Publications

Researchers associated with the UC Santa Cruz Genomics Institute write publications in genomics, bioinformatics, and a variety of other related fields.

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Complete Bibliography

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2018

M. Ryan Corces, Jeffrey M. Granja, Shadi Shams, Bryan H. Louie, Jose A. Seoane, Wanding Zhou, Tiago C. Silva, Clarice Groeneveld, Christopher K. Wong, Seung Woo Cho, Ansuman T. Satpathy, Maxwell R. Mumbach, Katherine A. Hoadley, A. Gordon Robertson, Nathan C. Sheffield, Ina Felau, Mauro A. A. Castro, Benjamin P. Berman, Louis M. Staudt, Jean C. Zenklusen, Peter W. Laird, Christina Curtis, The Cancer Genome Atlas Analysis Network, William J. Greenleaf, Howard Y. Chang. The chromatin accessibility landscape of primary human cancers. SCIENCE 26 OCT 2018

Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nat Genet. 2018 Oct 1.

Sasha A. LangleyKaren MigaGary H. KarpenCharles H. Langley; Diverse haplotypes span human centromeres and include archaic lineages within and out of Africa. bioRxiv (2018)

Hoadley, Katherine A.Caesar-Johnson, Samantha J; Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of CancerCell. (5 April 2018)

Jain, Miten and Koren, Sergey and Miga, Karen H and Quick, Josh and Rand, Arthur C and Sasani, Thomas A and Tyson, John R and Beggs, Andrew D and Dilthey, Alexander T and Fiddes, Ian T and others; Nanopore sequencing and assembly of a human genome with ultra-long readsNature Biotechnology. (2018) Nature Publishing Group

Jain, Miten and Olsen, Hugh E and Turner, Daniel J and Stoddart, David and Bulazel, Kira V and Paten, Benedict and Haussler, David and Willard, Huntington F and Akeson, Mark and Miga, Karen H; Linear Assembly of a Human Y CentromerebioRxiv.170373 (2018) Cold Spring Harbor Laboratory

Toor, Jugmohit S and Rao, Arjun A and McShan, Andrew C and Yarmarkovich, Mark and Nerli, Santrupti and Yamaguchi, Karissa and Madejska, Ada A and Nguyen, Son and Tripathi, Sarvind and Maris, John M and others; A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope ConformationsFrontiers in Immunology9. 99 (2018) Frontiers

Coulter ME, Dorobantu CM, Lodewijk GA, Delalande F, Cianferani S, Ganesh VS, Smith RS, Lim ET, Xu CS, Pang S, Wong ET, Lidov HGW, Calicchio ML, Yang E, Gonzalez DM, Schlaeger TM, Mochida GH, Hess H, Lee WA, Lehtinen MK, Kirchhausen T, Haussler D, et al.; The ESCRT-III Protein CHMP1A Mediates Secretion of Sonic Hedgehog on a Distinctive Subtype of Extracellular VesiclesCell Rep. 2018 Jul 24;24(4):973-986.e8. doi: 10.1016/j.celrep.2018.06.100. PMID: 30044992

Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B; Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res. 2018 Jul;28(7):1029-1038. doi: 10.1101/gr.233460.117. Epub 2018 Jun 8. PMID:29884752 | PMCID:PMC6028123

Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, et al.; High-resolution comparative analysis of great ape genomes. Science. 2018 Jun 8;360(6393). pii: eaar6343. doi: 10.1126/science.aar6343. PMID:29880660

Fiddes IT, Lodewijk GA, Mooring M, Bosworth CM, Ewing AD, Mantalas GL, Novak AM, van den Bout A, Bishara A, Rosenkrantz JL, Lorig-Roach R, Field AR, Haeussler M, Russo L, Bhaduri A, Nowakowski TJ, Pollen AA, Dougherty ML, Nuttle X, Addor MC, Zwolinski S, Katzman S, et al.; Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis. Cell. 2018 May 31;173(6):1356-1369.e22. doi: 10.1016/j.cell.2018.03.051. Epub 2018 May 31. PMID:29856954 | PMCID:PMC5986104

Haussler D, Smuga-Otto M, Eizenga JM, Paten B, Novak AM, Nikitin S, Zueva M, Miagkov D; A Flow Procedure for Linearization of Genome Sequence Graphs. J Comput Biol. 2018 Jul;25(7):664-676. doi: 10.1089/cmb.2017.0248. Epub 2018 May 24. PMID:29792514 | PMCID:PMC6067104

Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, Gilbert MTP, Goldstein MM, Grigoriev IV, Hackett KJ, Haussler D, Jarvis ED, Johnson WE, Patrinos A, Richards S, Castilla-Rubio JC, van Sluys MA, Soltis PS, Xu X, et al.; Earth BioGenome Project: Sequencing life for the future of life. Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4325-4333. doi: 10.1073/pnas.1720115115. PMID:29686065 | PMCID:PMC5924910

Jain M, Olsen HE, Turner DJ, Stoddart D, Bulazel KV, Paten B, Haussler D, Willard HF, Akeson M, Miga KH. Linear assembly of a human centromere on the Y chromosome. Nat Biotechnol. 2018 Apr;36(4):321-323. doi: 10.1038/nbt.4109. Epub 2018 Mar 19.PMID:29553574 | PMCID:PMC5886786

Toor JS, Rao AA, McShan AC, Yarmarkovich M, Nerli S, Yamaguchi K, Madejska AA, Nguyen S, Tripathi S, Maris JM, Salama SR, Haussler D, Sgourakis NG. A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations. Front Immunol. 2018 Jan 30;9:99. doi: 10.3389/fimmu.2018.00099. eCollection 2018. PMID:29441070 | PMCID:PMC5797543

Cooper CI, Yao D, Sendorek DH, Yamaguchi TN, P’ng C, Houlahan KE, Caloian C, Fraser M; SMC-DNA Challenge Participants., Ellrott K, Margolin AA, Bristow RG, Stuart JM, Boutros PC; Valection: design optimization for validation and verification studies. BMC Bioinformatics. 2018 Sep 25;19(1):339. doi: 10.1186/s12859-018-2391-z. PMID:30253747

Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, et al.; Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell. 2018 Jul 26;174(3):758-769.e9. doi: 10.1016/j.cell.2018.06.039. Epub 2018 Jul 19. PMID:30033370

Aggarwal R, Huang J, Alumkal JJ, Zhang L, Feng FY, Thomas GV, Weinstein AS, Friedl V, Zhang C, Witte ON, Lloyd P, Gleave M, Evans CP, Youngren J, Beer TM, Rettig M, Wong CK, True L, Foye A, Playdle D, Ryan CJ, Lara P, et al.; Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study. J Clin Oncol. 2018 Aug 20;36(24):2492-2503. doi: 10.1200/JCO.2017.77.6880. Epub 2018 Jul 9. PMID:29985747

Shen H, Shih J, Hollern DP, Wang L, Bowlby R, Tickoo SK, Thorsson V, Mungall AJ, Newton Y, Hegde AM, Armenia J, Sánchez-Vega F, Pluta J, Pyle LC, Mehra R, Reuter VE, Godoy G, Jones J, Shelley CS, Feldman DR, Vidal DO, Lessel D, et al.; Integrated Molecular Characterization of Testicular Germ Cell TumorsCell Rep. 2018 Jun 12;23(11):3392-3406. doi: 10.1016/j.celrep.2018.05.039. PMID:29898407 | PMCID:PMC6075738

Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ; Cancer Genome Atlas Research Network., Stuart JM, Hoadley KA, Laird PW, et al.; Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell. 2018 Apr 5;173(2):338-354.e15. doi: 10.1016/j.cell.2018.03.034. PMID:29625051 | PMCID:PMC5902191

Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, et al.; Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 2018 Apr 5;173(2):305-320.e10. doi: 10.1016/j.cell.2018.03.033. PMID:29625049 | PMCID:PMC5916814

Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM; Cancer Genome Atlas Network., Stuart JM, et al.; Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell. 2018 Apr 5;173(2):291-304.e6. doi: 10.1016/j.cell.2018.03.022. PMID:29625048 | PMCID:PMC5957518

Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, et al.; Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 Apr 3;23(1):194-212.e6. doi: 10.1016/j.celrep.2018.03.063. PMID:29617660 | PMCID:PMC6002769

Sendorek DH, Caloian C, Ellrott K, Bare JC, Yamaguchi TN, Ewing AD, Houlahan KE, Norman TC, Margolin AA, Stuart JM, Boutros PC; Germline contamination and leakage in whole genome somatic single nucleotide variant detection. BMC Bioinformatics. 2018 Jan 31;19(1):28. doi: 10.1186/s12859-018-2046-0. PMID:29385983 | PMCID:PMC5793408

Garrison E, Sirén J, Novak AM, Hickey G, Eizenga JM, Dawson ET, Jones W, Garg S, Markello C, Lin MF, Paten B, Durbin R; Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat Biotechnol. 2018 Oct;36(9):875-879. doi: 10.1038/nbt.4227. Epub 2018 Aug 20. PMID:30125266 | PMCID:PMC6126949

Tunstall T, Kock R, Vahala J, Diekhans M, Fiddes I, Armstrong J, Paten B, Ryder OA, Steiner CC; Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells. Genome Res. 2018 Jun;28(6):780-788. doi: 10.1101/gr.227603.117. Epub 2018 May 24. PMID:29798851 | PMCID:PMC5991516

Dang LT, Tondl M, Chiu MHH, Revote J, Paten B, Tano V, Tokolyi A, Besse F, Quaife-Ryan G, Cumming H, Drvodelic MJ, Eichenlaub MP, Hallab JC, Stolper JS, Rossello FJ, Bogoyevitch MA, Jans DA, Nim HT, Porrello ER, Hudson JE, Ramialison M; TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets. BMC Genomics. 2018 Apr 5;19(1):238. doi: 10.1186/s12864-018-4630-0. PMID:29621972 | PMCID:PMC5887194

Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, et al.; Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Res. 2018 Apr;28(4):448-459. doi: 10.1101/gr.234096.117. Epub 2018 Mar 21. PMID:29563166 | PMCID:PMC5880236

Paten B, Eizenga JM, Rosen YM, Novak AM, Garrison E, Hickey G; Superbubbles, Ultrabubbles, and Cacti. J Comput Biol. 2018 Jul;25(7):649-663. doi: 10.1089/cmb.2017.0251. Epub 2018 Feb 20. PMID:29461862 | PMCID:PMC6067107

Supple MA, Shapiro B; Conservation of biodiversity in the genomics era. Genome Biol. 2018 Sep 11;19(1):131. doi: 10.1186/s13059-018-1520-3. Review. PMID:30205843 | PMCID:PMC6131752

Anbar A, Elgin S, Jez J, O’Dowd D, Shapiro B, Zaman M; Improving societies’ harassment policies. Science. 2018 Sep 7;361(6406):984-985. doi: 10.1126/science.aav1362. No abstract available. PMID:30190397

Barlow A, Cahill JA, Hartmann S, Theunert C, Xenikoudakis G, Fortes GG, Paijmans JLA, Rabeder G, Frischauf C, Grandal-d’Anglade A, García-Vázquez A, Murtskhvaladze M, Saarma U, Anijalg P, Skrbinšek T, Bertorelle G, Gasparian B, Bar-Oz G, Pinhasi R, Slatkin M, Dalén L, Shapiro B, et al.; Partial genomic survival of cave bears in living brown bears. Nat Ecol Evol. 2018 Oct;2(10):1563-1570. doi: 10.1038/s41559-018-0654-8. Epub 2018 Aug 27. PMID:30150744

Mann DH, Groves P, Gaglioti BV, Shapiro BA; Climate-driven ecological stability as a globally shared cause of Late Quaternary megafaunal extinctions: the Plaids and Stripes Hypothesis. Biol Rev Camb Philos Soc. 2018 Aug 22. doi: 10.1111/brv.12456. [Epub ahead of print] PMID:30136433

Fregel R, Méndez FL, Bokbot Y, Martín-Socas D, Camalich-Massieu MD, Santana J, Morales J, Ávila-Arcos MC, Underhill PA, Shapiro B, Wojcik G, Rasmussen M, Soares AER, Kapp J, Sockell A, Rodríguez-Santos FJ, Mikdad A, Trujillo-Mederos A, Bustamante CD; Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6774-6779. doi: 10.1073/pnas.1800851115. Epub 2018 Jun 12. Erratum in: Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E7231. PMID:29895688 | PMCID:PMC6042094

Eerkens JW, Nichols RV, Murray GGR, Perez K, Murga E, Kaijankoski P, Rosenthal JS, Engbring L, Shapiro B; A probable prehistoric case of meningococcal disease from San Francisco Bay: Next generation sequencing of Neisseria meningitidis from dental calculus and osteological evidence. Int J Paleopathol. 2018 Sep;22:173-180. doi: 10.1016/j.ijpp.2018.05.001. Epub 2018 May 25. PMID:29807684

Nichols RV, Vollmers C, Newsom LA, Wang Y, Heintzman PD, Leighton M, Green RE, Shapiro B; Minimizing polymerase biases in metabarcoding. Mol Ecol Resour. 2018 May 24. doi: 10.1111/1755-0998.12895. [Epub ahead of print] PMID:29797549

Cahill JA, Heintzman PD, Harris K, Teasdale MD, Kapp J, Soares AER, Stirling I, Bradley D, Edwards CJ, Graim K, Kisleika AA, Malev AV, Monaghan N, Green RE, Shapiro B; Genomic Evidence of Widespread Admixture from Polar Bears into Brown Bears during the Last Ice Age. Mol Biol Evol. 2018 May 1;35(5):1120-1129. doi: 10.1093/molbev/msy018. PMID:29471451

Li J, Choi PS, Chaffer CL, Labella K, Hwang JH, Giacomelli AO, Kim JW, Ilic N, Doench JG, Ly SH, Dai C, Hagel K, Hong AL, Gjoerup O, Goel S, Ge JY, Root DE, Zhao JJ, Brooks AN, Weinberg RA, Hahn WC; An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. Elife. 2018 Jul 30;7. pii: e37184. doi: 10.7554/eLife.37184. PMID:30059005 | PMCID:PMC6103745

Khan SY, Ali M, Kabir F, Chen R, Na CH, Lee MW, Pourmand N, Hackett SF, Riazuddin SA; Identification of novel transcripts and peptides in developing murine lens. Sci Rep. 2018 Jul 24;8(1):11162. doi: 10.1038/s41598-018-28727-w. PMID:30042402 | PMCID:PMC6057992

Ozel RE, Bulbul G, Perez J, Pourmand N; Functionalized Quartz Nanopipette for Intracellular Superoxide Sensing: A Tool for Monitoring Reactive Oxygen Species Levels in Single Living Cell. ACS Sens. 2018 Jul 27;3(7):1316-1321. doi: 10.1021/acssensors.8b00185. Epub 2018 Jun 25. PMID:29893547

Bulbul G, Chaves G, Olivier J, Ozel RE, Pourmand N; Nanopipettes as Monitoring Probes for the Single Living Cell: State of the Art and Future Directions in Molecular Biology. Cells. 2018 Jun 6;7(6). pii: E55. doi: 10.3390/cells7060055. Review. PMID:29882813 | PMCID:PMC6024992

Tóth EN, Lohith A, Mondal M, Guo J, Fukamizu A, Pourmand N; Single-cell nanobiopsy reveals compartmentalization of mRNAs within neuronal cells. J Biol Chem. 2018 Mar 30;293(13):4940-4951. doi: 10.1074/jbc.M117.800763. Epub 2018 Jan 29. PMID:29378846 | PMCID:PMC5880154

 

2017

Adema, Coen M and Hillier, LaDeana W and Jones, Catherine S and Loker, Eric S and Knight, Matty and Minx, Patrick and Oliveira, Guilherme and Raghavan, Nithya and Shedlock, Andrew and Do Amaral, Laurence Rodrigues and others; Whole genome analysis of a schistosomiasis-transmitting freshwater snailNature communications8. 15451 (2017) Nature Publishing Group

Benazzo, Andrea and Trucchi, Emiliano and Cahill, James A and Delser, Pierpaolo Maisano and Mona, Stefano and Fumagalli, Matteo and Bunnefeld, Lynsey and Cornetti, Luca and Ghirotto, Silvia and Girardi, Matteo and others; Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglersProceedings of the National Academy of Sciences114-45. E9589–E9597 (2017) National Acad Sciences

Cahill, James A and Heintzman, Peter D and Harris, Kelley and Teasdale, Matthew and Kapp, Joshua and Soares, Andre E Rodrigues and Stirling, Ian and Bradley, Daniel and Edwards, Ceiridwen J and Kisleika, Aliaksandr A and others; Genomic evidence of globally widespread admixture from polar bears into brown bears during the last ice agebioRxiv. 154773 (2017) Cold Spring Harbor Laboratory

Cai, Binghuang and Li, Biao and Kiga, Nikki and Thusberg, Janita and Bergquist, Timothy and Chen, Yun-Ching and Niknafs, Noushin and Carter, Hannah and Tokheim, Collin and Beleva-Guthrie, Violeta and others; Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challengesHuman mutation.(2017) Wiley Online Library

