David Haussler, PhD

Title(s)Professor, Bioengineering
SchoolSchool of Pharmacy
Address3333 California Street
San Francisco CA 94118
Phone831-459-2105
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    Collapse Research 
    Collapse Research Activities and Funding
    Center for Live Cell Genomics
    NIH RM1HG011543Sep 15, 2021 - Jun 30, 2026
    Role: Principal Investigator
    Enhance UCSC Xena: extend interactive visualization to ultra-large-scale multi-omics data and integrate with analysis resources
    NIH U24CA258407Sep 1, 2021 - Aug 31, 2026
    Role: Co-Principal Investigator
    Development of Advanced Preclinical Models for Pediatric Solid Tumors
    NIH R01CA243555Mar 5, 2020 - Feb 28, 2025
    Role: Co-Principal Investigator
    Enabling Comparative Pangenomics
    NIH R01HG010485Mar 2, 2020 - Dec 31, 2023
    Role: Co-Principal Investigator
    Center for Human Reference Genome Diversity
    NIH U01HG010971Sep 18, 2019 - Jul 31, 2024
    Role: Principal Investigator
    The AnVIL Data Ecosystem
    NIH U24HG010262Sep 19, 2018 - Jun 30, 2023
    Role: Co-Principal Investigator
    Unbiased analysis of genomic correlates of gene expression in health and disease
    NIH U01HL137183Apr 15, 2017 - Mar 31, 2021
    Role: Principal Investigator
    Visualization hub for genomics data exploration and translational discovery
    NIH U24CA210974Sep 13, 2016 - Aug 31, 2021
    Role: Co-Principal Investigator
    UC Santa Cruz Training Program In Genomic Sciences
    NIH T32HG008345Jul 1, 2015 - Jun 30, 2021
    Role: Co-Principal Investigator
    Center for Big Data in Translational Genomics
    NIH U54HG007990Sep 29, 2014 - Aug 31, 2021
    Role: Principal Investigator
    Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Canc
    NIH U24CA180951Sep 17, 2013 - Aug 31, 2020
    Role: Principal Investigator
    UCSC-Buck Inst. Genome Data Analysis Center for TCGA Research Network (GDAC)
    NIH U24CA143858Sep 28, 2009 - Sep 1, 2017
    Role: Principal Investigator
    Visualization and Analysis of the TCGA Data Using the UCSC Cancer Genomics Browse
    NIH R21CA135937Sep 24, 2008 - Aug 31, 2011
    Role: Principal Investigator
    UCSC Center for Genomic Science and Minority Outreach Program
    NIH P41HG002371Jul 12, 2001 - Sep 11, 2012
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A complete pedigree-based graph workflow for rare candidate variant analysis. Genome Res. 2022 Apr 28. Markello C, Huang C, Rodriguez A, Carroll A, Chang PC, Eizenga J, Markello T, Haussler D, Paten B. PMID: 35483961.
      View in: PubMed   Mentions:
    2. The Human Pangenome Project: a global resource to map genomic diversity. Nature. 2022 04; 604(7906):437-446. Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison NA, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D, Human Pangenome Reference Consortium. PMID: 35444317.
      View in: PubMed   Mentions:
    3. A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci. Genome Res. 2022 04; 32(4):656-670. van Bree EJ, Guimarães RLFP, Lundberg M, Blujdea ER, Rosenkrantz JL, White FTG, Poppinga J, Ferrer-Raventós P, Schneider AE, Clayton I, Haussler D, Reinders MJT, Holstege H, Ewing AD, Moses C, Jacobs FMJ. PMID: 35332097; PMCID: PMC8997352.
      View in: PubMed   Mentions:
    4. The Earth BioGenome Project 2020: Starting the clock. Proc Natl Acad Sci U S A. 2022 01 25; 119(4). Lewin HA, Richards S, Lieberman Aiden E, Allende ML, Archibald JM, Bálint M, Barker KB, Baumgartner B, Belov K, Bertorelle G, Blaxter ML, Cai J, Caperello ND, Carlson K, Castilla-Rubio JC, Chaw SM, Chen L, Childers AK, Coddington JA, Conde DA, Corominas M, Crandall KA, Crawford AJ, DiPalma F, Durbin R, Ebenezer TE, Edwards SV, Fedrigo O, Flicek P, Formenti G, Gibbs RA, Gilbert MTP, Goldstein MM, Graves JM, Greely HT, Grigoriev IV, Hackett KJ, Hall N, Haussler D, Helgen KM, Hogg CJ, Isobe S, Jakobsen KS, Janke A, Jarvis ED, Johnson WE, Jones SJM, Karlsson EK, Kersey PJ, Kim JH, Kress WJ, Kuraku S, Lawniczak MKN, Leebens-Mack JH, Li X, Lindblad-Toh K, Liu X, Lopez JV, Marques-Bonet T, Mazard S, Mazet JAK, Mazet JAK, Mazzoni CJ, Myers EW, O'Neill RJ, Paez S, Park H, Robinson GE, Roquet C, Ryder OA, Sabir JSM, Shaffer HB, Shank TM, Sherkow JS, Soltis PS, Tang B, Tedersoo L, Uliano-Silva M, Wang K, Wei X, Wetzer R, Wilson JL, Xu X, Yang H, Yoder AD, Zhang G. PMID: 35042800; PMCID: PMC8795548.
