Publications

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

Featured Publications

Historical Sketch: The Santa Cruz Workshop

Robert L. Sinsheimer May, 1985. | Genomics. Volume 5, Issue 4, November 1989, Pages 954-956. The Santa Cruz Workshop in May 1985 resulted from the convergence of several lines of thought. The first complete genome to be sequenced was that of the bacterial virus ¢Xl 74...

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Complete Bibliography

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2019

The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data to support highly collaborative research activities. Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2. Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org. The purpose of the BRCA Exchange is to provide the community with a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype. More than 20,000 variants have been aggregated, three times the number found in the next-largest public database at the project’s outset, of which approximately 7,250 have expert classifications. The data set is based on shared information from existing clinical databases-Breast Cancer Information Core (BIC), ClinVar, and the Leiden Open Variation Database (LOVD)-as well as population databases, all linked to a single point of access. The BRCA Challenge has brought together the existing international Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium expert panel, along with expert clinicians, diagnosticians, researchers, and database providers, all with a common goal of advancing our understanding of BRCA1 and BRCA2 variation. Ongoing work includes direct contact with national centers with access to BRCA1 and BRCA2 diagnostic data to encourage data sharing, development of methods suitable for extraction of genetic variation at the level of individual laboratory reports, and engagement with participant communities to enable a more comprehensive understanding of the clinical significance of genetic variation in BRCA1 and BRCA2.

2018

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 

2017

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2016

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2015

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 

2014

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 

2012

Harrow, Jennifer and Frankish, Adam and Gonzalez, Jose M and Tapanari, Electra and Diekhans, Mark and Kokocinski, Felix and Aken, Bronwen L and Barrell, Daniel and Zadissa, Amonida and Searle, Stephen and