David Haussler, PhD

Title(s)Professor, Bioengineering
SchoolSchool of Pharmacy
Address3333 California Street, #103
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. The UCSC Genome Browser database: 2025 update. Nucleic Acids Res. 2024 Oct 26. Perez G, Barber GP, Benet-Pages A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Raney BJ, Speir ML, van Baren MJ, Vaske CJ, Haussler D, Kent WJ, Haeussler M. PMID: 39460617.
      View in: PubMed   Mentions:    Fields:    
    2. Model-agnostic neural mean field with a data-driven transfer function. Neuromorphic Comput Eng. 2024 Sep 01; 4(3):034013. Spaeth A, Haussler D, Teodorescu M. PMID: 39310743; PMCID: PMC11413991.
      View in: PubMed   Mentions:
    3. Reducing education inequalities through cloud-enabled live-cell biotechnology. Trends Biotechnol. 2024 Aug 28. Vera-Choqqueccota S, Belmekki BEY, Alouini MS, Teodorescu M, Haussler D, Mostajo-Radji MA. PMID: 39209603.
      View in: PubMed   Mentions:    Fields:    
    4. A nonoscillatory, millisecond-scale embedding of brain state provides insight into behavior. Nat Neurosci. 2024 Sep; 27(9):1829-1843. Parks DF, Schneider AM, Xu Y, Brunwasser SJ, Funderburk S, Thurber D, Blanche T, Dyer EL, Haussler D, Hengen KB. PMID: 39009836.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    5. Internet-enabled lab-on-a-chip technology for education. Sci Rep. 2024 06 22; 14(1):14364. Sano T, Sampad MJN, Gonzalez-Ferrer J, Hernandez S, Vera-Choqqueccota S, Vargas PA, Urcuyo R, Montellano Duran N, Teodorescu M, Haussler D, Schmidt H, Mostajo-Radji MA. PMID: 38906940; PMCID: PMC11192768.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    6. SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis. Cell Genom. 2024 Jun 12; 4(6):100581. Gonzalez-Ferrer J, Lehrer J, O'Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA. PMID: 38823397; PMCID: PMC11228957.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    7. A feedback-driven IoT microfluidic, electrophysiology, and imaging platform for brain organoid studies. bioRxiv. 2024 May 19. Voitiuk K, Seiler ST, Pessoa de Melo M, Geng J, Hernandez S, Schweiger HE, Sevetson JL, Parks DF, Robbins A, Torres-Montoya S, Ehrlich D, Elliott MAT, Sharf T, Haussler D, Mostajo-Radji MA, Salama SR, Teodorescu M. PMID: 38559212; PMCID: PMC10979982.
      View in: PubMed   Mentions:
    8. Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders. Cell Stem Cell. 2024 03 07; 31(3):421-432.e8. Shin D, Kim CN, Ross J, Hennick KM, Wu SR, Paranjape N, Leonard R, Wang JC, Keefe MG, Pavlovic BJ, Donohue KC, Moreau C, Wigdor EM, Larson HH, Allen DE, Cadwell CR, Bhaduri A, Popova G, Bearden CE, Pollen AA, Jacquemont S, Sanders SJ, Haussler D, Wiita AP, Frost NA, Sohal VS, Nowakowski TJ. PMID: 38382530; PMCID: PMC10939828.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    9. Model-Agnostic Neural Mean Field With The Refractory SoftPlus Transfer Function. bioRxiv. 2024 Feb 06. Spaeth A, Haussler D, Teodorescu M. PMID: 38370695; PMCID: PMC10871173.
      View in: PubMed   Mentions:
    10. The UCSC Genome Browser database: 2024 update. Nucleic Acids Res. 2024 Jan 05; 52(D1):D1082-D1088. Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline MS, Diekhans M, Fischer C, Navarro Gonzalez J, Hickey G, Hinrichs AS, Kuhn RM, Lee BT, Lee CM, Le Mercier P, Miga KH, Nassar LR, Nejad P, Paten B, Perez G, Schmelter D, Speir ML, Wick BD, Zweig AS, Haussler D, Kent WJ, Haeussler M. PMID: 37953330; PMCID: PMC10767968.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimals
    11. Internet-Connected Cortical Organoids for Project-Based Stem Cell and Neuroscience Education. eNeuro. 2023 Dec; 10(12). Elliott MAT, Schweiger HE, Robbins A, Vera-Choqqueccota S, Ehrlich D, Hernandez S, Voitiuk K, Geng J, Sevetson JL, Core C, Rosen YM, Teodorescu M, Wagner NO, Haussler D, Mostajo-Radji MA. PMID: 38016807; PMCID: PMC10755643.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    12. Unraveling Neuronal Identities Using SIMS: A Deep Learning Label Transfer Tool for Single-Cell RNA Sequencing Analysis. bioRxiv. 2023 Nov 17. Gonzalez-Ferrer J, Lehrer J, O'Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA. PMID: 36909548; PMCID: PMC10002667.
