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A draft human pangenome reference

A draft human pangenome reference

Abstract Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals (source). These assemblies cover more than 99% of the...

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As a reminder, preprints — many of which cited here are published in bioRxiv — are preliminary reports that have not been peer-reviewed. They should not be regarded as conclusive, guide health-related behavior, or be reported as established information.

2023

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2022

Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, et al. A complete reference genome improves analysis of human genetic variation. Science 376 (2022). doi:10.1126/science.abl3533

Alkan C, et al. Implications of the first complete human genome assembly. Genome Research (2022). doi:10.1101/gr.276723.122

Altemose N, et al. Complete genomic and epigenetic maps of human centromeres. Science 376 (2022). doi:10.1126/science.abl4178

Antonarakis S. Short arms of human acrocentric chromosomes and the completion of the human genome sequence. Genome Research (2022). doi:10.1101/gr.275350.121

Bailey, Andrew D et al. Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling. eLife vol. 11 e76562. 6 Apr. 2022, doi:10.7554/eLife.76562

Baudin PV, Sacksteder RE, Worthington AK, et al. Cloud-controlled microscopy enables Remote Project-based biology education in underserved Latinx communities. Heliyon. 2022;8(11). doi:10.1016/j.heliyon.2022.e11596

Casaletto J, Parsons M, et al. Federated analysis of BRCA1 and BRCA2 variation in a Japanese cohort. Cell Genomics (2022). doi:10.1016/j.xgen.2022.100109

De Maio N, Kalaghatgi P, Turakhia Y, Corbett-Detig R, Minh BQ, Goldman N. Maximum likelihood pandemic-scale phylogenetics. Nature Genetics. 2023. doi:10.1038/s41588-023-01368-0

Formenti G, Rhie A, et al. Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation. Nature Methods (2022). doi:10.1038/s41592-022-01445-y.

Gershman A, et al. Epigenetic patterns in a complete human genome. Science 376 (2022). doi:10.1126/science.abj5089

Goenka, Sneha D et al. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nature biotechnology, 10.1038/s41587-022-01221-5. 28 Mar. 2022, doi:10.1038/s41587-022-01221-5

Gozashti L, Roy SW, Thornlow B, Kramer A, Ares M, Corbett-Detig R. Transposable elements drive intron gain in diverse eukaryotes. Proceedings of the National Academy of Sciences. 2022;119(48). doi:10.1073/pnas.2209766119

Guarracino A, Buonaiuto S, de Lima LG, et al. Recombination between heterologous human acrocentric chromosomes. Nature. 2023;617(7960):335-343. doi:10.1038/s41586-023-05976-y

Hickey G, Monlong J, Ebler J, et al. Pangenome graph construction from genome alignments with minigraph-cactus. Nature Biotechnology. Published online 2023. doi:10.1038/s41587-023-01793-w

Hoyt SJ, et al. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science 376 (2022). doi:10.1126/science.abk3112

Laidre KL, Supple MA, Born EW, et al. Glacial ice supports a distinct and undocumented polar bear subpopulation persisting in late 21st-century sea-ice conditions. Science (2022). doi:10.1126/science.abk2793

Liao W-W, Asri M, Ebler J, et al. A draft human PANGENOME reference. Nature. 2023;617(7960):312-324. doi:10.1038/s41586-023-05896-x

Markello, Charles et al. A complete pedigree-based graph workflow for rare candidate variant analysis. Genome research, 10.1101/gr.276387.121. 28 Apr. 2022, doi:10.1101/gr.276387.121

McBroome J, Turakhia Y, Corbett-Detig R. BTE: a Python module for pandemic-scale mutation-annotated phylogenetic trees. J Open Source Softw (2022). doi:10.21105/joss.04433

McCartney AM, Shafin K, Alonge M, et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nature Methods (2022). doi:10.1038/s41592-022-01440-3

Moon KL, Huson HJ, Morrill K, et al. Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs. Science. 2023;380(6643). doi:10.1126/science.abn5887

Nassar LR, Barber GP, Benet-Pagès A, et al. The UCSC genome browser database: 2023 update. Nucleic Acids Research. 2022. doi:10.1093/nar/gkac1072

Nurk S, Koren S, Rhie A, Rautiainen M, et al. The complete sequence of a human genome. Science 376 (2022). doi:10.1126/science.abj698

Osmanski AB, Paulat NS, Korstian J, et al. Insights into mammalian te diversity through the curation of 248 genome assemblies. Science. 2023;380(6643). doi:10.1126/science.abn1430

Parks DF, Voitiuk K, Geng J, et al. IoT cloud laboratory: Internet of Things architecture for cellular biology. Internet of Things (2022). doi:10.1016/j.iot.2022.100618

Paez S, Kraus RHS, Shapiro B, et al. Reference genomes for conservation. Science (2022). doi:10.1126/science.abm8127

Reggiardo RE, Maroli SV, Halasz H, et al. Mutant KRAS regulates transposable element RNA and innate immunity via KRAB zinc-finger genes. Cell Rep (2022). doi:10.1016/j.celrep.2022.111104

Seiler ST, Mantalas GL, Selberg J, et al. Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids. Scientific Reports. 2022;12(1). doi:10.1038/s41598-022-20096-9

Shaffer, H. B., et al. Landscape Genomics to enable conservation actions: The California Conservation Genomics Project. Journal of Heredity (2022). doi:10.1093/jhered/esac020

Talbert P and Henikoff S. The genetics and epigenetics of satellite centromeres. Genome Research (2022). doi:10.1101/gr.275351.121

Turakhia Y, Thornlow B, Hinrichs A, et al. Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape. Nature (2022). doi:10.1038/s41586-022-05189-9

van Bree, E. J., Guimarães, R., Lundberg, M., et al. A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk lociGenome research (2022). doi:10.1101/gr.275515.121

Vollger MR, Dishuck PC, Harvey WT, et al. Increased mutation and gene conversion within human segmental duplications. Nature. 2023;617(7960):325-334. doi:10.1038/s41586-023-05895-y