Casper, Jonathan and Zweig, Ann S and Villarreal, Chris and Tyner, Cath and Speir, Matthew L and Rosenbloom, Kate R and Raney, Brian J and Lee, Christopher M and Lee, Brian T and Karolchik, Donna and others; The UCSC Genome Browser database: 2018 updateNucleic acids research46-D1. D762–D769 (2017) Oxford University Press

Chang, Dan and Knapp, Michael and Enk, Jacob and Lippold, Sebastian and Kircher, Martin and Lister, Adrian and MacPhee, Ross DE and Widga, Christopher and Czechowski, Paul and Sommer, Robert and others; The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysisScientific reports7. 44585 (2017) Nature Publishing Group

de Bourcy, Charles FA and Angel, Cesar J Lopez and Vollmers, Christopher and Dekker, Cornelia L and Davis, Mark M and Quake, Stephen R; Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and agingProceedings of the National Academy of Sciences114-5. 1105–1110 (2017) National Acad Sciences

Farshidfar, Farshad and Zheng, Siyuan and Gingras, Marie-Claude and Newton, Yulia and Shih, Juliann and Robertson, A Gordon and Hinoue, Toshinori and Hoadley, Katherine A and Gibb, Ewan A and Roszik, Jason and others; Integrative genomic analysis of cholangiocarcinoma identifies distinct IDH-mutant molecular profilesCell reports18-11. 2780–2794 (2017) Elsevier

Fehren-Schmitz, Lars and Harkins, Kelly M and Llamas, Bastien; A paleogenetic perspective on the early population history of the high altitude AndesQuaternary International. (2017) Elsevier

Fiddes, Ian T and Armstrong, Joel and Diekhans, Mark and Nachtweide, Stefanie and Kronenberg, Zev N and Underwood, Jason G and Gordon, David and Earl, Dent and Keane, Thomas and Eichler, Evan E and others; Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotationbioRxiv. 231118 (2017) Cold Spring Harbor Laboratory

Fiddes, Ian T and Lodewijk, Gerrald A and Mooring, Meghan M and Bosworth, Colleen M and Ewing, Adam D and Mantalas, Gary L and Novak, Adam M and van den Bout, Anouk and Bishara, Alex and Rosenkrantz, Jimi L and others; Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesisbioRxiv. 221226 (2017) Cold Spring Harbor Laboratory

Field, Andrew R and Jacobs, Frank MJ and Fiddes, Ian T and Phillips, Alex PR and Reyes-Ortiz, Andrea M and LaMontagne, Erin and Whitehead, Lila and Meng, Vincent and Rosenkrantz, Jimi L and Haeussler, Maximillian and others; Structurally conserved primate lncRNAs are transiently expressed during human cortical differentiation and influence cell type specific genesbioRxiv. 232553 (2017) Cold Spring Harbor Laboratory

Froese, Duane and Stiller, Mathias and Heintzman, Peter D and Reyes, Alberto V and Zazula, Grant D and Soares, Andr{\’e} ER and Meyer, Matthias and Hall, Elizabeth and Jensen, Britta JL and Arnold, Lee J and others; Fossil and genomic evidence constrains the timing of bison arrival in North AmericaProceedings of the National Academy of Sciences114-13. 3457–3462 (2017) National Acad Sciences

Garrison, Erik and Sir{\’e}n, Jouni and Novak, Adam M and Hickey, Glenn and Eizenga, Jordan M and Dawson, Eric T and Jones, William and Lin, Michael F and Paten, Benedict and Durbin, Richard; Sequence variation aware genome references and read mapping with the variation graph toolkitbioRxiv. 234856 (2017) Cold Spring Harbor Laboratory

Hamilton, Scott L and Logan, Cheryl A and Fennie, Hamilton W and Sogard, Susan M and Barry, James P and Makukhov, April D and Tobosa, Lauren R and Boyer, Kirsten and Lovera, Christopher F and Bernardi, Giacomo; Species-Specific Responses of Juvenile Rockfish to Elevated pCO2: From Behavior to GenomicsPloS one12-1. e0169670 (2017) Public Library of Science

Hrabeta-Robinson, Eva and Marcus, Erin and Cozen, Aaron E and Phizicky, Eric M and Lowe, Todd M; High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq)RNA Methylation: Methods and Protocols. 231–243 (2017) Springer

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

Kuderna, Lukas FK and Tomlinson, Chad and Hillier, LaDeana W and Tran, Annabel and Fiddes, Ian and Armstrong, Joel and Laayouni, Hafid and Gordon, David and Huddleston, John and Perez, Raquel Garcia and others; A 3-way hybrid approach to generate a new high quality chimpanzee reference genome (Pan\_tro\_3. 0)GigaScience. (2017)

Lee, Anna Ying-Wah and Ewing, Adam D and Ellrott, Kyle and Hu, Yin and Houlahan, Kathleen E and Bare, J Christopher and Espiritu, Shadrielle Melijah G and Huang, Vincent and Dang, Kristen and Chong, Zechen and others; Combining accurate tumour genome simulation with crowd sourcing to benchmark somatic structural variant detectionbioRxiv. 224733 (2017) Cold Spring Harbor Laboratory

Lincoln, Stephen E and Yang, Shan and Cline, Melissa S and Kobayashi, Yuya and Zhang, Can and Topper, Scott and Haussler, David and Paten, Benedict and Nussbaum, Robert L; Consistency of BRCA1 and BRCA2 variant classifications among clinical diagnostic laboratoriesJCO Precision Oncology1. 1–10 (2017) American Society of Clinical Oncology

Lui, Lauren M and Uzilov, Andrew V and Bernick, David L and Corredor, Andrea and Lowe, Todd M and Dennis, Patrick P; Evolutionary Insights On The Structure And Function Of Archaeal C/D Box sRNAs As Revealed By A Comprehensive Set From Six Pyrobaculum SpeciesbioRxiv. 121921 (2017) Cold Spring Harbor Labs Journals

Lui, Lauren M and Uzilov, Andrew V and Bernick, David L and Corredor, Andrea and Lowe, Todd M and Dennis, Patrick P; Methylation guide RNA evolution in archaea: structure, function, and genomic organization of 110 C/D box sRNA families across six Pyrobaculum speciesbioRxiv. 121921 (2017) Cold Spring Harbor Laboratory

Murray, Gemma GR and Soares, Andr{\’e} ER and Novak, Ben J and Schaefer, Nathan K and Cahill, James A and Baker, Allan J and Demboski, John R and Doll, Andrew and Da Fonseca, Rute R and Fulton, Tara L and others; Natural selection shaped the rise and fall of passenger pigeon genomic diversitybioRxiv. 154294 (2017) Cold Spring Harbor Laboratory

Novak, Adam M and Garrison, Erik and Paten, Benedict; A graph extension of the positional Burrows–Wheeler transform and its applicationsAlgorithms for Molecular Biology12-1. 18 (2017) BioMed Central

O’Connor, Brian D and Yuen, Denis and Chung, Vincent and Duncan, Andrew G and Liu, Xiang Kun and Patricia, Janice and Paten, Benedict and Stein, Lincoln and Ferretti, Vincent; The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflowsF1000Research6. (2017) Faculty of 1000 Ltd

Paten, Benedict and Novak, Adam M and Eizenga, Jordan M and Garrison, Erik; Genome graphs and the evolution of genome inferenceGenome research27-5. 665–676 (2017) Cold Spring Harbor Lab

Pujar, Shashikant and O’Leary, Nuala A and Farrell, Catherine M and Loveland, Jane E and Mudge, Jonathan M and Wallin, Craig and Gir{\’o}n, Carlos G and Diekhans, Mark and Barnes, If and Bennett, Ruth and others; Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curationNucleic acids research46-D1. D221–D228 (2017) Oxford University Press

Rand, Arthur C and Jain, Miten and Eizenga, Jordan M and Musselman-Brown, Audrey and Olsen, Hugh E and Akeson, Mark and Paten, Benedict; Mapping DNA methylation with high-throughput nanopore sequencingnature methods14-4. 411–413 (2017) Nature Research

Rand, Arthur C and Jain, Miten and Eizenga, Jordan M and Musselman-Brown, Audrey and Olsen, Hugh E and Akeson, Mark and Paten, Benedict; Mapping DNA methylation with high-throughput nanopore sequencingNature methods14-4. 411 (2017) Nature Publishing Group

Rice, Edward S and Kohno, Satomi and John, John St and Pham, Son and Howard, Jonathan and Lareau, Liana F and O’Connell, Brendan L and Hickey, Glenn and Armstrong, Joel and Deran, Alden and others; Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signalingGenome Research27-5. 686–696 (2017) Cold Spring Harbor Lab

Rosen, Yohei and Eizenga, Jordan and Paten, Benedict; Modelling haplotypes with respect to reference cohort variation graphsBioinformatics33-14. i118–i123 (2017) Oxford University Press

Rosen, Yohei and Eizenga, Jordan and Paten, Benedict; Supplement to “Modelling haplotypes with respect to reference cohort variation graphs”. (2017)

Shapiro, Beth; Pathways to de-extinction: how close can we get to resurrection of an extinct species?Functional Ecology31-5. 996–1002 (2017) Wiley Online Library

Thornlow, Bryan and Hough, Josh and Roger, Jackie and Gong, Henry and Lowe, Todd and Corbett-Detig, Russell; Transfer RNA genes experience exceptionally elevated mutation ratesbioRxiv. 229906 (2017) Cold Spring Harbor Laboratory

Thybert, David and Roller, Ma{\v{s}}a and Navarro, F{\’a}bio CP and Fiddes, Ian and Streeter, Ian and Feig, Christine and Martin-Galvez, David and Kolmogorov, Mikhail and Janou{\v{s}}ek, V{\’a}clav and Akanni, Wasiu and others; Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomesbioRxiv. 158659 (2017) Cold Spring Harbor Laboratory

Verdugo, Cristina and Kassadjikova, Kalina and Washburn, Eden and Harkins, KM and Fehren-Schmitz, Lars; Ancient DNA Clarifies Osteological Analyses of Commingled Remains from Midnight Terror Cave, BelizeInternational Journal of Osteoarchaeology27-3. 495–499 (2017) Wiley Online Library

Vivian, John and Rao, Arjun Arkal and Nothaft, Frank Austin and Ketchum, Christopher and Armstrong, Joel and Novak, Adam and Pfeil, Jacob and Narkizian, Jake and Deran, Alden D and Musselman-Brown, Audrey and others; Toil enables reproducible, open source, big biomedical data analysesNature biotechnology35-4. 314 (2017) Nature Publishing Group

Vohr, Samuel H and Gordon, Rachel and Eizenga, Jordan M and Erlich, Henry A and Calloway, Cassandra D and Green, Richard E; A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixturesForensic Science International: Genetics30. 93–105 (2017) Elsevier

Vohr, Samuel H and Gordon, Rachel and Eizenga, Jordan M and Erlich, Henry A and Calloway, Cassandra D and Green, Richard E; A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixturesForensic Science International: Genetics. (2017) Elsevier

Wang, Yue and Heintzman, Peter D and Newsom, Lee and Bigelow, Nancy H and Wooller, Matthew J and Shapiro, Beth and Williams, John W; The southern coastal Beringian land bridge: cryptic refugium or pseudorefugium for woody plants during the Last Glacial Maximum?Journal of Biogeography44-7. 1559–1571 (2017) Wiley Online Library

Zazula, Grant D and Hall, Elizabeth and Hare, P Gregory and Thomas, Christian and Mathewes, Rolf and La Farge, Catherine and Martel, Andr{\’e} L and Heintzman, Peter D and Shapiro, Beth; A middle Holocene steppe bison and paleoenvironments from the Versleuce Meadows, Whitehorse, Yukon, CanadaCanadian Journal of Earth Sciences-999. 1–15 (2017) NRC Research Press

2016

Ceccarelli, Michele and Barthel, Floris P and Malta, Tathiane M and Sabedot, Thais S and Salama, Sofie R and Murray, Bradley A and Morozova, Olena and Newton, Yulia and Radenbaugh, Amie and Pagnotta, Stefano M and others; Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse gliomaCell164-3. 550–563 (2016) Elsevier

Putnam, Nicholas H and O’Connell, Brendan L and Stites, Jonathan C and Rice, Brandon J and Blanchette, Marco and Calef, Robert and Troll, Christopher J and Fields, Andrew and Hartley, Paul D and Sugnet, Charles W and others; Chromosome-scale shotgun assembly using an in vitro method for long-range linkageGenome research26-3. 342–350 (2016) Cold Spring Harbor Lab

Gordon, David and Huddleston, John and Chaisson, Mark JP and Hill, Christopher M and Kronenberg, Zev N and Munson, Katherine M and Malig, Maika and Raja, Archana and Fiddes, Ian and Hillier, LaDeana W and others; Long-read sequence assembly of the gorilla genomeScience352-6281. aae0344 (2016) American Association for the Advancement of Science

Siu, Lillian L and Lawler, Mark and Haussler, David and Knoppers, Bartha Maria and Lewin, Jeremy and Vis, Daniel J and Liao, Rachel G and Andre, Fabrice and Banks, Ian and Barrett, J Carl and others; Facilitating a culture of responsible and effective sharing of cancer genome dataNature medicine22-5. 464 (2016) NIH Public Access

Small, Eric Jay and Aggarwal, Rahul Raj and Huang, Jiaoti and Sokolov, Artem and Zhang, Li and Alumkal, Joshi J and Youngren, Jack and Ryan, Charles J and Foye, Adam and Reiter, Robert Evan and others; Clinical and genomic characterization of metastatic small cell/neuroendocrine prostate cancer (SCNC) and intermediate atypical prostate cancer (IAC): Results from the SU2C/PCF/AACRWest Coast Prostate Cancer Dream Team (WCDT).. (2016) American Society of Clinical Oncology

Liu, Tiffany T and Achrol, Achal S and Mitchell, Lex A and Rodriguez, Scott A and Feroze, Abdullah and Iv, Michael and Kim, Christine and Chaudhary, Navjot and Gevaert, Olivier and Stuart, Josh M and others; Magnetic resonance perfusion image features uncover an angiogenic subgroup of glioblastoma patients with poor survival and better response to antiangiogenic treatmentNeuro-oncology. now270 (2016) Oxford University Press US

Morozova, Olena and Newton, Yulia and Cline, Melissa and Yip, Stephen and Rao, Arjun and Stuart, Josh and Goldstein, Ted and Salama, Sofie and Deyell, Rebecca and Rassekh, S Rod and others; Abstract PR14: Harnessing the power of big data to advance pediatric cancer care. (2016) AACR

Kim, Won and Ryan, Charles J and Zhang, Li and Youngren, Jack and Wilton, John and Alumkal, Joshi J and Beer, Tomasz M and Baertsch, Robert and Stuart, Josh and Chi, Kim N and others; Dehydroepiandrosterone in metastatic castration-resistant prostate cancer: Preliminary results from the SU2C-PCF West Coast Dream Team (WCDT).. (2016) American Society of Clinical Oncology

Tyner, Cath and Barber, Galt P and Casper, Jonathan and Clawson, Hiram and Diekhans, Mark and Eisenhart, Christopher and Fischer, Clayton M and Gibson, David and Gonzalez, Jairo Navarro and Guruvadoo, Luvina and others; The UCSC Genome Browser database: 2017 updateNucleic acids research45-D1. D626–D634 (2016) Oxford University Press

Hinrichs, Angie S and Raney, Brian J and Speir, Matthew L and Rhead, Brooke and Casper, Jonathan and Karolchik, Donna and Kuhn, Robert M and Rosenbloom, Kate R and Zweig, Ann S and Haussler, David and others; UCSC data integrator and variant annotation integratorBioinformatics32-9. 1430–1432 (2016) Oxford University Press

Gordon, David and Huddleston, John and Chaisson, Mark JP and Hill, Christopher M and Kronenberg, Zev N and Munson, Katherine M and Malig, Maika and Raja, Archana and Fiddes, Ian and Hillier, Ladeana W and others; Nonhuman Genomics: Long-read sequence assembly of the gorilla genomeScience352-6281. 52 (2016)

Lee, Jiwon and Boutz, Daniel R and Chromikova, Veronika and Joyce, M Gordon and Vollmers, Christopher and Leung, Kwanyee and Horton, Andrew P and DeKosky, Brandon J and Lee, Chang-Han and Lavinder, Jason J and others; Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccinationNature medicine22-12. 1456 (2016) NIH Public Access

Horns, Felix and Vollmers, Christopher and Croote, Derek and Mackey, Sally F and Swan, Gary E and Dekker, Cornelia L and Davis, Mark M and Quake, Stephen R; Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switchingElife5. e16578 (2016) eLife Sciences Publications Limited

Nair, Nitya and Newell, Evan W and Vollmers, Christopher and Quake, Stephen R and Morton, John M and Davis, Mark M and He, Xiao-Song and Greenberg, Harry B; High-dimensional immune profiling of total and rotavirus VP6-specific intestinal and circulating B cells by mass cytometryMucosal immunology9-1. 68 (2016) NIH Public Access

