David Haussler, PhD

Title(s)Professor, Bioengineering
SchoolSchool of Pharmacy
Address3333 California Street, #103
San Francisco CA 94118
Phone831-459-2105
PronounsHe/Him/His
vCardDownload vCard

    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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. RT-Sort: An action potential propagation-based algorithm for real time spike detection and sorting with millisecond latencies. PLoS One. 2024; 19(12):e0312438. van der Molen T, Lim M, Bartram J, Cheng Z, Robbins A, Parks DF, Petzold LR, Hierlemann A, Haussler D, Hansma PK, Tovar KR, Kosik KS. PMID: 39637133; PMCID: PMC11620616.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    2. Multimodal evaluation of network activity and optogenetic interventions in human hippocampal slices. Nat Neurosci. 2024 Nov 15. Andrews JP, Geng J, Voitiuk K, Elliott MAT, Shin D, Robbins A, Spaeth A, Wang A, Li L, Solis D, Keefe MG, Sevetson JL, Rivera de Jesús JA, Donohue KC, Larson HH, Ehrlich D, Auguste KI, Salama S, Sohal V, Sharf T, Haussler D, Cadwell CR, Schaffer DV, Chang EF, Teodorescu M, Nowakowski TJ. PMID: 39548326.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    3. Multiscale Cloud-based Pipeline for Neuronal Electrophysiology Analysis and Visualization. bioRxiv. 2024 Nov 14. Geng J, Voitiuk K, Parks DF, Robbins A, Spaeth A, Sevetson JL, Hernandez S, Schweiger HE, Andrews JP, Seiler ST, Elliott MAT, Chang EF, Nowakowski TJ, Currie R, Mostajo-Radji MA, Haussler D, Sharf T, Salama SR, Teodorescu M. PMID: 39605518; PMCID: PMC11601321.
      View in: PubMed   Mentions:
    4. Pathological microcircuits initiate epileptiform events in patient hippocampal slices. bioRxiv. 2024 Nov 14. Elliott MAT, Andrews JP, van der Molen T, Geng J, Spaeth A, Voituik K, Core C, Gillespie T, Sinervo A, Parks DF, Robbins A, Solís D, Chang EF, Nowakowski TJ, Teodorescu M, Haussler D, Sharf T. PMID: 39605666; PMCID: PMC11601452.
      View in: PubMed   Mentions:
    5. 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:    
    6. 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: 1  
    7. 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:    
    8. 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: 2     Fields:    Translation:AnimalsCells
    9. 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
    10. 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
    11. 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:
    12. 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
    13. 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:
    14. 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: 35     Fields:    Translation:HumansAnimals
    15. 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
    16. 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:
    17. 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: 2     Fields:    
    18. 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:
    19. 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:
    20. 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: 264     Fields:    Translation:Humans
    21. 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:
    22. 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:
    23. 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:
    24. 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: 175     Fields:    Translation:HumansCells
    25. 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
    26. 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:    
    27. 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  
    28. 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
    29. 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: 78     Fields:    Translation:HumansCells
    30. 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  
    31. 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: 76     Fields:    Translation:HumansCellsPHPublic Health
    32. 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:    
    33. 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:    
    34. 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: 150     Fields:    Translation:Humans
    35. 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: 12     Fields:    Translation:HumansCells
    36. 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: 84     Fields:    Translation:HumansAnimalsCells
    37. 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: 131     Fields:    Translation:HumansAnimalsCells
    38. 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: 99     Fields:    Translation:HumansAnimals
    39. 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
    40. 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
    41. 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: 83     Fields:    
    42. 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  Translation:Animals
    43. 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: 9     Fields:    Translation:HumansAnimals
    44. 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:
    45. 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; PMCID: PMC9248294.
      View in: PubMed   Mentions: 186     Fields:    Translation:HumansCells
    46. Cancer microenvironment and genomics: evolution in process. Clin Exp Metastasis. 2022 02; 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: 4     Fields:    Translation:HumansCells
    47. 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: 951     Fields:    Translation:AnimalsCells
    48. 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: 1  
    49. 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: 4     Fields:    
    50. 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: 2     Fields:    Translation:Humans
    51. 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:HumansAnimalsCells
    52. 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: 252     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    53. 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: 7     Fields:    Translation:Humans
    54. 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: 65     Fields:    Translation:HumansCells
    55. 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: 183     Fields:    Translation:HumansAnimals
    56. 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: 150     Fields:    Translation:HumansAnimals
    57. 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: 10     Fields:    Translation:HumansCells
    58. 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: 5     Fields:    Translation:HumansAnimalsCells
    59. 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: 56     Fields:    Translation:HumansCellsPHPublic Health
    60. 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:
    61. 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: 21     Fields:    Translation:Humans
    62. 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: 1756     Fields:    Translation:Humans
    63. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat Biotechnol. 2020 09; 38(9):1044-1053. Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B. PMID: 32686750; PMCID: PMC7483855.
