Selected Publications

This page lists publications directly funded by the NHGRI grant to the UCSC Genome Browser. View more publications by Genome Browser staff here:

2021

Gonzalez JN, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, Powell CC, Nassar LR, Maulding ND, Lee CM, Lee BT, Hinrichs AS, Fyfe AC, Fernandes JD, Diekhans M, Clawson H, Casper J, Benet-Pagés A, Barber GP, Haussler D, Kuhn RM, Haeussler M, Kent WJ The UCSC Genome Browser database: 2021 update Nucleic Acids Res. 2021 Jan 8;49(D1):D1046-D1057. PMID: 33221922 PMCID: PMC7779060

Moreno P, Huang N, Manning JR, Mohammed S, Solovyev A, Polanski K, Bacon W, Chazarra R, Talavera-López C, Doyle MA et al. User-friendly, scalable tools and workflows for single-cell RNA-seq analysis. Nat Methods. 2021 Apr;18(4):327-328. PMID: 33782609

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021 Apr;592(7856):737-746. PMID: 33911273; PMC: PMC8081667

Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ et al. UCSC Cell Browser: Visualize Your Single-Cell Data. Bioinformatics. 2021 Jul 9;. PMID: 34244710

2020

Birgmeier J, Deisseroth CA, Hayward LE, Galhardo LMT, Tierno AP, Jagadeesh KA, Stenson PD, Cooper DN, Bernstein JA, Haeussler M et al. AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature. Genet Med. 2020 Feb;22(2):362-370. PMID: 31467448; PMC: PMC7301356

Fernandes JD, Hinrichs AS, Clawson H, Gonzalez JN, Lee BT, Nassar LR, Raney BJ, Rosenbloom KR, Nerli S, Rao AA, Schmelter D, Fyfe A, Maulding N, Zweig AS, Lowe TM, Ares M, Corbet-Detig R, Kent WJ, Haussler D, Haeussler M. The UCSC SARS-CoV-2 Genome Browser. Nat Genet. 2020 Sep 9;. PMID: 32908258; PMC: PMC8016453

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. Mob DNA. 2020;11:13. PMID: 32266012; PMC: PMC7110667

Ferraro NM, Strober BJ, Einson J, Abell NS, Aguet F, Barbeira AN, Brandt M, Bucan M, Castel SE, Davis JR et al. Transcriptomic signatures across human tissues identify functional rare genetic variation. Science. 2020 Sep 11;369(6509). PMID: 32913073; PMC: PMC7646251

GTEx Consortium.. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science. 2020 Sep 11;369(6509):1318-1330. PMID: 32913098; PMC: PMC7737656

Haeussler M. CRISPR off-targets: a question of context. Cell Biol Toxicol. 2020 Feb;36(1):5-9. PMID: 31734746; PMC: PMC7056574

Kim-Hellmuth S, Aguet F, Oliva M, Muñoz-Aguirre M, Kasela S, Wucher V, Castel SE, Hamel AR, Viñuela A, Roberts AL et al. Cell type-specific genetic regulation of gene expression across human tissues. Science. 2020 Sep 11;369(6509). PMID: 32913075; PMC: PMC8051643

Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ. UCSC Genome Browser enters 20th year. Nucleic Acids Res. 2020 Jan 8;48(D1):D756-D761. PMID: 31691824; PMC: PMC7145642

Turakhia Y, De Maio N, Thornlow B, Gozashti L, Lanfear R, Walker CR, Hinrichs AS, Fernandes JD, Borges R, Slodkowicz G et al. Stability of SARS-CoV-2 phylogenies. PLoS Genet. 2020 Nov;16(11):e1009175. PMID: 33206635; PMC: PMC7721162

Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, Corbett-Detig R. Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS- CoV-2 Pandemic. bioRxiv. 2020 Sep 28;. PMID: 33024970; PMC: PMC7536873

2019

Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure J. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double- strand break repair. Nucleic Acids Res. 2019 Sep 5;47(15):7989-8003. PMID: 31165867; PMC: PMC6735782

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. PMID: 30407534; PMC: PMC6323953

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 RJM, Haeussler M et al. Neuronal vulnerability and multilineage diversity in multiple sclerosis. Nature. 2019 Sep;573(7772):75-82. PMID: 31316211; PMC: PMC6731122

2018

Anderson KR, Haeussler M, Watanabe C, Janakiraman V, Lund J, Modrusan Z, Stinson J, Bei Q, Buechler A, Yu C, Thamminana SR, Tam L, Sowick MA, Alcantar T, O'Neil N, Li J, Ta L, Lima L, Roose-Girma M, Rairdan X, Durinck S, Warming S. CRISPR off-target analysis in genetically engineered rats and mice. Nat Methods. 2018 Jul;15(7):512-514. PMID: 29786090; PMC: PMC6558654

Canver MC, Haeussler M, Bauer DE, Orkin SH, Sanjana NE, Shalem O, Yuan GC, Zhang F, Concordet JP, Pinello L. Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments. Nat Protoc. 2018 May;13(5):946-986. PMID: 29651054; PMC: PMC6182299

Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, Hinrichs AS, Haeussler M, Guruvadoo L, Navarro Gonzalez J, Gibson D, Fiddes IT, Eisenhart C, Diekhans M, Clawson H, Barber GP, Armstrong J, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2018 update. Nucleic Acids Res. 2018 Jan 4;46(D1):D762-D769. PMID: 29106570; PMC: PMC5753355

Concordet JP, Haeussler M. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Res. 2018 Jul 2;46(W1):W242-W245. PMID: 29762716; PMC: PMC6030908

Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, Flicek P. Registered access: authorizing data access. Eur J Hum Genet. 2018 Dec;26(12):1721-1731. PMID: 30069064; PMC: PMC6244209

Howard JM, Lin H, Wallace AJ, Kim G, Draper JM, Haeussler M, Katzman S, Toloue M, Liu Y, Sanford JR. HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo. Genome Res. 2018 May;28(5):689-698. PMID: 29650551; PMC: PMC5932609