Cole, Charles and Volden, Roger and Dharmadhikari, Sumedha and Scelfo-Dalbey, Camille and Vollmers, Christopher; Highly Accurate Sequencing of Full-Length Immune Repertoire Amplicons Using Tn5-Enabled and Molecular Identifier–Guided Amplicon AssemblyThe Journal of Immunology196-6. 2902–2907 (2016) Am Assoc Immnol

Okayasu, Isao and Nogawa, Haruo and Casper, Jonathan M and Morais, Duarte B; Recreational sports event participants’ attitudes and satisfaction: cross-cultural comparisons between runners in Japan and the USAManaging Sport and Leisure21-3. 164–180 (2016) Taylor \& Francis

Jeon, Jung-Hwan and Casper, Jonathan; Psychological antecedents of youth versus adult participation: An examination based on the Sport Commitment ModelJournal of Amateur Sport2-2. 103–125 (2016)

Peterson, Megan L and Kay, Kathleen M and Angert, Amy L; The scale of local adaptation in Mimulus guttatus: comparing life history races, ecotypes, and populationsNew Phytologist211-1. 345–356 (2016) Wiley Online Library

2015

Kundaje, Anshul and Meuleman, Wouter and Ernst, Jason and Bilenky, Misha and Yen, Angela and Kheradpour, Pouya and Zhang, Zhizhuo and Heravi-Moussavi, Alireza and Liu, Yaping and Amin, Viren and others; Integrative analysis of 111 reference human epigenomesNature518-7539. 317 (2015) NIH Public Access

Speir, Matthew L and Zweig, Ann S and Rosenbloom, Kate R and Raney, Brian J and Paten, Benedict and Nejad, Parisa and Lee, Brian T and Learned, Katrina and Karolchik, Donna and Hinrichs, Angie S and others; The UCSC genome browser database: 2016 updateNucleic acids research44-D1. D717–D725 (2015) Oxford University Press

Ewing, Adam D and Houlahan, Kathleen E and Hu, Yin and Ellrott, Kyle and Caloian, Cristian and Yamaguchi, Takafumi N and Bare, J Christopher and P’ng, Christine and Waggott, Daryl and Sabelnykova, Veronica Y and others; Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detectionNature methods12-7. 623–630 (2015) Nature Research

Paten, Benedict and Diekhans, Mark and Druker, Brian J and Friend, Stephen and Guinney, Justin and Gassner, Nadine and Guttman, Mitchell and James Kent, W and Mantey, Patrick and Margolin, Adam A and others; The NIH BD2K center for big data in translational genomicsJournal of the American Medical Informatics Association22-6. 1143–1147 (2015) Oxford University Press

Nguyen, Ngan and Hickey, Glenn and Zerbino, Daniel R and Raney, Brian and Earl, Dent and Armstrong, Joel and Kent, W James and Haussler, David and Paten, Benedict; Building a pan-genome reference for a populationJournal of Computational Biology22-5. 387–401 (2015) Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA

Small, Eric Jay and Huang, Jiaoti and Youngren, Jack and Sokolov, Artem and Aggarwal, Rahul Raj and Thomas, George and True, Lawrence D and Zhang, Li and Foye, Adam and Alumkal, Joshi J and others; Characterization of neuroendocrine prostate cancer (NEPC) in patients with metastatic castration resistant prostate cancer (mCRPC) resistant to abiraterone (Abi) or enzalutamide (Enz): Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT).. (2015) American Society of Clinical Oncology

Aggarwal, Rahul Raj and Thomas, George and Youngren, Jack and Foye, Adam and Olson, Susan and Paris, Pamela and Beer, Tomasz M and Ryan, Charles J and Witte, Owen and Evans, Christopher P and others; Androgen receptor (AR) amplification in patients (pts) with metastatic castration resistant prostate cancer (mCRPC) resistant to abiraterone (Abi) and enzalutamide (Enz): Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT)..(2015) American Society of Clinical Oncology

Woodward, Josha and King, Carly and Coleman, Daniel and Lisac, Robert and Schwartzman, Jacob and Wang, Nicholas and Gleave, Martin and Gray, Joe and Thomas, George and Beer, Tomasz M and others; Integrative genomic analysis to identify emergent enzalutamide resistance mechanisms in castration-resistant prostate cancer. (2015) AACR

Morozova, Olena and Ng, Sam and Rao, Arjun and Stuart, Josh and Haussler, David and Salama, Sofie; Abstract A2-52: Pan-cancer analysis reveals distinct effects of receptor tyrosine kinase mutations on downstream pathway activities. (2015) AACR

Hafner, Marc and Niepel, Mario and Duan, Qiaonan and Paull, Evan and Stuart, Josh and Subramanian, Aravind and Ma’ayan, Avi and Sorger, Peter; Abstract B20: Transcriptional landscape of drug response guides the design of specific and potent drug combinations. (2015) AACR

Stuart, Josh and Boutros, Paul and Lee, Anna Ying-Wah and Ellrott, Kyle and Margolin, Adam and Dang, Kristen and Houlahan, Kathleen and Bare, Christopher and Guinney, Justin and Espiritu, Shadrielle and others; Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic variant detectionF1000Research4. (2015)

Baertsch, Robert and Wong, Chris and Youngren, Jack and Stuart, Josh and Small, Eric and Goldstein, Ted; Abstract A1-46: Using Medbook Workbench to create evidence streams to guide medical decisions. (2015) AACR

Dobrynin, Pavel and Liu, Shiping and Tamazian, Gaik and Xiong, Zijun and Yurchenko, Andrey A and Krasheninnikova, Ksenia and Kliver, Sergey and Schmidt-K{\”u}ntzel, Anne and Koepfli, Klaus-Peter and Johnson, Warren and others; Genomic legacy of the African cheetah, Acinonyx jubatusGenome biology16-1. 277 (2015) BioMed Central

Zhu, Jingchun and Craft, Brian and Goldman, Mary and Cline, Melissa and Diekhans, Mark and Haussler, David; Abstract B1-07: Using the UCSC Xena Platform to integrate, visualize, and analyze your own data in the context of large external genomic datasets. (2015) AACR

Vollmers, Christopher and De Vlaminck, Iwijn and Valantine, Hannah A and Penland, Lolita and Luikart, Helen and Strehl, Calvin and Cohen, Garrett and Khush, Kiran K and Quake, Stephen R; Monitoring pharmacologically induced immunosuppression by immune repertoire sequencing to detect acute allograft rejection in heart transplant patients: a proof-of-concept diagnostic accuracy studyPLoS medicine12-10. e1001890 (2015) Public Library of Science

Vollmers, Christopher and Penland, Lolita and Kanbar, Jad N and Quake, Stephen R; Novel exons and splice variants in the human antibody heavy chain identified by single cell and single molecule sequencingPloS one10-1. e0117050 (2015) Public Library of Science

Pfahl, Michael and Casper, Jonathan and Trendafilova, Sylvia and McCullough, Brian P and Nguyen, Sheila N; Crossing boundaries: An examination of sustainability department and athletics department collaboration regarding environmental issuesCommunication \& Sport3-1. 27–56 (2015) Sage Publications Sage CA: Los Angeles, CA

Casper, Jonathan M and Pfahl, Michael E; Sport Management and the Natural Environment: Theory and Practice. (2015) Routledge

Casper, Jonathan M and Pfahl, Michael E; Environmental sustainability practices in US NCAA Division III athletics departmentsInternational Journal of Event Management Research10-1. (2015)

Mayer, Jessica and Seekamp, Erin and Casper, Jonathan and Blank, Gary; An examination of behavior change theories to predict behavioral intentions of organisms-in-trade hobbyistsHuman Ecology Review21-2. 65–92 (2015) JSTOR

Peterson, Megan L and Miller, Timothy J and Kay, Kathleen M; An ultraviolet floral polymorphism associated with life history drives pollinator discrimination in Mimulus guttatusAmerican journal of botany102-3. 396–406 (2015) Botanical Soc America

Biletch, Barry and Kay, Kathleen and Yu, Hongji; An Analysis of Mathematical Notations: For Better or For Worse. (2015)

 

2014

Jarvis, Erich D and Mirarab, Siavash and Aberer, Andre J and Li, Bo and Houde, Peter and Li, Cai and Ho, Simon YW and Faircloth, Brant C and Nabholz, Benoit and Howard, Jason T and others; Whole-genome analyses resolve early branches in the tree of life of modern birdsScience346-6215. 1320–1331 (2014) American Association for the Advancement of Science

Rosenbloom, Kate R and Armstrong, Joel and Barber, Galt P and Casper, Jonathan and Clawson, Hiram and Diekhans, Mark and Dreszer, Timothy R and Fujita, Pauline A and Guruvadoo, Luvina and Haeussler, Maximilian and others; The UCSC genome browser database: 2015 updateNucleic acids research43-D1. D670–D681 (2014) Oxford University Press

Zhang, Guojie and Li, Cai and Li, Qiye and Li, Bo and Larkin, Denis M and Lee, Chul and Storz, Jay F and Antunes, Agostinho and Greenwold, Matthew J and Meredith, Robert W and others; Comparative genomics reveals insights into avian genome evolution and adaptationScience346-6215. 1311–1320 (2014) American Association for the Advancement of Science

Jacobs, Frank MJ and Greenberg, David and Nguyen, Ngan and Haeussler, Maximilian and Ewing, Adam D and Katzman, Sol and Paten, Benedict and Salama, Sofie R and Haussler, David; An evolutionary arms race between KRAB zinc finger genes 91/93 and SVA/L1 retrotransposonsNature516-7530. 242 (2014) NIH Public Access

Green, Richard E and Braun, Edward L and Armstrong, Joel and Earl, Dent and Nguyen, Ngan and Hickey, Glenn and Vandewege, Michael W and John, John A St and Capella-Guti{\’e}rrez, Salvador and Castoe, Todd A and others; Three crocodilian genomes reveal ancestral patterns of evolution among archosaursScience346-6215. 1254449 (2014) American Association for the Advancement of Science

Wilks, Christopher and Cline, Melissa S and Weiler, Erich and Diehkans, Mark and Craft, Brian and Martin, Christy and Murphy, Daniel and Pierce, Howdy and Black, John and Nelson, Donavan and others; The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential dataDatabase2014. (2014) Oxford University Press

Goldman, Mary and Craft, Brian and Swatloski, Teresa and Cline, Melissa and Morozova, Olena and Diekhans, Mark and Haussler, David and Zhu, Jingchun; The UCSC cancer genomics browser: update 2015Nucleic acids research43-D1. D812–D817 (2014) Oxford University Press

Earl, Dent and Nguyen, Ngan and Hickey, Glenn and Harris, Robert S and Fitzgerald, Stephen and Beal, Kathryn and Seledtsov, Igor and Molodtsov, Vladimir and Raney, Brian J and Clawson, Hiram and others; Alignathon: a competitive assessment of whole-genome alignment methodsGenome research24-12. 2077–2089 (2014) Cold Spring Harbor Lab

Lowe, Craig B and Clarke, Julia A and Baker, Allan J and Haussler, David and Edwards, Scott V; Feather development genes and associated regulatory innovation predate the origin of DinosauriaMolecular biology and evolution32-1. 23–28 (2014) Oxford University Press

Paten, Benedict and Novak, Adam and Haussler, David; Mapping to a reference genome structurearXiv preprint arXiv:1404.5010. (2014)

Haeussler, Maximilian and Raney, Brian J and Hinrichs, Angie S and Clawson, Hiram and Zweig, Ann S and Karolchik, Donna and Casper, Jonathan and Speir, Matthew L and Haussler, David and Kent, W James; Navigating protected genomics data with UCSC Genome Browser in a BoxBioinformatics31-5. 764–766 (2014) Oxford University Press

Radenbaugh, Amie J and Ma, Singer and Ewing, Adam and Stuart, Joshua M and Collisson, Eric A and Zhu, Jingchun and Haussler, David; RADIA: RNA and DNA integrated analysis for somatic mutation detectionPloS one9-11. e111516 (2014) Public Library of Science

Yuan, Yuan and Van Allen, Eliezer M and Omberg, Larsson and Wagle, Nikhil and Amin-Mansour, Ali and Sokolov, Artem and Byers, Lauren A and Xu, Yanxun and Hess, Kenneth R and Diao, Lixia and others; Assessing the clinical utility of cancer genomic and proteomic data across tumor typesNature biotechnology32-7. 644–652 (2014) Nature Research

Small, Eric Jay and Youngren, Jack and Thomas, George and Olson, Susan and Toschi, Alexandria and Foye, Adam and Alumkal, Joshi J and Rettig, Matthew and Gleave, Martin Edwin and Evans, Christopher P and others; Androgen receptor (AR) amplification in patients with metastatic castration-resistant prostate cancer (mCRPC) refractory to therapy with abiraterone acetate or enzalutamide: Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT).. (2014) American Society of Clinical Oncology

Yau, Christina and Benz, Stephen and Vaske, Charles and Ng, Sam and Stuart, Josh and Benz, Christopher C; Differential pathway activation associated with domain-specific PIK3CA mutations. (2014) AACR

Wolf, Denise M and Fan, Cheng and Hoadley, Katherine A and Yau, Christina and Sokolov, Artem and Network, TCGA and Stuart, Josh and Perou, Charles and van’t Veer, Laura; Thousands of published cancer signatures and pathways can be collapsed into a handful of non-redundant gene programs: a TCGA pan-cancer analysis. (2014) AACR

Spellman, Paul T and Stuart, Josh and Gray, Joe W; Understanding and Using Information about Cancer Genomes. (2014) Elsevier Inc.

Bivol, Adrian and Graim, Kiley and Paull, Evan and Carlin, Dan and Baertsch, Robert and Sokolov, Artem and Stuart, Josh; Identification of pathways relevant for metastatic site prediction in prostate cancer. (2014) AACR

Alumkal, Joshi J and Heiser, Laura and Beer, Tomasz M and Small, Eric Jay and Baertsch, Robert and Stuart, Josh and King, Carly and Korkola, James and Cetnar, Jeremy and Graff, Julie Nicole and others; Identifying enzalutamide resistance mechanisms in men with castration-resistant prostate cancer.. (2014) American Society of Clinical Oncology

Nguyen, Ngan and Hickey, Glenn and Raney, Brian J and Armstrong, Joel and Clawson, Hiram and Zweig, Ann and Karolchik, Donna and Kent, William James and Haussler, David and Paten, Benedict; Comparative assembly hubs: web-accessible browsers for comparative genomicsBioinformatics30-23. 3293–3301 (2014) Oxford University Press

Haeussler, Maximilian and Karolchik, Donna and Clawson, Hiram and Raney, Brian J and Rosenbloom, Kate R and Fujita, Pauline A and Hinrichs, Angie S and Speir, Matthew L and Eisenhart, Chris and Zweig, Ann S and others; The UCSC Ebola genome portalPLoS currents6. (2014) Public Library of Science

Ezkurdia, Iakes and Juan, David and Rodriguez, Jose Manuel and Frankish, Adam and Diekhans, Mark and Harrow, Jennifer and Vazquez, Jesus and Valencia, Alfonso and Tress, Michael L; Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genesHuman molecular genetics23-22. 5866–5878 (2014) Oxford University Press

Sisu, Cristina and Pei, Baikang and Leng, Jing and Frankish, Adam and Zhang, Yan and Balasubramanian, Suganthi and Harte, Rachel and Wang, Daifeng and Rutenberg-Schoenberg, Michael and Clark, Wyatt and others; Comparative analysis of pseudogenes across three phylaProceedings of the National Academy of Sciences111-37. 13361–13366 (2014) National Acad Sciences

Casper, Jonathan M and Pfahl, Michael E and McCullough, Brian and others; Intercollegiate sport and the environment: Examining fan engagement based on athletics department sustainability effortsJournal of Issues in Intercollegiate Athletics7. 65–91 (2014) College Sport Research Institute

Bocarro, Jason N and Kanters, Michael A and Edwards, Michael B and Casper, Jonathan M and McKenzie, Thomas L; Prioritizing school intramural and interscholastic programs based on observed physical activityAmerican Journal of Health Promotion28-3\_suppl. S65–S71 (2014) SAGE Publications Sage CA: Los Angeles, CA

Kelley, Katharine and Harrolle, Michelle G and Casper, Jonathan M; Estimating Consumer Spending on Tickets, Merchandise, and Food and Beverage: A Case Study of a NHL TeamJournal of Sport Management28-3. 253–265 (2014)

Trendafilova, Sylvia and McCullough, Brian and Pfahl, Michael and Nguyen, Sheila N and Casper, Jonathan and Picariella, M; Environmental sustainability in sport: Current state and future trendsGlobal Journal on Advances in Pure and Applied Sciences3. 9–14 (2014)

Frick, Winifred F and Shipley, J Ryan and Kelly, Jeffrey F and Heady, Paul A and Kay, Kathleen M; Seasonal reliance on nectar by an insectivorous bat revealed by stable isotopesOecologia174-1. 55–65 (2014) Springer