      View in: PubMed   Mentions: 242     Fields:    Translation:HumansCells
    64. Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. PLoS Comput Biol. 2020 04; 16(4):e1007753. Pfeil J, Sanders LM, Anastopoulos I, Lyle AG, Weinstein AS, Xue Y, Blair A, Beale HC, Lee A, Leung SG, Dinh PT, Shah AT, Breese MR, Devine WP, Bjork I, Salama SR, Sweet-Cordero EA, Haussler D, Vaske OM. PMID: 32275708; PMCID: PMC7176284.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    65. 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.
      View in: PubMed   Mentions: 23  
    66. Blockchain-Authenticated Sharing of Genomic and Clinical Outcomes Data of Patients With Cancer: A Prospective Cohort Study. J Med Internet Res. 2020 03 20; 22(3):e16810. Glicksberg BS, Burns S, Currie R, Griffin A, Wang ZJ, Haussler D, Goldstein T, Collisson E. PMID: 32196460; PMCID: PMC7125440.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    67. 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.
      View in: PubMed   Mentions: 110     Fields:    Translation:Humans
    68. 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.
      View in: PubMed   Mentions:    Fields:    
    69. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Rep. 2019 11 05; 29(6):1675-1689.e9. Rokita JL, Rathi KS, Cardenas MF, Upton KA, Jayaseelan J, Cross KL, Pfeil J, Egolf LE, Way GP, Farrel A, Kendsersky NM, Patel K, Gaonkar KS, Modi A, Berko ER, Lopez G, Vaksman Z, Mayoh C, Nance J, McCoy K, Haber M, Evans K, McCalmont H, Bendak K, Böhm JW, Marshall GM, Tyrrell V, Kalletla K, Braun FK, Qi L, Du Y, Zhang H, Lindsay HB, Zhao S, Shu J, Baxter P, Morton C, Kurmashev D, Zheng S, Chen Y, Bowen J, Bryan AC, Leraas KM, Coppens SE, Doddapaneni H, Momin Z, Zhang W, Sacks GI, Hart LS, Krytska K, Mosse YP, Gatto GJ, Sanchez Y, Greene CS, Diskin SJ, Vaske OM, Haussler D, Gastier-Foster JM, Kolb EA, Gorlick R, Li XN, Reynolds CP, Kurmasheva RT, Houghton PJ, Smith MA, Lock RB, Raman P, Wheeler DA, Maris JM. PMID: 31693904; PMCID: PMC6880934.
      View in: PubMed   Mentions: 92     Fields:    Translation:HumansAnimalsCells
    70. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    71. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    72. 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.
      View in: PubMed   Mentions: 27     Fields:    Translation:Humans
    73. 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.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    74. 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.
      View in: PubMed   Mentions:    Fields:    
    75. Data sharing for pediatric cancers. Science. 2019 03 15; 363(6432):1125. Vaske OM, Haussler D. PMID: 30872493.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    76. 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.
      View in: PubMed   Mentions: 46     Fields:    Translation:Humans
    77. 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.
      View in: PubMed   Mentions: 261     Fields:    Translation:HumansAnimalsCells
    78. Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes. Stem Cell Reports. 2019 02 12; 12(2):245-257. Field AR, Jacobs FMJ, Fiddes IT, Phillips APR, Reyes-Ortiz AM, LaMontagne E, Whitehead L, Meng V, Rosenkrantz JL, Olsen M, Hauessler M, Katzman S, Salama SR, Haussler D. PMID: 30639214; PMCID: PMC6372947.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    79. The UCSC Genome Browser database: 2019 update. Nucleic Acids Res. 2019 01 08; 47(D1):D853-D858. Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ. PMID: 30407534; PMCID: PMC6323953.
      View in: PubMed   Mentions: 408     Fields:    Translation:HumansAnimals
    80. 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.
      View in: PubMed   Mentions: 109     Fields:    Translation:Humans
    81. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biol. 2018 11 06; 19(1):188. Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC. PMID: 30400818; PMCID: PMC6219177.
      View in: PubMed   Mentions: 28     Fields:    Translation:Humans
    82. 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.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansAnimalsCells
    83. High-resolution comparative analysis of great ape genomes. Science. 2018 06 08; 360(6393). Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE. PMID: 29880660; PMCID: PMC6178954.
      View in: PubMed   Mentions: 181     Fields:    Translation:HumansAnimals
    84. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res. 2018 07; 28(7):1029-1038. Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. PMID: 29884752; PMCID: PMC6028123.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansAnimals
    85. 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.
      View in: PubMed   Mentions: 221     Fields:    Translation:HumansAnimalsCells
    86. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    87. 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.
      View in: PubMed   Mentions: 303     Fields:    Translation:Animals
    88. 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.