      View in: PubMed   Mentions:
    5. The UCSC Genome Browser database: 2022 update. Nucleic Acids Res. 2022 01 07; 50(D1):D1115-D1122. Lee BT, Barber GP, Benet-Pagès A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Muthuraman P, Nassar LR, Nguy B, Pereira T, Perez G, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Wick BD, Zweig AS, Haussler D, Kuhn RM, Haeussler M, Kent WJ. PMID: 34718705; PMCID: PMC8728131.
      View in: PubMed   Mentions:
    6. Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science. 2021 Dec 17; 374(6574):abg8871. Sirén J, Monlong J, Chang X, Novak AM, Eizenga JM, Markello C, Sibbesen JA, Hickey G, Chang PC, Carroll A, Gupta N, Gabriel S, Blackwell TW, Ratan A, Taylor KD, Rich SS, Rotter JI, Haussler D, Garrison E, Paten B. PMID: 34914532.
      View in: PubMed   Mentions:
    7. A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees. Mol Biol Evol. 2021 12 09; 38(12):5819-5824. McBroome J, Thornlow B, Hinrichs AS, Kramer A, De Maio N, Goldman N, Haussler D, Corbett-Detig R, Turakhia Y. PMID: 34469548; PMCID: PMC8662617.
      View in: PubMed   Mentions: 1     Fields:    
    8. Light-weight electrophysiology hardware and software platform for cloud-based neural recording experiments. J Neural Eng. 2021 11 12; 18(6). Voitiuk K, Geng J, Keefe MG, Parks DF, Sanso SE, Hawthorne N, Freeman DB, Currie R, Mostajo-Radji MA, Pollen AA, Nowakowski TJ, Salama SR, Teodorescu M, Haussler D. PMID: 34666315; PMCID: PMC8667733.
      View in: PubMed   Mentions:    Fields:    
    9. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom. 2021 Nov 10; 1(2). Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Auvil JMG, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Udara Liyanage I, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O'Connor BD, Oesterle S, Ogishima S, Wang VO, Paglione LAD, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. PMID: 35072136; PMCID: PMC8774288.
      View in: PubMed   Mentions:
    10. Picroscope: low-cost system for simultaneous longitudinal biological imaging. Commun Biol. 2021 11 04; 4(1):1261. Ly VT, Baudin PV, Pansodtee P, Jung EA, Voitiuk K, Rosen YM, Willsey HR, Mantalas GL, Seiler ST, Selberg JA, Cordero SA, Ross JM, Rolandi M, Pollen AA, Nowakowski TJ, Haussler D, Mostajo-Radji MA, Salama SR, Teodorescu M. PMID: 34737378; PMCID: PMC8569150.
      View in: PubMed   Mentions:
    11. Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans. Genome Res. 2021 11; 31(11):2035-2049. Cahill JA, Armstrong J, Deran A, Khoury CJ, Paten B, Haussler D, Jarvis ED. PMID: 34667117; PMCID: PMC8559704.
      View in: PubMed   Mentions:    Fields:    
    12. A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees. bioRxiv. 2021 Jul 13. McBroome J, Thornlow B, Hinrichs AS, De Maio N, Goldman N, Haussler D, Corbett-Detig R, Turakhia Y. PMID: 33821270; PMCID: PMC8020970.
      View in: PubMed   Mentions:
    13. Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic. Nat Genet. 2021 06; 53(6):809-816. Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, Corbett-Detig R. PMID: 33972780.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    14. Cancer microenvironment and genomics: evolution in process. Clin Exp Metastasis. 2022 Feb; 39(1):85-99. Leong SP, Witz IP, Sagi-Assif O, Izraely S, Sleeman J, Piening B, Fox BA, Bifulco CB, Martini R, Newman L, Davis M, Sanders LM, Haussler D, Vaske OM, Witte M. PMID: 33970362.