Peterson, Megan L and Kay, Kathleen M; Mating system plasticity promotes persistence and adaptation of colonizing populations of hermaphroditic angiospermsThe American Naturalist185-1. 28–43 (2014) University of Chicago Press Chicago, IL

 

2012

Harrow, Jennifer and Frankish, Adam and Gonzalez, Jose M and Tapanari, Electra and Diekhans, Mark and Kokocinski, Felix and Aken, Bronwen L and Barrell, Daniel and Zadissa, Amonida and Searle, Stephen and others; GENCODE: the reference human genome annotation for The ENCODE ProjectGenome research22-9. 1760–1774 (2012) Cold Spring Harbor Lab

Meyer, Laurence R and Zweig, Ann S and Hinrichs, Angie S and Karolchik, Donna and Kuhn, Robert M and Wong, Matthew and Sloan, Cricket A and Rosenbloom, Kate R and Roe, Greg and Rhead, Brooke and others; The UCSC Genome Browser database: extensions and updates 2013Nucleic acids research41-D1. D64–D69 (2012) Oxford University Press

Rosenbloom, Kate R and Sloan, Cricket A and Malladi, Venkat S and Dreszer, Timothy R and Learned, Katrina and Kirkup, Vanessa M and Wong, Matthew C and Maddren, Morgan and Fang, Ruihua and Heitner, Steven G and others; ENCODE data in the UCSC Genome Browser: year 5 updateNucleic acids research41-D1. D56–D63 (2012) Oxford University Press

Heiser, Laura M and Sadanandam, Anguraj and Kuo, Wen-Lin and Benz, Stephen C and Goldstein, Theodore C and Ng, Sam and Gibb, William J and Wang, Nicholas J and Ziyad, Safiyyah and Tong, Frances and others; Subtype and pathway specific responses to anticancer compounds in breast cancerProceedings of the National Academy of Sciences109-8. 2724–2729 (2012) National Acad Sciences

Kuhn, Robert M and Haussler, David and Kent, W James; The UCSC genome browser and associated toolsBriefings in bioinformatics14-2. 144–161 (2012) Oxford University Press

Goldman, Mary and Craft, Brian and Swatloski, Teresa and Ellrott, Kyle and Cline, Melissa and Diekhans, Mark and Ma, Singer and Wilks, Chris and Stuart, Josh and Haussler, David and others; The UCSC cancer genomics browser: update 2013Nucleic acids research41-D1. D949–D954 (2012) Oxford University Press

Kristensen, Vessela N and Vaske, Charles J and Ursini-Siegel, Josie and Van Loo, Peter and Nordgard, Silje H and Sachidanandam, Ravi and S{\o}rlie, Therese and W{\”a}rnberg, Fredrik and Haakensen, Vilde D and Helland, {\AA}slaug and others; Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signalingProceedings of the National Academy of Sciences109-8. 2802–2807 (2012) National Acad Sciences

Raab, Jesse R and Chiu, Jonathan and Zhu, Jingchun and Katzman, Sol and Kurukuti, Sreenivasulu and Wade, Paul A and Haussler, David and Kamakaka, Rohinton T; Human tRNA genes function as chromatin insulatorsThe EMBO journal31-2. 330–350 (2012) EMBO Press

Ng, Sam and Collisson, Eric A and Sokolov, Artem and Goldstein, Theodore and Gonzalez-Perez, Abel and Lopez-Bigas, Nuria and Benz, Christopher and Haussler, David and Stuart, Joshua M; PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysisBioinformatics28-18. i640–i646 (2012) Oxford University Press

Bernardi, Giacomo and Wiley, Edward O and Mansour, Hicham and Miller, Michael R and Orti, Guillermo and Haussler, David and O’Brien, Stephen J and Ryder, Oliver A and Venkatesh, Byrappa; The fishes of Genome 10KMarine genomics7. 3–6 (2012) Elsevier

Lowe, Craig B and Haussler, David; 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genomePLoS One7-8. e43128 (2012) Public Library of Science

Wong, Pamela BY and Wiley, Edward O and Johnson, Warren E and Ryder, Oliver A and O’Brien, Stephen J and Haussler, David and Koepfli, Klaus-Peter and Houck, Marlys L and Perelman, Polina and Mastromonaco, Gabriela and others; Tissue sampling methods and standards for vertebrate genomicsGigaScience1-1. 8 (2012) BioMed Central

Onodera, Courtney S and Underwood, Jason G and Katzman, Sol and Jacobs, Frank and Greenberg, David and Salama, Sofie R and Haussler, David; Gene isoform specificity through enhancer-associated antisense transcriptionPloS one7-8. e43511 (2012) Public Library of Science

Pei, Baikang and Sisu, Cristina and Frankish, Adam and Howald, C{\’e}dric and Habegger, Lukas and Mu, Xinmeng Jasmine and Harte, Rachel and Balasubramanian, Suganthi and Tanzer, Andrea and Diekhans, Mark and others; The GENCODE pseudogene resourceGenome biology13-9. R51 (2012) BioMed Central

Harte, Rachel A and Farrell, Catherine M and Loveland, Jane E and Suner, Marie-Marthe and Wilming, Laurens and Aken, Bronwen and Barrell, Daniel and Frankish, Adam and Wallin, Craig and Searle, Steve and others; Tracking and coordinating an international curation effort for the CCDS ProjectDatabase2012. bas008 (2012) Oxford University Press

Hatori, Megumi and Vollmers, Christopher and Zarrinpar, Amir and DiTacchio, Luciano and Bushong, Eric A and Gill, Shubhroz and Leblanc, Mathias and Chaix, Amandine and Joens, Matthew and Fitzpatrick, James AJ and others; Time-restricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat dietCell metabolism15-6. 848–860 (2012) Elsevier

Vollmers, Christopher and Schmitz, Robert J and Nathanson, Jason and Yeo, Gene and Ecker, Joseph R and Panda, Satchidananda; Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenomeCell metabolism16-6. 833–845 (2012) Elsevier

Zarrinpar, Amir and Vollmers, Christopher and Panda, Satchidananda; 52 Temporally Restricted Feeding Prevents Obesity and Other Metabolic Disorders Associated With High Fat Diet in MiceGastroenterology142-5. S–14 (2012) WB Saunders

Bocarro, Jason N and Kanters, Michael A and Cerin, Ester and Floyd, Myron F and Casper, Jonathan M and Suau, Luis J and McKenzie, Thomas L; School sport policy and school-based physical activity environments and their association with observed physical activity in middle school childrenHealth \& Place18-1. 31–38 (2012) Elsevier

Casper, Jonathan and Pfahl, Michael and McSherry, Mark; Athletics department awareness and action regarding the environment: A study of NCAA athletics department sustainability practicesJournal of Sport Management26-1. 11–29 (2012)

Henderson, Karla A and Casper, Jonathan and Wilson, Beth E and Dern, Liana; Behaviors, reasons, and outcomes perceived by senior games participantsJournal of Park and Recreation Administration30-1. (2012) Sagamore Publishing LLC

Casper, Jonathan M and Pfahl, Michael E; Environmental behavior frameworks of sport and recreation undergraduate studentsSport Management Education Journal6-1. 8–20 (2012)

Kanters, Michael A and Bocarro, Jason N and Greenwood, P Brian and Casper, Jonathan M and Suau, Luis and McKenzie, Thomas L; Determinants of middle school sport participation: a comparison of different models for school sport deliveryInternational Journal of Sport Management and Marketing12-3-4. 159–179 (2012) Inderscience Publishers Ltd

Reardon, Jenny and TallBear, Kim; “Your DNA Is Our History” Genomics, Anthropology, and the Construction of Whiteness as PropertyCurrent Anthropology53-S5. S233–S245 (2012) University of Chicago Press Chicago, IL

Reardon, Jenny; The democratic, anti-racist genome? Technoscience at the limits of liberalismScience as Culture21-1. 25–47 (2012) Taylor \& Francis

Yost, Jenn M and Barry, Teri and Kay, Kathleen M and Rajakaruna, Nishanta; Edaphic adaptation maintains the coexistence of two cryptic species on serpentine soilsAmerican Journal of Botany99-5. 890–897 (2012) Botanical Soc America

Abreu, Aluana G and Albaina, A and Alpermann, Tilman J and Apkenas, Vanessa E and BANKHEAD-DRONNET, St{\’e}phanie and Bergek, Sara and Berumen, Michael L and CHO, CHANG-HUNG and Clobert, Jean and Coulon, Aur{\’e}lie and others; Permanent genetic resources added to molecular ecology resources database 1 October 2011–30 November 2011Molecular ecology resources12-2. 374–376 (2012) Wiley Online Library

Frick, Winifred F and Price, Ryan D and Heady III, Paul A and Kay, Kathleen M; Insectivorous bat pollinates columnar cactus more effectively per visit than specialized nectar batThe American Naturalist181-1. 137–144 (2012) University of Chicago Press Chicago, IL

2011

Earl, Dent and Bradnam, Keith and John, John St and Darling, Aaron and Lin, Dawei and Fass, Joseph and Yu, Hung On Ken and Buffalo, Vince and Zerbino, Daniel R and Diekhans, Mark and others; Assemblathon 1: a competitive assessment of de novo short read assembly methodsGenome research21-12. 2224–2241 (2011) Cold Spring Harbor Lab

Alf{\”o}ldi, Jessica and Di Palma, Federica and Grabherr, Manfred and Williams, Christina and Kong, Lesheng and Mauceli, Evan and Russell, Pamela and Lowe, Craig B and Glor, Richard and Jaffe, Jacob D and others; The genome of the green anole lizard and a comparative analysis with birds and mammalsNature477-7366. 587 (2011) NIH Public Access

Locke, Devin P and Hillier, LaDeana W and Warren, Wesley C and Worley, Kim C and Nazareth, Lynne V and Muzny, Donna M and Yang, Shiaw-Pyng and Wang, Zhengyuan and Chinwalla, Asif T and Minx, Pat and others; Comparative and demographic analysis of orangutan genomesNature469-7331. 529 (2011) NIH Public Access

Dreszer, Timothy R and Karolchik, Donna and Zweig, Ann S and Hinrichs, Angie S and Raney, Brian J and Kuhn, Robert M and Meyer, Laurence R and Wong, Mathew and Sloan, Cricket A and Rosenbloom, Kate R and others; The UCSC Genome Browser database: extensions and updates 2011Nucleic acids research40-D1. D918–D923 (2011) Oxford University Press

Gravel, Simon and Henn, Brenna M and Gutenkunst, Ryan N and Indap, Amit R and Marth, Gabor T and Clark, Andrew G and Yu, Fuli and Gibbs, Richard A and Bustamante, Carlos D and Altshuler, David L and others; Demographic history and rare allele sharing among human populationsProceedings of the National Academy of Sciences108-29. 11983–11988 (2011) National Acad Sciences

Wang, Nicholas J and Sanborn, Zachary and Arnett, Kelly L and Bayston, Laura J and Liao, Wilson and Proby, Charlotte M and Leigh, Irene M and Collisson, Eric A and Gordon, Patricia B and Jakkula, Lakshmi and others; Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinomaProceedings of the National Academy of Sciences108-43. 17761–17766 (2011) National Acad Sciences

Rosenbloom, Kate R and Dreszer, Timothy R and Long, Jeffrey C and Malladi, Venkat S and Sloan, Cricket A and Raney, Brian J and Cline, Melissa S and Karolchik, Donna and Barber, Galt P and Clawson, Hiram and others; ENCODE whole-genome data in the UCSC Genome Browser: update 2012Nucleic acids research40-D1. D912–D917 (2011) Oxford University Press

Zhou, Xin and Maricque, Brett and Xie, Mingchao and Li, Daofeng and Sundaram, Vasavi and Martin, Eric A and Koebbe, Brian C and Nielsen, Cydney and Hirst, Martin and Farnham, Peggy and others; The human epigenome browser at Washington UniversityNature methods8-12. 989–990 (2011) Nature Research

Lowe, Craig B and Kellis, Manolis and Siepel, Adam and Raney, Brian J and Clamp, Michele and Salama, Sofie R and Kingsley, David M and Lindblad-Toh, Kerstin and Haussler, David; Three periods of regulatory innovation during vertebrate evolutionscience333-6045. 1019–1024 (2011) American Association for the Advancement of Science

Paten, Benedict and Diekhans, Mark and Earl, Dent and John, John St and Ma, Jian and Suh, Bernard and Haussler, David; Cactus graphs for genome comparisonsJournal of Computational Biology18-3. 469–481 (2011) Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA

Katzman, Sol and Capra, John A and Haussler, David and Pollard, Katherine S; Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spotsGenome biology and evolution3. 614–626 (2011) Oxford University Press

Roskin, Krishna M and Paten, Benedict and Haussler, David; Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelizationBMC bioinformatics12-1. 144 (2011) BioMed Central

Craft, Brian and Ellrott, Kyle and Goldman, Mary and Wilks, Christopher and Szeto, Christopher and Ma, Singer and Stuart, Josh and Zhu, Jingchun and Haussler, David; Abstract A39: The UCSC Cancer Genomics Browser. (2011) AACR

Karolchik, Donna and Hinrichs, Angie S and Kent, W James; The UCSC genome browserCurrent protocols in human genetics.18–6 (2011) Wiley Online Library

Raney, Melissa S Cline and Karolchik, Donna and Barber, Galt P and Clawson, Hiram and others; Encode whole-genome 751 data in the ucsc genome browser: update 2012Nucleic acids research, page gkr1012752. (2011)

Wong, Wing Chung and Kim, Dewey and Carter, Hannah and Diekhans, Mark and Ryan, Michael C and Karchin, Rachel; CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancerBioinformatics27-15. 2147–2148 (2011) Oxford University Press

DiTacchio, Luciano and Le, Hiep D and Vollmers, Christopher and Hatori, Megumi and Witcher, Michael and Secombe, Julie and Panda, Satchidananda; Histone lysine demethylase JARID1a activates CLOCK-BMAL1 and influences the circadian clockScience333-6051. 1881–1885 (2011) American Association for the Advancement of Science

Casper, Jonathan M and Bocarro, Jason N and Kanters, Michael A and Floyd, Myron F; “Just let me play!”—understanding constraints that limit adolescent sport participationJournal of Physical Activity and Health8-s1. S32–S39 (2011)

Casper, Jonathan M and Bocarro, Jason N and Kanters, Michael A and Floyd, Myron F; Measurement properties of constraints to sport participation: A psychometric examination with adolescentsLeisure Sciences33-2. 127–146 (2011) Taylor \& Francis

Edwards, Michael B and Bocarro, Jason N and Kanters, Michael and Casper, Jonathan; Participation in interscholastic and intramural sport programs in middle schools: An exploratory investigation of race and genderRecreational Sports Journal35-2. 157–173 (2011)

Bruton, Candice M and Floyd, Myron F and Bocarro, Jason N and Henderson, Karla A and Casper, Jonathan M and Kanters, Michael A; Physical activity and health partnerships among park and recreation departments in North CarolinaJournal of Park and Recreation Administration29-2. (2011) Sagamore Publishing LLC

Menefee, W Chadwick and Casper, Jonathan M; Professional basketball fans in China: A comparison of National Basketball Association and Chinese Basketball Association team identificationInternational Journal of Sport Management and Marketing9-3-4. 185–200 (2011) Inderscience Publishers

Jonathan, Casper; Measurement Properties of Constraints to Sport Participation: A Psychometric Examination with Adolescents/Jonathan M. Casper, Jason N. Bocarro, Michael A. Kanters, Myron F. FloydLeisure Sciences33. (2011)

Casper, Jonathan and Pfahl, Michael and McSherry, Mark; Journal of Sport ManagementJournal of Sport Management. (2011)

Reardon, Jenny; The ‘persons’ and ‘genomics’ of personal genomicsPersonalized Medicine8-1. 95–107 (2011) Future Medicine

Kay, Kathleen M and Ward, Kimiora L and Watt, Lorna R and Schemske, Douglas W; Plant speciationSerpentine: Evolution and Ecology in a Model System (SP Harrison \& N. Rajakaruna, eds). 71–96 (2011)

Louthan, Allison M and Kay, Kathleen M; Comparing the adaptive landscape across trait types: larger QTL effect size in traits under biotic selectionBMC evolutionary biology11-1. 60 (2011) BioMed Central

2010

Maunakea, Alika K and Nagarajan, Raman P and Bilenky, Mikhail and Ballinger, Tracy J and D’Souza, Cletus and Fouse, Shaun D and Johnson, Brett E and Hong, Chibo and Nielsen, Cydney and Zhao, Yongjun and others; Conserved role of intragenic DNA methylation in regulating alternative promotersNature466-7303. 253 (2010) NIH Public Access

 

Fujita, Pauline A and Rhead, Brooke and Zweig, Ann S and Hinrichs, Angie S and Karolchik, Donna and Cline, Melissa S and Goldman, Mary and Barber, Galt P and Clawson, Hiram and Coelho, Antonio and others; The UCSC genome browser database: update 2011Nucleic acids research39-suppl\_1. D876–D882 (2010) Oxford University Press