Vollger MR, et al. Segmental duplications and their variation in a complete human genome. Science 376 (2022). doi:10.1126/science.abj6965

Vollger MR, et al. StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps. Bioinformatics (2022). doi:10.1093/bioinformatics/btac018

Wagner J, et al. Curated variation benchmarks for challenging medically relevant autosomal genes. Nature Biotechnology (2022). doi:10.1038/s41587-021-01158-1

Wang MS, Murray GGR, Mann D, et al. A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears. Nat Ecol Evol (2022). doi:10.1038/s41559-022-01753-8

Wang, Ting et al. The Human Pangenome Project: a global resource to map genomic diversity. Nature vol. 604,7906 (2022): 437-446. doi:10.1038/s41586-022-04601-8

Wilder AP, Supple MA, Subramanian A, et al. The contribution of historical processes to contemporary extinction risk in placental mammals. Science. 2023;380(6643). doi:10.1126/science.abn5856

Xue JR, Mackay-Smith A, Mouri K, et al. The functional and evolutionary impacts of human-specific deletions in conserved elements. Science. 2023;380(6643). doi:10.1126/science.abn2253

2021

Alpaslan-Roodenberg, S., Anthony, D., Babiker, H. Fehren-Schmitz, L. et al. Ethics of DNA research on human remains: five globally applicable guidelines. Nature (2021). doi:10.1038/s41586-021-04008-x

Ann M. Mc CartneyKishwar ShafinMichael Along, et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. bioRxiv (2021). doi:10.1101/2021.07.02.450803

Apple Cortez VollmersSergio CovarrubiasDaisy Kuang, et alA conserved long noncoding RNA, GAPLINC, modulates the immune response during endotoxic shock

Card, D. C., Shapiro, B., Giribet, G., Moritz, C., & Edwards, S. V. (2021). Museum Genomics. Annual Review of Genetics (2021). doi:10.1146/annurev-genet-071719-020506

Cleber A. Trujillo, Edward S. Rice, Nathan K. Schaefer, et al. Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment. ScienceMag (2021). doi:10.1126/science.aax2537

Curtin, L., D’Andrea, W.J., Balascio, N.L. et al. Sedimentary DNA and molecular evidence for early human occupation of the Faroe Islands. Commun Earth Environ 2, 253 (2021). https://doi.org/10.1038/s43247-021-00318-0

Daniel He, David Wu, Soren Muller, et al. miRNA-independent function of long noncoding pri-miRNA loci. National Academy of Sciences (2021). doi:10.1073/pnas.2017562118

Ding H, Anastopoulos I, Bailey AD 4th, Stuart J, Paten B. Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures. Nat Commun. 2021;12(1):6545. doi:10.1038/s41467-021-26929-x

Garg P, Martin-Trujillo A, Rodriguez OL, et al. Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression. Am J Hum Genet. 2021;108(5):809-824. doi:10.1016/j.ajhg.2021.03.016

Logan Mulroney, Madalee G. Wulf, Ira Schildkraut, et al. Identification of high confidence human poly(A) RNA isoform
scaffolds using nanopore sequencing. RNA (2021). doi:10.1261/rna.078703.121

Mao Y, Catacchio CR, Hillier LW, et al. A high-quality bonobo genome refines the analysis of hominid evolution [published online ahead of print, 2021 May 5]. Nature. 2021;10.1038/s41586-021-03519-x. doi:10.1038/s41586-021-03519-x

Phelan R, Baumgartner B, Brand S, et al. Intended consequences statement. Conservation Science and Practice. 2021;e371. PHELAN ET AL. 3 of 3. doi: 10.1111/csp2.371

Savannah J. HoytJessica M. StorerGabrielle A. Hartley, et al. From telomere to telomere: the transcriptional and epigenetic state of human repeat elements. bioRxiv (2021). doi:10.1101/2021.07.12.451456

Schmitz, M.T., Sandoval, K., Chen, C.P. et al. The development and evolution of inhibitory neurons in primate cerebrum. Nature (2022). doi:10.1038/s41586-022-04510-w

Schultz, D. T., Francis, W. R., McBroome, J. D., Christianson, L. M., Haddock, S. H., & Green, R. E. (2021). A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis. G3 Genes | Genomes | Genetics. https://doi.org/10.1093/g3journal/jkab302

Seninge, L., Anastopoulos, I., Ding, H. et al. VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics. Nat Commun 12, 5684 (2021). https://doi.org/10.1038/s41467-021-26017-0

Sergey AganezovStephanie M. YanDaniela C. Soto, et al. A complete reference genome improves analysis of human genetic variation. bioRxiv (2021). doi:10.1101/2021.07.12.452063

Sergey Nurk, Sergey Koren, Arang Rhie, et al. The complete sequence of a human genome. bioRxiv (2021). doi:10.1101/2021.05.26.445798

Shafin K, Pesout T, Chang P-C, et al. Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nat Methods. 2021;18(11):1322-1332. doi:10.1038/s41592-021-01299-w

Shapiro B, et al. The origins and spread of domestic horses from the Western Eurasian steppes. Nature (2021). doi:10.1038/s41586-021-04018-9

Simone Des Roches, Linwood H. Pendleton, Beth Shapiro & Eric P. Palkovacs. Conserving intraspecific variation for nature’s contributions to people. Nature Ecology & Evolution (2021). doi.org/10.1038/s41559-021-01403-5

Sirén J, Monlong J, Chang X, et al. Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science. 2021;374(6574):abg8871. doi:10.1126/science.abg8871

Stahl-Rommel, S., Jain, M., Nguyen, H. N., et al. Real-time culture-independent microbial profiling onboard the International Space Station using nanopore sequencing. Genes. 2021;12(1):106. doi:10.3390/genes12010106

Sun, C., Huang, J., Wang, Y., et al. Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution. 2021;38(2):486-501. doi:10.1093/molbev/msaa240

Tom van der Valk, Patrícia Pečnerová, David Díez-del-Molino, et al. Million-year-old DNA sheds light on the genomic history of mammoths. Nature (2021). doi: 10.1038/s41586-021-03224-9