      View in: PubMed   Mentions: 6     Fields:    
    89. 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.
      View in: PubMed   Mentions: 109     Fields:    Translation:HumansCells
    90. 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.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    91. 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.
      View in: PubMed   Mentions: 270     Fields:    Translation:Humans
    92. 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.
      View in: PubMed   Mentions: 39     Fields:    Translation:Humans
    93. 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.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    94. 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.
      View in: PubMed   Mentions: 16     Fields:    
    95. Toil enables reproducible, open source, big biomedical data analyses. Nat Biotechnol. 2017 04 11; 35(4):314-316. Vivian J, Rao AA, Nothaft FA, Ketchum C, Armstrong J, Novak A, Pfeil J, Narkizian J, Deran AD, Musselman-Brown A, Schmidt H, Amstutz P, Craft B, Goldman M, Rosenbloom K, Cline M, O'Connor B, Hanna M, Birger C, Kent WJ, Patterson DA, Joseph AD, Zhu J, Zaranek S, Getz G, Haussler D, Paten B. PMID: 28398314; PMCID: PMC5546205.
      View in: PubMed   Mentions: 621     Fields:    Translation:Humans
    96. The UCSC Genome Browser database: 2017 update. Nucleic Acids Res. 2017 01 04; 45(D1):D626-D634. Tyner C, Barber GP, Casper J, Clawson H, Diekhans M, Eisenhart C, Fischer CM, Gibson D, Gonzalez JN, Guruvadoo L, Haeussler M, Heitner S, Hinrichs AS, Karolchik D, Lee BT, Lee CM, Nejad P, Raney BJ, Rosenbloom KR, Speir ML, Villarreal C, Vivian J, Zweig AS, Haussler D, Kuhn RM, Kent WJ. PMID: 27899642; PMCID: PMC5210591.
      View in: PubMed   Mentions: 197     Fields:    Translation:HumansAnimals
    97. 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.
      View in: PubMed   Mentions: 4     Fields:    
    98. Facilitating a culture of responsible and effective sharing of cancer genome data. Nat Med. 2016 05 05; 22(5):464-71. Siu LL, Lawler M, Haussler D, Knoppers BM, Lewin J, Vis DJ, Liao RG, Andre F, Banks I, Barrett JC, Caldas C, Camargo AA, Fitzgerald RC, Mao M, Mattison JE, Pao W, Sellers WR, Sullivan P, Teh BT, Ward RL, ZenKlusen JC, Sawyers CL, Voest EE. PMID: 27149219; PMCID: PMC4995884.
      View in: PubMed   Mentions: 40     Fields:    Translation:Humans
    99. 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.
      View in: PubMed   Mentions: 180     Fields:    Translation:HumansAnimals
    100. 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.
      View in: PubMed   Mentions: 388     Fields:    Translation:HumansAnimalsCells
    101. 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.
      View in: PubMed   Mentions: 1131     Fields:    Translation:HumansCells
    102. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics. 2016 05 01; 32(9):1430-2. Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. PMID: 26740527; PMCID: PMC4848401.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimals
    103. 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.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    104. The UCSC Genome Browser database: 2016 update. Nucleic Acids Res. 2016 Jan 04; 44(D1):D717-25. Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, Eisenhart C, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ. PMID: 26590259; PMCID: PMC4702902.
      View in: PubMed   Mentions: 224     Fields:    Translation:HumansAnimals
    105. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med. 2016 Jan 14; 374(2):135-45. Cancer Genome Atlas Research Network, Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AA, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho TH, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni HV, Drummond JA, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R. PMID: 26536169; PMCID: PMC4775252.
      View in: PubMed   Mentions: 549     Fields:    Translation:HumansCells
    106. Canonical, stable, general mapping using context schemes. Bioinformatics. 2015 Nov 15; 31(22):3569-76. Novak AM, Rosen Y, Haussler D, Paten B. PMID: 26220960; PMCID: PMC4757953.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    107. The NIH BD2K center for big data in translational genomics. J Am Med Inform Assoc. 2015 Nov; 22(6):1143-7. Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, Kent WJ, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, Smuga-Otto M, Stuart JM, Van't Veer L, Wold B, Haussler D. PMID: 26174866; PMCID: PMC5009913.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    108. 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.
      View in: PubMed   Mentions: 1551     Fields:    Translation:HumansCells
    109. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat Methods. 2015 Jul; 12(7):623-30. Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY, ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC. PMID: 25984700; PMCID: PMC4856034.
      View in: PubMed   Mentions: 167     Fields:    Translation:Humans
    110. 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.
      View in: PubMed   Mentions: 3231     Fields:    Translation:HumansCells
    111. 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.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    112. 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.
      View in: PubMed   Mentions: 662     Fields:    Translation:AnimalsCells
    113. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014 Dec 12; 346(6215):1311-20. Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J. PMID: 25504712; PMCID: PMC4390078.