2017

Adema CM, Hillier LW, Jones CS, Loker ES, Knight M, Minx P, Oliveira G, Raghavan N, Shedlock A, do Amaral LR, Arican-Goktas HD, Assis JG, Baba EH, Baron OL, Bayne CJ, Bickham-Wright U, Biggar KK, Blouin M, Bonning BC, Botka C, Bridger JM, Buckley KM, Buddenborg SK, Lima Caldeira R, Carleton J, Carvalho OS, Castillo MG, Chalmers IW, Christensens M, Clifton S, Cosseau C, Coustau C, Cripps RM, Cuesta-Astroz Y, Cummins SF, di Stephano L, Dinguirard N, Duval D, Emrich S, Feschotte C, Feyereisen R, FitzGerald P, Fronick C, Fulton L, Galinier R, Gava SG, Geusz M, Geyer KK, Giraldo-Calderón GI, de Souza Gomes M, Gordy MA, Gourbal B, Grunau C, Hanington PC, Hoffmann KF, Hughes D, Humphries J, Jackson DJ, Jannotti-Passos LK, de Jesus Jeremias W, Jobling S, Kamel B, Kapusta A, Kaur S, Koene JM, Kohn AB, Lawson D, Lawton SP, Liang D, Limpanont Y, Liu S, Lockyer AE, Lovato TL, Ludolf F, Magrini V, McManus DP, Medina M, Misra M, Mitta G, Mkoji GM, Montague MJ, Montelongo C, Moroz LL, Munoz-Torres MC, Niazi U, Noble LR, Oliveira FS, Pais FS, Papenfuss AT, Peace R, Pena JJ, Pila EA, Quelais T, Raney BJ et al. Whole genome analysis of a schistosomiasis-transmitting freshwater snail. Nat Commun. 2017 May 16;8:15451. PMID: 28508897; PMC: PMC5440852

Brozovic M, Dantec C, Dardaillon J, Dauga D, Faure E, Gineste M, Louis A, Naville M, Nitta KR, Piette J, Reeves W, Scornavacca C, Simion P, Vincentelli R, Bellec M, Aicha SB, Fagotto M, Guéroult-Bellone M, Haeussler M, Jacox E, Lowe EK, Mendez M, Roberge A, Stolfi A, Yokomori R, Brown CT, Cambillau C, Christiaen L, Delsuc F, Douzery E, Dumollard R, Kusakabe T, Nakai K, Nishida H, Satou Y, Swalla B, Veeman M, Volff JN, Lemaire P. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res. 2018 Jan 4;46(D1):D718-D725. PMID: 29149270; PMC: PMC5753386

GTEx Consortium., Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group., Statistical Methods groups—Analysis Working Group., Enhancing GTEx (eGTEx) groups., NIH Common Fund., NIH/NCI., NIH/NHGRI., NIH/NIMH., NIH/NIDA., Biospecimen Collection Source Site—NDRI., Biospecimen Collection Source Site—RPCI., Biospecimen Core Resource—VARI., Brain Bank Repository—University of Miami Brain Endowment Bank., Leidos Biomedical—Project Management., ELSI Study., Genome Browser Data Integration &Visualization—EBI., Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz et al. Genetic effects on gene expression across human tissues. Nature. 2017 Oct 11;550(7675):204-213. PMID: 29022597; PMC: PMC5776756

He C, Hu X, Jung RS, Larsson M, Tu Y, Duarte-Vogel S, Kim P, Sandoval NP, Price TR, Allan CM, Raney B et al. Lipoprotein lipase reaches the capillary lumen in chickens despite an apparent absence of GPIHBP1. JCI Insight. 2017 Oct 19;2(20). PMID: 29046479; PMC: PMC5846916

Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, GTEx Consortium., Engelhardt BE, Battle A. Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res. 2017 Nov;27(11):1843-1858. PMID: 29021288; PMC: PMC5668942

Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, GTEx Consortium., Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group., Statistical Methods groups—Analysis Working Group., Enhancing GTEx (eGTEx) groups., NIH Common Fund., NIH/NCI., NIH/NHGRI., NIH/NIMH., NIH/NIDA., Biospecimen Collection Source Site—NDRI., Biospecimen Collection Source Site—RPCI., Biospecimen Core Resource—VARI., Brain Bank Repository—University of Miami Brain Endowment Bank., Leidos Biomedical—Project Management., ELSI Study., Genome Browser Data Integration & Visualization—EBI., Genome Browser Data Integration & Visualization—UCSC Genomics Institute, University of California Santa Cruz., Chawla A, Del Sal G, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB. Dynamic landscape and regulation of RNA editing in mammals. Nature. 2017 Oct 11;550(7675):249-254. PMID: 29022589; PMC: PMC5723435

Tyner C, Barber GP, Casper J, Clawson H, Diekhans M, Eisenhart C, Fischer CM, Gibson D, Gonzalez JN, Guruvadoo L, Haeussler M, Heitner S, Hinrichs AS, Karolchik D, Lee BT, Lee CM, Nejad P, Raney BJ, Rosenbloom KR, Speir ML, Villarreal C, Vivian J, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2017 update. Nucleic Acids Res. 2017 Jan 4;45(D1):D626-D634. PMID: 27899642; PMC: PMC5210591

Vivian J, Rao AA, Nothaft FA, Ketchum C, Armstrong J, Novak A, Pfeil J, Narkizian J, Deran AD, Musselman-Brown A, Schmidt H, Amstutz P, Craft B, Goldman M, Rosenbloom K, Cline M, O'Connor B, Hanna M, Birger C, Kent WJ, Patterson DA, Joseph AD, Zhu J, Zaranek S, Getz G, Haussler D, Paten B. Toil enables reproducible, open source, big biomedical data analyses. Nat Biotechnol. 2017 Apr 11;35(4):314-316. PMID: 28398314; PMC: PMC5546205

Yang F, Wang J, GTEx Consortium., Pierce BL, Chen LS. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Res. 2017 Nov;27(11):1859-1871. PMID: 29021290; PMC: PMC5668943

2016

Haeussler M, Concordet JP. Genome Editing with CRISPR-Cas9: Can It Get Any Better?. J Genet Genomics. 2016 May 20;43(5):239-50. PMID: 27210042; PMC: PMC5708852

Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016 Jul 5;17(1):148. PMID: 27380939; PMC: PMC4934014

Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics. 2016 May 1;32(9):1430-2. PMID: 26740527; PMC: PMC4848401

Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods. 2016 Mar;13(3):245-7. doi: 10.1038/nmeth.3732. Epub 2016 Jan 18. PMID: 26780094; PMC: PMC4767623

Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe G, Podduturi NR, Tanaka F, Hong EL, Cherry JM. ENCODE data at the ENCODE portal. Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32. doi: 10.1093/nar/gkv1160. Epub 2015 Nov 2. PMID: 26527727; PMC: PMC4702836

Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, Eisenhart C, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2016 update. Nucleic Acids Res. 2016 Jan 4;44(D1):D717-25. PMID: 26590259; PMC: PMC4702902

2015

1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA et al. A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. PMID: 26432245; PMC: PMC4750478

Foote AD, Liu Y, Thomas GW, Vinar T, Alfoldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu J, Raney BJ, Vijay N, Wolf JB, Hahn MW, Muzny DM, Worley KC, Gilbert MT, Gibbs RA. Convergent evolution of the genomes of marine mammals. Nat Genet. Epub 2015 Jan 26. doi: 10.1038/ng.3198. PMID: 25621460; PMC: PMC4644735

Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ. Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics 2015 Mar 1;31(5):764-6. doi: 10.1093/bioinformatics/btu712. Epub 2014 Oct 27. PMID: 25348212; PMC: PMC4341066

Koepfli KP, Paten B, Genome 10K Community of Scientists, O'Brien SJ. The Genome 10K Project: A way forward. Annu Rev Anim Biosci. 2015 Feb 16;3:57-111. doi: 10.1146/annurev-animal-090414-014900. PMID: 25689317

Lowe CB, Clarke JA, Baker AJ, Haussler D, Edwards SV. Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Mol Biol Evol. 2015 Jan;32(1):23-8. doi: 10.1093/molbev/msu309. Epub 2014 Nov 18. PMID: 25415961; PMC: PMC4271537

Miga KH. Completing the human genome: the progress and challenge of satellite DNA assembly. Chromosome Res. 2015 Sep;23(3):421-6. PMID: 26363799

Miga KH, Eisenhart C, Kent WJ. Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments. Nucleic Acids Res. 2015 Nov 16;43(20):e133. doi: 10.1093/nar/gkv671. Epub 2015 Jul 10. PMID: 26163063; PMC: PMC4787761

Novak AM, Rosen Y, Haussler D, Paten B. Canonical, stable, general mapping using context schemes. Bioinformatics. 2015 Nov 15;31(22):3569-76. doi: 10.1093/bioinformatics/btv435. Epub 2015 Jul 27. PMID: 26220960; PMC: PMC4757953

Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Building a pan-genome reference for a population. J Comput Biol. 2015 May;22(5):387-401. PMID: 25565268; PMC: PMC4424974

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19;518:317-30. doi: 10.1038/nature14248. PMID: 25693563; PMC: PMC4424974

Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D670-81. doi: 10.1093/nar/gku1177. Epub 2014 Nov 26. PMID: 25428374; PMC: PMC4383971

Singhal S, Leffler EM, Sannareddy K, Turner I, Venn O, Hooper DM, Strand AI, Li Q, Raney B, Balakrishnan CN, Griffith SC, McVean G, Przeworski M. Stable recombination hotspots in birds. Science. 2015 Nov 20;350(6263):928-32. PMID: 26586757

2014

Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B, Mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Principles of regulatory information conservation between mouse and human. Nature. 2014 Nov 20;515(7527):371-5. doi: 10.1038/nature13985. PMID: 25409826

Earl D, Nguyen NK, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney B, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B. Alignathon: A competitive assessment of whole genome alignment methods. Genome Res. 2014 Dec;24(12):2077-89. doi: 10.1101/gr.174920.114. Epub 2014 Oct 1. PMID: 25273068; PMC: PMC4248324

Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD. Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res. 2014 Jan 1;42(1):D865-72. Epub 2013 Nov 11. PMID: 24217909; PMC: PMC3965069

Haeussler M, Karolchik D, Clawson H, Raney BJ, Rosenbloom KR, Fujita PA, Hinrichs AS, Speir ML, Eisenhart C, Zweig AS, Haussler D, Kent WJ. The UCSC Ebola Genome Portal. PLOS Currents Outbreaks 2014 Nov 7. Edition 1.

Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014 Jan 1;42(1):D764-70. Epub 2013 Nov 21. PMID: 24270787; PMC: PMC3964947

Kolmogorov M, Raney B, Paten B, Pham S. Ragout—a reference-assisted assembly tool for bacterial genomes. Bioinformatics. 2014 June 15;30(12):i302-9. PMID: 24931998; PMC: PMC4058940

Mangan ME, Williams JM, Kuhn RM, Lathe WC 3rd. The UCSC Genome Browser: What every molecular biologist should know. Curr Protoc Mol Biol. 2014 Jul 1;107:19.9:19.9.1-19.9.36. PMID: 24984850; PMC: PMC4142428

Marmoset Genome Sequencing and Analysis Consortium. The common marmoset genome provides insight into primate biology and evolution. Nat Genet. 2014 Aug;46(8):850-7. doi: 10.1038/ng.3042. Epub 2014 Jul 20. PMID: 25038751; PMC: PMC4138798

Miga K. Our first view into the "blackout zones" of the human genome. Sci Am guest blog. 2014 Mar 6.

Miga KH, Newton Y, Jain M, Altemose N, Willard HF, Kent WJ. Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res. 2014 Apr;24(4):697-707. Epub 2014 Feb 5. PMID: 24501022; PMC: PMC3975068

Nilsson CL, Mostovenko E, Lichti CF, Ruggles K, Fenyö D, Rosenbloom KR, Hancock WS, Paik YK, Omenn GS, LaBaer J, Kroes RA, Uhlén M, Hober S, Végvári Á, Andrén PE, Sulman EP, Lang FF, Fuentes M, Carlsohn E, Emmett MR, Moskal JR, Berven FS, Fehniger TE, Marko-Varga G. Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome. J Proteome Res. 2015 Feb 6;14(2):603-8. doi: 10.1021/pr500564q. Epub 2014 Nov 26. PMID: 25369122

Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. Comparative assembly hubs: Web-accessible browsers for comparative genomics. Bioinformatics. 2014 Dec 1;30(23):3293-301. doi: 10.1093/bioinformatics/btu534. Epub 2014 Aug 18. PMID: 25138168

Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. 2014 Apr 1;30(7):1003-5. Epub 2013 Nov 13. PMID: 24227676; PMC: PMC3967101

Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC. Elephant shark genome provides unique insights into gnathostome evolution. Nature. 2014 Jan 9;505(7482):174-9. PMID: 24402279; PMC: PMC3964593

Wilks C, Cline MS, Weiler E, Diehkans M, Craft B, Martin C, Murphy D, Pierce H, Black J, Nelson D, Litzinger B, Hatton T, Maltbie L, Ainsworth M, Allen P, Rosewood L, Mitchell E, Smith B, Warner J, Groboske J, Telc H, Wilson D, Sanford B, Schmidt H, Haussler D, Maltbie D. The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Database (Oxford). 2014 Sep 29;2014. pii: bau093. doi: 10.1093/database/bau093. PMID: 25267794; PMC: PMC4178372

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992. PMID: 25409824; PMC: PMC4266106

2013

Brennan CW, Verhaak RGW, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH et al. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10;155(2):462-77. PMID: 24120142; PMC: PMC3910500

Ewing AD, Ballinger TJ, Earl D, Broad Institute Genome Sequencing and Analysis Program and Platform, Harris CC, Ding L, Wilson RK, Haussler D. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biol. 2013 Mar 13;14(3):R22. PMID: 23497673; PMC: PMC3663115

Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M, Ma S, Wilks C, Stuart J, Haussler D, Zhu J. The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D949-54. PMID: 23109555; PMC: PMC3531186

Hickey G, Paten B, Earl D, Zerbino D, Haussler D. HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics. 2013 May 15;29(10):1341-2. PMID: 23505295; PMC: PMC3654707

Kuhn RM, Haussler D, Kent WJ. The UCSC genome browser and associated tools. Brief Bioinform. 2013 Mar;14(2):144-61. PMID: 22908213; PMC: PMC3603215

Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9. PMID: 23155063; PMC: PMC3531082

Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 2013 Jan;41(Database issue):D56-63. PMID: 23193274; PMC: PMC3531152

Sanborn JZ, Salama SR, Grifford M, Brennan CW, Mikkelsen T, Jhanwar S, Katzman S, Chin L, Haussler D. Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Cancer Res. 2013 Oct 1;73(19):6036-45. Epub 2013 Aug 12. PMID: 23940299; PMC: PMC3800429

Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning AJ, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol. 2013 Mar 28;14(3):R28. PMID: 23537068; PMC: PMC4054807

Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D, Stuart JM. The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Res. 2013 Jul 1;41(Web Server issue):W218-24. PMID: 23748957; PMC: PMC3692096

Zerbino DR, Paten B, Hickey G, Haussler D. An algebraic framework to sample the rearrangement histories of a cancer metagenome with double cut and join, duplication and deletion events. arXiv:1303.5569v1 [q-bio.GN]. 2013 Mar 22.

2012

de Leeuw N, Dijkhuizen T, Hehir-Kwa JY, Carter NP, Feuk L, Firth HV, Kuhn RM, Ledbetter DH, Martin CL, van Ravenswaaij-Arts CM, Scherer SW, Shams S, Van Vooren S, Sijmons R, Swertz M, Hastings R. Diagnostic interpretation of array data using public databases and internet sources. Hum Mutat. 2012 Jun;33(6):930-40. PMID: 26285306; PMC: PMC5027376

Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS, Li CH, Learned K, Kirkup V, Hsu F, Harte RA, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 2012 Jan;40(Database issue):D918-23. PMID: 22086951; PMC: PMC3245018

ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMC: PMC3439153

Harte RA, Farrell CM, Loveland JE, Suner MM, Wilming L, Aken B, Barrell D, Frankish A, Wallin C, Searle S, Diekhans M, Harrow J, Pruitt KD. Tracking and coordinating an international curation effort for the CCDS Project. Database (Oxford). 2012;2012:bas008. PMID: 22434842; PMC: PMC3308164

Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, Bayani N, Hu Z, Billig JI, Dueregger A, Lewis S, Jakkula L, Korkola JE, Durinck S, Pepin F, Guan Y, Purdom E, Neuvial P, Bengtsson H, Wood KW, Smith PG, Vassilev LT, Hennessy BT, Greshock J, Bachman KE, Hardwicke MA, Park JW, Marton LJ, Wolf DM, Collisson EA, Neve RM, Mills GB, Speed TP, Feiler HS, Wooster RF, Haussler D, Stuart JM, Gray JW, Spellman PT. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2724-9. PMID: 22003129; PMC: PMC3286973

Karolchik D, Hinrichs AS, Kent WJ. The UCSC Genome Browser. Curr Protoc Bioinformatics. 2012 Dec;Chapter 1:Unit1.4. PMID: 23255150

Kristensen VN, Vaske CJ, Ursini-Siegel J, Van Loo P, Nordgard SH, Sachidanandam R, Sørlie T, Wärnberg F, Haakensen VD, Helland Å, Naume B, Perou CM, Haussler D, Troyanskaya OG, Børresen-Dale AL. Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2802-7. PMID: 21908711; PMC: PMC3286992

Lowe CB, Haussler D. 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS One. 2012;7(8):e43128. PMID: 22952639; PMC: PMC3428314

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie1 BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13;13(8):418. PMID: 22889292; PMC: PMC3491367

Riggs ER, Church DM, Hanson K, Horner VL, Kaminsky EB, Kuhn RM, Wain KE, Williams ES, Aradhya S, Kearney HM, Ledbetter DH, South ST, Thorland EC, Martin CL. Towards an evidence-based process for the clinical interpretation of copy number variation. Clin Genet. 2012 May;81(5):403-12. PMID: 22097934

Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, Goldman M, Gravell RC, Harte RA, Hinrichs AS, Kirkup VM, Kuhn RM, Learned K, Maddren M, Meyer LR, Pohl A, Rhead B, Wong MC, Zweig AS, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res. 2012 Jan;40(Database issue):D912-7. PMID: 22075998; PMC: PMC3245183

St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ Jr, Glenn TC, Green RE, Ray DA. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol. 2012 Jan 31;13(1):415. PMID: 22293439; PMC: PMC3334581

Wong PB, Wiley EO, Johnson WE, Ryder OA, O'Brien SJ, Haussler D, Koepfli KP, Houck ML, Perelman P, Mastromonaco G, Bentley AC, Venkatesh B, Zhang YP, Murphy RW, G10KCOS. Tissue sampling methods and standards for vertebrate genomics. Gigascience. 2012 Jul 12;1(1):8. PMID: 23587255; PMC: PMC3626508

Zerbino DR, Paten B, Haussler D. Integrating genomes. Science. 2012 Apr 13;336(6078):179-82. PMID: 22499938

2011

Alfoldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 2011 Aug 31;477(7366):587-91.