      View in: PubMed   Mentions: 1     Fields:    
    15. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021 04; 592(7856):737-746. Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sovic I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. PMID: 33911273; PMCID: PMC8081667.
      View in: PubMed   Mentions: 25     Fields:    
    16. A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. bioRxiv. 2021 Apr 06. Thornlow B, Hinrichs AS, Jain M, Dhillon N, La S, Kapp JD, Anigbogu I, Cassatt-Johnstone M, McBroome J, Haeussler M, Turakhia Y, Chang T, Olsen HE, Sanford J, Stone M, Vaske O, Bjork I, Akeson M, Shapiro B, Haussler D, Kilpatrick AM, Corbett-Detig R. PMID: 33851162; PMCID: PMC8043452.
      View in: PubMed   Mentions:
    17. Author Correction: Dense sampling of bird diversity increases power of comparative genomics. Nature. 2021 Apr; 592(7856):E24. Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sánchez S, Margaryan A, Howard JT, Parent C, Pacheco G, Sinding MS, Puetz L, Cavill E, Ribeiro ÂM, Eckhart L, Fjeldså J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Sicheritz-Ponten T, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jønsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Hansson B, Ponnikas S, Sigeman H, Stervander M, Frandsen PB, van der Zwan H, van der Sluis R, Visser C, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Edwards SV, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, González-Solís J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalén L, Urrutia AO, Székely T, Liu Y, Campana MG, Corvelo A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Milá B, Ketterson ED, Fidler AE, Friis G, Parody-Merino ÁM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, Zhang G. PMID: 33833441; PMCID: PMC8081657.
      View in: PubMed   Mentions:    Fields:    
    18. The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets. Gigascience. 2021 03 13; 10(3). Beale HC, Roger JM, Cattle MA, McKay LT, Thompson DKA, Learned K, Lyle AG, Kephart ET, Currie R, Lam DL, Sanders L, Pfeil J, Vivian J, Bjork I, Salama SR, Haussler D, Vaske OM. PMID: 33712853; PMCID: PMC7955155.
      View in: PubMed   Mentions: 1     Fields:    
    19. Share pandemic sequences openly and fast. Nature. 2021 03; 591(7849):202. Haussler D, Haeussler M, Hinrichs A, Corbett-Detig R, Bjork I. PMID: 33658678.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    20. The UCSC Genome Browser database: 2021 update. Nucleic Acids Res. 2021 01 08; 49(D1):D1046-D1057. Navarro Gonzalez J, 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-Pagès A, Barber GP, Haussler D, Kuhn RM, Haeussler M, Kent WJ. PMID: 33221922; PMCID: PMC7779060.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsPHPublic Health
    21. Identification of a differentiation stall in epithelial mesenchymal transition in histone H3-mutant diffuse midline glioma. Gigascience. 2020 12 15; 9(12). Sanders LM, Cheney A, Seninge L, van den Bout A, Chen M, Beale HC, Kephart ET, Pfeil J, Learned K, Lyle AG, Bjork I, Haussler D, Salama SR, Vaske OM. PMID: 33319914; PMCID: PMC7736793.
      View in: PubMed   Mentions:    Fields:    
    22. Stability of SARS-CoV-2 phylogenies. PLoS Genet. 2020 11; 16(11):e1009175. Turakhia Y, De Maio N, Thornlow B, Gozashti L, Lanfear R, Walker CR, Hinrichs AS, Fernandes JD, Borges R, Slodkowicz G, Weilguny L, Haussler D, Goldman N, Corbett-Detig R. PMID: 33206635; PMCID: PMC7721162.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    23. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 2020 11; 587(7833):246-251. Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, Lindblad-Toh K, Haussler D, Karlsson E, Jarvis ED, Zhang G, Paten B. PMID: 33177663; PMCID: PMC7673649.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimals
    24. Dense sampling of bird diversity increases power of comparative genomics. Nature. 2020 11; 587(7833):252-257. Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sánchez S, Margaryan A, Howard JT, Parent C, Pacheco G, Sinding MS, Puetz L, Cavill E, Ribeiro ÂM, Eckhart L, Fjeldså J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Sicheritz-Ponten T, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jønsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Hansson B, Ponnikas S, Sigeman H, Stervander M, Frandsen PB, van der Zwan H, van der Sluis R, Visser C, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Edwards SV, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, González-Solís J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalén L, Urrutia AO, Székely T, Liu Y, Campana MG, Corvelo A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Milá B, Ketterson ED, Fidler AE, Friis G, Parody-Merino ÁM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, Zhang G. PMID: 33177665; PMCID: PMC7759463.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimals
    25. ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy. Front Immunol. 2020; 11:483296. Rao AA, Madejska AA, Pfeil J, Paten B, Salama SR, Haussler D. PMID: 33244314; PMCID: PMC7683782.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    26. Spiking neural state machine for gait frequency entrainment in a flexible modular robot. PLoS One. 2020; 15(10):e0240267. Spaeth A, Tebyani M, Haussler D, Teodorescu M. PMID: 33085673; PMCID: PMC7577446.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    27. The UCSC SARS-CoV-2 Genome Browser. Nat Genet. 2020 10; 52(10):991-998. 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. PMID: 32908258; PMCID: PMC8016453.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCellsPHPublic Health
    28. Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic. bioRxiv. 2020 Sep 28. Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, Corbett-Detig R. PMID: 33024970; PMCID: PMC7536873.
