Kate R; Zweig, Ann S; Haussler, David; Kent, W James; Comparative genomic analysis using the UCSC genome browser. Genome Research. . 17-33 (2008) Humana Press

Berman, P; Hsu, F; Kent, J; Schweighardt, B; Zweig, A; Kuhn, R; Wrin, T; Sinangil, F; GSID HIV Sequence Database: A Powerful New Tool for HIV Vaccine Research that Relates HIV Sequence Information to Clinical Specimens and Data. Genome Research. 24. 103-104 (2008) MARY ANN LIEBERT INC 140 HUGUENOT STREET, 3RD FL, NEW ROCHELLE, NY 10801 USA

Paten, Benedict; Herrero, Javier; Beal, Kathryn; Fitzgerald, Stephen; Birney, Ewan; Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Genome Research. 18-11. 1814-1828 (2008) Cold Spring Harbor Lab

Paten, Benedict; Herrero, Javier; Fitzgerald, Stephen; Beal, Kathryn; Flicek, Paul; Holmes, Ian; Birney, Ewan; The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Research. 18-11. 1829-1843 (2008) Cold Spring Harbor Lab

Ho, Simon YW; Saarma, Urmas; Barnett, Ross; Haile, James; Shapiro, Beth; Response to comment on ‰ÛÏProtein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry‰Û. Genome Research. 3-2. e1615 (2008) Public Library of Science

Asara, John M; Schweitzer, Mary H; Cantley, Lewis C; Cottrell, John S; Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2. Genome Research. 321-5892. 1040c-1040c (2008) American Association for the Advancement of Science

Ho, Simon YW; Larson, Greger; Edwards, Ceiridwen J; Heupink, Tim H; Lakin, Kay E; Holland, Peter WH; Shapiro, Beth; No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al.). Genome Research. 4-4. 370-374 (2008) The Royal Society

Wilson, Michael C; Hills, Leonard V; Shapiro, Beth; Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Genome Research. 45-7. 827-859 (2008)

Shapiro, Beth; A Bayesian phylogenetic method to estimate unknown sequence ages. Genome Research. 26-6. 285-287 (2008) Elsevier

Kapoor, Amit; Shapiro, Beth; Shafer, Robert W; Shulman, Nancy; Rhee, Soo-Yon; Delwart, Eric L; Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons. Genome Research. 5-1. 7 (2008) BioMed Central

Lemey, Philippe; Pond, Sergei L Kosakovsky; Drummond, Alexei J; Pybus, Oliver G; Shapiro, Beth; Barroso, Helena; Taveira, Nuno; Rambaut, Andrew; Transoceanic drift and the domestication of African bottle gourds in the Americas. Genome Research. 8. S15-S16 (2008) ELSEVIER SCIENCE BV

Shapiro, Beth; Belshaw, Robert; Rambuat, Andrew; Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe. Genome Research. 8-4. S46-S46 (2008) ELSEVIER SCIENCE BV PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS

Barnett, Ross; Yamaguchi, Nobuyuki; Shapiro, Beth; Sabin, Richard; A revised evolutionary history of armadillos (Dasypus) in North America based on ancient mitochondrial DNA. Genome Research. 77-1(2008) NCB Naturals

Shapiro, B; Gilbert, MTP; Barnes, I; Pattern of extinction of the woolly mammoth in Beringia-Supplementary Information.. Genome Research. 1-56. 207-242 (2008) Cambridge University Press

Karolchik, Donna; Kuhn, Robert M; Baertsch, Robert; Barber, Galt P; Clawson, Hiram; Diekhans, Mark; Giardine, Belinda; Harte, Rachel A; Hinrichs, Angela S; Hsu, Fan; Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks. Genome Research. 36-suppl 1. D773-D779 (2008) Oxford University Press

Yeung, Natalie; Cline, Melissa S; Kuchinsky, Allan; Smoot, Michael E; Bader, Gary D; Ы ХЙЬ. Genome Research. . 8.13. 1-8.13. 20 (2008) Wiley Online Library

Emig, Dorothea; Cline, Melissa S; Lengauer, Thomas; Albrecht, Mario; Affymetrix Inc., 6550 Vallejo Street, Suite 100. Genome Research. 24-21. 2546-2548 (2008) Oxford Univ Press

Emig, Dorothea; Cline, Melissa S; Klein, Karsten; Kunert, Anne; Mutzel, Petra; Lengauer, Thomas; Albrecht, Mario; Variant classifications in BRCA1 and BRCA2: A systematic analysis of interlaboratory concordance. Genome Research. 5-2. 173-187 (2008)

Karolchik, Donna; Kuhn, Robert M; Baertsch, Robert; Barber, Galt P; Clawson, Hiram; Diekhans, Mark; Giardine, Belinda; Harte, Rachel A; Hinrichs, Angela S; Hsu, Fan; The GENCODE pseudogene resource. Genome Research. 36-suppl 1. D773-D779 (2008) Oxford University Press

Stanke, Mario; Diekhans, Mark; Baertsch, Robert; Haussler, David; The ORFeome Collaboration. Genome Research. 24-5. 637-644 (2008) Oxford University Press

Baertsch, Robert; Diekhans, Mark; Kent, W James; Haussler, David; Brosius, Jürgen; Genome Research. 9-1. 466 (2008) BioMed Central

Harte, Rachel; Diekhans, Mark; (2008)

Kuhn, Robert M; Karolchik, Donna; Zweig, Ann S; Wang, Ting; Smith, Kayla E; Rosenbloom, Kate R; Rhead, B; Raney, Brian J; Pohl, Andy; Pheasant, Michael; The UCSC genome browser database: update 2009. Genome Research. 37-suppl_1. D755-D761 (2008) Oxford University Press

Stanke, Mario; Diekhans, Mark; Baertsch, Robert; Haussler, David; Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Genome Research. 24-5. 637-644 (2008) Oxford University Press

Ma, Jian; Ratan, Aakrosh; Raney, Brian J; Suh, Bernard B; Miller, Webb; Haussler, David; The infinite sites model of genome evolution. Genome Research. 105-38. 14254-14261 (2008) National Acad Sciences

Baertsch, Robert; Diekhans, Mark; Kent, W James; Haussler, David; Brosius, Jürgen; Retrocopy contributions to the evolution of the human genome. Genome Research. 9-1. 466 (2008) BioMed Central

Ma, Jian; Ratan, Aakrosh; Raney, Brian J; Suh, Bernard B; Zhang, Louxin; Miller, Webb; Haussler, David; DUPCAR: reconstructing contiguous ancestral regions with duplications. Genome Research. 15-8. 1007-1027 (2008) Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA

Blanchette, Mathauieu; Diallo, Abdoulaye Baniré; Green, Eric D; Miller, Webb; Haussler, David; Computational reconstruction of ancestral DNA sequences. Genome Research. . 171-184 (2008) Humana Press

Rosenbloom, Kate; Taylor, James; Schaeffer, Stephen; Kent, Jim; Haussler, David; Miller, Webb; Phylogenomic resources at the UCSC Genome Browser. Genome Research. . 133-144 (2008) Humana Press

Haussler, David; Computing how we became human. Genome Research. . 639-640 (2008) ACM

Yeang, Chen-Hsiang; Darot, Jeremy FJ; Noller, Harry F; Haussler, David; Erratum to Detecting the Coevolution of Biosequences—An Example of RNA Interaction Prediction. Genome Research. 25-9. 2077-2077 (2008) SMBE

Zeng, Jue; Yan, Jizhou; Wang, Ting; Mosbrook-Davis, Deborah; Dolan, Kyle T; Christenensen, Ryan; Stormo, Gary D; Haussler, David; Lathrop, Richard H; Brachmann, Rainer K; Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding. (2008)

Zweig, Ann S; Karolchik, Donna; Kuhn, Robert M; Haussler, David; Kent, W James; UCSC genome browser tutorial. Genome Research. 92-2. 75-84 (2008) Elsevier

Karolchik, Donna; Bejerano, Gill; Hinrichs, Angie S; Kuhn, Robert M; Miller, Webb; Rosenbloom, Kate R; Zweig, Ann S; Haussler, David; Kent, W James; Comparative genomic analysis using the UCSC genome browser. Genome Research. . 17-33 (2008) Springer

Ho, Simon YW; Saarma, Urmas; Barnett, Ross; Haile, James; Shapiro, Beth; The effect of inappropriate calibration: three case studies in molecular ecology. Genome Research. 3-2. e1615 (2008) Public Library of Science

Asara, John M; Schweitzer, Mary H; Cantley, Lewis C; Cottrell, John S; Response to comment on ‰ŰĎProtein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry‰Űť. Genome Research. 321-5892. 1040c-1040c (2008) American Association for the Advancement of Science

Ho, Simon YW; Larson, Greger; Edwards, Ceiridwen J; Heupink, Tim H; Lakin, Kay E; Holland, Peter WH; Shapiro, Beth; Correlating Bayesian date estimates with climatic events and domestication using a bovine case study. Genome Research. 4-4. 370-374 (2008) The Royal Society

Wilson, Michael C; Hills, Leonard V; Shapiro, Beth; Late Pleistocene northward-dispersing Bison antiquus from the Bighill Creek Formation, Gallelli gravel pit, Alberta, Canada, and the fate of Bison occidentalis. Genome Research. 45-7. 827-859 (2008)

Shapiro, Beth; Engineered polymerases amplify the potential of ancient DNA. Genome Research. 26-6. 285-287 (2008) Elsevier

Kapoor, Amit; Shapiro, Beth; Shafer, Robert W; Shulman, Nancy; Rhee, Soo-Yon; Delwart, Eric L; Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients. Genome Research. 5-1. 7 (2008) BioMed Central

Lemey, Philippe; Pond, Sergei L Kosakovsky; Drummond, Alexei J; Pybus, Oliver G; Shapiro, Beth; Barroso, Helena; Taveira, Nuno; Rambaut, Andrew; Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. Genome Research. 8. S15-S16 (2008) ELSEVIER SCIENCE BV

Shapiro, Beth; Belshaw, Robert; Rambuat, Andrew; Identifying deeper taxonomic relationships among RNA viruses. Genome Research. 8-4. S46-S46 (2008) ELSEVIER SCIENCE BV PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS

Barnett, Ross; Yamaguchi, Nobuyuki; Shapiro, Beth; Sabin, Richard; Ancient DNA analysis indicates the first English lions originated from North Africa. Genome Research. 77-1(2008) NCB Naturals

Shapiro, B; Gilbert, MTP; Barnes, I; Using DNA to investigate the human past. Genome Research. 1-56. 207-242 (2008) Cambridge University Press

Paten, Benedict; Herrero, Javier; Beal, Kathryn; Fitzgerald, Stephen; Birney, Ewan; Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Research. 18-11. 1814-1828 (2008) Cold Spring Harbor Lab

Paten, Benedict; Herrero, Javier; Fitzgerald, Stephen; Beal, Kathryn; Flicek, Paul; Holmes, Ian; Birney, Ewan; Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Research. 18-11. 1829-1843 (2008) Cold Spring Harbor Lab

Clark, Andrew G; Eisen, Michael B; Smith, Douglas R; Bergman, Casey M; Oliver, Brian; Markow, Therese A; Kaufman, Thomas C; Kellis, Manolis; Gelbart, William; Iyer, Venky N; Evolution of genes and genomes on the Drosophila phylogeny. Genome Research. 450-7167. 203-218 (2007) Nature Publishing Group

Lareau, Liana F; Brooks, Angela N; Soergel, David AW; Meng, Qi; Brenner, Steven E; The coupling of alternative splicing and nonsense-mediated mRNA decay. Genome Research. 623(2007) Landes Biosciences

Birney, Ewan; Stamatoyannopoulos, John A; Dutta, Anindya; Guig岯, Roderic; Gingeras, Thomas R; Margulies, Elliott H; Weng, Zhiping; Snyder, Michael; Dermitzakis, Emmanouil T; Thurman, Robert E; Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Genome Research. 447-7146. 799-816 (2007) Nature Publishing Group

Kuhn, Robert M; Karolchik, Donna; Zweig, Ann S; Trumbower, Heather; Thomas, Daryl J; Thakkapallayil, Archana; Sugnet, Charles W; Stanke, Mario; Smith, Kayla E; Siepel, A; The UCSC genome browser database: update 2007. Genome Research. 35-suppl 1. D668-D673 (2007) Oxford University Press

Margulies, Elliott H; Cooper, Gregory M; Asimenos, George; Thomas, Daryl J; Dewey, Colin N; Siepel, Adam; Birney, Ewan; Keefe, Damian; Schwartz, Ariel S; Hou, Minmei; Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17-6. 760-774 (2007) Cold Spring Harbor Lab

Thomas, Daryl J; Rosenbloom, Kate R; Clawson, Hiram; Hinrichs, Angie S; Trumbower, Heather; Raney, Brian J; Karolchik, Donna; Barber, Galt P; Harte, Rachel A; Hillman-Jackson, Jennifer; The ENCODE project at UC santa cruz. Genome Research. 35-suppl 1. D663-D667 (2007) Oxford University Press