      View in: PubMed   Mentions:
    13. GenArk: towards a million UCSC genome browsers. Genome Biol. 2023 10 02; 24(1):217. Clawson H, Lee BT, Raney BJ, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Perez G, Wick B, Schmelter D, Speir ML, Armstrong J, Zweig AS, Kuhn RM, Kirilenko BM, Hiller M, Haussler D, Kent WJ, Haeussler M. PMID: 37784172; PMCID: PMC10544498.
      View in: PubMed   Mentions: 1     Fields:    
    14. Internet-connected cortical organoids for project-based stem cell and neuroscience education. bioRxiv. 2023 Jul 15. Elliott MAT, Schweiger HE, Robbins A, Vera-Choqqueccota S, Ehrlich D, Hernandez S, Voitiuk K, Geng J, Sevetson JL, Rosen YM, Teodorescu M, Wagner NO, Haussler D, Mostajo-Radji MA. PMID: 37503236; PMCID: PMC10369936.
      View in: PubMed   Mentions:
    15. A non-oscillatory, millisecond-scale embedding of brain state provides insight into behavior. bioRxiv. 2023 Jun 27. Parks DF, Schneider AM, Xu Y, Brunwasser SJ, Funderburk S, Thurber D, Blanche T, Dyer EL, Haussler D, Hengen KB. PMID: 37333381; PMCID: PMC10274881.
      View in: PubMed   Mentions:
    16. A draft human pangenome reference. Nature. 2023 05; 617(7960):312-324. Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H, Paten B. PMID: 37165242; PMCID: PMC10172123.
      View in: PubMed   Mentions: 230     Fields:    Translation:Humans
    17. Isoform-specific translational control is evolutionarily conserved in primates. bioRxiv. 2023 May 08. Draper JM, Philipp J, Neeb ZT, Thomas R, Katzman S, Salama S, Haussler D, Sanford J. PMID: 37131629; PMCID: PMC10153275.
      View in: PubMed   Mentions:
    18. Open-loop lab-on-a-chip technology enables remote computer science training in Latinx life sciences students. bioRxiv. 2023 May 01. Sano T, Sampad MJN, Gonzalez-Ferrer J, Hernandez S, Vera-Choqqueccota S, Vargas PA, Urcuyo R, Duran NM, Teodorescu M, Haussler D, Schmidt H, Mostajo-Radji MA. PMID: 37205466; PMCID: PMC10187215.
      View in: PubMed   Mentions:
    19. GenArk: Towards a million UCSC Genome Browsers. Res Sq. 2023 Apr 03. Clawson H, Lee BT, Raney BJ, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Perez G, Wick B, Schmelter D, Speir ML, Armstrong J, Zweig AS, Kuhn RM, Kirilenko BM, Hiller M, Haussler D, Kent WJ, Haeussler M. PMID: 37066427; PMCID: PMC10104252.
      View in: PubMed   Mentions:
    20. The UCSC Genome Browser database: 2023 update. Nucleic Acids Res. 2023 01 06; 51(D1):D1188-D1195. Nassar LR, Barber GP, Benet-Pagès A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee BT, Lee CM, Muthuraman P, Nguy B, Pereira T, Nejad P, Perez G, Raney BJ, Schmelter D, Speir ML, Wick BD, Zweig AS, Haussler D, Kuhn RM, Haeussler M, Kent WJ. PMID: 36420891; PMCID: PMC9825520.
      View in: PubMed   Mentions: 155     Fields:    Translation:HumansCells
    21. Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors. Commun Biol. 2022 12 13; 5(1):1367. Sanders LM, Chandra R, Zebarjadi N, Beale HC, Lyle AG, Rodriguez A, Kephart ET, Pfeil J, Cheney A, Learned K, Currie R, Gitlin L, Vengerov D, Haussler D, Salama SR, Vaske OM. PMID: 36513728; PMCID: PMC9747808.