      View in: PubMed   Mentions:
    29. A user guide for the online exploration and visualization of PCAWG data. Nat Commun. 2020 07 07; 11(1):3400. Goldman MJ, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O'Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez M. PMID: 32636365; PMCID: PMC7340791.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    30. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol. 2020 06; 38(6):675-678. Goldman MJ, Craft B, Hastie M, Repecka K, McDade F, Kamath A, Banerjee A, Luo Y, Rogers D, Brooks AN, Zhu J, Haussler D. PMID: 32444850; PMCID: PMC7386072.
      View in: PubMed   Mentions: 252     Fields:    Translation:Humans
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    33. The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. Mob DNA. 2020; 11:13. Fernandes JD, Zamudio-Hurtado A, Clawson H, Kent WJ, Haussler D, Salama SR, Haeussler M. PMID: 32266012; PMCID: PMC7110667.
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    35. UCSC Genome Browser enters 20th year. Nucleic Acids Res. 2020 01 08; 48(D1):D756-D761. 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. PMID: 31691824; PMCID: PMC7145642.
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    36. Erratum: Data sharing for clinical utility. Cold Spring Harb Mol Case Stud. 2019 Dec; 5(6). Bjork I, Peralez J, Haussler D, Spunt SL, Morozova Vaske O. PMID: 31836591; PMCID: PMC6913145.
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    38. Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor. Cold Spring Harb Mol Case Stud. 2019 10; 5(5). Sanders LM, Rangaswami A, Bjork I, Lam DL, Beale HC, Kephart ET, Durbin A, Learned K, Currie R, Lyle AG, Pfeil J, Shah AT, Lee AG, Leung SG, Behroozfard IH, Breese MR, Peralez J, Hazard FK, Lacayo N, Spunt SL, Haussler D, Salama SR, Sweet-Cordero EA, Vaske OM. PMID: 31645344; PMCID: PMC6824255.
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    39. Data sharing for clinical utility. Cold Spring Harb Mol Case Stud. 2019 10; 5(5). Bjork I, Peralez J, Haussler D, Spunt SL, Vaske OM. PMID: 31645349; PMCID: PMC6824251.
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    40. Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer. JAMA Netw Open. 2019 10 02; 2(10):e1913968. Vaske OM, Bjork I, Salama SR, Beale H, Tayi Shah A, Sanders L, Pfeil J, Lam DL, Learned K, Durbin A, Kephart ET, Currie R, Newton Y, Swatloski T, McColl D, Vivian J, Zhu J, Lee AG, Leung SG, Spillinger A, Liu HY, Liang WS, Byron SA, Berens ME, Resnick AC, Lacayo N, Spunt SL, Rangaswami A, Huynh V, Torno L, Plant A, Kirov I, Zabokrtsky KB, Rassekh SR, Deyell RJ, Laskin J, Marra MA, Sender LS, Mueller S, Sweet-Cordero EA, Goldstein TC, Haussler D. PMID: 31651965; PMCID: PMC6822083.
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    41. Barriers to accessing public cancer genomic data. Sci Data. 2019 06 20; 6(1):98. Learned K, Durbin A, Currie R, Kephart ET, Beale HC, Sanders LM, Pfeil J, Goldstein TC, Salama SR, Haussler D, Vaske OM, Bjork IM. PMID: 31222016; PMCID: PMC6586850.
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    42. Publisher Correction: Federated discovery and sharing of genomic data using Beacons. Nat Biotechnol. 2019 04; 37(4):480. Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, Haussler D, Varma S, Saunders G, Scollen S. PMID: 30894680; PMCID: PMC7608460.
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    43. Data sharing for pediatric cancers. Science. 2019 03 15; 363(6432):1125. Vaske OM, Haussler D. PMID: 30872493.
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    44. Federated discovery and sharing of genomic data using Beacons. Nat Biotechnol. 2019 03; 37(3):220-224. Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, Haussler D, Varma S, Saunders G, Scollen S. PMID: 30833764; PMCID: PMC6728157.