Birney, Ewan; Stamatoyannopoulos, John A; Dutta, Anindya; Guigó, Roderic; Gingeras, Thomas R; Margulies, Elliott H; Weng, Zhiping; Snyder, Michael; Dermitzakis, Emmanouil T; Thurman, Robert E; Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Genome Research. 447-7146. 799-816 (2007) Nature Publishing Group

Stark, Alexander; Lin, Michael F; Kheradpour, Pouya; Pedersen, Jakob S; Parts, Leopold; Carlson, Joseph W; Crosby, Madeline A; Rasmussen, Matthew D; Roy, Sushmita; Deoras, Ameya N; Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Research. 450-7167. 219-232 (2007) Nature publishing group

Margulies, Elliott H; Cooper, Gregory M; Asimenos, George; Thomas, Daryl J; Dewey, Colin N; Siepel, Adam; Birney, Ewan; Keefe, Damian; Schwartz, Ariel S; Hou, Minmei; Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Research. 17-6. 760-774 (2007) Cold Spring Harbor Lab

Ettwiller, Laurence; Paten, Benedict; Ramialison, Mirana; Birney, Ewan; Wittbrodt, Joachim; Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Genome Research. 4-7. 563-565 (2007) Nature Publishing Group

Paten, Benedict John; The Genome 10K Project: a way forward. (2007) University of Cambridge

Ho, Simon YW; Shapiro, Beth; Phillips, Matthew J; Cooper, Alan; Drummond, Alexei J; Ancient papillomavirus-host co-speciation in Felidae. Genome Research. 56-3. 515-522 (2007) Oxford University Press

Edwards, Ceiridwen J; Bollongino, Ruth; Scheu, Amelie; Chamberlain, Andrew; Tresset, Anne; Vigne, Jean-Denis; Baird, Jillian F; Larson, Greger; Ho, Simon YW; Heupink, Tim H; Ancient DNA provides new insights into the evolutionary history of New Zealand’s extinct giant eagle. Genome Research. 274-1616. 1377-1385 (2007) The Royal Society

Abecasis, Ana B; Lemey, Philippe; Vidal, Nicole; de Oliveira, T̼lio; Peeters, Martine; Camacho, Ricardo; Shapiro, Beth; Rambaut, Andrew; Vandamme, Anne-Mieke; Bayesian estimation of sequence damage in ancient DNA. Genome Research. 81-16. 8543-8551 (2007) American Society for Microbiology

Lemey, Philippe; Pond, Sergei L Kosakovsky; Drummond, Alexei J; Pybus, Oliver G; Shapiro, Beth; Barroso, Helena; Taveira, Nuno; Rambaut, Andrew; Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Genome Research. 3-2. e29 (2007) Public Library of Science

Barnes, Ian; Shapiro, Beth; Lister, Adrian; Kuznetsova, Tatiana; Sher, Andrei; Guthrie, Dale; Thomas, Mark G; Correlating Bayesian date estimates with climatic events and domestication using a bovine case study. Genome Research. 17-12. 1072-1075 (2007) Cell Press

Rector, Annabel; Lemey, Philippe; Tachezy, Ruth; Mostmans, Sara; Ghim, Shin-Je; Van Doorslaer, Koenraad; Roelke, Melody; Bush, Mitchell; Montali, Richard J; Joslin, Janis; The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis. Genome Research. 8-4. R57 (2007) BioMed Central

Haile, James; Holdaway, Richard; Oliver, Karen; Bunce, Michael; Gilbert, M Thomas P; Nielsen, Rasmus; Munch, Kasper; Ho, Simon YW; Shapiro, Beth; Willerslev, Eske; A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution. Genome Research. 24-4. 982-989 (2007) Oxford University Press

Ho, Simon YW; Heupink, Tim H; Rambaut, Andrew; Shapiro, Beth; Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Genome Research. 24-6. 1416-1422 (2007) Oxford University Press

Deforche, Koen; Camacho, Ricardo; Laethem, Kristel Van; Shapiro, Beth; Moreau, Yves; Rambaut, Andrew; Vandamme, Anne-Mieke; Lemey, Philippe; Mid-Holocene vertebrate bone Concentration-LagerstÌ_tte on oceanic island Mauritius provides a window into the ecosystem of the dodo (Raphus cucullatus). Genome Research. 14-8. 1105-1114 (2007) Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA

Barnett, Ross; Yamaguchi, Nobuyuki; Shapiro, Beth; Nijman, Vincent; Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients. Genome Research. 76-2(2007) Brill Academic Publishers, Inc.; NCB Naturals

Dal̩n, Love; G̦therstr̦m, Anders; Meijer, Tomas; Shapiro, Beth; The earliest evidence for anatomically modern humans in northwestern Europe. Genome Research. 121-3. 321-324 (2007)

Deforche, Koen; Lemey, Philippe; Camacho, Ricardo; Van Laethem, Kristel; Shapiro, Beth; Moreau, Yves; Rambaut, Andrew; Vandamme, Anne-Mieke; Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. (2007)

Shapiro, Beth; Lemey, Philippe; Schuster, S; Van Laethem, Kristel; Vandamme, Anne-Mieke; Rambaut, Andrew; Ancient DNA: Methods and Protocols. (2007)

Cline, Melissa S; Smoot, Michael; Cerami, Ethan; Kuchinsky, Allan; Landys, Nerius; Workman, Chris; Christmas, Rowan; Avila-Campilo, Iliana; Creech, Michael; Gross, Benjamin; Information‐theoretic dissection of pairwise contact potentials. Genome Research. 2-10. 2366-2382 (2007) Nature Publishing Group

Garcia, Olivier; Saveanu, Cosmin; Cline, Melissa; Fromont-Racine, Micheline; Jacquier, Alain; Schwikowski, Benno; Aittokallio, Tero; Method, system and computer software providing a genomic web portal for functional analysis of alternative splice variants. Genome Research. 23-3. 394-396 (2007) Oxford Univ Press

Kuhn, Robert M; Karolchik, Donna; Zweig, Ann S; Trumbower, Heather; Thomas, Daryl J; Thakkapallayil, Archana; Sugnet, Charles W; Stanke, Mario; Smith, Kayla E; Siepel, A; MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. Genome Research. 35-suppl 1. D668-D673 (2007) Oxford University Press

Miller, Webb; Rosenbloom, Kate; Hardison, Ross C; Hou, Minmei; Taylor, James; Raney, Brian; Burhans, Richard; King, David C; Baertsch, Robert; Blankenberg, Daniel; The shrinking human protein coding complement: are there now fewer than 20,000 genes?. Genome Research. 17-12. 1797-1808 (2007) Cold Spring Harbor Lab

Zhu, Jingchun; Sanborn, J Zachary; Diekhans, Mark; Lowe, Craig B; Pringle, Tom H; Haussler, David; Genome Research. 3-12. e247 (2007) Public Library of Science

Siepel, Adam; Diekhans, Mark; Brejová, Broňa; Langton, Laura; Stevens, Michael; Comstock, Charles LG; Davis, Colleen; Ewing, Brent; Oommen, Shelly; Lau, Christopher; Genome Research. 17-12. 1763-1773 (2007) Cold Spring Harbor Lab

ENCODE Project Consortium; Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Genome Research. 447-7146. 799 (2007) NIH Public Access

Gibbs, Richard A; Rogers, Jeffrey; Katze, Michael G; Bumgarner, Roger; Weinstock, George M; Mardis, Elaine R; Remington, Karin A; Strausberg, Robert L; Venter, J Craig; Wilson, Richard K; Evolutionary and biomedical insights from the rhesus macaque genome. Genome Research. 316-5822. 222-234 (2007) American Association for the Advancement of Science

Karolchik, Donna; Kuhn, Robert M; Baertsch, Robert; Barber, Galt P; Clawson, Hiram; Diekhans, Mark; Giardine, Belinda; Harte, Rachel A; Hinrichs, Angela S; Hsu, Fan; The UCSC genome browser database: 2008 update. Genome Research. 36-suppl_1. D773-D779 (2007) Oxford University Press

Stark, Alexander; Lin, Michael F; Kheradpour, Pouya; Pedersen, Jakob S; Parts, Leopold; Carlson, Joseph W; Crosby, Madeline A; Rasmussen, Matthew D; Roy, Sushmita; Deoras, Ameya N; Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Genome Research. 450-7167. 219 (2007) NIH Public Access

Lowe, Craig B; Bejerano, Gill; Haussler, David; Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Genome Research. 104-19. 8005-8010 (2007) National Acad Sciences

Miller, Webb; Rosenbloom, Kate; Hardison, Ross C; Hou, Minmei; Taylor, James; Raney, Brian; Burhans, Richard; King, David C; Baertsch, Robert; Blankenberg, Daniel; 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research. 17-12. 1797-1808 (2007) Cold Spring Harbor Lab

Katzman, Sol; Kern, Andrew D; Bejerano, Gill; Fewell, Ginger; Fulton, Lucinda; Wilson, Richard K; Salama, Sofie R; Haussler, David; Human genome ultraconserved elements are ultraselected. Genome Research. 317-5840. 915-915 (2007) American Association for the Advancement of Science

Wang, Ting; Zeng, Jue; Lowe, Craig B; Sellers, Robert G; Salama, Sofie R; Yang, Min; Burgess, Shawn M; Brachmann, Rainer K; Haussler, David; Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Genome Research. 104-47. 18613-18618 (2007) National Acad Sciences

Ohlson, Johan; Pedersen, Jakob Skou; Haussler, David; Öhman, Marie; Editing modifies the GABAA receptor subunit ?3. Genome Research. 13-5. 698-703 (2007) Cold Spring Harbor Lab

Yeang, Chen-Hsiang; Haussler, David; Detecting coevolution in and among protein domains. Genome Research. 3-11. e211 (2007) Public Library of Science

Zhu, Jingchun; Sanborn, J Zachary; Diekhans, Mark; Lowe, Craig B; Pringle, Tom H; Haussler, David; Comparative genomics search for losses of long-established genes on the human lineage. Genome Research. 3-12. e247 (2007) Public Library of Science

Siepel, Adam; Diekhans, Mark; Brejová, Bro?a; Langton, Laura; Stevens, Michael; Comstock, Charles LG; Davis, Colleen; Ewing, Brent; Oommen, Shelly; Lau, Christopher; Targeted discovery of novel human exons by comparative genomics. Genome Research. 17-12. 1763-1773 (2007) Cold Spring Harbor Lab

Yeang, Chen-Hsiang; Darot, Jeremy FJ; Noller, Harry F; Haussler, David; Detecting the coevolution of biosequences—an example of RNA interaction prediction. Genome Research. 24-9. 2119-2131 (2007) Oxford University Press

Zeng, Jue; Yan, Jizhou; Wang, Ting; Mosbrook-Davis, Deborah; Dolan, Kyle T; Christensen, Ryan; Stormo, Gary D; Haussler, David; Lathrop, Richard H; Brachmann, Rainer K; Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins. Genome Research. 36-1. e8-e8 (2007) Oxford University Press

Ma, Jian; Ratan, Aakrosh; Zhang, Louxin; Miller, Webb; Haussler, David; A heuristic algorithm for reconstructing ancestral gene orders with duplications. Genome Research. . 122-135 (2007) Springer, Berlin, Heidelberg

Yeom, Kyu Hyeon; Lee, Yoon Tae; Pedersen, Jakob; Haussler, David; Kim, V Narry; Han, Jin Ju; Symposia: Small RNA and gene Regulation; Autoregulation of Drosha and DGCR8. Genome Research. 2007. 218-218 (2007) ????????? (? ???????????)