Harris, R Alan and Wang, Ting and Coarfa, Cristian and Nagarajan, Raman P and Hong, Chibo and Downey, Sara L and Johnson, Brett E and Fouse, Shaun D and Delaney, Allen and Zhao, Yongjun and others; Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modificationsNature biotechnology28-10. 1097–1105 (2010) Nature Research

Vaske, Charles J and Benz, Stephen C and Sanborn, J Zachary and Earl, Dent and Szeto, Christopher and Zhu, Jingchun and Haussler, David and Stuart, Joshua M; Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGMBioinformatics26-12. i237–i245 (2010) Oxford University Press

Underwood, Jason G and Uzilov, Andrew V and Katzman, Sol and Onodera, Courtney S and Mainzer, Jacob E and Mathews, David H and Lowe, Todd M and Salama, Sofie R and Haussler, David; FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencingNature methods7-12. 995–1001 (2010) Nature Research

Raney, Brian J and Cline, Melissa S and Rosenbloom, Kate R and Dreszer, Timothy R and Learned, Katrina and Barber, Galt P and Meyer, Laurence R and Sloan, Cricket A and Malladi, Venkat S and Roskin, Krishna M and others; ENCODE whole-genome data in the UCSC genome browser (2011 update)Nucleic acids research39-suppl\_1. D871–D875 (2010) Oxford University Press

Sanborn, J Zachary and Benz, Stephen C and Craft, Brian and Szeto, Christopher and Kober, Kord M and Meyer, Laurence and Vaske, Charles J and Goldman, Mary and Smith, Kayla E and Kuhn, Robert M and others; The UCSC cancer genomics browser: update 2011Nucleic acids research39-suppl\_1. D951–D959 (2010) Oxford University Press

Katzman, Sol and Kern, Andrew D and Pollard, Katherine S and Salama, Sofie R and Haussler, David; GC-biased evolution near human accelerated regionsPLoS genetics6-5. e1000960 (2010) Public Library of Science

Kern, Andrew D and Haussler, David; A population genetic hidden Markov model for detecting genomic regions under selectionMolecular biology and evolution27-7. 1673–1685 (2010) Oxford University Press

Lowe, Craig B and Bejerano, Gill and Salama, Sofie R and Haussler, David; Endangered species hold clues to human evolutionJournal of heredity101-4. 437–447 (2010) Oxford University Press

Marshall, Heather and Stuart, Josh and Jaunzens, Tatiana; Community organizing goes greenSocial Policy39-4. 8–10 (2010)

Kent, W James and Zweig, Ann S and Barber, G and Hinrichs, Angie S and Karolchik, Donna; BigWig and BigBed: enabling browsing of large distributed datasetsBioinformatics26-17. 2204–2207 (2010) Oxford University Press

Paten, Benedict and Diekhans, Mark and Earl, Dent; John St. John, Jian Ma, Bernard Suh, and David Haussler. 410–425 (2010)

Miller, David T and Adam, Margaret P and Aradhya, Swaroop and Biesecker, Leslie G and Brothman, Arthur R and Carter, Nigel P and Church, Deanna M and Crolla, John A and Eichler, Evan E and Epstein, Charles J and others; Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomaliesThe American Journal of Human Genetics86-5. 749–764 (2010) Elsevier

Jones, Matthew A and Covington, Michael F and DiTacchio, Luciano and Vollmers, Christopher and Panda, Satchidananda and Harmer, Stacey L; Jumonji domain protein JMJD5 functions in both the plant and human circadian systemsProceedings of the National Academy of Sciences107-50. 21623–21628 (2010) National Acad Sciences

Casper, Jonathan M and Menefee, W Chadwick; Prior sport participation and spectator sport consumption: Socialization and soccerEuropean Sport Management Quarterly10-5. 595–611 (2010) Taylor \& Francis

Casper, Jonathan and Pfahl, Michael; Athletic Department Awareness and Action Regarding the Environment: An Exploratory Study of Athletic Department Sustainability Practices. (2010)

LaJeunesse, Dennis R and Johnson, Brooke and Presnell, Jason S and Catignas, Kathleen Kay and Zapotoczny, Grzegorz; Peristalsis in the junction region of the Drosophila larval midgut is modulated by DH31 expressing enteroendocrine cellsBMC physiology10-1. 14 (2010) BioMed Central

 

2009

Rhead, Brooke and Karolchik, Donna and Kuhn, Robert M and Hinrichs, Angie S and Zweig, Ann S and Fujita, Pauline A and Diekhans, Mark and Smith, Kayla E and Rosenbloom, Kate R and Raney, Brian J and others; The UCSC genome browser database: update 2010Nucleic acids research38-suppl\_1. D613–D619 (2009) Oxford University Press

Pruitt, Kim D and Harrow, Jennifer and Harte, Rachel A and Wallin, Craig and Diekhans, Mark and Maglott, Donna R and Searle, Steve and Farrell, Catherine M and Loveland, Jane E and Ruef, Barbara J and others; 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 Research19-8. 1506–1506 (2009) COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2924 USA

Han, Jinju and Pedersen, Jakob S and Kwon, S Chul and Belair, Cassandra D and Kim, Young-Kook and Yeom, Kyu-Hyeon and Yang, Woo-Young and Haussler, David and Blelloch, Robert and Kim, V Narry; Posttranscriptional crossregulation between Drosha and DGCR8Cell136-1. 75–84 (2009) Elsevier

Rosenbloom, Kate R and Dreszer, Timothy R and Pheasant, Michael and Barber, Galt P and Meyer, Laurence R and Pohl, Andy and Raney, Brian J and Wang, Ting and Hinrichs, Angie S and Zweig, Ann S and others; ENCODE whole-genome data in the UCSC Genome BrowserNucleic acids research38-suppl\_1. D620–D625 (2009) Oxford University Press

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

Zhu, Jingchun and Sanborn, J Zachary and Benz, Stephen and Szeto, Christopher and Hsu, Fan and Kuhn, Robert M and Karolchik, Donna and Archie, John and Lenburg, Marc E and Esserman, Laura J and others; The UCSC cancer genomics browserNature methods6-4. 239–240 (2009) Nature Publishing Group

Temple, Gary and Gerhard, Daniela S and Rasooly, Rebekah and Feingold, Elise A and Good, Peter J and Robinson, Cristen and Mandich, Allison and Derge, Jeffrey G and Lewis, Jeanne and Shoaf, Debonny and others; The completion of the mammalian gene collection (MGC)Genome research19-12. 2324–2333 (2009) Cold Spring Harbor Lab

Koeva, Martina and Forsberg, E Camilla and Stuart, Josh M; Core stemness mechanisms revealed through homologyBMC Bioinformatics10-S13. O4 (2009) Springer

Karolchik, Donna and Hinrichs, Angie S and Kent, W James; The UCSC genome browserCurrent protocols in bioinformatics. 1–4 (2009) Wiley Online Library

Ryan, Michael and Diekhans, Mark and Lien, Stephanie and Liu, Yun and Karchin, Rachel; LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structuresBioinformatics25-11. 1431–1432 (2009) Oxford University Press

Pruitt, Kim D and Harrow, Jennifer and Harte, Rachel A and Wallin, Craig and Diekhans, Mark and Maglott, Donna R and Searle, Steve and Farrell, Catherine M and Loveland, Jane E and Ruef, Barbara J; Clara Amid, Garth Brown, Oksana Dukhanina, Adam Frankish, Jennifer Hart, Bonnie L. (2009)

Flume, Patrick A and Mogayzel Jr, Peter J and Robinson, Karen A and Goss, Christopher H and Rosenblatt, Randall L and Kuhn, Robert J and Marshall, Bruce C and Clinical Practice Guidelines for Pulmonary Therapies Committee*; Cystic fibrosis pulmonary guidelines: treatment of pulmonary exacerbationsAmerican journal of respiratory and critical care medicine180-9. 802–808 (2009) Am Thoracic Soc

Hartnig, Christoph and Manke, Ingo and Kuhn, Robert and Kleinau, Sebastian and Goebbels, J{\”u}rgen and Banhart, John; High-resolution in-plane investigation of the water evolution and transport in PEM fuel cellsJournal of Power Sources188-2. 468–474 (2009) Elsevier

Hughes, Michael E and DiTacchio, Luciano and Hayes, Kevin R and Vollmers, Christopher and Pulivarthy, S and Baggs, Julie E and Panda, Satchidananda and Hogenesch, John B; Harmonics of circadian gene transcription in mammalsPLoS genetics5-4. e1000442 (2009) Public Library of Science

Vollmers, Christopher and Gill, Shubhroz and DiTacchio, Luciano and Pulivarthy, Sandhya R and Le, Hiep D and Panda, Satchidananda; Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expressionProceedings of the National Academy of Sciences106-50. 21453–21458 (2009) National Acad Sciences

Bocarro, Jason N and Casper, Jonathan and Henderson, Karla A and Floyd, Myron F and Moore, Roger and Kanters, Michael A and Laven, Kevin and Edwards, Michael B; Physical Activity Promotion in North Carolina: Perceptions of Public Park and Recreation Directors.Journal of Park \& Recreation Administration27-1. (2009)

Reardon, Jenny; Race to the Finish: Identity and Governance in an Age of Genomics. (2009) Princeton University Press

Kay, Kathleen M and Sargent, Risa D; The role of animal pollination in plant speciation: integrating ecology, geography, and geneticsAnnual Review of Ecology, Evolution, and Systematics40. 637–656 (2009) Annual Reviews

Yost, Jenn M and Kay, Kathleen M; The evolution of postpollination reproductive isolation in CostusSexual plant reproduction22-4. 247–255 (2009) Springer

 

2008

Kuhn, Robert M and Karolchik, Donna and Zweig, Ann S and Wang, Ting and Smith, Kayla E and Rosenbloom, Kate R and Rhead, B and Raney, Brian J and Pohl, Andy and Pheasant, Michael and others; The UCSC genome browser database: update 2009Nucleic acids research37-suppl\_1. D755–D761 (2008) Oxford University Press

Stanke, Mario and Diekhans, Mark and Baertsch, Robert and Haussler, David; Using native and syntenically mapped cDNA alignments to improve de novo gene findingBioinformatics24-5. 637–644 (2008) Oxford University Press

Baertsch, Robert and Diekhans, Mark and Kent, W James and Haussler, David and Brosius, J{\”u}rgen; Retrocopy contributions to the evolution of the human genomeBMC genomics9-1. 466 (2008) BioMed Central

Ma, Jian and Ratan, Aakrosh and Raney, Brian J and Suh, Bernard B and Miller, Webb and Haussler, David; The infinite sites model of genome evolutionProceedings of the National Academy of Sciences105-38. 14254–14261 (2008) National Acad Sciences

Zweig, Ann S and Karolchik, Donna and Kuhn, Robert M and Haussler, David and Kent, W James; UCSC genome browser tutorialGenomics92-2. 75–84 (2008) Elsevier

Ma, Jian and Ratan, Aakrosh and Raney, Brian J and Suh, Bernard B and Zhang, Louxin and Miller, Webb and Haussler, David; DUPCAR: reconstructing contiguous ancestral regions with duplicationsJournal of computational biology15-8. 1007–1027 (2008) Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA

Blanchette, Mathauieu and Diallo, Abdoulaye Banir{\’e} and Green, Eric D and Miller, Webb and Haussler, David; Computational reconstruction of ancestral DNA sequencesPhylogenomics. 171–184 (2008) Springer

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

Rosenbloom, Kate and Taylor, James and Schaeffer, Stephen and Kent, Jim and Haussler, David and Miller, Webb; Phylogenomic resources at the UCSC Genome BrowserPhylogenomics. 133–144 (2008) Springer

Twigger, Simon N and Pruitt, Kim D and Fern{\’a}ndez-Su{\’a}rez, Xos{\’e} M and Karolchik, Donna and Worley, Kim C and Maglott, Donna R and Brown, Garth and Weinstock, George and Gibbs, Richard A and Kent, Jim and others; What everybody should know about the rat genome and its online resourcesNature genetics40-5. 523–527 (2008) Nature Publishing Group

Mangan, Mary E and Williams, Jennifer M and Lathe, Scott M and Karolchik, Donna and Lathe, Warren C; UCSC genome browser: deep support for molecular biomedical researchBiotechnology annual review14. 63–108 (2008) Elsevier

Harte, Rachel and Diekhans, Mark; Fishing for Genes in the UCSC Browser A Tutorial. (2008)

Hartnig, Christoph and Manke, Ingo and Kuhn, Robert and Kardjilov, Nikolay and Banhart, John and Lehnert, Werner; Cross-sectional insight in the water evolution and transport in polymer electrolyte fuel cellsApplied Physics Letters92-13. 134106 (2008) AIP

Hatori, Megumi and Le, Hiep and Vollmers, Christopher and Keding, Sheena Racheal and Tanaka, Nobushige and Schmedt, Christian and Jegla, Timothy and Panda, Satchidananda; Inducible ablation of melanopsin-expressing retinal ganglion cells reveals their central role in non-image forming visual responsesPloS one3-6. e2451 (2008) Public Library of Science

Vollmers, Christopher and Panda, Satchidananda and DiTacchio, Luciano; A high-throughput assay for siRNA-based circadian screens in human U2OS cellsPloS one3-10. e3457 (2008) Public Library of Science

Kanters, Michael A and Bocarro, Jason and Casper, Jonathan; Supported or pressured? An examination of agreement among parent’s and children on parent’s role in youth sportsJournal of sport behavior31-1. 64 (2008) Journal of Sport Behavior

Bocarro, Jason and Kanters, Michael A and Casper, Jonathan and Forrester, Scott; School physical education, extracurricular sports, and lifelong active livingJournal of Teaching in Physical Education27-2. 155–166 (2008)

Casper, Jonathan M and Andrew, Damon PS; Sport commitment differences among tennis players on the basis of participation outlet and skill levelJournal of Sport Behavior31-3. 201 (2008) Journal of Sport Behavior

Casper, Jonathan M and Stellino, Megan Babkes; Demographic Predictors of Recreational Tennis Participants’ Sport Commitment.Journal of Park \& Recreation Administration26-3. (2008)

Casper, Jonathan M and Kanters, Michael A and James, Jeffrey D; Perceptions of constraints to NHL spectatorshipInternational Journal of Sport Management and Marketing5-1-2. 55–72 (2008) Inderscience Publishers

Kanters, Michael and Bocarro, Jason and Casper, Jonathan and Forrester, Scott; Determinants of sport participation in middle school children and the impact of intramural sportsRecreational sports journal32-2. 134–151 (2008)

Prainsack, Barbara and Reardon, Jenny and Hindmarsh, Richard and Gottweis, Herbert and Naue, Ursula and Lunshof, Jeantine E; Personal genomes: misdirected precautionNature456-7218. 34–35 (2008) Nature Publishing Group

Reardon, Jenny; Race without SalvationRevisiting Race in a Genomic Age (New Brunswick: Rutgers University Press, 2008). 304–19 (2008)

Bolnick, Deborah A and Fullwiley, Duana and Marks, Jonathan and Reverby, Susan M and Kahn, Jonathan and Tallbear, Kimberly and Reardon, Jenny and Cooper, Richard S and Duster, Troy and Fujimura, Joan H and others; The legitimacy of genetic ancestry tests-ResponseScience319-5866. 1039–1040 (2008) AMER ASSOC ADVANCEMENT SCIENCE 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA

Kay, Kathleen M and Schemske, Douglas W; Natural selection reinforces speciation in a radiation of neotropical rainforest plantsEvolution62-10. 2628–2642 (2008) Wiley Online Library

Rogers, Kathleen Kay; Editorial in English: Innovation, risk-taking, and collaboration: A celebration and history of CADE/ACED and distance education in CanadaInternational Journal of E-Learning \& Distance Education8-1. 1–7 (2008)

 

2007

Gibbs, Richard A and Rogers, Jeffrey and Katze, Michael G and Bumgarner, Roger and Weinstock, George M and Mardis, Elaine R and Remington, Karin A and Strausberg, Robert L and Venter, J Craig and Wilson, Richard K and others; Evolutionary and biomedical insights from the rhesus macaque genomescience316-5822. 222–234 (2007) American Association for the Advancement of Science

Karolchik, Donna and Kuhn, Robert M and Baertsch, Robert and Barber, Galt P and Clawson, Hiram and Diekhans, Mark and Giardine, Belinda and Harte, Rachel A and Hinrichs, Angela S and Hsu, Fan and others; The UCSC genome browser database: 2008 updateNucleic acids research36-suppl\_1. D773–D779 (2007) Oxford University Press

Miller, Webb and Rosenbloom, Kate and Hardison, Ross C and Hou, Minmei and Taylor, James and Raney, Brian and Burhans, Richard and King, David C and Baertsch, Robert and Blankenberg, Daniel and others; 28-way vertebrate alignment and conservation track in the UCSC Genome BrowserGenome research17-12. 1797–1808 (2007) Cold Spring Harbor Lab