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    45. Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. Cell. 2019 02 07; 176(4):743-756.e17. Pollen AA, Bhaduri A, Andrews MG, Nowakowski TJ, Meyerson OS, Mostajo-Radji MA, Di Lullo E, Alvarado B, Bedolli M, Dougherty ML, Fiddes IT, Kronenberg ZN, Shuga J, Leyrat AA, West JA, Bershteyn M, Lowe CB, Pavlovic BJ, Salama SR, Haussler D, Eichler EE, Kriegstein AR. PMID: 30735633; PMCID: PMC6544371.
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    48. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. PLoS Genet. 2018 12; 14(12):e1007752. Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R, Dlott CC, Dolman L, den Dunnen JT, Dyke SOM, Domchek SM, Easton D, Fischmann Z, Foulkes WD, Garber J, Goldgar D, Goldman MJ, Goodhand P, Harrison S, Haussler D, Kato K, Knoppers B, Markello C, Nussbaum R, Offit K, Plon SE, Rashbass J, Rehm HL, Robson M, Rubinstein WS, Stoppa-Lyonnet D, Tavtigian S, Thorogood A, Zhang C, Zimmermann M, BRCA Challenge Authors, Burn J, Chanock S, Rätsch G, Spurdle AB. PMID: 30586411; PMCID: PMC6324924.
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    50. The ESCRT-III Protein CHMP1A Mediates Secretion of Sonic Hedgehog on a Distinctive Subtype of Extracellular Vesicles. Cell Rep. 2018 07 24; 24(4):973-986.e8. 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, Jacobs FMJ, Gaudin R, Walsh CA. PMID: 30044992; PMCID: PMC6178983.
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    53. Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis. Cell. 2018 05 31; 173(6):1356-1369.e22. 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, Kriegstein A, Eichler EE, Salama SR, Jacobs FMJ, Haussler D. PMID: 29856954; PMCID: PMC5986104.
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    54. A Flow Procedure for Linearization of Genome Sequence Graphs. J Comput Biol. 2018 07; 25(7):664-676. Haussler D, Smuga-Otto M, Eizenga JM, Paten B, Novak AM, Nikitin S, Zueva M, Miagkov D. PMID: 29792514; PMCID: PMC6067104.
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    55. Earth BioGenome Project: Sequencing life for the future of life. Proc Natl Acad Sci U S A. 2018 04 24; 115(17):4325-4333. 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, Yang H, Zhang G. PMID: 29686065; PMCID: PMC5924910.
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    56. Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer. JCO Precis Oncol. 2018; 2. Newton Y, Rassekh SR, Deyell RJ, Shen Y, Jones MR, Dunham C, Yip S, Leelakumari S, Zhu J, McColl D, Swatloski T, Salama SR, Ng T, Hendson G, Lee AF, Ma Y, Moore R, Mungall AJ, Haussler D, Stuart JM, Jantzen C, Laskin J, Jones SJM, Marra MA, Morozova O. PMID: 31372595; PMCID: PMC6675034.
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    57. Linear assembly of a human centromere on the Y chromosome. Nat Biotechnol. 2018 04; 36(4):321-323. Jain M, Olsen HE, Turner DJ, Stoddart D, Bulazel KV, Paten B, Haussler D, Willard HF, Akeson M, Miga KH. PMID: 29553574; PMCID: PMC5886786.
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    58. A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations. Front Immunol. 2018; 9:99. 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. PMID: 29441070; PMCID: PMC5797543.
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    59. The UCSC Genome Browser database: 2018 update. Nucleic Acids Res. 2018 01 04; 46(D1):D762-D769. 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. PMID: 29106570; PMCID: PMC5753355.
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    60. TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal. Cancer Res. 2017 11 01; 77(21):e111-e114. Newton Y, Novak AM, Swatloski T, McColl DC, Chopra S, Graim K, Weinstein AS, Baertsch R, Salama SR, Ellrott K, Chopra M, Goldstein TC, Haussler D, Morozova O, Stuart JM. PMID: 29092953; PMCID: PMC5751940.
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    61. Sharing Clinical and Genomic Data on Cancer - The Need for Global Solutions. N Engl J Med. 2017 05 25; 376(21):2006-2009. Clinical Cancer Genome Task Team of the Global Alliance for Genomics and Health, Lawler M, Haussler D, Siu LL, Haendel MA, McMurry JA, Knoppers BM, Chanock SJ, Calvo F, The BT, Walia G, Banks I, Yu PP, Staudt LM, Sawyers CL. PMID: 28538124.