      View in: PubMed   Mentions: 2  Translation:HumansCells
    22. Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids. Sci Rep. 2022 11 23; 12(1):20173. Seiler ST, Mantalas GL, Selberg J, Cordero S, Torres-Montoya S, Baudin PV, Ly VT, Amend F, Tran L, Hoffman RN, Rolandi M, Green RE, Haussler D, Salama SR, Teodorescu M. PMID: 36418910; PMCID: PMC9684529.
      View in: PubMed   Mentions: 10     Fields:    
    23. Cloud-controlled microscopy enables remote project-based biology education in underserved Latinx communities. Heliyon. 2022 Nov; 8(11):e11596. Baudin PV, Sacksteder RE, Worthington AK, Voitiuk K, Ly VT, Hoffman RN, Elliott MAT, Parks DF, Ward R, Torres-Montoya S, Amend F, Montellano Duran N, Vargas PA, Martinez G, Ramirez SM, Alvarado-Arnez LE, Ehrlich D, Rosen YM, Breevoort A, Schouten T, Kurniawan S, Haussler D, Teodorescu M, Mostajo-Radji MA. PMID: 36439758; PMCID: PMC9681640.
      View in: PubMed   Mentions: 8  
    24. The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science. Neoplasia. 2023 01; 35:100846. Lilly JV, Rokita JL, Mason JL, Patton T, Stefankiewiz S, Higgins D, Trooskin G, Larouci CA, Arya K, Appert E, Heath AP, Zhu Y, Brown MA, Zhang B, Farrow BK, Robins S, Morgan AM, Nguyen TQ, Frenkel E, Lehmann K, Drake E, Sullivan C, Plisiewicz A, Coleman N, Patterson L, Koptyra M, Helili Z, Van Kuren N, Young N, Kim MC, Friedman C, Lubneuski A, Blackden C, Williams M, Baubet V, Tauhid L, Galanaugh J, Boucher K, Ijaz H, Cole KA, Choudhari N, Santi M, Moulder RW, Waller J, Rife W, Diskin SJ, Mateos M, Parsons DW, Pollack IF, Goldman S, Leary S, Caporalini C, Buccoliero AM, Scagnet M, Haussler D, Hanson D, Firestein R, Cain J, Phillips JJ, Gupta N, Mueller S, Grant G, Monje-Deisseroth M, Partap S, Greenfield JP, Hashizume R, Smith A, Zhu S, Johnston JM, Fangusaro JR, Miller M, Wood MD, Gardner S, Carter CL, Prolo LM, Pisapia J, Pehlivan K, Franson A, Niazi T, Rubin J, Abdelbaki M, Ziegler DS, Lindsay HB, Stucklin AG, Gerber N, Vaske OM, Quinsey C, Rood BR, Nazarian J, Raabe E, Jackson EM, Stapleton S, Lober RM, Kram DE, Koschmann C, Storm PB, Lulla RR, Prados M, Resnick AC, Waanders AJ. PMID: 36335802; PMCID: PMC9641002.
      View in: PubMed   Mentions: 20     Fields:    Translation:Humans
    25. Semi-automated assembly of high-quality diploid human reference genomes. Nature. 2022 Nov; 611(7936):519-531. Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, Chin CS, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton RS, Fulton LL, Garg S, Gerton JL, Ghurye J, Granat A, Green RE, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger EB, Jain M, Kirsche M, Kolmogorov M, Korbel JO, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell MW, McDaniel J, Nie F, Olsen HE, Olson ND, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg SL, Sanders AD, Schatz MC, Schmitt A, Schneider VA, Selvaraj S, Shafin K, Shumate A, Stitziel NO, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin AV, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook JM, Eichler EE, Phillippy AM, Paten B, Howe K, Miga KH, Human Pangenome Reference Consortium. PMID: 36261518; PMCID: PMC9668749.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCells
    26. IoT cloud laboratory: Internet of Things architecture for cellular biology. Internet Things (Amst). 2022 Nov; 20. Parks DF, Voitiuk K, Geng J, Elliott MAT, Keefe MG, Jung EA, Robbins A, Baudin PV, Ly VT, Hawthorne N, Yong D, Sanso SE, Rezaee N, Sevetson JL, Seiler ST, Currie R, Pollen AA, Hengen KB, Nowakowski TJ, Mostajo-Radji MA, Salama SR, Teodorescu M, Haussler D. PMID: 37383277; PMCID: PMC10305744.