      View in: PubMed   Mentions: 478     Fields:    Translation:AnimalsCells
    114. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science. 2014 Dec 12; 346(6215):1254449. Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA. PMID: 25504731; PMCID: PMC4386873.
      View in: PubMed   Mentions: 167     Fields:    Translation:AnimalsCells
    115. The birds of Genome10K. Gigascience. 2014; 3(1):32. OBrien SJ, Haussler D, Ryder O. PMID: 25685332; PMCID: PMC4326320.
      View in: PubMed   Mentions: 8     Fields:    
    116. 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.
      View in: PubMed   Mentions: 550     Fields:    Translation:AnimalsCells
    117. 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.
      View in: PubMed   Mentions: 27     Fields:    Translation:Animals
    118. 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.
      View in: PubMed   Mentions: 46     Fields:    Translation:Humans
    119. 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.
      View in: PubMed   Mentions: 175     Fields:    Translation:HumansCells
    120. 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.
      View in: PubMed   Mentions: 5  
    121. Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics. 2015 Mar 01; 31(5):764-6. Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ. PMID: 25348212; PMCID: PMC4341066.
      View in: PubMed   Mentions: 33     Fields:    Translation:Humans
    122. 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.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansAnimals
    123. 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.
      View in: PubMed   Mentions: 89     Fields:    Translation:Humans
    124. 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.
      View in: PubMed   Mentions: 258     Fields:    Translation:HumansAnimalsCells
    125. 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.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    126. 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.
      View in: PubMed   Mentions: 4     Fields:    
    127. 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.
      View in: PubMed   Mentions: 421     Fields:    Translation:HumansAnimals
    128. 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.
      View in: PubMed   Mentions: 91     Fields:    Translation:HumansAnimals
    129. 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.
      View in: PubMed   Mentions: 2666     Fields:    Translation:HumansCells
    130. 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.
      View in: PubMed   Mentions: 174     Fields:    Translation:HumansAnimals
    131. 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.
      View in: PubMed   Mentions: 107     Fields:    Translation:HumansCells
    132. 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.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    133. 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.
      View in: PubMed   Mentions: 310     Fields:    
    134. The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Res. 2013 Jul; 41(Web Server issue):W218-24. Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D, Stuart JM. PMID: 23748957; PMCID: PMC3692096.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    135. 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.
      View in: PubMed   Mentions: 103     Fields:    Translation:HumansAnimalsCells
    136. 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.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansAnimalsCells
    137. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    138. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 2013 Jan; 41(Database issue):D56-63. Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. PMID: 23193274; PMCID: PMC3531152.
      View in: PubMed   Mentions: 519     Fields:    Translation:HumansAnimals
    139. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2013 Jan; 41(Database issue):D64-9. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ. PMID: 23155063; PMCID: PMC3531082.
      View in: PubMed   Mentions: 497     Fields:    Translation:HumansAnimals
    140. 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.
      View in: PubMed   Mentions: 114     Fields:    Translation:HumansCells
    141. 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.
      View in: PubMed   Mentions: 58     Fields:    Translation:Humans
    142. 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.
      View in: PubMed   Mentions: 2594     Fields:    Translation:HumansAnimalsCells
    143. 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS One. 2012; 7(8):e43128. Lowe CB, Haussler D. PMID: 22952639; PMCID: PMC3428314.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    144. Gene isoform specificity through enhancer-associated antisense transcription. PLoS One. 2012; 7(8):e43511. Onodera CS, Underwood JG, Katzman S, Jacobs F, Greenberg D, Salama SR, Haussler D. PMID: 22937057; PMCID: PMC3427357.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    145. 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.
      View in: PubMed   Mentions: 451     Fields:    Translation:HumansAnimals
    146. 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.
      View in: PubMed   Mentions: 18     Fields:    
    147. 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.
      View in: PubMed   Mentions: 16     Fields:    Translation:Animals
    148. 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.
      View in: PubMed   Mentions: 195     Fields:    Translation:Humans
    149. 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.
      View in: PubMed   Mentions: 79     Fields:    Translation:HumansAnimalsCells
    150. 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.
      View in: PubMed   Mentions: 209     Fields:    Translation:HumansAnimals
    151. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res. 2012 Jan; 40(Database issue):D912-7. Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, Goldman M, Gravell RC, Harte RA, Hinrichs AS, Kirkup VM, Kuhn RM, Learned K, Maddren M, Meyer LR, Pohl A, Rhead B, Wong MC, Zweig AS, Haussler D, Kent WJ. PMID: 22075998; PMCID: PMC3245183.
      View in: PubMed   Mentions: 158     Fields:    Translation:HumansAnimals
    152. 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.