Birney, Ewan; Stamatoyannopoulos, John A; Dutta, Anindya; Guigó, Roderic; Gingeras, Thomas R; Margulies, Elliott H; Weng, Zhiping; Snyder, Michael; Dermitzakis, Emmanouil T; Thurman, Robert E; Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Genome Research. 447-7146. 799-816 (2007) Nature Publishing Group

Giardine, Belinda; Riemer, Cathy; Hefferon, Tim; Thomas, Daryl; Hsu, Fan; Zielenski, Julian; Sang, Yunhua; Elnitski, Laura; Cutting, Garry; Trumbower, Heather; PhenCode: connecting ENCODE data with mutations and phenotype. Genome Research. 28-6. 554-562 (2007) Wiley Online Library

Birney, E; Stamatoyannopoulos, JA; Dutta, A; Guigó, R; Gingeras, TR; Margulies, EH; Weng, Z; Snyder, M; Dermitzakis, ET; Thurman, RE; ENCODE Project Consortium NISC Comparative Sequencing Program Baylor College of Medicine Human Genome Sequencing Center Washington University Genome Sequencing Center Broad Institute Children’s Hospital Oakland Research Institute Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Genome Research. 447-7146. 799-816 (2007)

Ho, Simon YW; Shapiro, Beth; Phillips, Matthew J; Cooper, Alan; Drummond, Alexei J; Evidence for time dependency of molecular rate estimates. Genome Research. 56-3. 515-522 (2007) Oxford University Press

Edwards, Ceiridwen J; Bollongino, Ruth; Scheu, Amelie; Chamberlain, Andrew; Tresset, Anne; Vigne, Jean-Denis; Baird, Jillian F; Larson, Greger; Ho, Simon YW; Heupink, Tim H; Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Genome Research. 274-1616. 1377-1385 (2007) The Royal Society

Abecasis, Ana B; Lemey, Philippe; Vidal, Nicole; de Oliveira, TĚĽlio; Peeters, Martine; Camacho, Ricardo; Shapiro, Beth; Rambaut, Andrew; Vandamme, Anne-Mieke; Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. Genome Research. 81-16. 8543-8551 (2007) American Society for Microbiology

Lemey, Philippe; Pond, Sergei L Kosakovsky; Drummond, Alexei J; Pybus, Oliver G; Shapiro, Beth; Barroso, Helena; Taveira, Nuno; Rambaut, Andrew; Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. Genome Research. 3-2. e29 (2007) Public Library of Science

Barnes, Ian; Shapiro, Beth; Lister, Adrian; Kuznetsova, Tatiana; Sher, Andrei; Guthrie, Dale; Thomas, Mark G; Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Genome Research. 17-12. 1072-1075 (2007) Cell Press

Rector, Annabel; Lemey, Philippe; Tachezy, Ruth; Mostmans, Sara; Ghim, Shin-Je; Van Doorslaer, Koenraad; Roelke, Melody; Bush, Mitchell; Montali, Richard J; Joslin, Janis; Ancient papillomavirus-host co-speciation in Felidae. Genome Research. 8-4. R57 (2007) BioMed Central

Haile, James; Holdaway, Richard; Oliver, Karen; Bunce, Michael; Gilbert, M Thomas P; Nielsen, Rasmus; Munch, Kasper; Ho, Simon YW; Shapiro, Beth; Willerslev, Eske; Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor?. Genome Research. 24-4. 982-989 (2007) Oxford University Press

Ho, Simon YW; Heupink, Tim H; Rambaut, Andrew; Shapiro, Beth; Bayesian estimation of sequence damage in ancient DNA. Genome Research. 24-6. 1416-1422 (2007) Oxford University Press

Deforche, Koen; Camacho, Ricardo; Laethem, Kristel Van; Shapiro, Beth; Moreau, Yves; Rambaut, Andrew; Vandamme, Anne-Mieke; Lemey, Philippe; Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo. Genome Research. 14-8. 1105-1114 (2007) Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA

Barnett, Ross; Yamaguchi, Nobuyuki; Shapiro, Beth; Nijman, Vincent; Using ancient DNA techniques to identify the origin of unprovenanced museum specimens, as illustrated by the identification of a 19th century lion from Amsterdam. Genome Research. 76-2(2007) Brill Academic Publishers, Inc.; NCB Naturals

Dal̩n, Love; G̦therstr̦m, Anders; Meijer, Tomas; Shapiro, Beth; Recovery of DNA from footprints in the snow. Genome Research. 121-3. 321-324 (2007)

Deforche, Koen; Lemey, Philippe; Camacho, Ricardo; Van Laethem, Kristel; Shapiro, Beth; Moreau, Yves; Rambaut, Andrew; Vandamme, Anne-Mieke; Understanding the adenine richness of the HIV genome through the estimation of misincorporation rates in viv. (2007)

Shapiro, Beth; Lemey, Philippe; Schuster, S; Van Laethem, Kristel; Vandamme, Anne-Mieke; Rambaut, Andrew; Population genomic analysis of within-host HIV diversity. (2007)

Stark, Alexander; Lin, Michael F; Kheradpour, Pouya; Pedersen, Jakob S; Parts, Leopold; Carlson, Joseph W; Crosby, Madeline A; Rasmussen, Matthew D; Roy, Sushmita; Deoras, Ameya N; Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Genome Research. 450-7167. 219-232 (2007) Nature publishing group

Ettwiller, Laurence; Paten, Benedict; Ramialison, Mirana; Birney, Ewan; Wittbrodt, Joachim; Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Genome Research. 4-7. 563-565 (2007) Nature Publishing Group

Paten, Benedict John; Large-scale multiple alignment and transcriptionally-associated pattern discovery in vertebrate genomes. (2007) University of Cambridge

MacRae, Ian J; Zhou, Kaihong; Li, Fei; Repic, Adrian; Brooks, Angela N; Cande, W Zacheus; Adams, Paul D; Doudna, Jennifer A; Structural basis for double-stranded RNA processing by Dicer. Genome Research. 311-5758. 195-198 (2006) American Association for the Advancement of Science

Hinrichs, Angela S; Karolchik, Donna; Baertsch, Robert; Barber, Galt P; Bejerano, Gill; Clawson, Hiram; Diekhans, Mark; Furey, Terrence S; Harte, Rachel A; Hsu, Fan; The UCSC genome browser database: update 2006. Genome Research. 34-suppl 1. D590-D598 (2006) Oxford University Press

Shapiro, Beth; Rambaut, Andrew; Drummond, Alexei J; Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Genome Research. 23-1. 42925 (2006) Oxford University Press

Shapiro, Beth; Rambaut, Andrew; Pybus, Oliver G; Holmes, Edward C; Is amino acid racemization a useful tool for screening for ancient DNA in bone?. Genome Research. 23-9. 1724-1730 (2006) SMBE

Shapiro, Beth; Rambaut, Andrew; Gilbert, M Thomas P; Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo. Genome Research. 10-4. 334-335 (2006) Elsevier

Poinar, Hendrik N; Schwarz, Carsten; Qi, Ji; Shapiro, Beth; MacPhee, Ross DE; Buigues, Bernard; Tikhonov, Alexei; Huson, Daniel H; Tomsho, Lynn P; Auch, Alexander; Case study: recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon. Genome Research. 311-5759. 392-394 (2006) American Association for the Advancement of Science

Sugnet, Charles W; Srinivasan, Karpagam; Clark, Tyson A; O’Brien, Georgeann; Cline, Melissa S; Wang, Hui; Williams, Alan; Kulp, David; Blume, John E; Haussler, David; Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation. Genome Research. 2-1. e4 (2006) Public Library of Science

Hinrichs, Angela S; Karolchik, Donna; Baertsch, Robert; Barber, Galt P; Bejerano, Gill; Clawson, Hiram; Diekhans, Mark; Furey, Terrence S; Harte, Rachel A; Hsu, Fan; CRAVAT: cancer-related analysis of variants toolkit. Genome Research. 34-suppl 1. D590-D598 (2006) Oxford University Press

Hsu, Fan; Kent, W James; Clawson, Hiram; Kuhn, Robert M; Diekhans, Mark; Haussler, David; The shrinking human protein coding complement: are there fewer than 20,000 genes?. Genome Research. 22-9. 1036-1046 (2006) Oxford Univ Press

Schattner, Peter; Diekhans, Mark; Genome Research. 34-6. 1700-1710 (2006) Oxford University Press

Sanborn, J Zachary; Zhu, Jing; Diekhans, Mark; Haussler, David; (2006)

Pollard, Katherine S; Salama, Sofie R; Lambert, Nelle; Lambot, Marie-Alexandra; Coppens, Sandra; Pedersen, Jakob S; Katzman, Sol; King, Bryan; Onodera, Courtney; Siepel, Adam; An RNA gene expressed during cortical development evolved rapidly in humans. Genome Research. 443-7108. 167 (2006) Nature Publishing Group

Pedersen, Jakob Skou; Bejerano, Gill; Siepel, Adam; Rosenbloom, Kate; Lindblad-Toh, Kerstin; Lander, Eric S; Kent, Jim; Miller, Webb; Haussler, David; Identification and classification of conserved RNA secondary structures in the human genome. Genome Research. 2-4. e33 (2006) Public Library of Science

Hinrichs, Angela S; Karolchik, Donna; Baertsch, Robert; Barber, Galt P; Bejerano, Gill; Clawson, Hiram; Diekhans, Mark; Furey, Terrence S; Harte, Rachel A; Hsu, Fan; The UCSC genome browser database: update 2006. Genome Research. 34-suppl_1. D590-D598 (2006) Oxford University Press

Bejerano, Gill; Lowe, Craig B; Ahituv, Nadav; King, Bryan; Siepel, Adam; Salama, Sofie R; Rubin, Edward M; Kent, W James; Haussler, David; A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Genome Research. 441-7089. 87 (2006) Nature Publishing Group

Hsu, Fan; Kent, W James; Clawson, Hiram; Kuhn, Robert M; Diekhans, Mark; Haussler, David; The UCSC known genes. Genome Research. 22-9. 1036-1046 (2006) Oxford University Press

Kuhn, Robert M; Karolchik, Donna; Zweig, Ann S; Trumbower, Heather; Thomas, Daryl J; Thakkapallayil, Archana; Sugnet, Charles W; Stanke, Mario; Smith, Kayla E; Siepel, A; The UCSC genome browser database: update 2007. Genome Research. 35-suppl_1. D668-D673 (2006) Oxford University Press

Pollard, Katherine S; Salama, Sofie R; King, Bryan; Kern, Andrew D; Dreszer, Tim; Katzman, Sol; Siepel, Adam; Pedersen, Jakob S; Bejerano, Gill; Baertsch, Robert; Forces shaping the fastest evolving regions in the human genome. Genome Research. 2-10. e168 (2006) Public Library of Science

Ma, Jian; Zhang, Louxin; Suh, Bernard B; Raney, Brian J; Burhans, Richard C; Kent, W James; Blanchette, Mathieu; Haussler, David; Miller, Webb; Reconstructing contiguous regions of an ancestral genome. Genome Research. 16-12. 1557-1565 (2006) Cold Spring Harbor Lab

Sugnet, Charles W; Srinivasan, Karpagam; Clark, Tyson A; O’Brien, Georgeann; Cline, Melissa S; Wang, Hui; Williams, Alan; Kulp, David; Blume, John E; Haussler, David; Unusual intron conservation near tissue-regulated exons found by splicing microarrays. Genome Research. 2-1. e4 (2006) Public Library of Science

Siepel, Adam; Pollard, Katherine S; Haussler, David; New methods for detecting lineage-specific selection. Genome Research. 3909. 190-205 (2006) Berlin: Springer-Verlag, 1973-

Thomas, Daryl J; Rosenbloom, Kate R; Clawson, Hiram; Hinrichs, Angie S; Trumbower, Heather; Raney, Brian J; Karolchik, Donna; Barber, Galt P; Harte, Rachel A; Hillman-Jackson, Jennifer; The ENCODE project at UC santa cruz. Genome Research. 35-suppl_1. D663-D667 (2006) Oxford University Press

Thomas, Daryl J; Trumbower, Heather; Kern, Andrew D; Rhead, Brooke L; Kuhn, Robert M; Haussler, David; Kent, W James; Variation resources at UC Santa Cruz. Genome Research. 35-suppl_1. D716-D720 (2006) Oxford University Press

Wu, Jing; Haussler, David; Coding exon detection using comparative sequences. Genome Research. 13-6. 1148-1164 (2006) Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA

Darot, Jeremy; Yeang, Chen-Hsiang; Haussler, David; Detecting the dependent evolution of biosequences. Genome Research. 3909. 595 (2006) Springer-Verlag

Haussler, David; Ultraconserved elements, living fossil transposons, and rapid bursts of change: reconstructing the uneven evolutionary history of the human genome. Genome Research. . 336-337 (2006) Springer-Verlag

Sanborn, J Zachary; Zhu, Jing; Diekhans, Mark; Haussler, David; A Novel Method for Discovering Primate Gene Loss using the Ancestral Genome. (2006)

Smith, David I; Zhu, Yu; McAvoy, Sarah; Kuhn, Robert; Common fragile sites, extremely large genes, neural development and cancer. Genome Research. 232-1. 48-57 (2006) Elsevier

Zhu Y, McAvoy S, Kuhn R, Smith DI; RORA, a large common fragile site gene, is involved in cellular stress response.. Genome Research. 25-20. 2901-8 (2006)

Shapiro, Beth; Rambaut, Andrew; Drummond, Alexei J; Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Genome Research. 23-1. 42925 (2006) Oxford University Press

Shapiro, Beth; Rambaut, Andrew; Pybus, Oliver G; Holmes, Edward C; A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution. Genome Research. 23-9. 1724-1730 (2006) SMBE

Shapiro, Beth; Rambaut, Andrew; Gilbert, M Thomas P; No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al.). Genome Research. 10-4. 334-335 (2006) Elsevier