      View in: PubMed   Mentions: 7  
    27. Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape. Nature. 2022 09; 609(7929):994-997. Turakhia Y, Thornlow B, Hinrichs A, McBroome J, Ayala N, Ye C, Smith K, De Maio N, Haussler D, Lanfear R, Corbett-Detig R. PMID: 35952714; PMCID: PMC9519458.
      View in: PubMed   Mentions: 74     Fields:    Translation:HumansCellsPHPublic Health
    28. Author Correction: Comparative and demographic analysis of orang-utan genomes. Nature. 2022 Aug; 608(7924):E36. Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AFA, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, RoyChoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK. PMID: 35962045; PMCID: PMC9402433.
      View in: PubMed   Mentions: 1     Fields:    
    29. A complete pedigree-based graph workflow for rare candidate variant analysis. Genome Res. 2022 05; 32(5):893-903. Markello C, Huang C, Rodriguez A, Carroll A, Chang PC, Eizenga J, Markello T, Haussler D, Paten B. PMID: 35483961; PMCID: PMC9104704.
      View in: PubMed   Mentions: 4     Fields:    
    30. 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; PMCID: PMC9402379.
      View in: PubMed   Mentions: 136     Fields:    Translation:Humans
    31. 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: 11     Fields:    Translation:HumansCells
    32. 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: 79     Fields:    Translation:HumansAnimalsCells
    33. 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: 124     Fields:    Translation:HumansAnimalsCells
    34. 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; PMCID: PMC9365333.
      View in: PubMed   Mentions: 95     Fields:    Translation:HumansAnimals
    35. 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: 53     Fields:    Translation:HumansCells
    36. 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: 6     Fields:    Translation:Humans
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    73. 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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    78. 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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    81. 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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    84. 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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    88. 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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    89. 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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    90. 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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    93. Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. BMC Bioinformatics. 2016 Sep 29; 17(1):400. Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D. PMID: 27687569; PMCID: PMC5043639.
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    97. 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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    99. A Distributed Network for Intensive Longitudinal Monitoring in Metastatic Triple-Negative Breast Cancer. J Natl Compr Canc Netw. 2016 01; 14(1):8-17. Blau CA, Ramirez AB, Blau S, Pritchard CC, Dorschner MO, Schmechel SC, Martins TJ, Mahen EM, Burton KA, Komashko VM, Radenbaugh AJ, Dougherty K, Thomas A, Miller CP, Annis J, Fromm JR, Song C, Chang E, Howard K, Austin S, Schmidt RA, Linenberger ML, Becker PS, Senecal FM, Mecham BH, Lee SI, Madan A, Ronen R, Dutkowski J, Heimfeld S, Wood BL, Stilwell JL, Kaldjian EP, Haussler D, Zhu J. PMID: 26733551; PMCID: PMC4970582.
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    104. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 2015 Jun 25; 372(26):2481-98. Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J. PMID: 26061751; PMCID: PMC4530011.
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    106. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. PMID: 25693563; PMCID: PMC4530010.
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    107. Building a pan-genome reference for a population. J Comput Biol. 2015 May; 22(5):387-401. Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. PMID: 25565268; PMCID: PMC4424974.
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    108. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014 Dec 12; 346(6215):1320-31. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G. PMID: 25504713; PMCID: PMC4405904.
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    109. The birds of Genome10K. Gigascience. 2014; 3(1):32. OBrien SJ, Haussler D, Ryder O. PMID: 25685332; PMCID: PMC4326320.
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    112. The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 2015 Jan; 43(Database issue):D670-81. 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. PMID: 25428374; PMCID: PMC4383971.
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    113. Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Mol Biol Evol. 2015 Jan; 32(1):23-8. Lowe CB, Clarke JA, Baker AJ, Haussler D, Edwards SV. PMID: 25415961; PMCID: PMC4271537.
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    114. RADIA: RNA and DNA integrated analysis for somatic mutation detection. PLoS One. 2014; 9(11):e111516. Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D. PMID: 25405470; PMCID: PMC4236012.