Balasubramanian S, Habegger L, Frankish A, MacArthur DG, Harte R, Tyler-Smith C, Harrow J, Gerstein M. Gene inactivation and its implications for annotation in the era of personal genomics. Genes Dev. 2011 Jan 1;25(1):1-10.

Cline MS, Karchin R. Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. 2011 Feb 15;27(4):441-8. Epub 2010 Dec 15.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011 Dec;21(12):2224-41.

ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046. PMID: 21526222; PMC: PMC3079585

Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82. PMID: 20959295; PMC: PMC3242726

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82.

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P et al. Comparative and demographic analysis of orang-utan genomes. Nature. 2011 Jan 27;469(7331):529-53.

Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. Three periods of regulatory innovation during vertebrate evolution. Science. 2011 Aug 19;333(6045):1019-24.

Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D. Cactus graphs for genome comparisons. J Comput Biol. 2011 Mar;18(3):469-81.

Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 2011 Jan;39(Database issue):D871-5. PMID: 21037257; PMC: PMC3013645

Roskin KM, Paten B, Haussler D. Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization. BMC Bioinformatics. 2011 May 10;12(1):144.

Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J. The UCSC Cancer Genomics Browser database: update 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D951-9. Epub 2010 Nov 8.

The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 30;474:609-615.

Wang NJ, Sanborn Z, Arnett KL, Bayston LJ, Liao W, Proby CM, Leigh IM, Collisson EA, Gordon PB, Jakkula L et al. Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma. Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17761-6.

Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P et al. The Human Epigenome Browser at Washington University. Nat Methods. 2011 Nov;8:989-90. Epub 2011 Nov 29.

2010

1000 Genomes Project Consortium, Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73.

Churakov G, Sadasivuni MK, Rosenbloom KR, Huchon D, Brosius J, Schmitz J. Rodent evolution: back to the root. Mol Biol Evol. 2010 Jun;27(6):1315-26. PMID: 20100942

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct;28(10):1097-105. Epub 2010 Sep 19.

Harte, R. A., Diekhans, M., Kent, W. J. & Haussler, D. Guide to the UCSC Genome Browser. Cambridge, MA: NPG Education, 2010.

Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed data sets. Bioinformatics. 2010 Sep 1;26(17):2204-7. Epub 2010 Jul 17.

Kern AD, Haussler D. A population genetic hidden Markov model for detecting genomic regions under selection. Mol Biol Evol. 2010 Jul;27(7):1673-85. Epub 2010 Feb 25.

Lowe CB, Bejerano G, Salama SR, Haussler D. Endangered species hold clues to human evolution. J Hered. 2010 Jul-Aug;101(4):437-47. Epub 2010 Mar 23.

Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, Scherer SW, Spinner NB, Stavropoulos DJ, Tepperberg JH, Thorland EC, Vermeesch JR, Waggoner DJ, Watson MS, Martin CL, Ledbetter DH. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010 May 14;86(5):749-64.

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Feb 3;470(7332):59-65.

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823

Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9. PMID: 19906737; PMC: PMC2808870

Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5. PMID: 19920125; PMC: PMC2808953

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project, Eichler EE. Diversity of human copy number variation and multicopy genes. Science. 2010 Oct 29;330(6004):641-6.

Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods. 2010 Dec;7(12):995-1001. Epub 2010 Nov 7.

Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics. 2010 Jun 15;26(12):i237-45.

2009

Cline MS, Kent WJ. Understanding genome browsing. Nat Biotechnol. 2009 Feb;27(2):153-5.

Genome 10K Community of Scientists. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 2009 Nov;100:659-674.

Han J, Pedersen JS, Kwon SC, Belair CD, Kim YK, Yeom KH, Yang WY, Haussler D, Blelloch R, Kim VN. Posttranscriptional crossregulation between Drosha and DGCR8. Cell. 2009 Jan 9;136(1):75-84.

Harte RA, Karolchik D, Kuhn RM, Kent WJ, Haussler D. Databases and Genome Browsers. In Speicher M, Antonarakis S, Motulsky AG. (eds): Vogel and Motulsky's Human Genetics, Principles and Approaches, 4th Edition, Springer, New York, 2009.

Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 2009 Jan;37:D755-D761.

Mangan ME, Williams JM, Kuhn RM, Lathe WC 3rd. The UCSC genome browser: what every molecular biologist should know. Curr Protoc Mol Biol. 2009 Oct;Chapter 19:Unit19.9. PMID: 19816931

The MGC Project Team. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 Dec;19:2324-33.

Pohl AA, Sugnet CW, Clark TA, Smith K, Fujita PA, Cline MS. Affy Exon Tissues: exon levels in normal tissues in human, mouse, and rat. Bioinformatics. 2009 Sept 15;25(18):2442-3.

Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R, Lipman D. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009 Jul;19(7):1316-23.

Zhu J, Sanborn JZ, Benz S, Szeto C, Hsu F, Kuhn R, Karolchik D, Archie J, Lenburg M, Esserman L, Kent J, Haussler D, Wang T. The UCSC Cancer Genomics Browser. Nat Methods. 2009 Apr;6(4):239-40.

2008

Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics. 2008 Oct 8;9(1):466.

Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Computational reconstruction of ancestral DNA sequences. Methods Mol Biol. 2008;422:171-84.

Buckley M, Walker A, Ho SY, Yang Y, Smith C, Ashton P, Oates JT, Cappellini E, Koon H, Penkman K, Elsworth B, Ashford D, Solazzo C, Andrews P, Strahler J, Shapiro B, Ostrom P, Gandhi H, Miller W, Raney B, Zylber MI, Gilbert MT, Prigodich RV, Ryan M, Rijsdijk KF, Janoo A, Collins MJ. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science. 2008 Jan 4;319(5859):33; author reply 33.

Karolchik D, Kuhn, RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 2008 Jan;36:D773-9.

Lathe W, Williams J, Mangan M, Karolchik D. Genomic data resources: challenges and promises. Nature Education. 2008;1(3).