Poinar, Hendrik N; Schwarz, Carsten; Qi, Ji; Shapiro, Beth; MacPhee, Ross DE; Buigues, Bernard; Tikhonov, Alexei; Huson, Daniel H; Tomsho, Lynn P; Auch, Alexander; Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Genome Research. 311-5759. 392-394 (2006) American Association for the Advancement of Science

Schattner, Peter; Brooks, Angela N; Lowe, Todd M; The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Genome Research. 33-suppl 2. W686-W689 (2005) Oxford University Press

Ettwiller, Laurence; Paten, Benedict; Souren, Marcel; Loosli, Felix; Wittbrodt, Jochen; Birney, Ewan; Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation. Genome Research. 6-12. R104 (2005) BioMed Central

Drummond, Alexei J; Rambaut, Andrew; Shapiro, BETH; Pybus, Oliver G; Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. Genome Research. 22-5. 1185-1192 (2005) Oxford University Press

Bunce, Michael; Szulkin, Marta; Lerner, Heather RL; Barnes, Ian; Shapiro, Beth; Cooper, Alan; Holdaway, Richard N; The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Genome Research. 3-1. e9 (2005) Public Library of Science

Gilbert, MTP; Shapiro, B; Drummond, A; Cooper, A; The Late Pleistocene distribution of vicu̱as (Vicugna vicugna) and the ‰ÛÏextinction‰Û of the gracile llama (‰ÛÏLama gracilis‰Û): New molecular data. Genome Research. 32-7. 1053-1060 (2005) Academic Press

Ule, Jernej; Ule, Aljaž; Spencer, Joanna; Williams, Alan; Hu, Jing-Shan; Cline, Melissa; Wang, Hui; Clark, Tyson; Fraser, Claire; Ruggiu, Matteo; Using bioinformatics to predict the functional impact of SNVs. Genome Research. 37-8. 844-852 (2005) Nature Publishing Group

Cline, Melissa S; Blume, John; Cawley, Simon; Clark, Tyson A; Hu, Jing-Shan; Lu, Gang; Salomonis, Nathan; Wang, Hui; Williams, Alan; Expression Data Integrated with Domain Interaction Networks. Genome Research. 21-suppl 1. i107-i115 (2005) Oxford Univ Press

Karchin, Rachel; Diekhans, Mark; Kelly, Libusha; Thomas, Daryl J; Pieper, Ursula; Eswar, Narayanan; Haussler, David; Sali, Andrej; Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes. Genome Research. 21-12. 2814-2820 (2005) Oxford Univ Press

Hsu, Fan; Pringle, Tom H; Kuhn, Robert M; Karolchik, Donna; Diekhans, Mark; Haussler, David; Kent, W James; The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes (vol 19, pg 1316, 2009). Genome Research. 33-suppl 1. D454-D458 (2005) Oxford Univ Press

Di Bias, A; Dahle, David M; Diekhans, Mark; Grate, Leslie; Hirschberg, Jeffrey; Karplus, Kevin; Keller, Hansjörg; Kendrick, Mark; Mesa-Martinez, Francisco J; Pease, David; Genome Research. 16-1. 80-92 (2005) IEEE

Siepel, Adam; Bejerano, Gill; Pedersen, Jakob S; Hinrichs, Angie S; Hou, Minmei; Rosenbloom, Kate; Clawson, Hiram; Spieth, John; Hillier, LaDeana W; Richards, Stephen; Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research. 15-8. 1034-1050 (2005) Cold Spring Harbor Lab

Karchin, Rachel; Diekhans, Mark; Kelly, Libusha; Thomas, Daryl J; Pieper, Ursula; Eswar, Narayanan; Haussler, David; Sali, Andrej; LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Genome Research. 21-12. 2814-2820 (2005) Oxford University Press

Siepel, Adam; Haussler, David; Phylogenetic hidden Markov models. Genome Research. . 325-351 (2005) Springer New York

Kent, WJ; Hsu, Fan; Karolchik, Donna; Kuhn, Robert M; Clawson, Hiram; Trumbower, Heather; Haussler, David; Exploring relationships and mining data with the UCSC Gene Sorter. Genome Research. 15-5. 737-741 (2005) Cold Spring Harbor Lab

Bejerano, Gill; Siepel, Adam C; Kent, W James; Haussler, David; Computational screening of conserved genomic DNA in search of functional noncoding elements. Genome Research. 2-7. 535-545 (2005) Nature Publishing Group

Hsu, Fan; Pringle, Tom H; Kuhn, Robert M; Karolchik, Donna; Diekhans, Mark; Haussler, David; Kent, W James; The UCSC proteome browser. Genome Research. 33-suppl_1. D454-D458 (2005) Oxford University Press

Lucena, Brian; Haussler, David; Counterexample to a claim about the reconstruction of ancestral character states. Genome Research. 54-4. 693-695 (2005) Society of Systematic Zoology

Akeson, Mark; Vercoutere, Wenonah; Haussler, David; Winters-Hilt, Stephen; Methods and devices for characterizing duplex nucleic acid molecules. (2005) US Patent 6,936,433

Bejerano, Gill; Lowe, Craig; Ahituv, Nadav; King, Bryan; Siepel, Adam; Salama, Sofie; Rubin, Edward M; Kent, W James; Haussler, David; An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 are Derived from a Retroposon. Genome Research. (2005)

Blanchette, M; Green, ED; Miller, W; Haussler, D; Reconstructing large regions of an ancestral mammalian genome in silico (vol 14, pg 2412, 2004). Genome Research. 15-3. 451-451 (2005) COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2924 USA

Bejerano, Gill; Lowe, Craig; Ahituv, Nadav; King, Bryan; Siepel, Adam; Salama, Sofie; Rubin, Edward M; Kent, W James; Haussler, David; An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 areDerived from a Retroposon. Genome Research. 441-LBNL–59307(2005) Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)

Smith, David I; Wang, Fang; Zhu, Yu; McAvoy, Sarah; Kuhn, Robert; Large common fragile site genes link neurological development and cancer. (2005) American Association for Cancer Research

Drummond, Alexei J; Rambaut, Andrew; Shapiro, BETH; Pybus, Oliver G; Bayesian coalescent inference of past population dynamics from molecular sequences. Genome Research. 22-5. 1185-1192 (2005) Oxford University Press

Bunce, Michael; Szulkin, Marta; Lerner, Heather RL; Barnes, Ian; Shapiro, Beth; Cooper, Alan; Holdaway, Richard N; Ancient DNA provides new insights into the evolutionary history of New Zealand’s extinct giant eagle. Genome Research. 3-1. e9 (2005) Public Library of Science

Gilbert, MTP; Shapiro, B; Drummond, A; Cooper, A; Post-mortem DNA damage hotspots in Bison (Bison bison) provide evidence for both damage and mutational hotspots in human mitochondrial DNA. Genome Research. 32-7. 1053-1060 (2005) Academic Press

Ettwiller, Laurence; Paten, Benedict; Souren, Marcel; Loosli, Felix; Wittbrodt, Jochen; Birney, Ewan; The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Research. 6-12. R104 (2005) BioMed Central

Shapiro, Beth; Drummond, Alexei J; Rambaut, Andrew; Wilson, Michael C; Matheus, Paul E; Sher, Andrei V; Pybus, Oliver G; Gilbert, M Thomas P; Barnes, Ian; Binladen, Jonas; Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. Genome Research. 306-5701. 1561-1565 (2004) American Association for the Advancement of Science

Gilbert, M Thomas P; Wilson, Andrew S; Bunce, Michael; Hansen, Anders J; Willerslev, Eske; Shapiro, Beth; Higham, Thomas FG; Richards, Michael P; O’Connell, Tamsin C; Tobin, Desmond J; Sequence preservation of osteocalcin protein and mitochondrial DNA in bison bones older than 55 ka. Genome Research. 14-12. R463-R464 (2004) Cell Press

Shapiro, Beth; Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data. Genome Research. 79-2(2004)

Cheng, Jill; Sun, Shaw; Tracy, Adam; Hubbell, Earl; Morris, Joseph; Valmeekam, Venu; Kimbrough, Andrew; Cline, Melissa S; Liu, Guoying; Shigeta, Ron; GPCR-GRAPA-LIB—a refined library of hidden Markov Models for annotating GPCRs. Genome Research. 20-9. 1462-1463 (2004) Oxford Univ Press

Cheng, Jill; Cline, Melissa; Martin, John; Finkelstein, David; Awad, Tarif; Kulp, David; Siani-Rose, Michael A; Structure-based comparison of four eukaryotic genomes. Genome Research. 14-3. 687-700 (2004) Taylor & Francis

Karchin, Rachel; Cline, Melissa; Karplus, Kevin; RBPmap: a web server for mapping binding sites of RNA-binding proteins. Genome Research. 55-3. 508-518 (2004) Wiley Online Library

Cline, Melissa S; Shigeta, Ron; Wheeler, Raymond; Siani-Rose, Michael A; Kulp, David; Loraine, Ann E; The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Genome Research. 9. 17-28 (2004)

Furey, Terrence S; Diekhans, Mark; Lu, Yontao; Graves, Tina A; Oddy, Lachlan; Randall-Maher, Jennifer; Hillier, LaDeana W; Wilson, Richard K; Haussler, David; Genome Research. 14-10b. 2034-2040 (2004) Cold Spring Harbor Lab

Roskin, Krishna M; Diekhans, Mark; Haussler, David; Genome Research. 11-42769. 395-411 (2004) Mary Ann Liebert, Inc.

Gerhard, Daniela S; Wagner, Lukas; Feingold, Elise A; Shenmen, Carolyn M; Grouse, Lynette H; Schuler, Greg; Klein, Steven L; Old, Susan; Rasooly, Rebekah; Good, Peter; Genome Research. 14-10B. 2121-2127 (2004)

Bejerano, Gill; Pheasant, Michael; Makunin, Igor; Stephen, Stuart; Kent, W James; Mattick, John S; Haussler, David; Ultraconserved elements in the human genome. Genome Research. 304-5675. 1321-1325 (2004) American Association for the Advancement of Science

Blanchette, Mathieu; Kent, W James; Riemer, Cathy; Elnitski, Laura; Smit, Arian FA; Roskin, Krishna M; Baertsch, Robert; Rosenbloom, Kate; Clawson, Hiram; Green, Eric D; Aligning multiple genomic sequences with the threaded blockset aligner. Genome Research. 14-4. 708-715 (2004) Cold Spring Harbor Lab

Karolchik, Donna; Hinrichs, Angela S; Furey, Terrence S; Roskin, Krishna M; Sugnet, Charles W; Haussler, David; Kent, W James; The UCSC Table Browser data retrieval tool. Genome Research. 32-suppl_1. D493-D496 (2004) Oxford University Press

Gerhard, Daniela S; Wagner, Lukas; Feingold, Elise A; Shenmen, Carolyn M; Grouse, Lynette H; Schuler, Greg; Klein, Steven L; Old, Susan; Rasooly, Rebekah; Good, Peter; The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).. Genome Research. 14-10B. 2121-2127 (2004) Cold Spring Harbor Laboratory Press

Siepel, Adam; Haussler, David; Combining phylogenetic and hidden Markov models in biosequence analysis. Genome Research. 11-42769. 413-428 (2004) Mary Ann Liebert, Inc.

Siepel, Adam; Haussler, David; Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Genome Research. 21-3. 468-488 (2004) Oxford University Press

Jensen-Seaman, Michael I; Furey, Terrence S; Payseur, Bret A; Lu, Yontao; Roskin, Krishna M; Chen, Chin-Fu; Thomas, Michael A; Haussler, David; Jacob, Howard J; Comparative recombination rates in the rat, mouse, and human genomes. Genome Research. 14-4. 528-538 (2004) Cold Spring Harbor Lab

Bailey, Jeffrey A; Baertsch, Robert; Kent, W James; Haussler, David; Eichler, Evan E; Hotspots of mammalian chromosomal evolution. Genome Research. 5-4. R23 (2004) BioMed Central

Sugnet, Charles W; Kent, W James; Ares, Manuel; Haussler, David; Transcriptome and genome conservation of alternative splicing events in humans and mice.. Genome Research. 9. 66-77 (2004)

She, Xinwei; Horvath, Julie E; Jiang, Zhaoshi; Liu, Ge; The structure and evolution of centromeric transition regions within the human genome. Genome Research. 430-7002. 857 (2004) Nature Publishing Group

Siepel, Adam; Haussler, David; Computational identification of evolutionarily conserved exons. Genome Research. . 177-186 (2004) ACM

Bejerano, Gill; Haussler, David; Blanchette, Mathieu; Into the heart of darkness: large-scale clustering of human non-coding DNA. Genome Research. 20-suppl_1. i40-i48 (2004) Oxford University Press

Yang, Shan; Smit, Arian F; Schwartz, Scott; Chiaromonte, Francesca; Roskin, Krishna M; Haussler, David; Miller, Webb; Hardison, Ross C; Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Research. 14-4. 517-527 (2004) Cold Spring Harbor Lab

Robertson, Michael P; Igel, Haller; Baertsch, Robert; Haussler, David; Ares Jr, Manuel; Scott, William G; The structure of a rigorously conserved RNA element within the SARS virus genome. Genome Research. 3-1. e5 (2004) Public Library of Science

Furey, Terrence S; Diekhans, Mark; Lu, Yontao; Graves, Tina A; Oddy, Lachlan; Randall-Maher, Jennifer; Hillier, LaDeana W; Wilson, Richard K; Haussler, David; Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. Genome Research. 14-10b. 2034-2040 (2004) Cold Spring Harbor Lab

Jojic, Vladimir; Jojic, Nebojsa; Meek, Chris; Geiger, Dan; Siepel, Adam; Haussler, David; Heckerman, David; Efficient approximations for learning phylogenetic HMM models from data. Genome Research. 20-suppl_1. i161-i168 (2004) Oxford University Press

Roskin, Krishna M; Diekhans, Mark; Haussler, David; Score functions for determining regional conservation in two-species local alignments. Genome Research. 11-42769. 395-411 (2004) Mary Ann Liebert, Inc.