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    62. Consistency of BRCA1 and BRCA2 Variant Classifications Among Clinical Diagnostic Laboratories. JCO Precis Oncol. 2017 Jul; 1. Lincoln SE, Yang S, Cline MS, Kobayashi Y, Zhang C, Topper S, Haussler D, Paten B, Nussbaum RL. PMID: 28782058; PMCID: PMC5542009.
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    67. Long-read sequence assembly of the gorilla genome. Science. 2016 Apr 01; 352(6281):aae0344. Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin CS, Eichler EE. PMID: 27034376; PMCID: PMC4920363.
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    68. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 2016 Mar; 26(3):342-50. Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE. PMID: 26848124; PMCID: PMC4772016.
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    69. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell. 2016 Jan 28; 164(3):550-63. Ceccarelli M, Barthel FP, Malta TM, Sabedot TS, Salama SR, Murray BA, Morozova O, Newton Y, Radenbaugh A, Pagnotta SM, Anjum S, Wang J, Manyam G, Zoppoli P, Ling S, Rao AA, Grifford M, Cherniack AD, Zhang H, Poisson L, Carlotti CG, Tirapelli DP, Rao A, Mikkelsen T, Lau CC, Yung WK, Rabadan R, Huse J, Brat DJ, Lehman NL, Barnholtz-Sloan JS, Zheng S, Hess K, Rao G, Meyerson M, Beroukhim R, Cooper L, Akbani R, Wrensch M, Haussler D, Aldape KD, Laird PW, Gutmann DH, TCGA Research Network, Noushmehr H, Iavarone A, Verhaak RG. PMID: 26824661; PMCID: PMC4754110.
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    88. The UCSC Ebola Genome Portal. PLoS Curr. 2014 Nov 07; 6. Haeussler M, Karolchik D, Clawson H, Raney BJ, Rosenbloom KR, Fujita PA, Hinrichs AS, Speir ML, Eisenhart C, Zweig AS, Haussler D, Kent WJ. PMID: 25685613; PMCID: PMC4318873.
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    152. The infinite sites model of genome evolution. Proc Natl Acad Sci U S A. 2008 Sep 23; 105(38):14254-61. Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D. PMID: 18787111; PMCID: PMC2533685.
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    154. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 01; 24(5):637-44. Stanke M, Diekhans M, Baertsch R, Haussler D. PMID: 18218656.
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    156. Computational reconstruction of ancestral DNA sequences. Methods Mol Biol. 2008; 422:171-84. Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. PMID: 18629667.
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    157. 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. Zeng J, Yan J, Wang T, Mosbrook-Davis D, Dolan KT, Christensen R, Stormo GD, Haussler D, Lathrop RH, Brachmann RK, Burgess SM. PMID: 18086703; PMCID: PMC2248728.
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    158. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec; 3(12):e247. Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. PMID: 18085818; PMCID: PMC2134963.
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    159. 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. Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D. PMID: 18003932; PMCID: PMC2141825.
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    160. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007 Nov 08; 450(7167):219-32. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Harvard FlyBase curators, Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. PMID: 17994088; PMCID: PMC2474711.
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      View in: PubMed   Mentions: 640     Fields:    Translation:HumansAnimals
    171. Editing modifies the GABA(A) receptor subunit alpha3. RNA. 2007 May; 13(5):698-703. Ohlson J, Pedersen JS, Haussler D, Ohman M. PMID: 17369310; PMCID: PMC1852825.
      View in: PubMed   Mentions: 97     Fields:    Translation:HumansAnimalsCells
    172. Comparative genomic analysis using the UCSC genome browser. Methods Mol Biol. 2007; 395:17-34. Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. PMID: 17993665.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimals
    173. The ENCODE Project at UC Santa Cruz. Nucleic Acids Res. 2007 Jan; 35(Database issue):D663-7. 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, ENCODE Project Consortium, Haussler D, Kent WJ. PMID: 17166863; PMCID: PMC1781110.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    174. Variation resources at UC Santa Cruz. Nucleic Acids Res. 2007 Jan; 35(Database issue):D716-20. Thomas DJ, Trumbower H, Kern AD, Rhead BL, Kuhn RM, Haussler D, Kent WJ. PMID: 17151077; PMCID: PMC1781230.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimals
    175. Reconstructing contiguous regions of an ancestral genome. Genome Res. 2006 Dec; 16(12):1557-65. Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W. PMID: 16983148; PMCID: PMC1665639.
      View in: PubMed   Mentions: 101     Fields:    Translation:HumansAnimalsCells
    176. Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2006 Oct 13; 2(10):e168. 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. PMID: 17040131; PMCID: PMC1599772.