Margulies, Elliott H and Cooper, Gregory M and Asimenos, George and Thomas, Daryl J and Dewey, Colin N and Siepel, Adam and Birney, Ewan and Keefe, Damian and Schwartz, Ariel S and Hou, Minmei and others; Analyses of deep mammalian sequence alignments and constraint predictions for 1\% of the human genomeGenome research17-6. 760–774 (2007) Cold Spring Harbor Lab

Wang, Ting and Zeng, Jue and Lowe, Craig B and Sellers, Robert G and Salama, Sofie R and Yang, Min and Burgess, Shawn M and Brachmann, Rainer K and Haussler, David; Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53Proceedings of the National Academy of Sciences104-47. 18613–18618 (2007) National Acad Sciences

Lowe, Craig B and Bejerano, Gill and Haussler, David; Thousands of human mobile element fragments undergo strong purifying selection near developmental genesProceedings of the National Academy of Sciences104-19. 8005–8010 (2007) National Acad Sciences

Katzman, Sol and Kern, Andrew D and Bejerano, Gill and Fewell, Ginger and Fulton, Lucinda and Wilson, Richard K and Salama, Sofie R and Haussler, David; Human genome ultraconserved elements are ultraselectedScience317-5840. 915–915 (2007) American Association for the Advancement of Science

Yeang, Chen-Hsiang and Darot, Jeremy FJ and Noller, Harry F and Haussler, David; Detecting the coevolution of biosequences—an example of RNA interaction predictionMolecular biology and evolution24-9. 2119–2131 (2007) Oxford University Press

Ohlson, Johan and Pedersen, Jakob Skou and Haussler, David and {\”O}hman, Marie; Editing modifies the GABAA receptor subunit $\alpha$3Rna13-5. 698–703 (2007) Cold Spring Harbor Lab

Zhu, Jingchun and Sanborn, J Zachary and Diekhans, Mark and Lowe, Craig B and Pringle, Tom H and Haussler, David; Comparative genomics search for losses of long-established genes on the human lineagePLoS computational biology3-12. e247 (2007) Public Library of Science

Dreszer, Timothy R and Wall, Gregory D and Haussler, David and Pollard, Katherine S; Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversionGenome research17-10. 1420–1430 (2007) Cold Spring Harbor Lab

Siepel, Adam and Diekhans, Mark and Brejov{\’a}, Bro{\v{n}}a and Langton, Laura and Stevens, Michael and Comstock, Charles LG and Davis, Colleen and Ewing, Brent and Oommen, Shelly and Lau, Christopher and others; Targeted discovery of novel human exons by comparative genomicsGenome research17-12. 1763–1773 (2007) Cold Spring Harbor Lab

Zeng, Jue and Yan, Jizhou and Wang, Ting and Mosbrook-Davis, Deborah and Dolan, Kyle T and Christensen, Ryan and Stormo, Gary D and Haussler, David and Lathrop, Richard H and Brachmann, Rainer K and others; Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteinsNucleic acids research36-1. e8–e8 (2007) Oxford University Press

Salomonis, Nathan and Hanspers, Kristina and Zambon, Alexander C and Vranizan, Karen and Lawlor, Steven C and Dahlquist, Kam D and Doniger, Scott W and Stuart, Josh and Conklin, Bruce R and Pico, Alexander R; GenMAPP 2: new features and resources for pathway analysisBMC bioinformatics8-1. 217 (2007) BioMed Central

Casper, Jonathan; Sport commitment, participation frequency and purchase intention segmentation based on age, gender, income and skill level with US tennis participantsEuropean Sport Management Quarterly7-3. 269–282 (2007) Taylor \& Francis

Casper, Jonathan and Kanters, Michael A and Bocarro, Jason and Forrester, Scott and Greenwood, P Brian; Youth Sport Market Segmentation with the Theory of Planned Behavior. (2007)

Kanters, Michael and Bocarro, Jason and Casper, Jonathan and Forrester, Scott and Ballard, Kymm; Middle School Intramurals in Promoting Lifelong Active Living. (2007)

Bolnick, Deborah A and Fullwiley, Duana and Duster, Troy and Cooper, Richard S and Fujimura, Joan H and Kahn, Jonathan and Kaufman, Jay S and Marks, Jonathan and Morning, Ann and Nelson, Alondra and others; The science and business of genetic ancestry testingSCIENCE-NEW YORK THEN WASHINGTON-318-5849. 399 (2007) American Association for the Advancement of Science

Reardon, Jenny; Democratic mis-haps: the problem of democratization in a time of biopoliticsBioSocieties2-2. 239–256 (2007) Springer

 

2006

Hinrichs, Angela S and Karolchik, Donna and Baertsch, Robert and Barber, Galt P and Bejerano, Gill and Clawson, Hiram and Diekhans, Mark and Furey, Terrence S and Harte, Rachel A and Hsu, Fan and others; The UCSC genome browser database: update 2006Nucleic acids research34-suppl\_1. D590–D598 (2006) Oxford University Press

Pedersen, Jakob Skou and Bejerano, Gill and Siepel, Adam and Rosenbloom, Kate and Lindblad-Toh, Kerstin and Lander, Eric S and Kent, Jim and Miller, Webb and Haussler, David; Identification and classification of conserved RNA secondary structures in the human genomePLoS computational biology2-4. e33 (2006) Public Library of Science

Hsu, Fan and Kent, W James and Clawson, Hiram and Kuhn, Robert M and Diekhans, Mark and Haussler, David; The UCSC known genesBioinformatics22-9. 1036–1046 (2006) Oxford University Press

Bejerano, Gill and Lowe, Craig B and Ahituv, Nadav and King, Bryan and Siepel, Adam and Salama, Sofie R and Rubin, Edward M and Kent, W James and Haussler, David; A distal enhancer and an ultraconserved exon are derived from a novel retroposonNature441-7089. 87 (2006) Nature Publishing Group

Kuhn, Robert M and Karolchik, Donna and Zweig, Ann S and Trumbower, Heather and Thomas, Daryl J and Thakkapallayil, Archana and Sugnet, Charles W and Stanke, Mario and Smith, Kayla E and Siepel, A and others; The UCSC genome browser database: update 2007Nucleic acids research35-suppl\_1. D668–D673 (2006) Oxford University Press

Pollard, Katherine S and Salama, Sofie R and King, Bryan and Kern, Andrew D and Dreszer, Tim and Katzman, Sol and Siepel, Adam and Pedersen, Jakob S and Bejerano, Gill and Baertsch, Robert and others; Forces shaping the fastest evolving regions in the human genomePLoS genetics2-10. e168 (2006) Public Library of Science

Ma, Jian and Zhang, Louxin and Suh, Bernard B and Raney, Brian J and Burhans, Richard C and Kent, W James and Blanchette, Mathieu and Haussler, David and Miller, Webb; Reconstructing contiguous regions of an ancestral genomeGenome research16-12. 1557–1565 (2006) Cold Spring Harbor Lab

Sugnet, Charles W and Srinivasan, Karpagam and Clark, Tyson A and O’Brien, Georgeann and Cline, Melissa S and Wang, Hui and Williams, Alan and Kulp, David and Blume, John E and Haussler, David and others; Unusual intron conservation near tissue-regulated exons found by splicing microarraysPLoS computational biology2-1. e4 (2006) Public Library of Science

Siepel, Adam and Pollard, Katherine S and Haussler, David; New methods for detecting lineage-specific selectionLecture Notes in Computer Science3909. 190–205 (2006) Springer

Thomas, Daryl J and Rosenbloom, Kate R and Clawson, Hiram and Hinrichs, Angie S and Trumbower, Heather and Raney, Brian J and Karolchik, Donna and Barber, Galt P and Harte, Rachel A and Hillman-Jackson, Jennifer and others; The ENCODE project at UC santa cruzNucleic acids research35-suppl\_1. D663–D667 (2006) Oxford University Press

Thomas, Daryl J and Trumbower, Heather and Kern, Andrew D and Rhead, Brooke L and Kuhn, Robert M and Haussler, David and Kent, W James; Variation resources at UC Santa CruzNucleic acids research35-suppl\_1. D716–D720 (2006) Oxford University Press

Wu, Jing and Haussler, David; Coding exon detection using comparative sequencesJournal of Computational Biology13-6. 1148–1164 (2006) Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA

Schattner, Peter and Diekhans, Mark; Regions of extreme synonymous codon selection in mammalian genesNucleic acids research34-6. 1700–1710 (2006) Oxford University Press

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

Smith, David I and Zhu, Yu and McAvoy, Sarah and Kuhn, Robert; Common fragile sites, extremely large genes, neural development and cancerCancer letters232-1. 48–57 (2006) Elsevier

Brian Greenwood, P and Kanters, Michael A and Casper, Jonathan M; Sport fan team identification formation in mid-level professional sportEuropean Sport Management Quarterly6-3. 253–265 (2006) Taylor \& Francis

Casper, Jonathan; You Can’t be Serious, that Ball was IN: An Investigation of Junior Tennis Cheating BehaviorThe qualitative report11-1. 20–36 (2006)

Casper, Jonathan D; Eminent Domain: Property Rights vs. Redevelopment. (2006)

Kay, Kathleen M and Whittall, Justen B and Hodges, Scott A; A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effectsBMC Evolutionary Biology6-1. 36 (2006) BioMed Central

Kay, Kathleen M; Reproductive isolation between two closely related hummingbird-pollinated neotropical gingersEvolution60-3. 538–552 (2006) BioOne

Kay, Kathleen M and Voelckel, Claudia and Yang, Ji Y and Hufford, Kristina M and Kaska, Debora D and Hodges, Scott A; Floral characters and species diversificationEcology and evolution of flowers. 311–25 (2006) Oxford Univ. Press Oxford

 

2005

Siepel, Adam and Bejerano, Gill and Pedersen, Jakob S and Hinrichs, Angie S and Hou, Minmei and Rosenbloom, Kate and Clawson, Hiram and Spieth, John and Hillier, LaDeana W and Richards, Stephen and others; Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomesGenome research15-8. 1034–1050 (2005) Cold Spring Harbor Lab

 

Karchin, Rachel and Diekhans, Mark and Kelly, Libusha and Thomas, Daryl J and Pieper, Ursula and Eswar, Narayanan and Haussler, David and Sali, Andrej; LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sourcesBioinformatics21-12. 2814–2820 (2005) Oxford University Press

Siepel, Adam and Haussler, David; Phylogenetic hidden Markov models. 325–351 (2005) Springer

Kent, WJ and Hsu, Fan and Karolchik, Donna and Kuhn, Robert M and Clawson, Hiram and Trumbower, Heather and Haussler, David; Exploring relationships and mining data with the UCSC Gene SorterGenome research15-5. 737–741 (2005) Cold Spring Harbor Lab

Bejerano, Gill and Siepel, Adam C and Kent, W James and Haussler, David; Computational screening of conserved genomic DNA in search of functional noncoding elementsNature Methods2-7. 535–545 (2005) Nature Publishing Group

Hsu, Fan and Pringle, Tom H and Kuhn, Robert M and Karolchik, Donna and Diekhans, Mark and Haussler, David and Kent, W James; The UCSC proteome browserNucleic acids research33-suppl\_1. D454–D458 (2005) Oxford University Press

Lucena, Brian and Haussler, David; Counterexample to a claim about the reconstruction of ancestral character statesSystematic biology54-4. 693–695 (2005) Society of Systematic Zoology

Forsberg, E Camilla and Prohaska, Susan S and Katzman, Sol and Heffner, Garrett C and Stuart, Josh M and Weissman, Irving L; Differential expression of novel potential regulators in hematopoietic stem cellsPLoS genetics1-3. e28 (2005) Public Library of Science

Di Bias, A and Dahle, David M and Diekhans, Mark and Grate, Leslie and Hirschberg, Jeffrey and Karplus, Kevin and Keller, Hansj{\”o}rg and Kendrick, Mark and Mesa-Martinez, Francisco J and Pease, David and others; The UCSC Kestrel parallel processorIEEE Transactions on Parallel and Distributed Systems16-1. 80–92 (2005) IEEE

Kay, Kathleen M and Reeves, Patrick A and Olmstead, Richard G and Schemske, Douglas W; Rapid speciation and the evolution of hummingbird pollination in neotropical Costus subgenus Costus (Costaceae): evidence from nrDNA ITS and ETS sequencesAmerican Journal of Botany92-11. 1899–1910 (2005) Botanical Soc America

2005

Siepel, Adam and Bejerano, Gill and Pedersen, Jakob S and Hinrichs, Angie S and Hou, Minmei and Rosenbloom, Kate and Clawson, Hiram and Spieth, John and Hillier, LaDeana W and Richards, Stephen and others; Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomesGenome research15-8. 1034–1050 (2005) Cold Spring Harbor Lab

 

Karchin, Rachel and Diekhans, Mark and Kelly, Libusha and Thomas, Daryl J and Pieper, Ursula and Eswar, Narayanan and Haussler, David and Sali, Andrej; LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sourcesBioinformatics21-12. 2814–2820 (2005) Oxford University Press

Siepel, Adam and Haussler, David; Phylogenetic hidden Markov models. 325–351 (2005) Springer

Kent, WJ and Hsu, Fan and Karolchik, Donna and Kuhn, Robert M and Clawson, Hiram and Trumbower, Heather and Haussler, David; Exploring relationships and mining data with the UCSC Gene SorterGenome research15-5. 737–741 (2005) Cold Spring Harbor Lab

Bejerano, Gill and Siepel, Adam C and Kent, W James and Haussler, David; Computational screening of conserved genomic DNA in search of functional noncoding elementsNature Methods2-7. 535–545 (2005) Nature Publishing Group

Hsu, Fan and Pringle, Tom H and Kuhn, Robert M and Karolchik, Donna and Diekhans, Mark and Haussler, David and Kent, W James; The UCSC proteome browserNucleic acids research33-suppl\_1. D454–D458 (2005) Oxford University Press

Lucena, Brian and Haussler, David; Counterexample to a claim about the reconstruction of ancestral character statesSystematic biology54-4. 693–695 (2005) Society of Systematic Zoology

Forsberg, E Camilla and Prohaska, Susan S and Katzman, Sol and Heffner, Garrett C and Stuart, Josh M and Weissman, Irving L; Differential expression of novel potential regulators in hematopoietic stem cellsPLoS genetics1-3. e28 (2005) Public Library of Science

Di Bias, A and Dahle, David M and Diekhans, Mark and Grate, Leslie and Hirschberg, Jeffrey and Karplus, Kevin and Keller, Hansj{\”o}rg and Kendrick, Mark and Mesa-Martinez, Francisco J and Pease, David and others; The UCSC Kestrel parallel processorIEEE Transactions on Parallel and Distributed Systems16-1. 80–92 (2005) IEEE

Kay, Kathleen M and Reeves, Patrick A and Olmstead, Richard G and Schemske, Douglas W; Rapid speciation and the evolution of hummingbird pollination in neotropical Costus subgenus Costus (Costaceae): evidence from nrDNA ITS and ETS sequencesAmerican Journal of Botany92-11. 1899–1910 (2005) Botanical Soc America

2004

Hillier, LaDeana W and Miller, Webb and Birney, Ewan and Warren, Wesley and Hardison, Ross C and Ponting, Chris P and Bork, Peer and Burt, David W and Groenen, Martien AM and Delany, Mary E and others; Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolutionNature432-7018. 695–716 (2004) Nature Publishing Group

 

Gibbs, Richard A and Weinstock, George M and Metzker, Michael L and Muzny, Donna M and Sodergren, Erica J and Scherer, Steven and Scott, Graham and Steffen, David and Worley, Kim C and Burch, Paula E and others; Genome sequence of the Brown Norway rat yields insights into mammalian evolutionNature428-6982. 493–521 (2004) Nature Publishing Group

Bejerano, Gill and Pheasant, Michael and Makunin, Igor and Stephen, Stuart and Kent, W James and Mattick, John S and Haussler, David; Ultraconserved elements in the human genomeScience304-5675. 1321–1325 (2004) American Association for the Advancement of Science

Karolchik, Donna and Hinrichs, Angela S and Furey, Terrence S and Roskin, Krishna M and Sugnet, Charles W and Haussler, David and Kent, W James; The UCSC Table Browser data retrieval toolNucleic acids research32-suppl\_1. D493–D496 (2004) Oxford University Press

Blanchette, Mathieu and Kent, W James and Riemer, Cathy and Elnitski, Laura and Smit, Arian FA and Roskin, Krishna M and Baertsch, Robert and Rosenbloom, Kate and Clawson, Hiram and Green, Eric D and others; Aligning multiple genomic sequences with the threaded blockset alignerGenome research14-4. 708–715 (2004) Cold Spring Harbor Lab

Gerhard, Daniela S and Wagner, Lukas and Feingold, Elise A and Shenmen, Carolyn M and Grouse, Lynette H and Schuler, Greg and Klein, Steven L and Old, Susan and Rasooly, Rebekah and Good, Peter and others; The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).Genome research14-10B. 2121–2127 (2004) Cold Spring Harbor Laboratory Press

Jensen-Seaman, Michael I and Furey, Terrence S and Payseur, Bret A and Lu, Yontao and Roskin, Krishna M and Chen, Chin-Fu and Thomas, Michael A and Haussler, David and Jacob, Howard J; Comparative recombination rates in the rat, mouse, and human genomesGenome research14-4. 528–538 (2004) Cold Spring Harbor Lab

Siepel, Adam and Haussler, David; Combining phylogenetic and hidden Markov models in biosequence analysisJournal of Computational Biology11-2-3. 413–428 (2004) Mary Ann Liebert, Inc.