Hillier, LaDeana W; Miller, Webb; Birney, Ewan; Warren, Wesley; Hardison, Ross C; Ponting, Chris P; Bork, Peer; Burt, David W; Groenen, Martien AM; Delany, Mary E; Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Genome Research. 432-7018. 695-716 (2004) Nature Publishing Group

Metzker, Michael L; Muzny, Donna M; Sodergren, Erica J; Scherer, Steven; Scott, Graham; Steffen, David; Worley, Kim C; Burch, Paula E; Okwuonu, Geoffrey; Hines, Sandra; Genome sequence of the Brown Norway rat yields insights into mammalian evolution. (2004) Macmillian Magazines Ltd.

Shapiro, Beth; Drummond, Alexei J; Rambaut, Andrew; Wilson, Michael C; Matheus, Paul E; Sher, Andrei V; Pybus, Oliver G; Gilbert, M Thomas P; Barnes, Ian; Binladen, Jonas; Rise and fall of the Beringian steppe bison. Genome Research. 306-5701. 1561-1565 (2004) American Association for the Advancement of Science

Gilbert, M Thomas P; Wilson, Andrew S; Bunce, Michael; Hansen, Anders J; Willerslev, Eske; Shapiro, Beth; Higham, Thomas FG; Richards, Michael P; O’Connell, Tamsin C; Tobin, Desmond J; Ancient mitochondrial DNA from hair. Genome Research. 14-12. R463-R464 (2004) Cell Press

Shapiro, Beth; History, Philosophy & Ethics Return of the Crazy Bird: The Sad, Strange Tale of the Dodo. By Clara Pinto‰Ű�Correia. Copernicus Books. New York: Springer‰Ű�Verlag. $27.50. xv+ 216 p; ill.; index. ISBN: 0‰ŰŇ387‰ŰŇ98876‰ŰŇ9. 2003.. Genome Research. 79-2(2004)

Willerslev, Eske; Hansen, Anders J; Binladen, Jonas; Brand, Tina B; Gilbert, M Thomas P; Shapiro, Beth; Bunce, Michael; Wiuf, Carsten; Gilichinsky, David A; Cooper, Alan; Ancient mitochondrial DNA from hair. Genome Research. 300-5620. 791-795 (2003) American Association for the Advancement of Science

Shapiro, Beth; Cooper, Alan; Using ancient DNA techniques to identify the origin of unprovenanced museum specimens, as illustrated by the identification of a 19th century lion from Amsterdam. Genome Research. 60-1. 94-100 (2003) Elsevier

Shapiro, Beth Alison; Case study: ancient DNA recovered from Pleistocene-age remains of a Florida armadillo. (2003) University of Oxford

Liu, Guoying; Loraine, Ann E; Shigeta, Ron; Cline, Melissa; Cheng, Jill; Valmeekam, Venu; Sun, Shaw; Kulp, David; Siani-Rose, Michael A; The UCSC cancer genomics browser: update 2013. Genome Research. 31-1. 82-86 (2003) Oxford Univ Press

Karchin, Rachel; Cline, Melissa; Mandel‐Gutfreund, Yael; Karplus, Kevin; Understanding genome browsing. Genome Research. 51-4. 504-514 (2003) Wiley Online Library

Wang, Hui; Hubbell, Earl; Hu, Jing-shan; Mei, Gangwu; Cline, Melissa; Lu, Gang; Clark, Tyson; Siani-Rose, Michael A; Ares, Manuel; Kulp, David C; On alignment shift and its measures. Genome Research. 19-suppl 1. i315-i322 (2003) Oxford Univ Press

Loraine, Ann E; Helt, Gregg A; Cline, Melissa S; Siani-Rose, Michael A; E-mail: melissa_cline® affymetrix. com. Genome Research. 1-2. 289-306 (2003) World Scientific

Shigeta, Ron; Cline, Melissa; Liu, Guoying; Siani-Rose, Michael A; Abstract PR14: Harnessing the power of big data to advance pediatric cancer care. Genome Research. 19-5. 667-668 (2003) Oxford Univ Press

Loraine, Ann; Cline, Melissa; Helt, Gregg; Siani-Rose, Michael; Kulp, David; Shigeta, Ron; Initial sequencing and comparative analysis of the mouse genome. (2003) US Patent App. 10/423,403

Loraine, Ann; Cline, Melissa; Helt, Gregg; Siani-Rose, Michael; Kulp, David; Shigeta, Ron; The UCSC known genes. (2003) US Patent App. 10/423,403

CLINE, MS; SHIGETA, R; WHEELER, RL; SIANI-ROSE, MA; KULP, D; LORAINE, AE; Retrocopy contributions to the evolution of the human genome. Genome Research. . 17 (2003) World Scientific

Diekhans, Mark; Grate, Leslie; Barrett, Christian; Brown, Michael; Casper, Jonathan; Cline, Melissa; Figel, Terry; Karchin, Rachel; Sjölander, Kimmen; Tarnas, Christopher; The completion of the mammalian gene collection (MGC). (2003)

Karplus, Kevin; Karchin, Rachel; Draper, Jenny; Casper, Jonathan; Mandel‐Gutfreund, Yael; Diekhans, Mark; Hughey, Richard; The UCSC genome browser database. Genome Research. 53-S6. 491-496 (2003) Wiley Subscription Services, Inc., A Wiley Company

Hardison, Ross C; Roskin, Krishna M; Yang, Shan; Diekhans, Mark; Kent, W James; Weber, Ryan; Elnitski, Laura; Li, Jia; O’Connor, Michael; Kolbe, Diana; Current status and new features of the Consensus Coding Sequence database. Genome Research. 13-1. 13-26 (2003) Cold Spring Harbor Lab

Chiaromonte, F; Weber, RJ; Roskin, KM; Diekhans, M; Kent, WJ; Haussler, D; The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).. Genome Research. 68. 245-254 (2003) Cold Spring Harbor Laboratory Press

Hardison, RC; Chiaromonte, F; Kolbe, D; Wang, Hao; Petrykowska, H; Elnitski, L; Yang, S; Giardine, B; Zhang, Y; Riemer, C; Genome Research. 68-1. 335-344 (2003)

Roskin, Krishna M; Diekhans, Mark; Haussler, David; Genome Research. . 257-266 (2003) ACM

Karolchik, Donna; Baertsch, Robert; Diekhans, Mark; Furey, Terrence S; Hinrichs, Angie; Lu, YT; Roskin, Krishna M; Schwartz, Matthias; Sugnet, Charles W; Thomas, Daryl J; Genome Research. 31-1. 51-54 (2003) Oxford University Press

Hardison, R; Smit, A; Chiaromonte, F; Diekhans, M; Elnitski, L; Goldman, N; Kent, J; Li, J; Miller, W; Roskin, K; Genome Research. 31-1. 145-145 (2003) ACADEMIC PRESS INC ELSEVIER SCIENCE 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA

Diekhans, Mark; Grate, Leslie; Barrett, Christian; Brown, Michael; Casper, Jonathan; Cline, Melissa; Figel, Terry; Karchin, Rachel; Sjölander, Kimmen; Tarnas, Christopher; (2003)

Karolchik, Donna; Baertsch, Robert; Diekhans, Mark; Furey, Terrence S; Hinrichs, Angie; Lu, YT; Roskin, Krishna M; Schwartz, Matthias; Sugnet, Charles W; Thomas, Daryl J; The UCSC genome browser database. Genome Research. 31-1. 51-54 (2003) Oxford University Press

Schwartz, Scott; Kent, W James; Smit, Arian; Zhang, Zheng; Baertsch, Robert; Hardison, Ross C; Haussler, David; Miller, Webb; Human–mouse alignments with BLASTZ. Genome Research. 13-1. 103-107 (2003) Cold Spring Harbor Lab

Thomas, JW; Touchman, JW; Blakesley, RW; Bouffard, GG; Comparative analyses of multi-species sequences from targeted genomic regions. Genome Research. 424-6950. 788 (2003) Nature Publishing Group

Kent, W James; Baertsch, Robert; Hinrichs, Angie; Miller, Webb; Haussler, David; Evolution’s cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Genome Research. 100-20. 11484-11489 (2003) National Acad Sciences

Hardison, Ross C; Roskin, Krishna M; Yang, Shan; Diekhans, Mark; Kent, W James; Weber, Ryan; Elnitski, Laura; Li, Jia; O’Connor, Michael; Kolbe, Diana; Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Research. 13-1. 13-26 (2003) Cold Spring Harbor Lab

Margulies, Elliott H; Blanchette, Mathieu; Haussler, David; Green, Eric D; NISC Comparative Sequencing Program; Identification and characterization of multi-species conserved sequences. Genome Research. 13-12. 2507-2518 (2003) Cold Spring Harbor Lab

Wang, Hui; Hubbell, Earl; Hu, Jing-shan; Mei, Gangwu; Cline, Melissa; Lu, Gang; Clark, Tyson; Siani-Rose, Michael A; Ares, Manuel; Kulp, David C; Gene structure-based splice variant deconvolution using a microarry platform. Genome Research. 19-suppl_1. i315-i322 (2003) Oxford University Press

Winters-Hilt, Stephen; Vercoutere, Wenonah; DeGuzman, Veronica S; Deamer, David; Akeson, Mark; Haussler, David; Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules. Genome Research. 84-2. 967-976 (2003) Cell Press

Furey, Terrence S; Haussler, David; Integration of the cytogenetic map with the draft human genome sequence. Genome Research. 12-9. 1037-1044 (2003) Oxford Univ Press

Chiaromonte, F; Weber, RJ; Roskin, KM; Diekhans, M; Kent, WJ; Haussler, D; The share of human genomic DNA under selection estimated from human–mouse genomic alignments. Genome Research. 68. 245-254 (2003) Cold Spring Harbor Laboratory Press

Roskin, Krishna M; Diekhans, Mark; Haussler, David; Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments. Genome Research. . 257-266 (2003) ACM

Hardison, RC; Chiaromonte, F; Kolbe, D; Wang, Hao; Petrykowska, H; Elnitski, L; Yang, S; Giardine, B; Zhang, Y; Riemer, C; Global predictions and tests of erythroid regulatory regions. Genome Research. 68. 335-344 (2003) Cold Spring Harbor Laboratory Press

DeGuzman, V; Winters-Hilt, S; Solbrig, A; Sughrue, W; Deamer, D; Haussler, D; Akeson, M; Sequence-dependent fraying of single DNA molecules measured in real time at 5 angstrom resolution using an ion channel. Genome Research. 84-2. 490A-490A (2003) BIOPHYSICAL SOCIETY 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA

Haussler, David; Computational analysis of the human and other mammalian genomes. Genome Research. . 138-138 (2003) ACM

ARES JR, M; HAUSSLER, D; TRANSCRIPTOME AND GENOME CONSERVATION OF ALTERNATIVE SPLICING EVENTS. Genome Research. . 66 (2003) World Scientific

Hardison, R; Smit, A; Chiaromonte, F; Diekhans, M; Elnitski, L; Goldman, N; Kent, J; Li, J; Miller, W; Roskin, K; Lessons from the alignment of human and mouse genomes: Finding candidate functional sequences despite variation in conservation.. Genome Research. 31-1. 145-145 (2003) ACADEMIC PRESS INC ELSEVIER SCIENCE 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA

ARES JR, M; HAUSSLER, D; CW SUGNET, WJ KENT. Genome Research. . 66 (2003) World Scientific

Willerslev, Eske; Hansen, Anders J; Binladen, Jonas; Brand, Tina B; Gilbert, M Thomas P; Shapiro, Beth; Bunce, Michael; Wiuf, Carsten; Gilichinsky, David A; Cooper, Alan; Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Genome Research. 300-5620. 791-795 (2003) American Association for the Advancement of Science

Shapiro, Beth; Cooper, Alan; Beringia as an Ice Age genetic museum. Genome Research. 60-1. 94-100 (2003) Elsevier

Shapiro, Beth Alison; Inferring evolutionary history and processes using ancient DNA. (2003) University of Oxford

Barnes, Ian; Matheus, P; Shapiro, Beth; Jensen, D; Cooper, Alan; The effect of inappropriate calibration: three case studies in molecular ecology. Genome Research. 295-5563. 2267-2270 (2002) American Association for the Advancement of Science

Shapiro, Beth; Sibthorpe, Dean; Rambaut, Andrew; Austin, Jeremy; Wragg, Graham M; Bininda-Emonds, Olaf RP; Lee, Patricia LM; Cooper, Alan; Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor?. Genome Research. 295-5560. 1683-1683 (2002) American Association for the Advancement of Science

Nielsen-Marsh, Christina M; Ostrom, Peggy H; Gandhi, Hasand; Shapiro, Beth; Cooper, Alan; Hauschka, Peter V; Collins, Matthew J; Accommodating the effect of ancient DNA damage on inferences of demographic histories. Genome Research. 30-12. 1099-1102 (2002) Geological Society of America

Lalueza-Fox, Carles; Shapiro, Beth; Bover, Pere; Alcover, Josep Antoni; Bertranpetit, Jaume; Post-mortem DNA damage hotspots in Bison (Bison bison) provide evidence for both damage and mutational hotspots in human mitochondrial DNA. Genome Research. 25-3. 501-510 (2002) Academic Press

Beck, Christopher W; Shapiro, Beth; Choksi, Semil; Promislow, Daniel EL; The evolutionary consequences of interspecies hybridization: insights from ancient and modern bear genomes. Genome Research. 4-2. 275-292 (2002) Evolutionary Ecology, Ltd.