Turakhia, Y., Thornlow, B., Hinrichs, A.S. et al. Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic. Nat Genet (2021). doi: 10.1038/s41588-021-00862-7

Vladimir Shchur, Vadim Spirin, Victor Pokrovskii, Evgeni Burovski, Nicola De Maio, Russell Corbett-Detig. VGsim: scalable viral genealogy simulator for global pandemic. MedRxiv (2021). doi.org/10.1101/2021.04.21.21255891

Yafei Mao, Claudia R. Catacchio, LaDeana W. Hillier, et al. A high-quality bonobo genome refines the analysis of hominid evolution. Nature (2021). doi.org/10.1038/s41586-021-03519-x

Yatish Turkahia, Bryan Thornlow, Angie Hinrichs, et al. Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region. bioRxiv (2021). doi:

Yuen D, Cabansay L, Duncan A, et al. The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols [published online ahead of print, 2021 May 12]. Nucleic Acids Res. 2021;gkab346. doi:10.1093/nar/gkab346

2020

Aashish N. Adhikari, Renata C. Gallagher, Yaqiong Wang, Robert J. Currier, George Amatuni, Laia Bassaganyas, Flavia Chen, Kunal Kundu, Mark Kvale, Sean D. Mooney, Robert L. Nussbaum, Savanna S. Randi, Jeremy Sanford, Joseph T. Shieh, Rajgopal Srinivasan, Uma Sunderam, Hao Tang, Dedeepya Vaka, Yangyun Zou, Barbara A. Koenig, Pui-Yan Kwok, Neil Risch, Jennifer M. Puck & Steven E. Brenner. The role of exome sequencing in newborn screening for inborn errors of metabolism. Nature Medicine (2020). doi:10.1038/s41591-020-0966-5

Abascal, F., Acosta, R., Addleman, N.J. et al. Expanded encyclopaedias of DNA elements in the human and mouse genomesNature 583, 699–710 (2020). doi:10.1038/s41586-020-2493-4

Aggarwal, R., Romero, G.R., Friedl, V. et al. Clinical and genomic characterization of Low PSA Secretors: a unique subset of metastatic castration resistant prostate cancerProstate Cancer Prostatic Dis (2020). doi:10.1038/s41391-020-0228-0

Alumkal JJ, Sun D, Lu E, et al. Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistanceProc Natl Acad Sci USA. 2020;117(22):12315-12323. doi:10.1073/pnas.1922207117

Aparna Bhaduri, Madeline G. Andrews, Walter Mancia Leon, Diane Jung, David Shin, Denise Allen, Dana Jung, Galina Schmunk, Maximilian Haeussler, Jahan Salma, Alex A. Pollen, Tomasz J. Nowakowski, Arnold R. Kriegstein. Cell stress in cortical organoids impairs molecular subtype specificationNature. 2020. doi:10.1038/s41586-020-1962-0

Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., et al.  Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 587(7833), 246–251 (2020). doi:10.1038/s41586-020-2871-y

Benz CC, Kang T, Yau C, et al. Abstract P3-08-20: The normal breast Active transcriptome associated with future breast cancer risk is driven by a dysregulated adipocyte microenvironmentCancer Res. 2020;80(4 Supplement):P3-08-20. doi:10.1158/1538-7445.SABCS19-P3-08-20

Carpenter, Susan et al. High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways. Cell Reports. 2020;33(13). doi:10.1016/j.celrep.2020.108541

Cristina Sisu, Paul Muir, Adam Frankish, Ian Fiddes, Mark Diekhans, David Thybert, Duncan T. Odom, Paul Flicek, Thomas M. Keane, Tim Hubbard, Jennifer Harrow & Mark Gerstein. Transcriptional activity and strain-specific history of mouse pseudogenes. Nature Communications volume 11, Article number: 3695 (2020). doi:10.1038/s41467-020-17157-w

Edana Lord, Nicolas Dussex, Marcin Kierczak, …, Joshua D. Kapp, Beth Shapiro, …, Sergey Vartanyan, Anders Götherström, Love Dalén. Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros. Current Biology. August 13, 2020, doi:10.1016/j.cub.2020.07.046

Eizenga, J. M., Novak, A. M., Kobayashi, E., Villani, F., Cisar, C., et al. Efficient dynamic variation graphs. Bioinformatics (Oxford, England) (2020). doi:10.1093/bioinformatics/btaa640

Feng, S., Stiller, J., Deng, Y., et al.  Dense sampling of bird diversity increases power of comparative genomics. Nature 587(7833), 252–257 (2020). doi:10.1038/s41586-020-2873-9

Fernandes, J.D., Hinrichs, A.S., Clawson, H. et al. The UCSC SARS-CoV-2 Genome Browser. Nat Genet (2020). doi:10.1038/s41588-020-0700-8

Fernandes JD, Zamudio-Hurtado A, Clawson H, Kent WJ, Haussler D, Salama SR, Haeussler M. The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. Mobile DNA volume 11, Article number: 13 (2020). doi:10.1101/429613v2

Frankish, A., Diekhans, M., Jungreis, I., Lagarde, J., Loveland, J. E., et al. GENCODE 2021. Nucleic Acids Research (2020). doi:10.1093/nar/gkaa1087

Füllgrabe, A., George, N., Green, M. et al. Guidelines for reporting single-cell RNA-seq experiments. Nat Biotechnol (2020). doi:10.1038/s41587-020-00744-z

Goenka, SD., Turakhia, Y,. Paten, B. et al. SegAlign: a scalable GPU-based whole genome aligner. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis. IEEE Press (2020). doi:10.5555/3433701.3433752

Goldman MJ, Craft B, Hastie M, Repečka K, McDade F, Kamath A, Banerjee A, Luo Y, Rogers D, Brooks AN, Zhu J, Haussler. D. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol (2020). doi:10.1038/s41587-020-0546-8

Haan D, Tao R, Friedl V, et al. Using Transcriptional Signatures to Find Cancer Drivers with LUREPac Symp Biocomput. 2020;25:343-354. https://doi.org/10.1142/9789811215636_0031