Siepel, Adam and Haussler, David; Phylogenetic estimation of context-dependent substitution rates by maximum likelihoodMolecular biology and evolution21-3. 468–488 (2004) Oxford University Press

Bailey, Jeffrey A and Baertsch, Robert and Kent, W James and Haussler, David and Eichler, Evan E; Hotspots of mammalian chromosomal evolutionGenome biology5-4. R23 (2004) BioMed Central

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

Blanchette, Mathieu and Green, Eric D and Miller, Webb and Haussler, David; Reconstructing large regions of an ancestral mammalian genome in silicoGenome research14-12. 2412–2423 (2004) Cold Spring Harbor Lab

Bejerano, Gill and Haussler, David and Blanchette, Mathieu; Into the heart of darkness: large-scale clustering of human non-coding DNABioinformatics20-suppl\_1. i40–i48 (2004) Oxford University Press

Yang, Shan and Smit, Arian F and Schwartz, Scott and Chiaromonte, Francesca and Roskin, Krishna M and Haussler, David and Miller, Webb and Hardison, Ross C; Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomesGenome research14-4. 517–527 (2004) Cold Spring Harbor Lab

Robertson, Michael P and Igel, Haller and Baertsch, Robert and Haussler, David and Ares Jr, Manuel and Scott, William G; The structure of a rigorously conserved RNA element within the SARS virus genomePLoS biology3-1. e5 (2004) Public Library of Science

Jojic, Vladimir and Jojic, Nebojsa and Meek, Chris and Geiger, Dan and Siepel, Adam and Haussler, David and Heckerman, David; Efficient approximations for learning phylogenetic HMM models from dataBioinformatics20-suppl\_1. i161–i168 (2004) Oxford University Press

Furey, Terrence S and Diekhans, Mark and Lu, Yontao and Graves, Tina A and Oddy, Lachlan and Randall-Maher, Jennifer and Hillier, LaDeana W and Wilson, Richard K and Haussler, David; Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editingGenome research14-10b. 2034–2040 (2004) Cold Spring Harbor Lab

Roskin, Krishna M and Diekhans, Mark and Haussler, David; Score functions for determining regional conservation in two-species local alignmentsJournal of Computational Biology11-2-3. 395–411 (2004) Mary Ann Liebert, Inc.

Br{\”a}ndlein, Stephanie and Pohle, Tina and Vollmers, Christopher and Wozniak, Ewa and Ruoff, Nele and M{\”u}ller-Hermelink, Hans Konrad and Vollmers, H Peter; CFR-1 receptor as target for tumor-specific apoptosis induced by the natural human monoclonal antibody PAM-1Oncology reports11-4. 777–784 (2004) Spandidos Publications

Casper, Jonathan; Explaining adult tennis participants’ participation frequency and purchase intention with the sport commitment model.. (2004)

Casper, Jonathan and Finley, Peter S and others; Teams web sites as aids in the recruiting process: NCAA Tennis coaches attitudes toward their use.The Sport Journal7-1. (2004) United States Sports Academy

Reardon, Jenny; Decoding race and human difference in a genomic ageDifferences: A journal of feminist cultural studies15-3. 38–65 (2004) Duke University Press

Kay, Kathleen M and Schemske, Douglas W; Geographic patterns in plant-pollinator mutualistic networks: commentEcology. 875–878 (2004) JSTOR

2003

Karolchik, Donna and Baertsch, Robert and Diekhans, Mark and Furey, Terrence S and Hinrichs, Angie and Lu, YT and Roskin, Krishna M and Schwartz, Matthias and Sugnet, Charles W and Thomas, Daryl J and others; The UCSC genome browser databaseNucleic acids research31-1. 51–54 (2003) Oxford University Press

Schwartz, Scott and Kent, W James and Smit, Arian and Zhang, Zheng and Baertsch, Robert and Hardison, Ross C and Haussler, David and Miller, Webb; Human–mouse alignments with BLASTZGenome research13-1. 103–107 (2003) Cold Spring Harbor Lab

Kent, W James and Baertsch, Robert and Hinrichs, Angie and Miller, Webb and Haussler, David; Evolution’s cauldron: duplication, deletion, and rearrangement in the mouse and human genomesProceedings of the National Academy of Sciences100-20. 11484–11489 (2003) National Acad Sciences

Margulies, Elliott H and Blanchette, Mathieu and Haussler, David and Green, Eric D and NISC Comparative Sequencing Program and others; Identification and characterization of multi-species conserved sequencesGenome research13-12. 2507–2518 (2003) Cold Spring Harbor Lab

Hardison, Ross C and Roskin, Krishna M and Yang, Shan and Diekhans, Mark and Kent, W James and Weber, Ryan and Elnitski, Laura and Li, Jia and O’Connor, Michael and Kolbe, Diana and others; Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolutionGenome research13-1. 13–26 (2003) Cold Spring Harbor Lab

Wang, Hui and Hubbell, Earl and Hu, Jing-shan and Mei, Gangwu and Cline, Melissa and Lu, Gang and Clark, Tyson and Siani-Rose, Michael A and Ares, Manuel and Kulp, David C and others; Gene structure-based splice variant deconvolution using a microarry platformBioinformatics19-suppl\_1. i315–i322 (2003) Oxford University Press

Winters-Hilt, Stephen and Vercoutere, Wenonah and DeGuzman, Veronica S and Deamer, David and Akeson, Mark and Haussler, David; Highly accurate classification of Watson-Crick basepairs on termini of single DNA moleculesBiophysical Journal84-2. 967–976 (2003) Elsevier

Furey, Terrence S and Haussler, David; Integration of the cytogenetic map with the draft human genome sequenceHuman Molecular Genetics12-9. 1037–1044 (2003) Oxford University Press

Owen, Art B and Stuart, Josh and Mach, Kathy and Villeneuve, Anne and Kim, Stuart; A Gene Recommender for C. elegans.(2003)

Picone, Joseph and Johnson, Wesley and Dyess, Matthew and Stuart, Josh and Trobough, Chris and Parker, Brock and Tate, Kevin and Riddell, Shaw and Anderson, Matthew; KARMA: A Mobile Acquisition Unit. (2003)

Karplus, Kevin and Karchin, Rachel and Draper, Jenny and Casper, Jonathan and Mandel-Gutfreund, Yael and Diekhans, Mark and Hughey, Richard; Combining local-structure, fold-recognition, and new fold methods for protein structure predictionProteins: Structure, Function, and Bioinformatics53-S6. 491–496 (2003) Wiley Online Library

Diekhans, Mark and Grate, Leslie and Barrett, Christian and Brown, Michael and Casper, Jonathan and Cline, Melissa and Figel, Terry and Karchin, Rachel and Sj{\”o}lander, Kimmen and Tarnas, Christopher; Sequence Alignment and Modeling Software System. (2003)

Kay, Kathleen M and Schemske, Douglas W; Pollinator assemblages and visitation rates for 11 species of Neotropical Costus (Costaceae)Biotropica35-2. 198–207 (2003) BioOne

Beauregard, Mary A and Deck, Dinah S and Kay, Kathleen Coughlin and Haynes, Jodi and Inman, Ruth and Perry, Martha and Richardson, Sharon and Rose, Beverly A and Silver, Kimberly N and White, Cathy and others; Improving our image a nurse at a timeJournal of nursing administration33-10. 510–511 (2003) LWW

2002

Kent, W James and Sugnet, Charles W and Furey, Terrence S and Roskin, Krishna M and Pringle, Tom H and Zahler, Alan M and Haussler, David; The human genome browser at UCSCGenome research12-6. 996–1006 (2002) Cold Spring Harbor Lab

Karchin, Rachel and Karplus, Kevin and Haussler, David; Classifying G-protein coupled receptors with support vector machinesBioinformatics18-1. 147–159 (2002) Oxford University Press

Asif T, Chinwalla and Lisa L, Cook and Kimberly D, Delehaunty and Ginger A, Fewell and Lucinda A, Fulton and Robert S, Fulton and Tina A, Graves and LaDeana W, Hillier and Elaine R, Mardis and Tracie L, Miner and others; Initial sequencing and comparative analysis of the mouse genomeNature420-6915. (2002) Joint Genome Institute (JGI)

Cline, Melissa S and Karplus, Kevin and Lathrop, Richard H and Smith, Temple F and Rogers, Robert G and Haussler, David; Information-theoretic dissection of pairwise contact potentialsProteins: Structure, Function, and Bioinformatics49-1. 7–14 (2002) Wiley Online Library

Roskin KM, Diekhans M, Kent WJ, Haussler D. Score functions for assessing conservation in locally aligned regions of DNA from two species. UCSC Tech Report UCSC-CRL-02-30 July 13, 2002.

2001

McPherson, John D and Marra, Marco and Hillier, LaDeana and Waterston, Robert H and Chinwalla, Asif and Wallis, John and Sekhon, Mandeep and Wylie, Kristine and Mardis, Elaine R and Wilson, Richard K and others; A physical map of the human genomeNature409-6822. 934–941 (2001) Nature Publishing Group

Vercoutere, Wenonah and Winters-Hilt, Stephen and Olsen, Hugh and Deamer, David and Haussler, David and Akeson, Mark; Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channelNature biotechnology19-3. 248 (2001) Nature Publishing Group

Kent, W James and Haussler, David; Assembly of the working draft of the human genome with GigAssemblerGenome Research11-9. 1541–1548 (2001) Cold Spring Harbor Lab

Marra, Marco and Hillier, LaDeana and Waterston, Robert H and Chinwalla, Asif and Wallis, John and Sekhon, Mandeep and Wylie, Kristine and Mardis, Elaine R and Wilson, Richard K and Fulton, Robert and others; A physical map of the human genomeNature409. 934–941 (2001)

Karplus, Kevin and Karchin, Rachel and Barrett, Christian and Tu, Spencer and Cline, Melissa and Diekhans, Mark and Grate, Leslie and Casper, Jonathan and Hughey, Richard; What is the value added by human intervention in protein structure prediction?Proteins: Structure, Function, and Bioinformatics45-S5. 86–91 (2001) Wiley Online Library

Reardon, Jenny; The human genome diversity project: a case study in coproductionSocial studies of science31-3. 357–388 (2001) Sage Publications London

2000

Jaakkola, Tommi and Haussler, David; Exploiting generative models in discriminative classifiers. 487–493 (1999)

Jaakkola, Tommi S and Diekhans, Mark and Haussler, David; Using the Fisher kernel method to detect remote protein homologies.99. 149–158 (1999)

Jaakkola, Tommi S and Haussler, David; Probabilistic kernel regression models.. (1999)

SPINGOLA, MARC and GRATE, LESLIE and HAUSSLER, DAVID and ARES, MANUEL; Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiaeRna5-2. 221–234 (1999) Cambridge University Press

Brown, Michael PS and Grundy, William Noble and Lin, David and Cristianini, Nello and Sugnet, Charles and Ares, Manuel and Haussler, David; Support vector machine classification of microarray gene expression dataUniversity of California, Santa Cruz, Technical Report UCSC-CRL-99-09. (1999)

Opper, Manfred and Haussler, David; Worst case prediction over sequences under log loss. 81–90 (1999) Springer

Haussler, David; Technical Report UCSC-CRL-99-10Computer Science Department, UC Santa Cruz. (1999)

Karplus, Kevin and Barrett, Christian and Cline, Melissa and Diekhans, Mark and Grate, Leslie and Hughey, Richard; Predicting protein structure using only sequence informationProteins: Structure, Function, and Bioinformatics37-S3. 121–125 (1999) Wiley Online Library

Kuhn, D Robert and Shibley, Nofa J and Austin, William M and Yochum, Terry R; Radiographic evaluation of weight-bearing orthotics and their effect on flexible pes planusJournal of manipulative and physiological therapeutics22-4. 221–226 (1999) Elsevier

Roskin, Krish M and Casper, Jonathan B; From chaos to cryptographyDisposn{\’\i}vel em:< http://www. gaianxaos. com/pdf/unsorted/chaos\_and\_cryptography. pdf>. Acesso em10. (1999)

 

1999

Brown, Michael PS and Grundy, William Noble and Lin, David and Cristianini, Nello and Sugnet, Charles Walsh and Furey, Terrence S and Ares, Manuel and Haussler, David; Knowledge-based analysis of microarray gene expression data by using support vector machinesProceedings of the National Academy of Sciences97-1. 262–267 (2000) National Acad Sciences

Furey, Terrence S and Cristianini, Nello and Duffy, Nigel and Bednarski, David W and Schummer, Michel and Haussler, David; Support vector machine classification and validation of cancer tissue samples using microarray expression dataBioinformatics16-10. 906–914 (2000) Oxford University Press

Jaakkola, Tommi and Diekhans, Mark and Haussler, David; A discriminative framework for detecting remote protein homologiesJournal of computational biology7-1-2. 95–114 (2000) Mary Ann Liebert, Inc.

Reese, Martin G and Kulp, David and Tammana, Hari and Haussler, David; Genie—gene finding in Drosophila melanogasterGenome Research10-4. 529–538 (2000) Cold Spring Harbor Lab

Grate, Leslie and Diekhans, Mark and Dahle, David and Hughey, Richard; Sequence analysis with the Kestrel SIMD parallel processor2001. 263–274 (2000)

Mandelberg, Joshua H and Kuhn, Robert E and Kohn, Michael A; Epidemiologic analysis of an urban, public emergency department’s frequent usersAcademic emergency medicine7-6. 637–646 (2000) Wiley Online Library

1998

Park, Jong and Karplus, Kevin and Barrett, Christian and Hughey, Richard and Haussler, David and Hubbard, Tim and Chothia, Cyrus; Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methodsJournal of molecular biology284-4. 1201–1210 (1998) Elsevier

Haussler, David and Kivinen, Jyrki and Warmuth, Manfred K; Sequential prediction of individual sequences under general loss functionsIEEE Transactions on Information Theory44-5. 1906–1925 (1998) IEEE

Haussler, David; Computational genefindingTrends in biotechnology16. 12–15 (1998) Elsevier

Casper, Jonathan D; Remembering Herbert JacobLaw \& Soc. Inquiry23. 745 (1998) HeinOnline

CASPER, JONATHAN D; Crossing Boundaries in Sociolegal ResearchCrossing boundaries: traditions and transformations in law and society research4. 81 (1998) Northwestern University Press

Abram, Karen and Gilsinan, James and Applebaum, Paul S and Golding, Jonathan M and Bagby, Michael and Golding, Stephen L and Bersoff, Donald N and Goldner, Jesse and Borgida, Eugene and Goodman, Gail S and others; Reviewers for Volume 22Law and Human Behavior22-6. (1998) Springer

Treseder, Kathleen Kay; Plant-soil interactions across a fertility gradient in Hawaii: nutrient acquisition strategies and effects of genetic variation on ecosystem function. (1998) Stanford University

1997

Reese, Martin G and Eeckman, Frank H and Kulp, David and Haussler, David; Improved splice site detection in GenieJournal of computational biology4-3. 311–323 (1997)

Cesa-Bianchi, Nicolo and Freund, Yoav and Haussler, David and Helmbold, David P and Schapire, Robert E and Warmuth, Manfred K; How to use expert adviceJournal of the ACM (JACM)44-3. 427–485 (1997) ACM

Alon, Noga and Ben-David, Shai and Cesa-Bianchi, Nicolo and Haussler, David; Scale-sensitive dimensions, uniform convergence, and learnabilityJournal of the ACM (JACM)44-4. 615–631 (1997) ACM

Karplus, Kevin and Sj{\”o}lander, Kimmen and Barrett, Christian and Cline, Melissa and Haussler, David and Hughey, Richard and Holm, Liisa and Sander, Chris; Predicting protein structure using hidden Markov modelsProteins Structure Function and Genetics29-s 1. 134–139 (1997)

Haussler, David and Opper, Manfred and others; Mutual information, metric entropy and cumulative relative entropy riskThe Annals of Statistics25-6. 2451–2492 (1997) Institute of Mathematical Statistics

Haussler, David; A general minimax result for relative entropyIEEE Transactions on Information Theory43-4. 1276–1280 (1997) IEEE

Kulp, David and Haussler, David and Reese, Martin G and Eeckman, Frank H; Integrating database homology in a probabilistic gene structure model2. 232–244 (1997)

Harrison, Mark and Brighton, Allan and Clarke, De and Crowley, Charles and Diekhans, Mark and Greenberg, Saul and Hill, D Richard and Howlett, George A and Lam, Ioi and Libes, Don and others; Tcl/Tk Tools. (1997) O’Reilly \& Associates, Inc.