      View in: PubMed   Mentions: 230     Fields:    Translation:HumansCells
    153. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):2724-9. Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, Bayani N, Hu Z, Billig JI, Dueregger A, Lewis S, Jakkula L, Korkola JE, Durinck S, Pepin F, Guan Y, Purdom E, Neuvial P, Bengtsson H, Wood KW, Smith PG, Vassilev LT, Hennessy BT, Greshock J, Bachman KE, Hardwicke MA, Park JW, Marton LJ, Wolf DM, Collisson EA, Neve RM, Mills GB, Speed TP, Feiler HS, Wooster RF, Haussler D, Stuart JM, Gray JW, Spellman PT. PMID: 22003129; PMCID: PMC3286973.
      View in: PubMed   Mentions: 283     Fields:    Translation:HumansCells
    154. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12; 478(7370):476-82. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. PMID: 21993624; PMCID: PMC3207357.
      View in: PubMed   Mentions: 607     Fields:    Translation:HumansAnimals
    155. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011 Dec; 21(12):2224-41. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. PMID: 21926179; PMCID: PMC3227110.
      View in: PubMed   Mentions: 225     Fields:    
    156. Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):2802-7. Kristensen VN, Vaske CJ, Ursini-Siegel J, Van Loo P, Nordgard SH, Sachidanandam R, Sørlie T, Wärnberg F, Haakensen VD, Helland Å, Naume B, Perou CM, Haussler D, Troyanskaya OG, Børresen-Dale AL. PMID: 21908711; PMCID: PMC3286992.
      View in: PubMed   Mentions: 90     Fields:    Translation:HumansCells
    157. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 2011 Aug 31; 477(7366):587-91. Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K. PMID: 21881562; PMCID: PMC3184186.
      View in: PubMed   Mentions: 293     Fields:    Translation:HumansAnimalsCells
    158. Three periods of regulatory innovation during vertebrate evolution. Science. 2011 Aug 19; 333(6045):1019-24. Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. PMID: 21852499; PMCID: PMC3511857.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansAnimalsCells
    159. Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Biol Evol. 2011; 3:614-26. Katzman S, Capra JA, Haussler D, Pollard KS. PMID: 21697099; PMCID: PMC3157837.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    160. Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 2011 Sep; 21(9):1512-28. Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. PMID: 21665927; PMCID: PMC3166836.
      View in: PubMed   Mentions: 125     Fields:    Translation:HumansAnimals
    161. Meta-alignment with crumble and prune: partitioning very large alignment problems for performance and parallelization. BMC Bioinformatics. 2011 May 10; 12:144. Roskin KM, Paten B, Haussler D. PMID: 21569267; PMCID: PMC3114744.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    162. David Haussler. Nat Biotechnol. 2011 Mar; 29(3):243. Haussler D. PMID: 21390032.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    163. Cactus graphs for genome comparisons. J Comput Biol. 2011 Mar; 18(3):469-81. Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D. PMID: 21385048; PMCID: PMC8884192.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    164. Comparative and demographic analysis of orang-utan genomes. Nature. 2011 Jan 27; 469(7331):529-33. 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 AF, 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: 21270892; PMCID: PMC3060778.
      View in: PubMed   Mentions: 250     Fields:    Translation:HumansAnimalsCells
    165. The UCSC Cancer Genomics Browser: update 2011. Nucleic Acids Res. 2011 Jan; 39(Database issue):D951-9. Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J. PMID: 21059681; PMCID: PMC3013705.
      View in: PubMed   Mentions: 37     Fields:    Translation:Humans
    166. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods. 2010 Dec; 7(12):995-1001. Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. PMID: 21057495; PMCID: PMC3247016.
      View in: PubMed   Mentions: 180     Fields:    Translation:HumansAnimalsCells
    167. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 2011 Jan; 39(Database issue):D871-5. Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ. PMID: 21037257; PMCID: PMC3013645.
      View in: PubMed   Mentions: 115     Fields:    Translation:Humans
    168. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2011 Jan; 39(Database issue):D876-82. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. PMID: 20959295; PMCID: PMC3242726.
      View in: PubMed   Mentions: 627     Fields:    Translation:HumansAnimalsCells
    169. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. PMID: 20852635; PMCID: PMC2955169.
      View in: PubMed   Mentions: 350     Fields:    Translation:HumansCells
    170. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 08; 466(7303):253-7. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. PMID: 20613842; PMCID: PMC3998662.
      View in: PubMed   Mentions: 866     Fields:    Translation:HumansAnimalsCells
    171. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics. 2010 Jun 15; 26(12):i237-45. Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM. PMID: 20529912; PMCID: PMC2881367.