Huang, H.H., Ferguson, I.D., Thornton, A.M. et al. Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myelomaNat Commun. 2020;11(1):1931. doi:10.1038/s41467-020-15521-4

JD Fernandes, AS Hinrichs, H Clawson, JN Gonzalez, BT Lee, LR Nassar, BJ Raney, KR Rosenbloom, S Nerli, A Rao, D Schmelter, AS Zweig, TM Lowe, M Ares Jr, R Corbet-Detig , WJ Kent, D Haussler, M Haeussler. The UCSC SARS-CoV-2 Genome Browser. May 4, 2020. doi:10.1101/2020.05.04.075945

Jian Carrot-Zhang, Nyasha Chambwe, Jeffrey S. Damrauer, Theo A. Knijnenburg, A. Gordon Robertson, Christina Yau, Wanding Zhou, Ashton C. Berger, Kuan-lin Huang, Justin Y. Newberg, R. Jay Mashl, Alessandro Romanel, Rosalyn W. Sayaman, Francesca Demichelis, Ina Felau, Garrett M. Frampton, Seunghun Han, Katherine A. Hoadley, Anab Kemal, Peter W. Laird, Alexander J. Lazar, Xiuning Le, Ninad Oak, Hui Shen, Christopher K. Wong, Jean C. Zenklusen, Elad Ziv, Cancer Genome Atlas Analysis Network, Andrew D. Cherniack, Rameen Beroukhim. Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer. Cancer Cell. Volume 37Issue 5p619-734. DOI:https://doi.org/10.1016/j.ccell.2020.04.012

Johannes Birgmeier, Maximilian Haeussler, Cole A. Deisseroth, Ethan H. Steinberg, Karthik A. Jagadeesh, Alexander J. Ratner, Harendra Guturu, Aaron M. Wenger, Mark E. Diekhans, Peter D. Stenson, David N. Cooper, Christopher Ré, Alan H. Beggs, Jonathan A. Bernstein and Gill Bejerano. AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature. Science Translational Medicine 20 May 2020: Vol. 12, Issue 544, eaau9113 doi: 10.1126/scitranslmed.aau9113

Jordan M Eizenga, Adam M Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar, Simon Heumos, Glenn Hickey, Vincenza Colonna, Benedict Paten, Erik Garrison. Efficient dynamic variation graphs. Bioinformatics, btaa640 doi: 10.1093/bioinformatics/btaa640

K Shafin, T Pesout, R Lorig-Roach, M Haukness, HE Olsen, C Bosworth, J Armstrong, K Tigyi, N Maurer, S Koren, FJ Sedlazeck, T Marschall, S Mayes, V Costa, JM Zook, KJ Liu, D Kilburn, M Sorensen, KM Munson, MR Vollger, J Monlong, E Garrison, EE Eichler, S Salama, D Haussler, RE Green, M Akeson, A Phillippy, KH. Miga, P Carnevali, M Jain, B Paten. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat Biotechnol (2020). doi:10.1038/s41587-020-0503-6

Karen H. Miga, Sergey Koren, […]Adam M. Phillippy. Telomere-to-telomere assembly of a complete human X chromosome. Nature (2020). doi:10.1038/s41586-020-2547-7

Kathiriya et al., Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease, Developmental Cell (2020), https://doi.org/10.1016/j.devcel.2020.11.020

Lee CM, Barber GP, Casper J, et al. UCSC Genome Browser enters 20th yearNucleic Acids Res. 2019;48(D1):D756-D761. doi:10.1093/nar/gkz1012

Nakatsuka N, Lazaridis I, Barbieri C, Skoglund P, Rohland N, Mallick S, Harkins-Kinkaid K, Ferry M, Harney E, Michel M, Stewardson K, Novak-Forst J, Posth C, Capriles JM, Alfonso Durruty M, Aranda Álvarez K, Beresford-Jones D, Burger R, Cadwallader, Lauren, Fujita R, Isla J, Lau G, Lémuz Aguirre C, LeBlanc S, Calla Maldonado S, Meddens F, Messineo PG Culleton BJ, Harper TK, Quilter J, Politis G, Reindel M, Rivera M, Salazar L, Sandoval JR, Santoro CM, Scheifler N, Standen V, Barreto MI, Flores Espinoza I, Tomasto-Cagigao E, Valverde G, Kennett DJ, Cooper A, Krause J, Haak W, Llamas B, Reich D, Fehren-Schmitz L. A Paleogenomic Reconstruction of the Deep Population History of the Andes. Cell. May 7, 2020. doi:10.17863/CAM.50732

PCAWG Transcriptome Core Group., Calabrese, C., Davidson, N.R. et al. Genomic basis for RNA alterations in cancerNature. 2020;578(7793):129-136. doi:10.1038/s41586-020-1970-0

Pfeil J, Sanders L, Anastopoulos I, Lyle A, Weinstein A, Xue Y, Blair A, Beale H, Lee A, Leung S, Dinh P, Shah A, Breese M, Devine W, Bjork I, Salama S, Sweet-Cordero E, Haussler D, Vaske O. Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. PLOS Computational Biology. April 2020. 16. e1007753. doi:10.1371/journal.pcbi.1007753

Porubsky, D., Ebert, P., Audano, P. A., Vollger, M. R., Harvey, W. T., et al. Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nature Biotechnology (2020). doi:10.1038/s41587-020-0719-5

Rheinbay, E., Nielsen, M.M., Abascal, F. et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomesNature. 2020;578(7793):102-111. doi:10.1038/s41586-020-1965-x

S. Chen M.D. Christopher K. Wong M.S.Felix Y. Feng M.D. Adina Bailey Ph.D.JiaotiHuang M.D., Ph.D.Joshua M.Stuart Ph.D. VerenaFriedl M.S. Alana S.Weinstein B.A. Tomasz M.Beer M.D. Joshi J.Alumkal M.D. MatthewRettig M.D. Martin Gleave M.D. Primo N.Lara Jr. M.D. George V. Thomas M.D. Patricia Li B.A. Austin Lui M.S. Eric J.Small M.D. Rahul R. Aggarwal M.D. Down-regulation of ADRB2 expression is associated with small cell neuroendocrine prostate cancer and adverse clinical outcomes in castration-resistant prostate cancer. doi:10.1016/j.urolonc.2020.06.002