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    115. The UCSC Cancer Genomics Browser: update 2015. Nucleic Acids Res. 2015 Jan; 43(Database issue):D812-7. Goldman M, Craft B, Swatloski T, Cline M, Morozova O, Diekhans M, Haussler D, Zhu J. PMID: 25392408; PMCID: PMC4383911.
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    116. 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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    118. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Res. 2014 Dec; 24(12):2077-89. Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B. PMID: 25273068; PMCID: PMC4248324.
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    119. The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Database (Oxford). 2014; 2014. 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. PMID: 25267794; PMCID: PMC4178372.
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    120. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature. 2014 Dec 11; 516(7530):242-5. Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D. PMID: 25274305; PMCID: PMC4268317.
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    121. Comparative assembly hubs: web-accessible browsers for comparative genomics. Bioinformatics. 2014 Dec 01; 30(23):3293-301. Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. PMID: 25138168; PMCID: PMC4296145.
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    122. A unifying model of genome evolution under parsimony. BMC Bioinformatics. 2014 Jun 19; 15:206. Paten B, Zerbino DR, Hickey G, Haussler D. PMID: 24946830; PMCID: PMC4082375.
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    123. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014 Jan; 42(Database issue):D764-70. 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. PMID: 24270787; PMCID: PMC3964947.
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    124. Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res. 2014 Jan; 42(Database issue):D865-72. 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. PMID: 24217909; PMCID: PMC3965069.
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    125. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10; 155(2):462-77. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L, TCGA Research Network. PMID: 24120142; PMCID: PMC3910500.
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    126. Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser. Sci Rep. 2013 Oct 02; 3:2652. Cline MS, Craft B, Swatloski T, Goldman M, Ma S, Haussler D, Zhu J. PMID: 24084870; PMCID: PMC3788369.
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    127. Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinformatics. 2013 Nov 01; 29(21):2757-64. Paull EO, Carlin DE, Niepel M, Sorger PK, Haussler D, Stuart JM. PMID: 23986566; PMCID: PMC3799471.
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    128. Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Cancer Res. 2013 Oct 01; 73(19):6036-45. Sanborn JZ, Salama SR, Grifford M, Brennan CW, Mikkelsen T, Jhanwar S, Katzman S, Chin L, Haussler D. PMID: 23940299; PMCID: PMC3800429.
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    129. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013 Jul 22; 2(1):10. Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. PMID: 23870653; PMCID: PMC3844414.
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    131. HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics. 2013 May 15; 29(10):1341-2. Hickey G, Paten B, Earl D, Zerbino D, Haussler D. PMID: 23505295; PMCID: PMC3654707.
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    132. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biol. 2013 Mar 13; 14(3):R22. Ewing AD, Ballinger TJ, Earl D, Broad Institute Genome Sequencing and Analysis Program and Platform, Harris CC, Ding L, Wilson RK, Haussler D. PMID: 23497673; PMCID: PMC3663115.
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    133. Life, the universe, and everything: an interview with David Haussler. Interviewed by Jane Gitschier. PLoS Genet. 2013; 9(1):e1003282. Haussler D. PMID: 23382705; PMCID: PMC3561096.
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    136. The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Res. 2013 Jan; 41(Database issue):D949-54. Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M, Ma S, Wilks C, Stuart J, Haussler D, Zhu J. PMID: 23109555; PMCID: PMC3531186.
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    137. PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinformatics. 2012 Sep 15; 28(18):i640-i646. Ng S, Collisson EA, Sokolov A, Goldstein T, Gonzalez-Perez A, Lopez-Bigas N, Benz C, Haussler D, Stuart JM. PMID: 22962493; PMCID: PMC3436829.
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    138. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012 Sep; 22(9):1760-74. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ. PMID: 22955987; PMCID: PMC3431492.
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    141. The UCSC genome browser and associated tools. Brief Bioinform. 2013 Mar; 14(2):144-61. Kuhn RM, Haussler D, Kent WJ. PMID: 22908213; PMCID: PMC3603215.
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    142. Tissue sampling methods and standards for vertebrate genomics. Gigascience. 2012 Jul 12; 1(1):8. 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. PMID: 23587255; PMCID: PMC3626508.
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    143. The fishes of Genome 10K. Mar Genomics. 2012 Sep; 7:3-6. Bernardi G, Wiley EO, Mansour H, Miller MR, Orti G, Haussler D, O'Brien SJ, Ryder OA, Venkatesh B. PMID: 22897955.