      View in: PubMed   Mentions: 415     Fields:    Translation:Humans
    172. GC-biased evolution near human accelerated regions. PLoS Genet. 2010 May 20; 6(5):e1000960. Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. PMID: 20502635; PMCID: PMC2873926.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    173. International network of cancer genome projects. Nature. 2010 Apr 15; 464(7291):993-8. International Cancer Genome Consortium, Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, Kerr D, Klatt P, Kolar P, Kusada J, Lane DP, Laplace F, Youyong L, Nettekoven G, Ozenberger B, Peterson J, Rao TS, Remacle J, Schafer AJ, Shibata T, Stratton MR, Vockley JG, Watanabe K, Yang H, Yuen MM, Knoppers BM, Bobrow M, Cambon-Thomsen A, Dressler LG, Dyke SO, Joly Y, Kato K, Kennedy KL, Nicolás P, Parker MJ, Rial-Sebbag E, Romeo-Casabona CM, Shaw KM, Wallace S, Wiesner GL, Zeps N, Lichter P, Biankin AV, Chabannon C, Chin L, Clément B, de Alava E, Degos F, Ferguson ML, Geary P, Hayes DN, Hudson TJ, Johns AL, Kasprzyk A, Nakagawa H, Penny R, Piris MA, Sarin R, Scarpa A, Shibata T, van de Vijver M, Futreal PA, Aburatani H, Bayés M, Botwell DD, Campbell PJ, Estivill X, Gerhard DS, Grimmond SM, Gut I, Hirst M, López-Otín C, Majumder P, Marra M, McPherson JD, Nakagawa H, Ning Z, Puente XS, Ruan Y, Shibata T, Stratton MR, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, Yang L, Spellman PT, Bader GD, Boutros PC, Campbell PJ, Flicek P, Getz G, Guigó R, Guo G, Haussler D, Heath S, Hubbard TJ, Jiang T, Jones SM, Li Q, López-Bigas N, Luo R, Muthuswamy L, Ouellette BF, Pearson JV, Puente XS, Quesada V, Raphael BJ, Sander C, Shibata T, Speed TP, Stein LD, Stuart JM, Teague JW, Totoki Y, Tsunoda T, Valencia A, Wheeler DA, Wu H, Zhao S, Zhou G, Stein LD, Guigó R, Hubbard TJ, Joly Y, Jones SM, Kasprzyk A, Lathrop M, López-Bigas N, Ouellette BF, Spellman PT, Teague JW, Thomas G, Valencia A, Yoshida T, Kennedy KL, Axton M, Dyke SO, Futreal PA, Gerhard DS, Gunter C, Guyer M, Hudson TJ, McPherson JD, Miller LJ, Ozenberger B, Shaw KM, Kasprzyk A, Stein LD, Zhang J, Haider SA, Wang J, Yung CK, Cros A, Cross A, Liang Y, Gnaneshan S, Guberman J, Hsu J, Bobrow M, Chalmers DR, Hasel KW, Joly Y, Kaan TS, Kennedy KL, Knoppers BM, Lowrance WW, Masui T, Nicolás P, Rial-Sebbag E, Rodriguez LL, Vergely C, Yoshida T, Grimmond SM, Biankin AV, Bowtell DD, Cloonan N, deFazio A, Eshleman JR, Etemadmoghadam D, Gardiner BB, Gardiner BA, Kench JG, Scarpa A, Sutherland RL, Tempero MA, Waddell NJ, Wilson PJ, McPherson JD, Gallinger S, Tsao MS, Shaw PA, Petersen GM, Mukhopadhyay D, Chin L, DePinho RA, Thayer S, Muthuswamy L, Shazand K, Beck T, Sam M, Timms L, Ballin V, Lu Y, Ji J, Zhang X, Chen F, Hu X, Zhou G, Yang Q, Tian G, Zhang L, Xing X, Li X, Zhu Z, Yu Y, Yu J, Yang H, Lathrop M, Tost J, Brennan P, Holcatova I, Zaridze D, Brazma A, Egevard L, Prokhortchouk E, Banks RE, Uhlén M, Cambon-Thomsen A, Viksna J, Ponten F, Skryabin K, Stratton MR, Futreal PA, Birney E, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Martin S, Reis-Filho JS, Richardson AL, Sotiriou C, Stunnenberg HG, Thoms G, van de Vijver M, van't Veer L, Calvo F, Birnbaum D, Blanche H, Boucher P, Boyault S, Chabannon C, Gut I, Masson-Jacquemier JD, Lathrop M, Pauporté I, Pivot X, Vincent-Salomon A, Tabone E, Theillet C, Thomas G, Tost J, Treilleux I, Calvo F, Bioulac-Sage P, Clément B, Decaens T, Degos F, Franco D, Gut I, Gut M, Heath S, Lathrop M, Samuel D, Thomas G, Zucman-Rossi J, Lichter P, Eils R, Brors B, Korbel JO, Korshunov A, Landgraf P, Lehrach H, Pfister S, Radlwimmer B, Reifenberger G, Taylor MD, von Kalle C, Majumder PP, Sarin R, Rao TS, Bhan MK, Scarpa A, Pederzoli P, Lawlor RA, Delledonne M, Bardelli A, Biankin AV, Grimmond SM, Gress T, Klimstra D, Zamboni G, Shibata T, Nakamura Y, Nakagawa H, Kusada J, Tsunoda T, Miyano S, Aburatani H, Kato K, Fujimoto A, Yoshida T, Campo E, López-Otín C, Estivill X, Guigó R, de Sanjosé S, Piris MA, Montserrat E, González-Díaz M, Puente XS, Jares P, Valencia A, Himmelbauer H, et al. PMID: 20393554; PMCID: PMC2902243.