Shuai, S., PCAWG Drivers and Functional Interpretation Working Group., Abascal, F. et al. Combined burden and functional impact tests for cancer driver discovery using DriverPowerNat Commun. 2020;11(1):734. doi:10.1038/s41467-019-13929-1

Small EJ, Aggarwal RR, Friedl V, et al. Intermediate atypical carcinoma (IAC): A discrete subtype of metastatic castration-resistant prostate cancer (mCRPC) suggesting that treatment-associated small cell/neuroendocrine prostate cancer (t-SCNC) may evolve from mCRPC adenocarcinoma (adeno)—Results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT).  JCO. 2020;38(6_suppl):158. doi:10.1200/JCO.2020.38.6_suppl.158

Struck A, Walsh B, Buchanan A, et al. Exploring Integrative Analysis Using the BioMedical Evidence GraphJCO Clinical Cancer Informatics. 2020;4:147-159. doi:10.1200/CCI.19.00110

Tang, A.D., Soulette, C.M., van Baren, M.J. et al. Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained intronsNat Commun. 2020;11(1438). doi:10.1038/s41467-020-15171-6

Turakhia Y, De Maio N, Thornlow B, et al. Stability of SARS-CoV-2 phylogenies. PLoS Genet (2020). doi:10.1371/journal.pgen.1009175

Vladislav Uzunangelov, Christopher K. Wong, Joshua M. Stuart. Highly Accurate Cancer Phenotype Prediction with AKLIMATE, a Stacked Kernel Learner Integrating Multimodal Genomic Data and Pathway Knowledge. doi.org/10.1101/2020.07.15.205575

Wesley C. Warren, Alan R. Harris, Marina Haukness. et alSequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science (2020). doi:10.1126/science.abc6617

William J. Dally, Yatish Turakhia, Song Han. Domain-Specific Hardware Accelerators Communications of the ACM, July 2020, Vol. 63 No. 7, Pages 48-57 10.1145/3361682

Xiangnan Guan, Duanchen Sun, Eric Lu, Joshua A. Urrutia, Robert Evan Reiter, Matthew Rettig, Christopher P. Evans, Primo Lara Jr, Martin Gleave, Tomasz M. Beer, George V. Thomas, Jiaoti Huang, Rahul R. Aggarwal, David A. Quigley, Adam Foye, William S. Chen, Jack Youngren, Alana S. Weinstein, Joshua M. Stuart, Felix Y. Feng, Eric J. Small, Zheng Xia and Joshi J. Alumkal. Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer. doi:10.1158/1078-0432.CCR-19-2303

Yatish Turakhia, Bryan Thornlow, Landen Gozashti, Angie S. Hinrichs, Jason D. Fernandes, David Haussler, and Russell Corbett-Detig. Stability of SARS-CoV-2 Phylogenies. bioRxiv preprint. June 9, 2020. doi:10.1101/2020.06.08.141127

Zoonomia Consortium. A comparative genomics multitool for scientific discovery and conservation. Nature 587(7833), 240–245 (2020).

2019

Aggarwal R, Huang J, Alumkal J, Feng FY, Zhang L, Stuart JM, Small EJ. Transformation of Prostate Adenocarcinoma Into Small-Cell Neuroendocrine Cancer Under Androgen Deprivation Therapy: Much Is Achieved But More Information Is Needed Reply. DOI: 10.1200/JCO.18.01487 Journal of Clinical Oncology 37, no. 4 (February 1 2019) 351-352., PMID: 30557523

Alexis M. ThorntonLishan FangCasey O’BrienAlice H. BergerMarios GiannakisAngela N. Brooks. eVIP2: Expression-based variant impact phenotyping to predict the function of gene variantsBioRxiv. 2019. doi:10.1101/872028v1

Anthony D. Long, James Baldwin-Brown, Yuan Tao, Vanessa J. Cook, Gabriela Balderrama-Gutierrez, Russell Corbett-Detig, Ali Mortazavi, Alan G. Barbour. The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections. 24 July 2019.

Armstrong JFiddes ITDiekhans MPaten B. Whole-Genome Alignment and Comparative Annotation. Annual Review of Animal Biosciences. 2019 Feb. doi: 10.1146/annurev-animal-020518-115005.

Beale H.C., Roger J.M., Cattle M.A., McKay L.T., Learned K, Lyle A.G., Kephart E.T., Currie R, Lam D.L., Sanders L, Pfeil J, Vivian J, Bjork I, Salama S.R., Haussler D, Vaske O.M. Framework for determining accuracy of RNA sequencing data for gene expression profiling of single samples. bioRxiv preprint. Posted July 30, 2019. doi:10.1101/716829

Bernardi G, Crane N. Benthic coverage data collected from 2012 to 2014 in the Federated States of Micronesia and the Caroline Islands (Disturb Impacts Coral project). 2019 Apr 4. doi: 10.1575/1912/bco-dmo.684031.1, https://hdl.handle.net/1912/23958.

Bernardi G, Crane N. Fish count data from the Caroline Islands and the Federal States of Micronesia collected from 2012-2014. 2019 Apr 4. doi: 10.1575/1912/bco-dmo.684177.1.

Bittman D, Alvaro P, Long D, Miller EL.Optimizing systems for byte-addressable NVM by reducing bit flipping. In Proceedings of the 17th USENIX Conference on File and Storage Technologies (FAST’19). USENIX Association, Berkeley, CA, USA, 17-30.