Casper, Jonathan D; Herbert JacobPS: Political Science \& Politics30-1. 88–89 (1997) Cambridge University Press

 

1996

Haussler, David Kulp David and Eeckman, Martin G Reese Frank H; A generalized hidden Markov model for the recognition of human genes in DNA. 134–142 (1996)

Sj{\”o}lander, Kimmen and Karplus, Kevin and Brown, Michael and Hughey, Richard and Krogh, Anders and Mian, I Saira and Haussler, David; Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homologyBioinformatics12-4. 327–345 (1996) Oxford University Press

Fayyad, Usama and Haussler, David and Stolorz, Paul; Mining scientific dataCommunications of the ACM39-11. 51–57 (1996) ACM

Haussler, David and Kearns, Michael and Seung, H Sebastian and Tishby, Naftali; Rigorous learning curve bounds from statistical mechanicsMachine Learning25-2-3. 195–236 (1996) Springer

Fayyad, Usama M and Haussler, David and Stolorz, Paul E; KDD for Science Data Analysis: Issues and Examples.. 50–56 (1996)

Haussler, David; Probably Approximately Correct learning and decision-theoretic generalizationsMathematical perspectives on neural networks. Hillsdale, NJ: Lawrence Erlbaum Publishers. (1996)

Wagner, Doris and Fairchild, Craig D and Kuhn, Robert M and Quail, Peter H; Chromophore-bearing NH2-terminal domains of phytochromes A and B determine their photosensory specificity and differential light labilityProceedings of the National Academy of Sciences93-9. 4011–4015 (1996) National Acad Sciences

Diamond, Shari Seidman and Casper, Jonathan D and Heiert, Cami L and Marshall, Anna-Maria; Juror reactions to attorneys at trialThe Journal of Criminal Law and Criminology (1973-)87-1. 17–47 (1996) JSTOR

1995

Haussler, David; Sphere packing numbers for subsets of the Boolean n-cube with bounded Vapnik-Chervonenkis dimensionJournal of Combinatorial Theory, Series A69-2. 217–232 (1995) Elsevier

Bendavid, Shai and Cesabianchi, Nicolo and Haussler, David and Long, Philip M; Characterizations of Learnability for Classes of $\{$0,…, n)-Valued FunctionsJournal of Computer and System Sciences50-1. 74–86 (1995) Elsevier

Haussler, David and Long, Philip M; A generalization of Sauer’s lemmaJournal of Combinatorial Theory, Series A71-2. 219–240 (1995) Elsevier

Opper, Manfred and Haussler, David; Bounds for predictive errors in the statistical mechanics of supervised learningPhysical Review Letters75-20. 3772 (1995) APS

Goldstein, Susan T and Watkins, G Todd and Kuhn, Robert M; Microhabitats of salt marsh foraminifera: St. Catherines island, Georgia, USAMarine Micropaleontology26-1-4. 17–29 (1995) Elsevier

Baume, Peter and Kay, Kathleen; Working solution: Report of the strategic review of the Commonwealth Disability Services Program. (1995) Australian Government Pub. Service

 

1994

Krogh, Anders and Mian, I Saira and Haussler, David; A hidden Markov model that finds genes in E. coli DNANucleic Acids Research22-22. 4768–4778 (1994) Oxford University Press

Sakakibara, Yasubumi and Brown, Michael and Hughey, Richard and Mian, I Saira and Sj{\”o}lander, Kimmen and Underwood, Rebecca C and Haussler, David; Stochastic context-free grammers for tRNA modelingNucleic acids research22-23. 5112–5120 (1994) Oxford University Press

Haussler, David and Kearns, Michael and Schapire, Robert E; Bounds on the sample complexity of Bayesian learning using information theory and the VC dimensionMachine learning14-1. 83–113 (1994) Springer

Haussler, David and Littlestone, Nick and Warmuth, Manfred K; Predicting $\{$0, 1$\}$-functions on randomly drawn pointsInformation and Computation115-2. 248–292 (1994) Elsevier

Grate, Leslie and Herbster, Mark and Hughey, Richard and Haussler, David and Mian, I Saira and Noller, Harry; RNA modeling using Gibbs sampling and stochastic context free grammars.2. 138–146 (1994)

Stormo, Gary D and Haussler, David; Optimally parsing a sequence into different classes based on multiple types of evidence.2. 369–375 (1994)

Diamond, Shari Seidman and Casper, Jonathan D; Empirical evidence and the death penalty: Past and futureJournal of Social Issues50-2. 177–197 (1994) Wiley Online Library

Adams, Kenneth and Adler, Jeffrey and Ageton, Suzanne and Agnew, Robert and Akers, Ronald and Albonetti, Celesta and Allen, Harry and Alpert, Geoffrey and Anderson, Patrick and Andrews, Don and others; Justice quarterly 1994 reviewersJustice Quarterly11-4. (1994) Taylor \& Francis

Abel, Richard and Albonetti, Celesta and Alfieri, Anthony and Alschuler, Albert and Aleson, James and Banks, Taunya L and Barak, Gregg and Barkai, John and Barreto, Emilcar and Baumgartner, Mary P and others; the Trustees, and the Editorial Advisory Board, as well as the following individuals who reviewed manuscripts for Volume 28.Law \& Society Review28-5. (1994) HeinOnline

 

1993

Brown, Michael and Hughey, Richard and Krogh, Anders and Mian, I Saira and Sj{\”o}lander, Kimmen and Haussler, David; Using Dirichlet mixture priors to derive hidden Markov models for protein families.1. 47–55 (1993)

Haussler, David and Warmuth, Manfred; The probably approximately correct (PAC) and other learning modelsKLUWER INTERNATIONAL SERIES IN ENGINEERING AND COMPUTER SCIENCE. 291–291 (1993) Springer

Casper, Jonathan D and Benedict, Kennette M; The influence of outcome information and attitudes on juror decision making in search and seizure casesInside the juror. 65–83 (1993) Cambridge University Press Cambridge,, UK

Casper, Jonathan D; Restructuring the traditional civil jury: The effects of changes in composition and proceduresVerdict: Assessing the civil jury system. 414–459 (1993)

Casper, Jonathan D and Diamond, Shari Seidman; Estimating damages and predicting violence: The influence of experts in the courtroom. (1993)

Ambuel, Bruce and Casper, Jonathan and Clark, Charles and Dvoskin, Joel and Ewing, Charles P and Faigman, David and FoUingstad, Diane and Fulero, Solomon and Greer, Alexander and Griffin, Patty and others; Reviewers for volume 17Law and Human Behavior17-6. (1993) Springer

O’Neil, Kathleen Kay; An evaluation of student retention efforts at a small collegeNASPA Journal31-1. 36–40 (1993) Routledge

 

1992

Haussler, David; Decision theoretic generalizations of the PAC model for neural net and other learning applicationsInformation and computation100-1. 78–150 (1992) Elsevier

Freund, Yoav and Haussler, David; Unsupervised learning of distributions on binary vectors using two layer networks. 912–919 (1992)

Haussler, David and Barron, Andrew; How well do Bayes methods work for on-line prediction of f+ 1; 1g values. (1992)

Haussler, David and Kearns, Michael and Opper, Manfred and Schapire, Robert; Estimating average-case learning curves using Bayesian, statistical physics and VC dimension methods. 855–862 (1992)

Diamond, Shari and Casper, Jonathan; Blindfolding the Jury to Verdict Consequences, 26L\& Soc’y Rev513. 553 (1992)

Abel, Richard and Adler, Patricia and Albonetti, Celesta and Atleson, James B and Banks, Taunya L and Barkai, John and Barnett, Laurence and Baum, Lawrence and Baumgartner, Mary P and Beattie, John and others; 0 1993 by The Law and Society Association. All rights reserved.Law \& Society Review27-4. (1992) HeinOnline

Burstein, James Acker Paul and Buzawa, Patricia Adler Eva and Cahn, Celesta Albonetti Naomi and Caiger, Francis Allen Andrew and Call, Albert Alschuler Jack and Canan, Anthony Amsterdam Penelope and Cannell, Andrew Arno Fenella and Carp, Burton Atkins Robert and Carroll, James Atleson John and Carson, Dianne Avery William and others; The Law \& Society Review would like to thank the Officers, Trustees, and Editorial Board, as well as the following individu-als who reviewed manuscripts for Volume 26.Law \& Society Review26-4. (1992) JSTOR

Schutte, Kathleen Kay; Personality and social support: A proposed causal model.. (1992)

1991

Haussler, David and Kearns, Michael and Littlestone, Nick and Warmuth, Manfred K; Equivalence of models for polynomial learnabilityInformation and Computation95-2. 129–161 (1991) Elsevier

Opper, Manfred and Haussler, David; Generalization performance of Bayes optimal classification algorithm for learning a perceptronPhysical Review Letters66-20. 2677 (1991) APS

Opper, Manfred and Haussler, David; Calculation of the learning curve of Bayes optimal classification algorithm for learning a perceptron with noise5-07. 75–87 (1991)

Sabatino, Frank and Masoro, Edward J and McMahan, C Alex and Kuhn, Robert W; Assessment of the role of the glucocorticoid system in aging processes and in the action of food restrictionJournal of gerontology46-5. B171–B179 (1991) The Gerontological Society of America

Mann, Jonathan M and Kay, Kathleen; Confronting the pandemic: the world health organization’s global programme on AIDS, 1986–1989Aids5-2. 221–229 (1991) LWW

 

1990

Bagallo, Giulia and Haussler, David; Boolean feature discovery in empirical learningMachine learning5-1. 71–99 (1990) Springer

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 and 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

Mann, Jonathan and Dam, Marjorie and Kay, Kathleen; Global Coordination of National Public Health StrategiesThe Journal of Law, Medicine \& Ethics18-1-2. 20–28 (1990) Wiley Online Library

Stromer, Kathleen Kay; GAO report: A long way from equality (promotion for men and women in the US military)Armed Forces Journal International127-8. 56 (1990)

Marcus, Ruthanne and Kay, Kathleen and Mann, Jonathan M; Transmisi{\’o}n del virus de la inmunodeficiencia humana (VIH) en establecimientos de atenci{\’o}n de salud de todo el mundo. (1990)

1989

Baum, Eric B and Haussler, David; What size net gives valid generalization?. 81–90 (1989)

Blumer, Anselm and Ehrenfeucht, Andrzej and Haussler, David and Warmuth, Manfred K; Learnability and the Vapnik-Chervonenkis dimensionJournal of the ACM (JACM)36-4. 929–965 (1989) ACM

Ehrenfeucht, Andrzej and Haussler, David and Kearns, Michael and Valiant, Leslie; A general lower bound on the number of examples needed for learningInformation and Computation82-3. 247–261 (1989) Elsevier

Haussler, David; Learning conjunctive concepts in structural domainsMachine learning4-1. 7–40 (1989) Springer

Ehrenfeucht, Andrzej and Haussler, David; Learning decision trees from random examplesInformation and Computation82-3. 231–246 (1989) Elsevier

Blumer, Anselm and Ehrenfeucht, Andrzej and Haussler, David; Average sizes of suffix trees and dawgsDiscrete Applied Mathematics24-1-3. 37–45 (1989) Elsevier

Haussler, David; Generalizing the PAC model for neural net and other learning applications. (1989) University of California, Santa Cruz, Computer Research Laboratory

Pagallo, Giulia and Haussler, David; A Greedy Method for Learning [mu] DNF Functions Under the Uniform Distribution.(1989) University of California, Santa Cruz, Computer Research Laboratory

DALLMAN, MARY F and LEVIN, NANCY and CASCIO, CAREN S and AKANA, SUSAN F and JACOBSON, LAUREN and KUHN, ROBERT W; Pharmacological evidence that the inhibition of diurnal adrenocorticotropin secretion by corticosteroids is mediated via type I corticosterone-preferring receptorsEndocrinology124-6. 2844–2850 (1989) The Endocrine Society

Tyler, Tom R and Casper, Jonathan D and Fisher, Bonnie; Maintaining allegiance toward political authorities: The role of prior attitudes and the use of fair proceduresAmerican Journal of Political Science. 629–652 (1989) JSTOR

Casper, Jonathan D and Benedict, Kennette and Perry, Jo L; Juror Decision Making, Attitudes, and the Hindsight Bias, 13 LAW \& HUMBEHAV291. 300 (1989)

Diamond, Shari Seidman and Casper, Jonathan D and Ostergren, Lynne; Blindfolding the juryLaw and Contemporary Problems52-4. 247–267 (1989) JSTOR

Casper, Jonathan D; Public Opinion and the Supreme Court: Introductory RemarksNw. UL Rev.84. 983 (1989) HeinOnline

Casper, Jonathan D and Tyler, Tom R and Fisher, Bonnie; Maintaining allegiance toward political authoritiesAmerican Journal of Political Science33. 629–625 (1989)

Marcus, Ruthanne and Kay, Kathleen and Mann, Jonathan M; Transmission of human immunodeficiency virus (HIV) in health-care settings worldwide.Bulletin of the World Health Organization67-5. 577 (1989) World Health Organization

O’neil, Kathleen Kay and Gajdostik, Karen Lee; The head nurse’s managerial role.Nursing management20-6. 39–41 (1989) LWW

Kay, Kathleen; AIDS—a global concernMidwifery5-2. 84–95 (1989) Elsevier

Sinsheimer, Robert L. Historical Sketch: The Santa Cruz Workshop. Genomics 5, 954-956 (1989)

Other

Johnson, Wesley and Dyess, Matthew and Stuart, Josh and Trobough, Chris and Parker, Brock and Tate, Kevin and Riddell, Shaw and Anderson, Matthew; Professor Joseph Picone E-mail: picone@ isip. msstate. edu ECE 4542: Senior Design II Department of Electrical and Computer Engineering Mississippi State University.

Stuart, Josh and Koller, Daphne and Friedman, Nir; Graphical Models for Joint Learning, Part II..

Craft, Brian and Swatloski, Teresa and Goldman, Mary and Ellrott, Kyle and Ma, Singer and Wilks, Chris and Stuart, Josh and Haussler, David and Zhu, Jingchun; The New UCSC Cancer Genomics Browser.

Jaakkola, Tommi and Diekhans, Mark and Haussler, David; A discriminative framework for detecting remote protein homologies, 1998Unpublished, available from http://www. cse. ucsc. edu/research/compbio/research. html.

Diekhans, Mark and Lehenbauer, Karl; TclX-Extended Tcl.

ROSKIN, KRISHNA M and DIEKHANS, MARK and KENT, W JAMES and HAUSSLER, DAVID; SCORE FUNCTIONS FOR ASSESSING CONSERVATION IN LOCALLY ALIGNED REGIONS OF DNA FROM TWO SPECIES UCSC TECH REPORT UCSC-CRL-02-30.

Nguyen, Ngan and Diekhans, Mark; Genome 10K Data Submission Guidelines.

Hsu, Fan and Pringle, Tom H and Kuhn, Robert M and Karolchik, Donna and Diekhans, Mark and Haussler, David and Kent, W James; Nucleic acids research Volume: 33 ISSN: 1362-4962 ISO Abbreviation: Nucleic Acids Res. Publication Date: 2005 JanDetail:.

Ableson, A and Akmaev, Viatcheslav R and Anantharaman, Thomas and Andersen, Claus A and Andrade, Miguel A and Ankerst, Mihael and Benson, Gary and Blackwell, Thomas W and Blaschke, Christian and Brass, Andy and others; From: ISMB-99 Proceedings. Copyright{\copyright} 1999, AAAI (www. aaai. org). All rights reserved..

Ezkurdia, Iakes and Juan, David and Rodriguez, Jose Manuel and Frankish, Adam and Diekhans, Mark and Harrow, Jennifer and Vazquez, Jesus and Valencia, Alfonso and Tress, Michael L; 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..

Rosenbloom, Kate and Dreszer, Timothy and Malladi, Venkat and Long, Jeffrey and Sloan, Cricket and Raney, Brian and Cline, Melissa and Karolchik, Donna and Barber, Galt and Clawson, Hiram and others; ENCODE Project at UCSC.

Diamond, Shari Seidman and Casper, Jonathan D; Blindfolding the Jury to Verdict Consequences: Damages, Experts and the Civil Jury’(1992)Law \& Society Review26. 513
AARONSON, David E and ALEXANDER, Sue C and BARONTI, Giancarlo and PITCH, Tamar and BAYER, Ronald and Decriminalization, Heroin and BOLAND, Barbara and BREDA, Jef and VAN HOUTTE, Jean and CASPER, Jonathan D and others; ” Race as a Determinant of Criminal Sentences: A Methodologi-cal Critique and a Case Study,” Gibson, 455.” Rationalist and Normative Approaches to the Sociological Study of Law”(review essay on Donald Black, The Behav-ior of Law, and Roberto Mangabeira Unger, Law in Mod. HeinOnline