      View in: PubMed   Mentions: 1136     Fields:    Translation:HumansCells
    174. Endangered species hold clues to human evolution. J Hered. 2010 Jul-Aug; 101(4):437-47. Lowe CB, Bejerano G, Salama SR, Haussler D. PMID: 20332163; PMCID: PMC2884192.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    175. A population genetic hidden Markov model for detecting genomic regions under selection. Mol Biol Evol. 2010 Jul; 27(7):1673-85. Kern AD, Haussler D. PMID: 20185453; PMCID: PMC2912474.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    176. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 2010 Jan; 38(Database issue):D620-5. Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ. PMID: 19920125; PMCID: PMC2808953.
      View in: PubMed   Mentions: 159     Fields:    Translation:HumansAnimalsCells
    177. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 2010 Jan; 38(Database issue):D613-9. Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ. PMID: 19906737; PMCID: PMC2808870.
      View in: PubMed   Mentions: 368     Fields:    Translation:HumansAnimals
    178. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 Dec; 19(12):2324-33. MGC Project Team, Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, Riddick L, Webb D, Weber J, Wu W, Pruitt KD, Maglott D, Siepel A, Brejova B, Diekhans M, Harte R, Baertsch R, Kent J, Haussler D, Brent M, Langton L, Comstock CL, Stevens M, Wei C, van Baren MJ, Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E, Lin C, Pennacchio C, Schreiber K, Shapiro N, Marsh A, Pardes E, Moore T, Lebeau A, Muratet M, Simmons B, Kloske D, Sieja S, Hudson J, Sethupathy P, Brownstein M, Bhat N, Lazar J, Jacob H, Gruber CE, Smith MR, McPherson J, Garcia AM, Gunaratne PH, Wu J, Muzny D, Gibbs RA, Young AC, Bouffard GG, Blakesley RW, Mullikin J, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJ, Holt RA, Marra MA, Lu S, Yang S, Hartigan J, Graf M, Wagner R, Letovksy S, Pulido JC, Robison K, Esposito D, Hartley J, Wall VE, Hopkins RF, Ohara O, Wiemann S. PMID: 19767417; PMCID: PMC2792178.
      View in: PubMed   Mentions: 79     Fields:    Translation:HumansAnimals
    179. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009 Jul; 19(7):1316-23. Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R, Lipman D. PMID: 19498102; PMCID: PMC2704439.
      View in: PubMed   Mentions: 321     Fields:    Translation:HumansAnimalsCells
    180. The UCSC Cancer Genomics Browser. Nat Methods. 2009 Apr; 6(4):239-40. Zhu J, Sanborn JZ, Benz S, Szeto C, Hsu F, Kuhn RM, Karolchik D, Archie J, Lenburg ME, Esserman LJ, Kent WJ, Haussler D, Wang T. PMID: 19333237; PMCID: PMC5027375.
      View in: PubMed   Mentions: 111     Fields:    Translation:Humans
    181. Posttranscriptional crossregulation between Drosha and DGCR8. Cell. 2009 Jan 09; 136(1):75-84. Han J, Pedersen JS, Kwon SC, Belair CD, Kim YK, Yeom KH, Yang WY, Haussler D, Blelloch R, Kim VN. PMID: 19135890; PMCID: PMC2680683.
      View in: PubMed   Mentions: 240     Fields:    Translation:HumansAnimalsCells
    182. Retrocopy contributions to the evolution of the human genome. BMC Genomics. 2008 Oct 08; 9:466. Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. PMID: 18842134; PMCID: PMC2584115.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansAnimalsCells
    183. DUPCAR: reconstructing contiguous ancestral regions with duplications. J Comput Biol. 2008 Oct; 15(8):1007-27. Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D. PMID: 18774902; PMCID: PMC3205822.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimals
    184. 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.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansAnimalsCells
    185. UCSC genome browser tutorial. Genomics. 2008 Aug; 92(2):75-84. Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. PMID: 18514479.
      View in: PubMed   Mentions: 53     Fields:    Translation:Cells
    186. 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.
      View in: PubMed   Mentions: 1027     Fields:    Translation:HumansAnimalsCells
    187. Phylogenomic resources at the UCSC Genome Browser. Methods Mol Biol. 2008; 422:133-44. Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W. PMID: 18629665.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    188. 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.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    189. 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.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    190. 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.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansAnimals
    191. 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.