Bjork I, Peralez J, Haussler D, Spunt SL, Vaske OM. Data sharing for clinical utility. Cold Spring Harb Mol Case Stud. 2019;5(5):a004689. Published 2019 Oct 23. doi:10.1101/mcs.a004689

Birgmeier, J., Deisseroth, C.A., Hayward, L.E. et al. AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literatureGenet Med. 2019;22(2):362-370. doi:10.1038/s41436-019-0643-6

Byrne ASupple MAVolden RLaidre KLShapiro BVollmers C. Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus). bioRxiv. 2019 Jan 27. doi: 10.1101/527978.

Cameron M. SouletteEva Hrabeta-RobinsonAlison TangMaximillian G. MarinAngela N. Brooks. Nanopore sequencing reveals U2AF1 S34F-associated full-length isoformsBioRxiv. 2019. doi:10.1101/871863v2

Campbell, P.J., Getz, G., Korbel, J.O. et al. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020). doi:10.1038/s41586-020-1969-6

Chiara Barbieri, Rodrigo Barquera, Leonardo Arias, José R Sandoval, Oscar Acosta, Camilo Zurita, Abraham Aguilar-Campos, Ana M Tito-Álvarez, Ricardo Serrano-Osuna, Russell Gray, Fabrizio Mafessoni, Paul Heggarty, Kentaro K Shimizu, Ricardo Fujita, Mark Stoneking, Irina Pugach, Lars Fehren-Schmitz, The current genomic landscape of western South America: Andes, Amazonia and Pacific Coast, Molecular Biology and Evolution (2019). DOI: 10.1093/molbev/msz174

Corbett‐Detig R, Medina P, Frérot H, Blassiau C, Castric V. Bulk pollen sequencing reveals rapid evolution of segregation distortion in the male germline of Arabidopsis hybrids. Evolution Letters, 3: 93-103. 2019 Jan 30. doi: 10.1002/evl3.96

Demircioglu Deniz, Cukuroglu, Kindermans Martin, et al. A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative PromotersCell. 2019;178(8):1465-1477doi:10.1016/j.cell.2019.08.018

Ding H, Blair A, Stuart J. Cross-Species Alignment of Single Cell States with Biological Process Activity. bioRxiv. 2019 Feb 19; doi:10.1101/555268

Ding, H., Blair, A., Yang, Y. et al. Biological process activity transformation of single cell gene expression for cross-species alignmentNat Commun. 2019;10(1):4899. doi:10.1038/s41467-019-12924-w

Ellrott, K., Buchanan, A., Creason, A. et al. Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challengesGenome Biol. 2019;20(1):195. doi:10.1186/s13059-019-1794-0

Field AR, Jacobs FMJ, Fiddes IT, Phillips APR, Reyes-Ortiz AM, LaMontagne E, Whitehead L, Meng V, Rosenkrantz JL, Olsen M, Hauessler M, Katzman S, Salama SR, Haussler D. Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes. Stem Cell Reports. 2019 Feb 12;12(2):245-257. doi: 10.1016/j.stemcr.2018.12.006. Epub 2019 Jan 10.

Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, et al. Federated discovery and sharing of genomic data using Beacons. Nat Biotechnol. 2019 Mar;37(3):220-224. doi: 10.1038/s41587-019-0046-x.

Frederik V. Seersholm, Daniel J. Werndly, Alicia Grealy, Taryn Johnson, Erin M. Keenan Early, Ernest L. Lundelius Jr., Barbara Winsborough, Grayal Earle Farr, Rickard Toomey, Anders J. Hansen, Beth Shapiro, Michael R. Waters, Gregory McDonald, Anna Linderholm, Thomas W. Stafford Jr. & Michael Bunce. Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change. June 2020 Nature Communications 11:2770(1) doi: 10.1038/s41467-020-16502-3

Fregel R, Ordóñez AC, Santana-Cabrera J, et al. Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary IslandsPLoS One. 2019;14(3):e0209125. Published 2019 Mar 20. doi:10.1371/journal.pone.0209125

Fulton TL, Shapiro B. Setting Up an Ancient DNA Laboratory. Springer. 2019 Mar 16. doi: 10.1007/978-1-4939-9176-1_1.

Galvén-Peña S, Carroll RG, Newman C, Hinchy EC, Palsson-McDermott E, Robinson EK, Covarrubias S, Nadin A, James AM, Haneklaus M, Carpenter S, Kelly VP, Murphy MP, Modis LK, O’Neill LA. Malonylation of GAPDH is an inflammatory signal in macrophages. Nat Commun. 2019 Jan 18;10(1):338. doi: 10.1038/s41467-018-08187-6.

Goldman MCraft BHastie MRepečka KKamath AMcDade FRogers DBrooks ANZhu JHaussler D. The UCSC Xena platform for public and private cancer genomics data visualization and interpretation. bioRxiv. 2019 Mar 5. doi: https://doi.org/10.1101/326470.

Graim K, Friedl V, Houlahan KE, Stuart JM. PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity PredictionPac Symp Biocomput. 2019;24:136–147.

Haeussler, M. CRISPR off-targets: a question of contextCell Biol Toxicol. 2019;36(1):5-9. doi:10.1007/s10565-019-09497-1

Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2019 update. Nucleic Acids Res. 2019 Jan 8;47(D1):D853-D858. doi: 10.1093/nar/gky1095.

Hongxu Ding, Andrew D Bailey, IV, Miten Jain, Hugh Olsen, Benedict Paten. Gaussian Mixture Model-Based Unsupervised Nucleotide Modification Number Detection Using Nanopore Sequencing Readouts. Bioinformatics, btaa601, doi:10.1093/bioinformatics/btaa601

Horns F, Vollmers C, Dekker CL, Quake SR. Signatures of selection in the human antibody repertoire: Selective sweeps, competing subclones, and neutral drift. Proc Natl Acad Sci U S A. 2019 Jan 22;116(4):1261-1266. doi: 10.1073/pnas.1814213116. Epub 2019 Jan 8.

Hu D, Feng D, Xie Y, Xu G, Gu X, Long D. Efficient Provenance Management via Clustering and Hybrid Storage in Big Data EnvironmentsIEEE Transactions on Big Datadoi: 10.1109/TBDATA.2019.2907116.