Cline, Melissa; Hughey, Richard; Karplus, Kevin; Protein-based analysis of alternative splicing in the human genome. Genome Research. 18-2. 306-314 (2002) Oxford Univ Press

Cline, Melissa S; Karplus, Kevin; Lathrop, Richard H; Smith, Temple F; Rogers, Robert G; Haussler, David; Bioinformatics (Oxford, England) Volume: 24 ISSN: 1367-4811 ISO Abbreviation: Bioinformatics Publication Date: 2008 Nov. Genome Research. 49-1. 42930 (2002) Wiley Online Library

Loraine, Ann E; Helt, Gregg A; Cline, Melissa S; Siani-Rose, Michael A; The UCSC Xena system for integrating and visualizing functional genomics. Genome Research. . 118-124 (2002) IEEE

Chinwalla, Asif T; Cook, Lisa L; Delehaunty, Kimberly D; Fewell, Ginger A; Fulton, Lucinda A; Fulton, Robert S; Graves, Tina A; Hillier, LaDeana W; Mardis, Elaine R; McPherson, John D; Genome 10K Data Submission Guidelines. Genome Research. 420-6915. 520-562 (2002) Nature Publishing Group

Waterston, Robert H; Pachter, Lior; Initial sequencing and comparative analysis of the mouse genome. Genome Research. 420-6915. 520-562 (2002) Nature Publishing Group

Kent, W James; Sugnet, Charles W; Furey, Terrence S; Roskin, Krishna M; Pringle, Tom H; Zahler, Alan M; Haussler, David; The human genome browser at UCSC. Genome Research. 12-6. 996-1006 (2002) Cold Spring Harbor Lab

Karchin, Rachel; Karplus, Kevin; Haussler, David; Classifying G-protein coupled receptors with support vector machines. Genome Research. 18-1. 147-159 (2002) Oxford Univ Press

Cline, Melissa S; Karplus, Kevin; Lathrop, Richard H; Smith, Temple F; Rogers, Robert G; Haussler, David; Information?theoretic dissection of pairwise contact potentials. Genome Research. 49-1. 42930 (2002) Wiley Online Library

Winters-Hilt, S; Vercoutere, WA; DeGuzman, VS; Deamer, DW; Akeson, M; Haussler, D; Highly accurate real-time classification of Watson-Crick termini on single DNA molecules. Genome Research. 82-1. 52A-52A (2002) BIOPHYSICAL SOCIETY 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA

Barnes, Ian; Matheus, P; Shapiro, Beth; Jensen, D; Cooper, Alan; Dynamics of Pleistocene population extinctions in Beringian brown bears. Genome Research. 295-5563. 2267-2270 (2002) American Association for the Advancement of Science

Shapiro, Beth; Sibthorpe, Dean; Rambaut, Andrew; Austin, Jeremy; Wragg, Graham M; Bininda-Emonds, Olaf RP; Lee, Patricia LM; Cooper, Alan; Flight of the dodo. Genome Research. 295-5560. 1683-1683 (2002) American Association for the Advancement of Science

Nielsen-Marsh, Christina M; Ostrom, Peggy H; Gandhi, Hasand; Shapiro, Beth; Cooper, Alan; Hauschka, Peter V; Collins, Matthew J; Sequence preservation of osteocalcin protein and mitochondrial DNA in bison bones older than 55 ka. Genome Research. 30-12. 1099-1102 (2002) Geological Society of America

Lalueza-Fox, Carles; Shapiro, Beth; Bover, Pere; Alcover, Josep Antoni; Bertranpetit, Jaume; Molecular phylogeny and evolution of the extinct bovid Myotragus balearicus. Genome Research. 25-3. 501-510 (2002) Academic Press

Beck, Christopher W; Shapiro, Beth; Choksi, Semil; Promislow, Daniel EL; A genetic algorithm approach to study the evolution of female preference based on male age. Genome Research. 4-2. 275-292 (2002) Evolutionary Ecology, Ltd.

Karplus, Kevin; Karchin, Rachel; Barrett, Christian; Tu, Spencer; Cline, Melissa; Diekhans, Mark; Grate, Leslie; Casper, Jonathan; Hughey, Richard; Splicing biomarkers of disease severity in myotonic dystrophy. Genome Research. 45-S5. 86-91 (2001) Wiley Online Library

Cline, Melissa; Liu, Guoying; LORAINE, ANNE; Shigeta, Ronald; Cheng, Jill; Mei, Gangwu; Kulp, David; Siani-Rose, Michael A; Sequence Alignment and Modeling Software System. Genome Research. . 127 (2001) World Scientific

CLINE, MELISSA; LIU, GUOYING; ANNE, LORAINE; SHIGETA, RONALD; Targeted discovery of novel human exons by comparative genomics. Genome Research. . 127 (2001) World Scientific

Karplus, Kevin; Karchin, Rachel; Barrett, Christian; Tu, Spencer; Cline, Melissa; Diekhans, Mark; Grate, Leslie; Casper, Jonathan; Hughey, Richard; 1. The potential non-coding set, expanded version, page 3. 2. Detecting expression of proteins in the non-coding set from other sources, page 6. 3. Coding genes not in GENCODE 19, page 8. 4. Supplementary figures, page 9.. Genome Research. 45-S5. 86-91 (2001) Wiley Online Library

Lander, Eric S; Linton, Lauren M; Birren, Bruce; Nusbaum, Chad; Zody, Michael C; Baldwin, Jennifer; Devon, Keri; Dewar, Ken; Doyle, Michael; FitzHugh, William; Initial sequencing and analysis of the human genome. (2001) Macmillan Publishers Ltd.

McPherson, John D; Marra, Marco; Hillier, LaDeana; Waterston, Robert H; Chinwalla, Asif; Wallis, John; Sekhon, Mandeep; Wylie, Kristine; Mardis, Elaine R; Wilson, Richard K; A physical map of the human genome. (2001) Macmillian Magazines Ltd.

Cheung, VG; Nowak, N; Jang, W; Kirsch, IR; Zhao, S; Chen, X-N; Furey, TS; Kim, U-J; Kuo, W-L; Olivier, M; Integration of cytogenetic landmarks into the draft sequence of the human genome. Genome Research. 409-6822. 953-959 (2001) Nature Publishing Group

Kent, W James; Haussler, David; Assembly of the working draft of the human genome with GigAssembler. Genome Research. 11-9. 1541-1548 (2001) Cold Spring Harbor Lab

Pavlidis, P; Furey, TS; Liberto, M; Haussler, D; Grundy, WN; PROMOTER RE ION-ASED CLASSIFICATION OF ENES. Genome Research. 6. 151-164 (2001)

Vercoutere, W; Winters-Hilt, S; Olsen, H; Deamer, D; Haussler, D; Akeson, M; Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Genome Research. 19-7. 681-681 (2001) NATURE AMERICA INC

Winters-Hilt, SN; Vercoutere, W; Olsen, H; Deamer, D; Akeson, M; Haussler, D; Channel current analysis using generative feature extraction and support vector machine discrimination enables single nucleotide resolution in an alpha-hemolysin nanopore detector. Genome Research. 80-1. 498A-498A (2001) BIOPHYSICAL SOCIETY 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA

Vercoutere, WA; Winters-Hilt, S; Olsen, H; Deamer, D; Haussler, D; Akeson, M; Rapid discrimination among individual DNA molecules at single nucleotide resolution with a nanopore instrument. Genome Research. 80-1. 200A-200A (2001) BIOPHYSICAL SOCIETY 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA

Shapiro, BA; Pickering, John; The Rise and Fall of the Passenger Pigeon. Genome Research. 2-1. 39-47 (2000) Wiley Online Library

Cline, Melissa Suzanne; Abstract B1-07: Using the UCSC Xena Platform to integrate, visualize, and analyze your own data in the context of large external genomic datasets. (2000) UNIVERSITY of CALIFORNIA SANTA CRUZ

Jaakkola, Tommi; Diekhans, Mark; Haussler, David; CGHub Client Security Guide. Genome Research. 7-42737. 95-114 (2000) Mary Ann Liebert, Inc.

Grate, Leslie; Diekhans, Mark; Dahle, David; Hughey, Richard; Genome Research. 2001. 263-274 (2000)

Brown, Michael PS; Grundy, William Noble; Lin, David; Cristianini, Nello; Sugnet, Charles Walsh; Furey, Terrence S; Ares, Manuel; Haussler, David; Knowledge-based analysis of microarray gene expression data by using support vector machines. Genome Research. 97-1. 262-267 (2000) National Acad Sciences

Furey, Terrence S; Cristianini, Nello; Duffy, Nigel; Bednarski, David W; Schummer, Michel; Haussler, David; Support vector machine classification and validation of cancer tissue samples using microarray expression data. Genome Research. 16-10. 906-914 (2000) Oxford Univ Press

Jaakkola, Tommi; Diekhans, Mark; Haussler, David; A discriminative framework for detecting remote protein homologies. Genome Research. 7-42737. 95-114 (2000) Mary Ann Liebert, Inc.

Reese, Martin G; Kulp, David; Tammana, Hari; Haussler, David; Genie—gene finding in Drosophila melanogaster. Genome Research. 10-4. 529-538 (2000) Cold Spring Harbor Lab

Brwon, MPS; Grundy, WN; Lin, D; Cristianini, N; Sugnet, CW; Furey, TS; Ares, MA; Haussler, D; Knowledge-based analysis of microarray gene expression. (2000) University of California-Santa Cruz (US)

Brown, MP; Grundy, WN; Lin, D; Cristianini, N; Sugnet, CW; Furey Jr, TS; Haussler, D; Brazma, A; Vilo, J; Bäck, T; Group: EvolutionaryComputation-library 1330 articles. Genome Research. 97-1. 262-267 (2000)

Shapiro, BA; Pickering, John; Rainfall and parasitic wasp (Hymenoptera: Ichneumonoidea) activity in successional forest stages at Barro Colorado Nature Monument, Panama, and La Selva Biological Station, Costa Rica. Genome Research. 2-1. 39-47 (2000) Wiley Online Library

Karplus, Kevin; Barrett, Christian; Cline, Melissa; Diekhans, Mark; Grate, Leslie; Hughey, Richard; Rbfox1 downregulation and altered calpain 3 splicing by FRG1 in a mouse model of Facioscapulohumeral muscular dystrophy (FSHD). Genome Research. 37-S3. 121-125 (1999) Wiley Online Library

Jaakkola, Tommi S; Diekhans, Mark; Haussler, David; GENCODE: the reference human genome annotation for The ENCODE Project. Genome Research. 99. 149-158 (1999)

Karplus, Kevin; Barrett, Christian; Cline, Melissa; Diekhans, Mark; Grate, Leslie; Hughey, Richard; Comparative analysis of pseudogenes across three phyla. Genome Research. 37-S3. 121-125 (1999) John Wiley & Sons, Inc.