      View in: PubMed   Mentions: 160     Fields:    Translation:HumansAnimalsCells
    177. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14; 443(7108):167-72. 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, Vanderhaeghen P, Haussler D. PMID: 16915236.
      View in: PubMed   Mentions: 338     Fields:    Translation:HumansAnimalsCells
    178. Coding exon detection using comparative sequences. J Comput Biol. 2006 Jul-Aug; 13(6):1148-64. Wu J, Haussler D. PMID: 16901234.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    179. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006 Apr; 2(4):e33. Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. PMID: 16628248; PMCID: PMC1440920.
      View in: PubMed   Mentions: 247     Fields:    Translation:HumansAnimalsCells
    180. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 2006 May 04; 441(7089):87-90. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. PMID: 16625209.
      View in: PubMed   Mentions: 225     Fields:    Translation:HumansAnimalsCells
    181. The UCSC Known Genes. Bioinformatics. 2006 May 01; 22(9):1036-46. Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. PMID: 16500937.
      View in: PubMed   Mentions: 307     Fields:    Translation:Cells
    182. Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol. 2006 Jan; 2(1):e4. Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D, Ares M. PMID: 16424921; PMCID: PMC1331982.
      View in: PubMed   Mentions: 121     Fields:    Translation:HumansAnimalsCells
    183. Counterexample to a claim about the reconstruction of ancestral character states. Syst Biol. 2005 Aug; 54(4):693-5. Lucena B, Haussler D. PMID: 16126665.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    184. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug; 15(8):1034-50. 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. PMID: 16024819; PMCID: PMC1182216.
      View in: PubMed   Mentions: 1788     Fields:    Translation:HumansAnimalsCells
    185. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat Methods. 2005 Jul; 2(7):535-45. Bejerano G, Siepel AC, Kent WJ, Haussler D. PMID: 16170870.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsCells
    186. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. 2005 May; 15(5):737-41. Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. PMID: 15867434; PMCID: PMC1088302.
      View in: PubMed   Mentions: 31     Fields:    Translation:Humans
    187. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 2005 Jun 15; 21(12):2814-20. Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. PMID: 15827081.
      View in: PubMed   Mentions: 99     Fields:    
    188. The UCSC Proteome Browser. Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D454-8. Hsu F, Pringle TH, Kuhn RM, Karolchik D, Diekhans M, Haussler D, Kent WJ. PMID: 15608236; PMCID: PMC540054.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    189. The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol. 2005 Jan; 3(1):e5. Robertson MP, Igel H, Baertsch R, Haussler D, Ares M, Scott WG. PMID: 15630477; PMCID: PMC539059.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansCells
    190. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res. 2004 Dec; 14(12):2412-23. Blanchette M, Green ED, Miller W, Haussler D. PMID: 15574820; PMCID: PMC534665.
      View in: PubMed   Mentions: 47     Fields:    Translation:AnimalsCells
    191. 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. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Morrin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J, MGC Project Team. PMID: 15489334; PMCID: PMC528928.
      View in: PubMed   Mentions: 216     Fields:    Translation:HumansAnimals
    192. Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. Genome Res. 2004 Oct; 14(10B):2034-40. Furey TS, Diekhans M, Lu Y, Graves TA, Oddy L, Randall-Maher J, Hillier LW, Wilson RK, Haussler D. PMID: 15489323; PMCID: PMC528917.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    193. The structure and evolution of centromeric transition regions within the human genome. Nature. 2004 Aug 19; 430(7002):857-64. She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE. PMID: 15318213.
      View in: PubMed   Mentions: 93     Fields:    Translation:HumansAnimalsCells
    194. Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics. 2004 Aug 04; 20 Suppl 1:i40-8. Bejerano G, Haussler D, Blanchette M. PMID: 15262779.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimalsCells
    195. Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics. 2004 Aug 04; 20 Suppl 1:i161-8. Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D. PMID: 15262795.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    196. Ultraconserved elements in the human genome. Science. 2004 May 28; 304(5675):1321-5. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. PMID: 15131266.
      View in: PubMed   Mentions: 630     Fields:    Translation:HumansAnimalsCells
    197. Comparative recombination rates in the rat, mouse, and human genomes. Genome Res. 2004 Apr; 14(4):528-38. Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ. PMID: 15059993; PMCID: PMC383296.
      View in: PubMed   Mentions: 206     Fields:    Translation:HumansAnimalsCells
    198. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr; 14(4):708-15. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. PMID: 15060014; PMCID: PMC383317.
      View in: PubMed   Mentions: 656     Fields:    Translation:HumansAnimalsCells
    199. Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res. 2004 Apr; 14(4):517-27. Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC. PMID: 15059992; PMCID: PMC383295.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimalsCells
    200. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 01; 428(6982):493-521. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Rat Genome Sequencing Project Consortium. PMID: 15057822.