IS Kathiriya, KS Rao, G Iacono, WP Devine, AP Blair. Modeling human TBX5 haploinsufficiency predicts regulatory networks for congenital heart disease

Jung E, Ly V, Buderi A, Appleton E, Teodorescu M. Design and Selection of Muscle Excitation Patterns for Modeling a Lower Extremity Joint Inspired Tensegrity.  IEEE International Conference on Robotic Computing (IRC). 2019 Feb. doi: 10.1109/IRC.2019.00053.

Kelly M Harkins, Nathan K Schaefer, Christopher J Troll, Varsha Rao, Joshua Kapp, Colin Naughton, Beth Shapiro, Richard E Green. A novel NGS library preparation method to characterize native termini of fragmented DNA. Nucleic Acids Research, Volume 48, Issue 8, 07 May 2020, Page e47, https://doi.org/10.1093/nar/gkaa128

Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Colleen Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas Maurer, Sergey Koren, Fritz J. Sedlazeck, Tobias Marschall, Simon Mayes, Vania Costa, Justin M. Zook, Kelvin J. Liu, Duncan Kilburn, Melanie Sorensen, Katy M. Munson, Mitchell R. Vollger, Evan E. Eichler, Sofie Salama, David Haussler, Richard E. Green, Mark Akeson, Adam Phillippy, Karen H. Miga, Paolo Carnevali, Miten Jain, Benedict Paten. Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit. bioRxiv preprint, July 26, 2019. 715722; doi: 10.1101/715722

Learned K, Durbin A, Currie R, Kephart E, Beale H, Sanders L, Pfeil J, Goldstein T, Salama S, Haussler D, Morozova Vaske O, Bjork I. Barriers to accessing public cancer genomic data. Scientific Data. 20 June 2019.

Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, Jose M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M. Stuart, Benjamin J. Raphael & PCAWG Consortium. Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications 2020-12. doi: 10.1038/s41467-020-14367-0

Mesa KA, Yu B, Wrin T, Petropoulos CJ, Pogson GH, Alexander DL, Perez G, O’Rourke SM, Sinangil F, Robinson J, Conant MA, Berman PW.
Ancestral sequences from an elite neutralizer proximal to the development of neutralization resistance as a potential source of HIV vaccine immunogens. PLoS One. 2019 Apr 10;14(4):e0213409. doi: 10.1371/journal.pone.0213409. eCollection 2019.

Meyer RCurd EESchweizer TGold ZRamos DRShirazi SKandlikar GKwan WLin MFriese AMoberg-Parker JRamos MMShapiro BSexton JPipes LVedrenne AGMejia MP, Aronson EMoore TNielsen RLewin H, Barber PWall JKraft NWayne R. The California Environmental DNA “CALeDNA” Program. bioRxiv. 2019 Jan 4. doi: 10.1101/503383.

Nedda F. Saremi, Megan A. Supple, Ashley Byrne, James A. Cahill, Luiz Lehmann Coutinho, Love Dalén, Henrique V. Figueiró, Warren E. Johnson, Heather J. Milne, Stephen J. O’Brien, Brendan O’Connell, David P. Onorato, Seth P. D. Riley, Jeff A. Sikich, Daniel R. Stahler, Priscilla Marqui Schmidt Villela, Christopher Vollmers, Robert K. Wayne, Eduardo Eizirik, Russell B. Corbett-Detig, Richard E. Green, Christopher C. Wilmers & Beth Shapiro. Puma genomes from North and South America provide insights into the genomic consequences of inbreeding. Nature Communications volume 10, Article number: 4769 (2019). doi:10.1038/s41467-019-12741-1

New B, Spradley M, Fehren-Schmitz L. A Forensic Anthropological Perspective on Latin American Genetic Diversity. 2019 Mar. doi: 10.13140/RG.2.2.24217.47207.

Nichols RV, Curd E, Heintzman PD, Shapiro B. Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA. Methods Mol Biol. 2019;1963:149-161. doi: 10.1007/978-1-4939-9176-1_16.

Nickols NG, Nazarian R, Zhao SG, Tan V, Uzunangelov V, Xia Z, Baertsch R, Neeman E, Gao AC, Thomas GV, Howard L, De Hoedt AM, Stuart J, Goldstein T, Chi K, Gleave ME, Graff JN, Beer TM, Drake JM, Evans CP, Aggarwal R, Foye A, et al. MEK-ERK signaling is a therapeutic target in metastatic castration resistant prostate cancer. Prostate Cancer Prostatic Dis. 2019 Feb 25. doi: 10.1038/s41391-019-0134-5. [Epub ahead of print].

O’Rourke SM, Yu B, Morales JF, Didinger CM, Alexander DL, Vollmers C, Berman PW. Production of a recombinant monoclonal antibody to Herpes Simplex Virus glycoprotein D for immunoaffinity purification of tagged proteins. J Immunol Methods. 2019 Feb;465:31-38. doi: 10.1016/j.jim.2018.11.015. Epub 2018 Nov 28.

Pollock DD. Society for Molecular Biology and Evolution, Council and Business Meetings, 2018, Yokohama, JapanMol Biol Evol. 2019;36(1):204–206. doi: 10.1093/molbev/msy240.

Porubsky D, Ebert P, Audano PA, et al. A fully phased accurate assembly of an individual human genome. BioRxiv. 2019. doi:10.1101/855049.

Prieto G, Verano JW, Goepfert N, Kennett D, Quilter J, LeBlanc S, Fehren-Schmitz L, Forst J, Lund M, Dement B, Dufour E, Tombret O, Calmon M, Gadison D, Tschinkel K. A mass sacrifice of children and camelids at the Huanchaquito-Las Llamas site, Moche Valley, Peru. PLoS One. 2019 Mar 6;14(3):e0211691. doi: 10.1371/journal.pone.0211691.

Rao A, Madejska A.A., Pfeil J, Paten B, Salama S.R., Haussler D. ProTECT – Prediction of T-cell Epitopes for Cancer Therapy. bioRxiv preprint. Posted July 09, 2019. doi:10.1101/696526

Ratjen A, Au J, Carpenter S, John P, Ratjen F. Growth of Pulmonary Arteriovenous Malformations in Pediatric Patients with Hereditary Hemorrhagic Telangiectasia. J Pediatr. 2019 May;208:279-281. doi: 10.1016/j.jpeds.2018.12.069. Epub 2019 Mar 8.