Ma J. Reconstructing ancient DNA sequences in silico. In Cooper DN and Kehrer-Sawatzki H. (ed): Handbook of Human Molecular Evolution, John Wiley & Sons, Inc., New Jersey, 2008.

Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D. The infinite sites model of genome evolution. Proc Natl Acad Sci USA. 2008 Sep 23;105(38):14254-61.

Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, and Haussler D. DUPCAR: Reconstructing contiguous ancestral regions with duplications. J Computational Biol. 2008 Oct;15(8):1007-27.

Mangan ME, Williams JM, Lathe SM, Karolchik D, Lathe WC 3rd. UCSC genome browser: deep support for molecular biomedical research. Biotechnol Annu Rev. 2008;14:63-108. PMID: 18606360

Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, Tomsho LP, Packard MD, Zhao F, Sher A, Tikhonov A, Raney B, Patterson N, Lindblad-Toh K, Lander ES, Knight JR, Irzyk GP, Fredrikson KM, Harkins TT, Sheridan S, Pringle T, Schuster SC. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 2008 Nov 20;456(7220):387-90.

Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W. Phylogenomic resources at the UCSC Genome Browser. In Murphy WJ. (ed): Methods in Molecular Biology: Phylogenomics, Springer, New York, 2008.

Schattner P. Genomes, Browsers and Databases: Data-Mining Tools for Integrated Genomic Databases. Cambridge University Press, Cambridge, UK, 2008.

Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44.

Twigger SN, Pruitt KD, Fernández-Suárez XM, Karolchik D, Worley KC, Maglott DR, Brown G, Weinstock G, Gibbs RA, Kent J, Birney E, Jacob HJ. What everybody should know about the rat genome and its online resources. Nat Genet. 2008 May;40(5):523-7.

Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18613-8. PMID: 18003932; PMC: PMC2141825

Zheng J, Yan J, Wang T, Mosbrook-Davis D, Dolan K, Christensen R, Stormo G, Haussler D, Lathrop R, Brachmann R, Burgess SM. Genome wide screens in yeast to identify potential binding sites and target genes of DNA binding proteins. Nucleic Acids Res. 2008 Jan;36(1):e8.

Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247.

Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. UCSC genome browser tutorial. Genomics. 2008 Aug;92(2):75-84. PMID: 18514479

2007

Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Computational reconstruction of ancestral DNA sequences. In Murphy WJ. (ed): Methods in Molecular Biology: Phylogenomics, Springer, New York, 2007.

Dreszer TR, Wall GD, Haussler D, Pollard KS. Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res. 2007 Oct;17(10):1420-30.

Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-218.

The ENCODE Project Consortium et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.

Giardine B, Riemer C, Hefferon T, Thomas D, Hsu F, Zielenski J, Sang Y, Elnitski L, Cutting G, Trumbower H, Kern A, Kuhn R, Patrinos GP, Hughes J, Higgs D, Chui D, Scriver C, Phommarinh M, Patnaik SK, Blumenfeld O, Gottlieb B, Vihinen M, Väliaho J, Kent J, Miller W, Hardison RC. PhenCode: connecting ENCODE data with mutations and phenotype. Hum Mutat. 2007 Jun;28(6):554-62. PMID: 17326095

The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18;449(7164):851-861.

Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. Comparative genomic analysis using the UCSC Genome Browser. In Bergman NH. (ed): Methods in Molecular Biology: Comparative Genomics, Volume 1, Springer, New York, 2007.

Karolchik D, Hinrichs AS, Kent WJ. The UCSC Genome Browser. Curr Protoc Bioinformatics. 2007 Mar;Chapter 1:Unit 1.4.

Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D. Human genome ultraconserved elements are ultraselected. Science. 2007 Aug 17;317(5840):915. [reprints] [supporting online materials] [materials and methods]

Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D, Kent, WJ. The UCSC Genome Browser database: update 2007. Nucleic Acids Res. 2007 Jan;35(Database issue):D668-73.

Li G, Ma J, Zhang L. Selecting genomes for reconstruction of ancestral genomes. 5th Annual RECOMB Satellite Workshop on Comparative Genomics. In McLysaght and A, Huson, DH. Lecture Notes in Computer Science: Comparative Genomics, 4751: 110-21, Springer, Berlin/Heidelberg, 2007.

Lowe CB, Bejerano G, Haussler D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci USA. 2007 May 8;104(19):8005-10.

Ma J, Ratan A, Zhang L, Miller W, Haussler D. A heuristic algorithm for reconstructing ancestral gene orders with duplications. In Lecture Notes in Computer Science: Comparative Genomics, Springer, Berlin/Heidelberg, 2007;4751:122-135.

Margulies E, Cooper G, Asimenos G, Thomas D, Dewey C, Siepel A, Birney E, Keefe D, Schwartz A, Hou M, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007 Jun;17(6):760-74.

Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 2007 Dec;17(12):1797-808.

Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M Jr. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev 2007 Mar 15;21(6):708-18.

Ohlson J, Pedersen JS, Haussler D, Öhman M. Editing modifies the GABAA receptor subunit a3. RNA. 2007 Mar;13:1-6.

Rhesus Macaque Genome Sequencing and Analysis Consortium et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13;316(5822):222-34.

Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73.

Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007 Nov 8;450(7167):219-232.

Thomas DJ, Rosenbloom KR, Clawson H, Hinrichs, AS, Trumbower H, Raney BJ, Karolchik D, Barber GP, Harte RA, Hillman-Jackson J, Kuhn RM, Rhead BL, Smith KE, Thakkapallayil A, Zweig AS, The ENCODE Project Consortium, Haussler D, Kent WJ. The ENCODE project at UC Santa Cruz. Nucleic Acids Res. 2007 Jan;35(Database issue):D663-7.

Thomas DJ, Trumbower H, Kern AD, Rhead BL, Kuhn RM, Haussler D, Kent WJ. Variation resources at UC Santa Cruz. Nucleic Acids Res. 2007 Jan;35(Database issue):D716-20.

Wang, T. Using PhyloCon to Identify Conserved Regulatory Motifs. Curr Protoc Bioinformatics. 2007 Sep;Chapter 2:Unit 2.12.

Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci USA. 2007 Nov 20;104(47):18613-8.

Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007 Jun;17(6):852-64.