      View in: PubMed   Mentions: 788     Fields:    Translation:HumansAnimalsCells
    201. Hotspots of mammalian chromosomal evolution. Genome Biol. 2004; 5(4):R23. Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. PMID: 15059256; PMCID: PMC395782.
      View in: PubMed   Mentions: 101     Fields:    Translation:HumansAnimalsCells
    202. Score functions for determining regional conservation in two-species local alignments. J Comput Biol. 2004; 11(2-3):395-411. Roskin KM, Diekhans M, Haussler D. PMID: 15285898.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    203. Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol. 2004; 11(2-3):413-28. Siepel A, Haussler D. PMID: 15285899.
      View in: PubMed   Mentions: 88     Fields:    
    204. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D493-6. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. PMID: 14681465; PMCID: PMC308837.
      View in: PubMed   Mentions: 1013     Fields:    Translation:HumansAnimals
    205. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol. 2004 Mar; 21(3):468-88. Siepel A, Haussler D. PMID: 14660683.
      View in: PubMed   Mentions: 153     Fields:    
    206. Identification and characterization of multi-species conserved sequences. Genome Res. 2003 Dec; 13(12):2507-18. Margulies EH, Blanchette M, NISC Comparative Sequencing Program, Haussler D, Green ED. PMID: 14656959; PMCID: PMC403793.
      View in: PubMed   Mentions: 144     Fields:    Translation:HumansAnimalsCells
    207. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30; 100(20):11484-9. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. PMID: 14500911; PMCID: PMC208784.
      View in: PubMed   Mentions: 392     Fields:    Translation:Animals
    208. Integration of the cytogenetic map with the draft human genome sequence. Hum Mol Genet. 2003 May 01; 12(9):1037-44. Furey TS, Haussler D. PMID: 12700172.
      View in: PubMed   Mentions: 44     Fields:    Translation:Humans
    209. Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules. Biophys J. 2003 Feb; 84(2 Pt 1):967-76. Winters-Hilt S, Vercoutere W, DeGuzman VS, Deamer D, Akeson M, Haussler D. PMID: 12547778; PMCID: PMC1302674.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    210. Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics. 2003; 19 Suppl 1:i315-22. Wang H, Hubbell E, Hu JS, Mei G, Cline M, Lu G, Clark T, Siani-Rose MA, Ares M, Kulp DC, Haussler D. PMID: 12855476.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    211. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 2003 Jan; 13(1):13-26. Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D. PMID: 12529302; PMCID: PMC430971.
      View in: PubMed   Mentions: 147     Fields:    Translation:HumansAnimalsCells
    212. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan; 13(1):103-7. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. PMID: 12529312; PMCID: PMC430961.
      View in: PubMed   Mentions: 559     Fields:    Translation:HumansAnimals
    213. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 05; 420(6915):520-62. Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. PMID: 12466850.
      View in: PubMed   Mentions: 2632     Fields:    Translation:HumansAnimalsCells
    214. Information-theoretic dissection of pairwise contact potentials. Proteins. 2002 Oct 01; 49(1):7-14. Cline MS, Karplus K, Lathrop RH, Smith TF, Rogers RG, Haussler D. PMID: 12211011.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    215. The human genome browser at UCSC. Genome Res. 2002 Jun; 12(6):996-1006. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. PMID: 12045153; PMCID: PMC186604.
      View in: PubMed   Mentions: 4083     Fields:    Translation:Humans
    216. Classifying G-protein coupled receptors with support vector machines. Bioinformatics. 2002 Jan; 18(1):147-59. Karchin R, Karplus K, Haussler D. PMID: 11836223.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCells
    217. Filter assay for 1alpha, 25-dihydroxyvitamin D3. Utilization of the hormone's target tissue chromatin receptor. Biochemistry. 1974 Sep 24; 13(20):4091-7. Brumbaugh PF, Haussler DH, Bursac KM, Haussler MR. PMID: 4370023.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    218. 1Alpha-hydroxyvitamin D3. An analog of vitamin D which apparently acts by metabolism to 1alpha, 25-dihydroxyvitamin D3. Biochemistry. 1974 Sep 24; 13(20):4097-102. Zerwekh JE, Brumbaugh PF, Haussler DH, Cork DJ, Haussler MR. PMID: 4370560.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    219. Radioreceptor assay for 1 alpha,25-dihydroxyvitamin D3. Science. 1974 Mar 15; 183(4129):1089-91. Brumbaugh PF, Haussler DH, Bressler R, Haussler MR. PMID: 4812038.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
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