Rosen YM, Paten BJ. An average-case sublinear forward algorithm for the haploid Li and Stephens model. Algorithms Mol Biol. 2019 Apr 2;14:11. doi: 10.1186/s13015-019-0144-9. eCollection 2019.

Sanders L, Cheney A, Beale H, Kephart E, Bjork I, Pfeil J, Salama S, Haussler D, Morozova O. Shared dysregulation of long non-coding RNA and developmental gene networks in histone H3 K27M gliomas and PF-A ependymomas. Journal of Clinical Oncology 2019 37:15_suppl, e21523-e21523

Sanders LM, Rangaswami A, Bjork I, et al. Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor. Cold Spring Harb Mol Case Stud. 2019;5(5):a004317. Published 2019 Oct 23. doi:10.1101/mcs.a004317

Sarsani VK, Raghupathy N, Fiddes IT, Armstrong J, Thibaud-Nissen F, Zinder O, Bolisetty M, Howe K, Hinerfeld D, Ruan X, Rowe L, Barter M, Ananda G, Paten B, Weinstock GM, Churchill GA, Wiles MV, Schneider VA, Srivastava A, Reinholdt LG. The Genome of C57BL/6J “Eve”, the Mother of the Laboratory Mouse Genome Reference Strain. G3 (Bethesda). 2019 Apr 17. pii: g3.400071.2019. doi: 10.1534/g3.119.400071. [Epub ahead of print].

Schirmer L, Velmeshev D, Holmqvist S, Kaufmann M, Werneburg S, Jung D, Vistnes S, Stockley JH, Young A, Steindel M, Tung B, Goyal N, Bhaduri A, Mayer S, Engler, JB, Bayraktar, OA, Franklin Robin JM, Haeussler M, et al. Neuronal vulnerability and multilineage diversity in multiple sclerosis. Nature. 17 July 2019.

Sirén JGarrison ENovak AMPaten BDurbin R. Haplotype-aware graph indexes. bioRxiv. 2019 Feb 24. doi: 10.1101/559583.

Smith AM, Jain M, Mulroney L, Garalde DR, Akeson M. Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing. PLoS One. 2019 May 16;14(5) 

Vaske OM, Bjork I, Salama SR, et al. Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer. JAMA Netw Open. 2019;2(10):e1913968. Published 2019 Oct 2. doi:10.1001/jamanetworkopen.2019.13968

Vaske OM, Haussler D. Data sharing for pediatric cancers. Science. 2019 Mar 15;363(6432):1125. doi: 10.1126/science.aax2739. No abstract available.

Velmeshev D, Schirmer L, Jung D, Haeussler M, Perez Y, Mayer S, Bhaduri A, Goyal N, Rowitch DH, Kriegstein AR. Single-cell genomics identifies cell type-specific molecular changes in autism. Science. 2019 May 17;364(6441):685-689. 

Workman, R.E., Tang, A.D., Tang, P.S. et al. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nat Methods. 2019;16: 1297–1305. doi:10.1038/s41592-019-0617-2

Wolfgang Beyer, Adam M Novak, Glenn Hickey, Jeffrey Chan, Vanessa Tan, Benedict Paten, Daniel R Zerbino. Sequence tube maps: making graph genomes intuitive to commuters. Bioinformatics, 01 August 2019.

Xian ChangJordan EizengaAdam M. NovakJouni SirénBenedict Paten. Distance Indexing and Seed Clustering in Sequence GraphsBioRxiv. 2019. doi:10.1101/2019.12.20.884924.

Yin S, Gambe RG, Sun J, Martinez AZ, Cartun ZJ, Regis FFD, Wan Y, Fan J, Brooks AN, Herman SEM, Ten Hacken E, Taylor-Weiner A, Rassenti LZ, Ghia EM, Kipps TJ, Obeng EA, Cibulskis CL, Neuberg D, Campagna DR, Fleming MD, Ebert BL, Wiestner A, et al. A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion. Cancer Cell. 2019 Feb 11;35(2):283-296.e5. doi: 10.1016/j.ccell.2018.12.013. Epub 2019 Jan 31.

Zhang C, Sharma R, Satbir T, Cheney A, Vaske O, Sanders L, Boklan J, Lewis V.A., Anderson R, Kovalchuk O, Lacayo N.J., Narendran A. and Bielamowicz K.J. Establishing a Novel in Vitro Informed Precision Clinical Trial Pathway for Refractory Pediatric Leukemia. Blood, [online]. Posted November 13, 2019. doi:10.1182/blood-2019-131444

2018

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

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

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

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

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

Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R, Dlott CC, Dolman L, den Dunnen JT, Dyke SOM, Domchek SM, Easton D, Fischmann Z, Foulkes WD, Garber J, et al. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. PLoS Genet. 2018 Dec 26;14(12):e1007752. doi: 10.1371/journal.pgen.1007752. eCollection 2018 Dec. PMID:30586411 | PMCID:PMC6324924

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

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

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

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

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

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

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

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

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

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

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)

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

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

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

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

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

Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants., Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, et al. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5.

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, Belize. International 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 2011. Molecular 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 browser. Current 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; Sustainable Athletics Project Final ReportJournal 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

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 Browser. Nucleic 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 2009. Nucleic 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 cells. Applied 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

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

Karolchik D, Hinrichs AS, Furey TS, et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004;32(Database issue):D493‐D496. doi:10.1093/nar/gkh103

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 prediction. Proteins: 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 time. Journal 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. 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 data. Bioinformatics16-10. 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 functions. IEEE 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 entropy. IEEE 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 homology. Bioinformatics12-4. 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 DNA. Nucleic 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 modeling. Nucleic 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 procedures. Verdict: 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 restriction. Journal 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
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 Jan. Detail:.
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 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 fro m 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