Haussler, David; Convolution kernels on discrete structures. (1999) Technical report, Department of Computer Science, University of California at Santa Cruz

Jaakkola, Tommi; Haussler, David; Exploiting generative models in discriminative classifiers. Genome Research. . 487-493 (1999)

Jaakkola, Tommi S; Diekhans, Mark; Haussler, David; Using the Fisher kernel method to detect remote protein homologies.. Genome Research. 99. 149-158 (1999)

Jaakkola, Tommi S; Haussler, David; Probabilistic kernel regression models.. Genome Research. (1999)

SPINGOLA, MARC; GRATE, LESLIE; HAUSSLER, DAVID; ARES, MANUEL; Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. Genome Research. 5-2. 221-234 (1999) Cambridge University Press

Brown, Michael PS; Grundy, William Noble; Lin, David; Cristianini, Nello; Sugnet, Charles; Ares, Manuel; Haussler, David; Support vector machine classification of microarray gene expression data. Genome Research. (1999) Citeseer

Opper, Manfred; Haussler, David; Worst case prediction over sequences under log loss. Genome Research. . 81-90 (1999) Springer New York

Lazareva-Ulitsky, Betty; Haussler, David; A Probabilistic Approach to a Consensus Multiple Alignment.. Genome Research. 4. 150-161 (1999)

Haussler, David; Hughey, Richard; Karplus, Keven; HMM-Based Gene Annotation Methods. (1999) University of California, Santa Cruz, CA (US)(US)

Haussler, David; Computational Analysis of High-throughput Genomics Data Using Hidden Markov Models and Support Vector Machines. Genome Research. 10. 199-199 (1999) Japanese Society for Bioinformatics

Cline, Melissa; Karplus, Kevin; SEMANTIC WEB FOR DATA INTERPRETATION & INTEGRATION: LESSONS LEARNED FROM SCIENTIFIC PUBLISHING AND THE DISTRIBUTED ANNOTATION SYSTEM. (1998) Technical Report UCSC-CRL-97-27, University of California, Santa Cruz, Jack Baskin School of Engineering, UC Santa Cruz, CA 95064

Haussler, D; Hughey, R; Karplus, K; Cline, M; Grate, L; Kulp, D; Sjolander, K; Lapedes, AS; Using native and syntenically mapped cDNA alignments to improve de novo gene finding. (1998) Los Alamos National Lab., NM (United States)

Park, Jong; Karplus, Kevin; Barrett, Christian; Hughey, Richard; Haussler, David; Hubbard, Tim; Chothia, Cyrus; Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. Genome Research. 284-4. 1201-1210 (1998) Elsevier

Haussler, David; Kivinen, Jyrki; Warmuth, Manfred K; Sequential prediction of individual sequences under general loss functions. Genome Research. 44-5. 1906-1925 (1998) IEEE

Haussler, David; Computational genefinding. Genome Research. 16. 43084 (1998) Elsevier Current Trends

Cesa-Bianchi, Nicolò; Haussler, David; A graph-theoretic generalization of the Sauer-Shelah lemma. Genome Research. 86-1. 27-35 (1998) Elsevier

Haussler, D; Hughey, R; Karplus, K; Cline, M; Grate, L; Kulp, D; Sjolander, K; Lapedes, AS; Covariation of mutations: A computational approach for determination of function and structure from sequence. (1998) Los Alamos National Lab., NM (United States)

Karplus, Kevin; Sjölander, Kimmen; Barrett, Christian; Cline, Melissa; Haussler, David; Hughey, Richard; Holm, Liisa; Sander, Chris; Exploring TCGA pan-cancer data at the UCSC cancer genomics browser. Genome Research. 29-s 1. 134-139 (1997)

Reese, Martin G; Eeckman, Frank H; Kulp, David; Haussler, David; Improved splice site detection in Genie. Genome Research. 4-3. 311-323 (1997)

Cesa-Bianchi, Nicolo; Freund, Yoav; Haussler, David; Helmbold, David P; Schapire, Robert E; Warmuth, Manfred K; How to use expert advice. Genome Research. 44-3. 427-485 (1997) ACM

Alon, Noga; Ben-David, Shai; Cesa-Bianchi, Nicolo; Haussler, David; Scale-sensitive dimensions, uniform convergence, and learnability. Genome Research. 44-4. 615-631 (1997) ACM

Karplus, Kevin; Sjölander, Kimmen; Barrett, Christian; Cline, Melissa; Haussler, David; Hughey, Richard; Holm, Liisa; Sander, Chris; Predicting protein structure using hidden Markov models. Genome Research. 29-s 1. 134-139 (1997)

Haussler, David; Opper, Manfred; Mutual information, metric entropy and cumulative relative entropy risk. Genome Research. 25-6. 2451-2492 (1997) Institute of Mathematical Statistics

Haussler, David; A general minimax result for relative entropy. Genome Research. 43-4. 1276-1280 (1997) IEEE

Kulp, David; Haussler, David; Reese, Martin G; Eeckman, Frank H; Integrating database homology in a probabilistic gene structure model. Genome Research. 2. 232-244 (1997) Citeseer

Haussler, David; A brief look at some machine learning problems in genomics. Genome Research. . 109-113 (1997) ACM

Haussler, David; Opper, Manfred; Metric entropy and minimax risk in classification. Genome Research. . 212-235 (1997) Springer Berlin/Heidelberg

Freund, Yoav; Haussler, DAVID; Helmbold, D; Schapire, R; Warmuth, Manfred K; How to use expert advice. Genome Research. 44-3. 427-485 (1997)

Haussler, David; Generalized Hidden Markov Models for Genomic Sequence Analysis. Genome Research. 42-5. 34 (1997)

Qin, Minmin; Kuhn, Robert; Moran, Sharon; Quail, Peter H; Overexpressed phytochrome C has similar photosensory specificity to phytochrome B but a distinctive capacity to enhance primary leaf expansion. Genome Research. 12-5. 1163-1172 (1997) Wiley Online Library

Haussler, David Kulp David; Eeckman, Martin G Reese Frank H; A generalized hidden Markov model for the recognition of human genes in DNA. Genome Research. . 134-142 (1996)

Sjölander, Kimmen; Karplus, Kevin; Brown, Michael; Hughey, Richard; Krogh, Anders; Mian, I Saira; Haussler, David; Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Genome Research. 12-4. 327-345 (1996) Oxford University Press

Fayyad, Usama; Haussler, David; Stolorz, Paul; Mining scientific data. Genome Research. 39-11. 51-57 (1996) ACM

Fayyad, Usama M; Haussler, David; Stolorz, Paul E; KDD for Science Data Analysis: Issues and Examples.. Genome Research. . 50-56 (1996)

Haussler, David; Kearns, Michael; Seung, H Sebastian; Tishby, Naftali; Rigorous learning curve bounds from statistical mechanics. Genome Research. 25-42769. 195-236 (1996) Kluwer Academic Publishers-Plenum Publishers

Gulko, Brad; Haussler, David; Using multiple alignments and phylogenetic trees to detect RNA secondary structure. Genome Research. . 350-367 (1996)

Haussler, David; Opper, Manfred; Mutual information, metric entropy, and risk in estimation of probability distributions. (1996) Technical Report UCSC-CRL-96-27, Univ. of Calif. Computer Research Lab, Santa Cruz, CA

Karplus, Kevin; Brown, Michael; Hughey, Richard; Krogh, Anders; Mian, I Saira; Haussler, David; Dirichlet Mixtures: A Method for Improving Detection of Weak but Significant Protein Sequence Homology. Genome Research. 12(1996)

Hsu, Chang Y; Editorial Comment. Genome Research. 27-12. 2298 (1996)

Wagner, Doris; Fairchild, Craig D; Kuhn, Robert M; Quail, Peter H; Chromophore-bearing NH2-terminal domains of phytochromes A and B determine their photosensory specificity and differential light lability. Genome Research. 93-9. 4011-4015 (1996) National Acad Sciences

Haussler, David; Sphere packing numbers for subsets of the Boolean n-cube with bounded Vapnik-Chervonenkis dimension. Genome Research. 69-2. 217-232 (1995) Academic Press

Haussler, David; Kivinen, Jyrki; Warmuth, Manfred; Tight worst-case loss bounds for predicting with expert advice. Genome Research. . 69-83 (1995) Springer Berlin/Heidelberg

Bendavid, Shai; Cesabianchi, Nicolo; Haussler, David; Long, Philip M; Characterizations of Learnability for Classes of {0,…, n)-Valued Functions. Genome Research. 50-1. 74-86 (1995) Academic Press

Haussler, David; Long, Philip M; A generalization of Sauer’s lemma. Genome Research. 71-2. 219-240 (1995) Elsevier

Opper, Manfred; Haussler, David; Bounds for predictive errors in the statistical mechanics of supervised learning. Genome Research. 75-20. 3772 (1995) APS

Haussler, David; Opper, Manfred; General bounds on the mutual information between a parameter and n conditionally independent observations. Genome Research. . 402-411 (1995) ACM

Opper, Manfred; Haussler, David; General bounds for predictive errors in supervised learning. Genome Research. (1995)

Haussler, David; Opper, Manfred; Mutual information and Bayes methods for learning a distribution. Genome Research. (1995)

Haussler, David; Part 1: Overview of the probably approximately correct (pac) learning framework. Genome Research. (1995)

Knill, Emanuel; Ehrenfeucht, Andrzej; Haussler, David; The size of k-pseudotrees. Genome Research. 141-42738. 185-194 (1995) North-Holland

Reklaw, Jesse; Hanna, Rebecca; Haussler, David; Prediction of ribosomal RNA base-pairing by neural networks. Genome Research. (1995)

Cline, Melissa S; Werner, Linda Louise; PUBLICATIONS AND SCHOLARLY WORK. (1994) Computer Research Laboratory [University of California, Santa Cruz]

Krogh, Anders; Brown, Michael; Mian, I Saira; Sjölander, Kimmen; Haussler, David; Hidden Markov models in computational biology: Applications to protein modeling. Genome Research. 235-5. 1501-1531 (1994) Elsevier

Sakakibara, Yasubumi; Brown, Michael; Hughey, Richard; Mian, I Saira; Sjölander, Kimmen; Underwood, Rebecca C; Haussler, David; Stochastic context-free grammers for tRNA modeling. Genome Research. 22-23. 5112-5120 (1994) Oxford Univ Press

Krogh, Anders; Mian, I Saira; Haussler, David; A hidden Markov model that finds genes in E. coli DNA. Genome Research. 22-22. 4768-4778 (1994) Oxford Univ Press

Haussler, David; Kearns, Michael; Schapire, Robert E; Bounds on the sample complexity of Bayesian learning using information theory and the VC dimension. Genome Research. 14-1. 83-113 (1994) Springer Netherlands

Haussler, David; Littlestone, Nick; Warmuth, Manfred K; Predicting {0, 1}-functions on randomly drawn points. Genome Research. 115-2. 248-292 (1994) Academic Press

Sakakibaratt, Yasubumi; Underwoodt, C; Stochastic context-free grammars for modeling RNA. (1994)

Grate, Leslie; Herbster, Mark; Hughey, Richard; Haussler, David; Mian, I Saira; Noller, Harry; RNA modeling using Gibbs sampling and stochastic context free grammars.. Genome Research. 2. 138-146 (1994)

Sakakibara, Yasubumi; Brown, Michael; Hughey, Richard; Mian, Saira; Sjölander, Kimmen; Underwood, Rebecca C; Haussler, David; Recent methods for RNA modeling using stochastic context-free grammars. Genome Research. . 289-306 (1994) Springer, Berlin, Heidelberg

Stormo, Gary D; Haussler, David; Optimally parsing a sequence into different classes based on multiple types of evidence.. Genome Research. 2. 369-375 (1994)

Underwood, Rebecca C; Haussler, David; Stochastic context-free grammars for tRNA modeling. Genome Research. 22-23. 5113 (1994)

Krogh’f, Anders; Brown, I; Hidden markov models in computational biology. Genome Research. 235. 1501-1531 (1994)

Mian, I Saira; Haussler, David; A Hidden Markov Model that finds genes in E. coli DNA Anders Krogh Nordita Blegdamsvej 17, DK-2100 Copenhagen, Denmark. Genome Research. 22. 4768-4778 (1994)

Kuhn, Robert M; Ludwig, Robert A; Complete sequence of the yeast artificial chromosome cloning vector pYAC4. Genome Research. 141-1. 125-127 (1994) Elsevier

Brown, Michael; Hughey, Richard; Krogh, Anders; Mian, I Saira; Sjölander, Kimmen; Haussler, David; Using Dirichlet mixture priors to derive hidden Markov models for protein families.. Genome Research. 1. 47-55 (1993)

Haussler, David; Krogh, Anders; Mian, I Saira; SJolander, KIMMEN; Protein modeling using hidden Markov models: Analysis of globins. Genome Research. 1. 792-802 (1993) IEEE

Haussler, David; Warmuth, Manfred; The probably approximately correct (PAC) and other learning models. Genome Research. . 291-291 (1993) KLUWER ACADEMIC PUBLISHERS GROUP

Barren, A; Clarke, Bertrand; Haussler, David; Information bounds for the risk of bayesian predictions and the redundancy of universal codes. Genome Research. . 54-54 (1993) IEEE