Yeang CH, Darot JF, Noller HF, Haussler D. Detecting the coevolution of biosequences--an example of RNA interaction prediction. Mol Biol Evol. 2007 Sep;24(9):2119-31.

Yeang CH and Haussler D. Detecting coevolution in and among protein domains. PLoS Comput Biol. 2007 Nov;3(11):e211.

Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, et al. Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription and evolution. Genome Res. 2007 Jun;17(6):839-51.

Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle T, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247.

2006

Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 2006 May 4;441(7089):87-90.

Darot J, Yeang CH, Haussler D. Detecting the dependent evolution of biosequences. In Proc. 10th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '06) (2006).

DiBiase A, Harte RA, Zhou Y, Zon L, Kent WJ. Piloting the zebrafish genome browser. Dev Dyn. 2006 Mar;235(3):747-53.

Drake JA, Bird C, Nemesh J, Thomas DJ, Newton-Cheh C, Reymond A, Excoffier L, Attar H, Antonarakis SE, Dermitzakis ET, Hirschhorn JN. Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet. 2006 Feb;38(2):223-7.

Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8.

Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC Known Genes. Bioinformatics. 2006 May 1;22(9):1036-46. PMID: 16500937

Kabat JL, Barberan-Soler S, McKenna P, Clawson H, Farrer T, Zahler AM. Intronic Alternative Splicing Regulators Identified by Comparative Genomics in Nematodes. PLoS Comput Biol. 2006 Jul 14;2(7):e86.

Kent J. XML, SQL, and C. Dr. Dobb's. 2006 Dec;31(12):32-9.

Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W. Reconstructing contiguous regions of an ancestral genome. Genome Res. 2006 Dec;16(12):1557-65.

Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006 Apr;2(4):e33.

Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D. Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2006 Oct 13;2(10):e168.

Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussler D. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14;443(7108):167-72.

Schattner P, Diekhans M. Regions of extreme synonymous codon selection in mammalian genes Nucleic Acids Res. 2006 Mar 23;34(6):1700-10.

Siepel A, Pollard KS, Haussler D. New methods for detecting lineage-specific selection. In Proc. 10th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '06).

Smith DI, Zhu Y, McAvoy S, Kuhn R. Common fragile sites, extremely large genes, neural development and cancer. Cancer Lett. 2006 Jan 28;232(1):48-57. PMID: 16221525

Taylor TD, Noguchi H, Totoki Y, Toyoda A, Kuroki Y, Dewar K, Lloyd C, Itoh T, Takeda T, Kim DW et al. Human chromosome 11 DNA sequence and analysis including novel gene identification. Nature. 2006 Mar 23;440(7083):497-500.

Zhu Y, McAvoy S, Kuhn R, Smith DI. RORA, a large common fragile site gene, is involved in cellular stress response. Oncogene. 2006 May 11;25(20):2901-8. PMID: 16462772

2005

Bejerano G, Siepel AC, Kent WJ, Haussler D. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat Methods. 2005 Jul;2(7):535-45. [reprint]

Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res. 2005 Nov;15(11):1553-65.

The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005 Sep 1;437(7055):69-87.

Glazov EA, Pheasant M, McGraw EA, Bejerano G, Mattick JS. Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res. 2005 Jun;15(6):800-8.

Hsu F, Pringle TH, Kuhn RM, Karolchik D, Diekhans M, Haussler D, Kent WJ. The UCSC Proteome Browser. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D454-8.

The International HapMap Consortium. A haplotype map of the human genome. Nature. 2005 Oct 27;437(7063):1299-320.

Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. LS-SNP: Large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 2005 Jun 15;21(12):2814-20.

Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. 2005 May;15(5):737-41.

Lucena B, Haussler D. Counterexample to a Claim About the Reconstruction of Ancestral Character States. Syst Biol. 2005 Aug;54(4):693-5.

Nusbaum C, Zody MC, Borowsky ML, Kamal M, Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K et al. DNA sequence and analysis of human chromosome 18. Nature. 2005 Sep 22;437(7058):551-5.

Robertson MP, Igel H, Baertsch R, Haussler D, Ares M Jr, Scott WG. The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol. 2005 Jan;3(1):e5.

Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP et al. The DNA sequence of the human X chromosome. Nature. 2005 Mar 17;434(7031):325-37.

Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. Identifying genetic networks underlying myometrial transition to labor. Genome Biol. 2005;6(2):R12.

Scherer SE, Muzny DM, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA et al. The finished DNA sequence of human chromosome 12. Nature. 2006 Mar 16;440(7082):346-51.

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50.

Siepel A, Haussler D. Phylogenetic hidden Markov models. In Nielsen R. (ed): Statistical Methods in Molecular Evolution, Springer, New York, 2005; 325-251.

Smith AV, Thomas DJ, Munro HM, Abecasis GR. Sequence features in regions of weak and strong linkage disequilibrium. Genome Res. 2005 Nov;15(11):1519-34.

2004

Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. Hotspots of mammalian chromosomal evolution. Genome Biol. 2004;5(4):R23.

Bejerano G. Algorithms for variable length Markov chain modeling. Bioinformatics. 2004 Mar 22;20(5):788-9.

Bejerano G, Friedman N, Tishby N. Efficient Exact p-Value Computation for Small Sample, Sparse and Surprising Categorical Data. J Comput Biol. 2004;11(5):867-86.

Bejerano G, Haussler D, Blanchette M. Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics. 2004 Aug 4;20 Suppl 1:I40-I48.

Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved elements in the human genome. Science. 2004 May 28;304(5675):1321-5. [reprint] [supplement] [website]

Blanchette M, Green ED, Miller W, Haussler D. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res. 2004 Dec;14(12):2412-23.

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15.

Dudoit S, van der Laan MJ, Pollard KS. Multiple testing. Part I. Single-step procedures for control of general type I error rates. Stat Appl Genet Mol Biol. 2004;3(1):Article13.

The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40.

Furey TS, Diekhans M, Lu Y, Graves TA, Oddy L, Randall-Maher J, Hillier LW, Wilson RK, Haussler D. Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. Genome Res. 2004 Oct;14(10B):2034-40.

Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M et al. The DNA sequence and biology of human chromosome 19. Nature. 2004 Apr 1;428(6982):529-35.

International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 9;432(7018):695-716.

International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004 Oct 21;431(7011):931-45.

Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ. Comparative recombination rates in the rat, mouse, and human genomes. Genome Res. 2004 Apr;14(4):528-38.

Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D. Efficient approximations for learning phylogenetic HMM models from data. Proc of ISMB 2004 and Bioinformatics. 2004 Aug 4;20 Suppl 1:I161-I168.

Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6.

MGC Project Team. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7.

Pollard KS, van der Laan MJ. Choice of a null distribution in resampling-based multiple testing. J Statistical Planning and Inference. 2004;125: 85-100.

Rat Genome Sequencing Project Consortium. Genome sequence of the brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521.

Roskin KM, Diekhans M, Haussler D. Score functions for determining regional conservation in two-species local alignments. J Comput Biol. 2004;11(2-3):395-411.

She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C et al. The structure and evolution of centromeric transition regions within the human genome. Nature. 2004 Aug 19;430(7002):857-64.

Siepel A, Haussler D. Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol. 2004;11(2-3):413-28.

Siepel A, Haussler D. Computational identification of evolutionarily conserved exons. Proc. 8th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '04):177-186.

Siepel A, Haussler D. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol. 2004 Mar;21(3):468-88.

Sugnet CW, Kent WJ, Ares M Jr, Haussler D. Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput. 2004;:66-77.

van der Laan MJ, Dudoit S, Pollard KS. Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Stat Appl Genet Mol Biol. 2004;3(1):Article15.

van der Laan MJ, Dudoit S, Pollard KS. Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Stat Appl Genet Mol Biol. 2004;3(1):Article14.

Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC. Patterns of insertions and their covariation with substitutions in the rat, mouse and human genomes. Genome Res. 2004 Apr;14(4):517-27.

2003

Blanchette M. A comparative analysis method for detecting binding sites in coding regions. Proc. 7th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '03):57-65.

Chiaromonte F, Weber RJ, Roskin KM, Diekhans M, Kent WJ, Haussler D. The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harb Symp Quant Biol. 2003;68:245-54.

DeGuzman V, Winters-Hilt S, Solbrig A, Sughrue W, Deamer D, Haussler D, Akeson M. Sequence-dependent fraying of single DNA molecules measured in real time at 5 angstrom resolution using an ion channel. Biophys J. 2003 84(2):490A-490A Part 2 Suppl.

Furey TS, Haussler D. Integration of the cytogenic map with the draft human genome sequence. Hum Mol Genet. 2003 May 1;12(9):1037-1044.

Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang S, Giardine B, Zhang Y, Riemer C et al. Global predictions and tests of erythroid regulatory regions. Cold Spring Harb Symp Quant Biol. 2003;68:335-44.

Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D et al. Covariation in frequencies of substitution, deletion, transposition and recombination during eutherian evolution. Genome Res. 2003 Jan;13(1):13-26.

Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R et al. The DNA sequence of human chromosome 7. Nature 2003 Jul 10;424(6945):157-64.

Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ. The UCSC Genome Browser database. Nucleic Acids Res. 2003 Jan 1;31(1):51-4.

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA. 2003 Sep 30;100(20):11484-9.

Margulies EH, Blanchette M; NISC Comparative Sequencing Program; Haussler D, Green ED. Identification and characterization of multi-species conserved sequences. Genome Res. 2003 Dec;13(12):2507-18.

Pollard KS, van der Laan MJ. Multiple testing for gene expression data: an investigation of null distributions with consequences for the permutation test. Proceedings of the 2003 International MultiConference in Computer Science and Engineering, METMBS'03 Conference, pp.3-9.

Roskin KM, Diekhans M, Haussler D. Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments. Proc. 7th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '03):257-266.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7.

Siepel A, Haussler D. Combining phylogenetic and hidden markov models in biosequence analysis. Proc. 7th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '03):277-286.

Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 2003 Aug 14;424(6950):788-93.

Wang H, Hubbell E, Hu JS, Mei G, Cline M, Lu G, Clark T, Siani-Rose MA, Ares M, Kulp DC, Haussler D. Gene structure-based splice variant deconvolution using a microarray platform. Proc. of ISMB 2003 and Bioinformatics. 2003;19 Suppl 1:i315-22.

Winters-Hilt S, Vercoutere W, DeGuzman VS, Deamer D, Akeson M, Haussler D. Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules. Biophys J. 2003 Feb;84(2 Pt 1):967-76.

Wolfsberg TG, Wetterstrand KA, Guyer MS, Collins FS, Baxevanis AD. A user's guide to the human genome. Nat Genet. 2003 Sep;35 Suppl 1:4.

2002

Clark TA, Sugnet CW, Ares M Jr. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science. 2002 May 3;296(5569):907-10.

Cline MS, Karplus K, Lathrop RH, Smith TF, Rogers RG Jr, Haussler D. Information theoretic dissection of pairwise contact potentials. Proteins. 2002 Oct 1;49(1):7-14.

Karchin R, Karplus K, Haussler D. Classifying G-protein coupled receptors with support vector machines. Bioinformatics. 2002 Jan;18(1):147-59.

Karolchik D, Kent WJ. The UCSC Genome Browser. Curr Protoc Bioinformatics. 2002;Chapter 1:Unit 1.4.

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250

Kent WJ, Brumbaugh H. autoSql and autoXml: code generators from the Genome Project. Linux J. 2002;99:68-77.

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006. PMID: 12045153

Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 5;420(6915):520-62.

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 Jul. 2002.

Wolfsberg TG, Wetterstrand KA, Guyer MS, Collins FS, Baxevanis AD. A user's guide to the human genome. Nat Genet. 2002 Sep;32 Suppl:1-79.

2001

BAC Resource Consortium. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 2001 Feb 15;409(6822):953-8.

The Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921.

International Human Genome Mapping Consortium. A physical map of the human genome. Nature. 2001 Feb 15;409(6822):934-941.

Kent WJ, Haussler D. Assembly of the working draft of the human genome with gigAssembler. Genome Res. 2001 Sep;11(9)1541-1548.

Pavlidis P, Furey TS, Liberto M, Haussler D, Grundy WN. Promoter region-based classification of genes. Pac Symp Biocomput. 2001;151-63.

2000

Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D. Knowledge-based analysis of microarray gene expression data using support vector machines. Proc Natl Acad Sci USA. 2000 Jan 4;97(1):262-7.

Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M, Haussler D. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics. 2000 Oct;16(10):906-14.