      View in: PubMed   Mentions: 218     Fields:    Translation:HumansCells
    192. 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.
      View in: PubMed   Mentions: 336     Fields:    Translation:AnimalsCells
    193. 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.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    194. 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.
      View in: PubMed   Mentions: 168     Fields:    Translation:HumansAnimalsCells
    195. Detecting coevolution in and among protein domains. PLoS Comput Biol. 2007 Nov; 3(11):e211. Yeang CH, Haussler D. PMID: 17983264; PMCID: PMC2098842.
      View in: PubMed   Mentions: 87     Fields:    Translation:Cells
    196. 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.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansAnimalsCells
    197. 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.
      View in: PubMed   Mentions: 126     Fields:    Translation:HumansCells
    198. 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.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    199. 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.
      View in: PubMed   Mentions: 2651     Fields:    Translation:HumansCells
    200. 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.
      View in: PubMed   Mentions: 118     Fields:    Translation:HumansAnimals
    201. 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.
      View in: PubMed   Mentions: 133     Fields:    Translation:HumansCells
    202. 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.
      View in: PubMed   Mentions: 725     Fields:    Translation:HumansAnimals
    203. 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: 110     Fields:    Translation:HumansAnimalsCells
    204. 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: 12     Fields:    Translation:HumansAnimals
    205. 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
    206. 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: 10     Fields:    Translation:HumansAnimals
    207. 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: 108     Fields:    Translation:HumansAnimalsCells
    208. 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: 233     Fields:    Translation:HumansAnimalsCells
    209. 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: 405     Fields:    Translation:HumansAnimalsCells
    210. 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
    211. 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: 267     Fields:    Translation:HumansAnimalsCells
    212. 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: 250     Fields:    Translation:HumansAnimalsCells
    213. 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: 338     Fields:    Translation:Cells
    214. 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: 122     Fields:    Translation:HumansAnimalsCells
    215. 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
    216. 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: 2245     Fields:    Translation:HumansAnimalsCells
    217. 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: 23     Fields:    Translation:HumansAnimalsCells
    218. 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: 32     Fields:    Translation:Humans
    219. 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: 103     Fields:    
    220. 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: 17     Fields:    Translation:Humans
    221. 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: 91     Fields:    Translation:HumansCells
    222. 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: 56     Fields:    Translation:AnimalsCells
    223. 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: 11     Fields:    Translation:HumansCells
    224. 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: 250     Fields:    Translation:HumansAnimals
    225. 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: 97     Fields:    Translation:HumansAnimalsCells
    226. 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
    227. 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: 36     Fields:    Translation:HumansAnimalsCells
    228. 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: 738     Fields:    Translation:HumansAnimalsCells
    229. 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: 244     Fields:    Translation:HumansAnimalsCells
    230. 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: 45     Fields:    Translation:HumansAnimalsCells
    231. 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.
      View in: PubMed   Mentions: 863     Fields:    Translation:HumansAnimalsCells
    232. 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: 793     Fields:    Translation:HumansAnimalsCells
    233. 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: 109     Fields:    Translation:HumansAnimalsCells
    234. 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: 1361     Fields:    Translation:HumansAnimals
    235. 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
    236. 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: 104     Fields:    
    237. 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: 170     Fields:    
    238. 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: 149     Fields:    Translation:HumansAnimalsCells
    239. 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: 466     Fields:    Translation:Animals
    240. 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: 52     Fields:    Translation:Humans
    241. 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: 35     Fields:    Translation:Cells
    242. 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: 143     Fields:    Translation:HumansAnimalsCells
    243. 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: 580     Fields:    Translation:HumansAnimals
    244. 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
    245. 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: 2892     Fields:    Translation:HumansAnimalsCells
    246. 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: 14     Fields:    Translation:Cells
    247. 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: 5636     Fields:    Translation:Humans
    248. 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
    249. 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
    250. 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
    251. 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: 28     Fields:    Translation:HumansAnimalsCells
    David's Networks
    Concepts (607)
    Derived automatically from this person's publications.
    Explore
    _
    Co-Authors (88)
    People in Profiles who have published with this person.
    Explore
    _
    Similar People (60)
    People who share similar concepts with this person.
    Explore
    _
    Same Department
    Search Department
    _

    UCSF Profiles is managed by the UCSF Clinical and Translational Science Institute (CTSI), part of the Clinical and Translational Science Award program funded by the National Center for Advancing Translational Sciences (Grant Number UL1 TR000004) at the National Institutes of Health (NIH).

    We use cookies to operate our website. We also use cookies to analyze our site’s performance and improve your experience on our site. For more information about how we use cookies, please see our Website Terms of Use. This site is running Profiles RNS version UCSF-v3.1.0-6-g69de2244 on PROFILES-PWEB04.

    Copyright © The Regents of the University of California.