Haussler, David; Warmuth, Manfred K; Analyzing the Performance of Learning Algorithms.. (1993) DTIC Document

Sakakibara, Yasubumi; Brown, Michael; Underwood, Rebecca C; Mian, Saira I; Haussler, David; Stochastic Context-Free Grammars in Computational Biology. Genome Research. 4. 36-45 (1993) Japanese Society for Bioinformatics

Kuhn, Robert M; Caspar, Timothy; Dehesh, Katayoon; Quail, Peter H; DNA binding factor GT-2 from Arabidopsis. Genome Research. 23-2. 337-348 (1993) Springer

Haussler, David; Decision theoretic generalizations of the PAC model for neural net and other learning applications. Genome Research. 100-1. 78-150 (1992) Academic Press

Freund, Yoav; Haussler, David; Unsupervised learning of distributions on binary vectors using two layer networks. Genome Research. . 912-919 (1992)

Haussler, David; Barron, Andrew; How well do Bayes methods work for on-line prediction of f+ 1; 1g values. Genome Research. (1992)

Haussler, David; Kearns, Michael; Opper, Manfred; Schapire, Robert; Estimating average-case learning curves using Bayesian, statistical physics and VC dimension methods. Genome Research. . 855-862 (1992)

Kuhn, Robert Michael; ClusteredtRNA genes in the centromeres of the fission yeast, Schizosaccharomyces pombe.. (1992)

Haussler, David; Kearns, Michael; Littlestone, Nick; Warmuth, Manfred K; Equivalence of models for polynomial learnability. Genome Research. 95-2. 129-161 (1991) Academic Press

Opper, Manfred; Haussler, David; Generalization performance of Bayes optimal classification algorithm for learning a perceptron. Genome Research. 66-20. 2677 (1991) APS

Opper, Manfred; Haussler, David; Calculation of the learning curve of Bayes optimal classification algorithm for learning a perceptron with noise. Genome Research. 5-7. 75-87 (1991) Citeseer

Haussler, David; Opper, Manfred; Calculation of the learning curve of Bayes optimal classification algorithm for learning a perceptron with noise. (1991) University of California at Santa Cruz

Ehrenfeucht, Andrzej; Haussler, David; Knill, E; A Combinatorial Analysis of K-pseudo Trees. (1991) University of Colorado, Boulder, Department of Computer Science

Kuhn, Robert M; Clarke, Louise; Carbon, John; Clustered tRNA genes in Schizosaccharomyces pombe centromeric DNA sequence repeats.. Genome Research. 88-4. 1306-1310 (1991) National Acad Sciences

Bagallo, Giulia; Haussler, David; Boolean feature discovery in empirical learning. Genome Research. 5-1. 71-99 (1990) Springer Netherlands

Haussler, David; Probably approximately correct learning. (1990) University of California, Santa Cruz, Computer Research Laboratory

Haussler, David; Applying valiant’s learning framework to Al concept-learning problems. (1990) Morgan Kaufmann Publishers Inc.

Haussler, David; Long, Philip M; A generalization of Sauer’s lemma. (1990) University of California, Santa Cruz, Computer Research Laboratory

Haussler, David; Decision theoretic generalizations of the PAC learning model. (1990) University of California, Santa Cruz, Computer Research Laboratory

Haussler, David; Warmuth, Manfred K; Efficient Learning Algorithms.. (1990) DTIC Document

Baum, Eric B; Haussler, David; What size net gives valid generalization?. Genome Research. . 81-90 (1989)

Blumer, Anselm; Ehrenfeucht, Andrzej; Haussler, David; Warmuth, Manfred K; Learnability and the Vapnik-Chervonenkis dimension. Genome Research. 36-4. 929-965 (1989) ACM

Ehrenfeucht, Andrzej; Haussler, David; Kearns, Michael; Valiant, Leslie; A general lower bound on the number of examples needed for learning. Genome Research. 82-3. 247-261 (1989) Academic Press

Haussler, David; Learning conjunctive concepts in structural domains. Genome Research. 4-1. 14793 (1989) Springer Netherlands

Ehrenfeucht, Andrzej; Haussler, David; Learning decision trees from random examples. Genome Research. 82-3. 231-246 (1989) Academic Press

Haussler, David; Generalizing the PAC model: sample size bounds from metric dimension-based uniform convergence results. Genome Research. . 40-45 (1989) IEEE

Blumer, Anselm; Ehrenfeucht, Andrzej; Haussler, David; Average sizes of suffix trees and dawgs. Genome Research. 24-42738. 37-45 (1989) North-Holland

Haussler, David; Generalizing the PAC model for neural net and other learning applications. (1989) University of California, Santa Cruz, Computer Research Laboratory

Pagallo, Giulia; Haussler, David; Two algorithms that learn DNF by discovering relevant features. Genome Research. . 119-123 (1989) Morgan Kaufmann Publishers Inc.

Pagallo, Giulia; Haussler, David; A Greedy Method for Learning [mu] DNF Functions Under the Uniform Distribution. (1989) University of California, Santa Cruz, Computer Research Laboratory

Haussler, David; Quantifying inductive bias: AI learning algorithms and Valiant’s learning framework. Genome Research. 36-2. 177-221 (1988) Elsevier

Haussler, David; Littlestone, Nick; Warmuth, Manfred K; Predicting (0, 1)-functions on randomly drawn points. Genome Research. . 100-109 (1988) IEEE

Ehrenfeucht, Andrzej; Haussler, David; A new distance metric on strings computable in linear time. Genome Research. 20-3. 191-203 (1988) North-Holland

Haussler, David; Space efficient learning algorithms. (1988) University of California, Santa Cruz, Computer Research Laboratory

Pagallo, Giulia M; Haussler, David; Feature discovery in empirical learning. 88-8(1988) Computer Research Laboratory,[University of California, Santa Cruz

Haussler, David; New theoretical directions in machine learning. Genome Research. 2-4. 281-284 (1988) Springer

Blumer, Anselm; Ehrenfeucht, Andrzej; Haussler, David; Warmuth, Manfred K; Occam’s razor. Genome Research. 24-6. 377-380 (1987) Elsevier

Haussler, David; Welzl, Emo; ?-nets and simplex range queries. Genome Research. 2-2. 127-151 (1987) Springer New York

Blumer, Anselm; Blumer, Janet; Haussler, David; McConnell, Ross; Ehrenfeucht, Andrzej; Complete inverted files for efficient text retrieval and analysis. Genome Research. 34-3. 578-595 (1987) ACM

Haussler, David; Bias, version spaces and valiant’s learning framework. Genome Research. . 324-336 (1987)

Alon, Noga; Haussler, David; Welzl, Emo; Partitioning and geometric embedding of range spaces of finite Vapnik-Chervonenkis dimension. Genome Research. . 331-340 (1987) ACM

Main, Michael G; Bucher, Walter; Haussler, David; Applications of an infinite square-free co-CFL. Genome Research. 49-42769. 113-119 (1987) Elsevier

Ehrenfeucht, Andrzej; Haemer, Jeffrey; Haussler, David; Quasi-monotonic sequences: theory, algorithms and applications. Genome Research. 8-3. 410-429 (1987) SIAM

Haussler, David; Learning Internal Disjunctive Concepts. Genome Research. 20. 356 (1987) IEEE Computer Society

Blumer, Anselm; Ehrenfeucht, Andrzej; Haussler, David; Warmuth, Manfred; Classifying learnable geometric concepts with the Vapnik-Chervonenkis dimension. Genome Research. . 273-282 (1986) ACM

Clift, B; Haussler, David; McConnell, R_; Schneider, Thomas D; Stormo, Gary D; Sequence landscapes. Genome Research. 14-1. 141-158 (1986) Oxford Univ Press

Haussler, David; Quantifying the inductive bias in concept learning. Genome Research. . 485-489 (1986)

Edelsbrunner, Herbert; Haussler, David; The complexity of cells in three-dimensional arrangements. Genome Research. 60. 139-146 (1986) North-Holland

Blumer, Anselm; Blumer, Janet; Haussler, David; Ehrenfeucht, Andrzej; Chen, Mu-Tian; Seiferas, Joel; The smallest automation recognizing the subwords of a text. Genome Research. 40. 31-55 (1985) Elsevier

Bucher, Walter; Ehrenfeucht, Andrzej; Haussler, David; On total regulators generated by derivation relations. Genome Research. 40. 131-148 (1985) Elsevier

Haussler, David; Another generalization of Higman’s well quasi order result on ??. Genome Research. 57-3. 237-243 (1985) North-Holland

Main, Michael; Bucher, Walter; Haussler, David; Applications of an infinite squarefree CO-CFL. Genome Research. . 404-412 (1985) Springer Berlin/Heidelberg

Warmuth, Manfred K; Haussler, David; On the complexity of iterated shuffle. Genome Research. 28-3. 345-358 (1984) Academic Press

Blumer, Anselm; Blumer, J; Ehrenfeucht, Andrzej; Haussler, David; McConnell, R; Building a complete inverted file for a set of text files in linear time. Genome Research. . 349-358 (1984) ACM

Blumer, Anselm; Blumer, J; Ehrenfeucht, Andrzej; Haussler, David; McConnell, R; Building the minimal DFA for the set of all subwords of a word on-line in linear time. Genome Research. . 109-118 (1984) Springer Berlin/Heidelberg

Ehrenfeucht, Andrzej; Haussler, David; Rozenberg, Grzegorz; Zeiger, Paul; On DOS languages and DOS mappings. Genome Research. 29-1. 123-148 (1984) Springer New York

Ehrenfeucht, Andrzej; Haussler, David; Rozenberg, Grzegorz; On ambiguity in DOS systems. Genome Research. 18-3. 279-295 (1984) EDP Sciences

Ehrenfeucht, Andrzej; Haussler, David; On Total Regulators Generated by Derivation Relations; CU-CS-301-85. (1984)

Ehrenfeucht, Andrzej; Haussler, David; The Smallest Automaton Recognizing the Subwords of a Text; CU-CS-300-84. (1984)

Ehrenfeucht, Andrzej; Haussler, David; Quasi-Monotonic Sequences: Theory, Algorithms and Applications; CU-CS-277-84. (1984)

Ehrenfeucht, Andrzej; Haussler, David; Rozenberg, Grzegorz; On regularity of context-free languages. Genome Research. 27-3. 311-332 (1983) Elsevier

Blumer, Anselm; Blumer, Janet; Ehrenfeucht, Andrzej; Haussler, David; McConnell, Ross M.; Linear size finite automata for the set of all subwords of a word – an outline of results. Genome Research. 21. 43089 (1983)

Haussler, David; Insertion languages. Genome Research. 31-1. 77-89 (1983) Elsevier

Ehrenfeucht, Andrzej; Rozenberg, Grzegorz; Haussler, David; Conditions Enforcing Regularity of Context-Free Languages; CU-CS-223-82. (1983)

Ehrenfeucht, Andrzej; Haussler, David; Rozenberg, Grzegorz; Conditions enforcing regularity of context-free languages. Genome Research. . 187-191 (1982) Springer Berlin/Heidelberg

Ehrenfeucht, Andrzej; Haussler, David; Rozenberg, Grezgorz; On Ambiguity in DOS Systems; CU-CS-215-82. (1982)

Ehrenfeucht, Andrzej; Haussler, David; Rozenberg, Grezgorz; Zeiger, Paul; On DOS Languages and DOS Mappings; CU-CS-213-82. (1982)

Ehrenfeucht, Andrzej; Haussler, David; Rozenberg, Grezgorz; On Regularity of Context-Free Languages; CU-CS-235-82. (1982)

Ehrenfeucht, Andrzej; Haussler, David; On DOS Languages and DOS Mappings 5 CU. (1982)

Haussler, David; Model completeness of an algebra of languages. Genome Research. 83-2. 371-374 (1981)

Warmuth, Manfred K; Haussler, David; On the Complexity of Iterated Shuffle; CU-CS-201-81. (1981)

Haussler, David; A Generalization of the Nerode Characterization of Regular Sets Using Well Quasi Orderings; CU-CS-218-81. (1981)

Ehrenfeucht, Andrzej; Haussler, David; A Generalization of a Theorem of Graham Higman; CU-CS-219-81. (1981)

Haussler, David; Zeiger, H Paul; Very special languages and representations of recursively enumerable languages via computation histories. Genome Research. 47-3. 201-212 (1980) Academic Press

Haussler, David; Zeiger, Paul; Very Special Languages and Representations of Recursively Enumerable Languages Via Computation Histories; CU-CS-177-80. (1980)

Haussler, David; Model Completeness of an Algebra of Languages; CU-CS-178-80. (1980)

Haussler, David; Some Results on Symmetric DGSM’s and DGSM Equivalence; CU-CS-199-79. (1979)

Goodman, Nelson G; Granville, George E; Law, Sam W; Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments. Genome Research. 12-3. 249-251 (1963) American Diabetes Association