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    144. The Human Epigenome Browser at Washington University. Nat Methods. 2011 Nov 29; 8(12):989-90. Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P, Kuhn RM, Zhu J, Smirnov I, Kent WJ, Haussler D, Madden PA, Costello JF, Wang T. PMID: 22127213; PMCID: PMC3552640.
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    145. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 2012 Jan; 40(Database issue):D918-23. 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, James Kent W. PMID: 22086951; PMCID: PMC3245018.
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    146. Human tRNA genes function as chromatin insulators. EMBO J. 2012 Jan 18; 31(2):330-50. Raab JR, Chiu J, Zhu J, Katzman S, Kurukuti S, Wade PA, Haussler D, Kamakaka RT. PMID: 22085927; PMCID: PMC3261562.
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    148. 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. Wang NJ, Sanborn Z, Arnett KL, Bayston LJ, Liao W, Proby CM, Leigh IM, Collisson EA, Gordon PB, Jakkula L, Pennypacker S, Zou Y, Sharma M, North JP, Vemula SS, Mauro TM, Neuhaus IM, Leboit PE, Hur JS, Park K, Huh N, Kwok PY, Arron ST, Massion PP, Bale AE, Haussler D, Cleaver JE, Gray JW, Spellman PT, South AP, Aster JC, Blacklow SC, Cho RJ. PMID: 22006338; PMCID: PMC3203814.
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    188. 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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    189. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec; 17(12):1763-73. Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C, Yu HC, Li J, Roe BA, Green P, Gerhard DS, Temple G, Haussler D, Brent MR. PMID: 17989246; PMCID: PMC2099585.
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    190. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 2007 Dec; 17(12):1797-808. 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. PMID: 17984227; PMCID: PMC2099589.
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    191. Detecting coevolution in and among protein domains. PLoS Comput Biol. 2007 Nov; 3(11):e211. Yeang CH, Haussler D. PMID: 17983264; PMCID: PMC2098842.
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    192. Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res. 2007 Oct; 17(10):1420-30. Dreszer TR, Wall GD, Haussler D, Pollard KS. PMID: 17785536; PMCID: PMC1987345.
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    193. Human genome ultraconserved elements are ultraselected. Science. 2007 Aug 17; 317(5840):915. Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D. PMID: 17702936.
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    194. Detecting the coevolution of biosequences--an example of RNA interaction prediction. Mol Biol Evol. 2007 Sep; 24(9):2119-31. Yeang CH, Darot JF, Noller HF, Haussler D. PMID: 17636042.
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    195. 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. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. PMID: 17571346; PMCID: PMC2212820.
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    196. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007 Jun; 17(6):760-74. Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A. PMID: 17567995; PMCID: PMC1891336.
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    197. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A. 2007 May 08; 104(19):8005-10. Lowe CB, Bejerano G, Haussler D. PMID: 17463089; PMCID: PMC1876562.
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    198. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13; 316(5822):222-34. Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS. PMID: 17431167.
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    199. 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.
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    200. 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.
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    201. 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.
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    202. 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.
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    203. 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.
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    204. 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.
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    205. 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.
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    206. Coding exon detection using comparative sequences. J Comput Biol. 2006 Jul-Aug; 13(6):1148-64. Wu J, Haussler D. PMID: 16901234.
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    207. 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.
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    208. 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.
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    209. 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.
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    210. 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.
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    211. 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.
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    212. 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.
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    213. 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.
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    214. 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.
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    215. 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.
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    216. 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.
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    217. 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.
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    222. 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.
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    223. 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.
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    224. 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.
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    225. 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.
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    226. 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.
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    227. 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.
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    228. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 04 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, Simons R, 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.
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    229. 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.
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    230. 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.
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    231. Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol. 2004; 11(2-3):413-28. Siepel A, Haussler D. PMID: 15285899.
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    232. 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.
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    233. 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.
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    234. 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.
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    235. 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.
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    236. 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.
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    237. 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.
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    238. 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.
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    239. 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.
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    240. 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.
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    241. 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.
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    242. 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.
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    243. 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.
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    244. 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: 73     Fields:    Translation:HumansCells
    245. 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: 15     Fields:    Translation:HumansAnimalsCells
    246. 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: 8     Fields:    Translation:AnimalsCells
    247. 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.
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