David Haussler, PhD
Professor
Bioengineering
School of Pharmacy

Grants and Projects

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• Enhance UCSC Xena: extend interactive visualization to ultra-large-scale multi-omics data and integrate with analysis resources, NIH, 2021-2026
• Center for Live Cell Genomics, NIH, 2021-2026
• Development of Advanced Preclinical Models for Pediatric Solid Tumors, NIH, 2020-2025
• Center for Human Reference Genome Diversity, NIH, 2019-2024
• Enabling Comparative Pangenomics, NIH, 2020-2023
• The AnVIL Data Ecosystem, NIH, 2018-2023
• Visualization hub for genomics data exploration and translational discovery, NIH, 2016-2021
• Center for Big Data in Translational Genomics, NIH, 2014-2021
• UC Santa Cruz Training Program In Genomic Sciences, NIH, 2015-2021
• Unbiased analysis of genomic correlates of gene expression in health and disease, NIH, 2017-2021
• Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Canc, NIH, 2013-2020
• UCSC-Buck Inst. Genome Data Analysis Center for TCGA Research Network (GDAC), NIH, 2009-2017
• UCSC Center for Genomic Science and Minority Outreach Program, NIH, 2001-2012
• Visualization and Analysis of the TCGA Data Using the UCSC Cancer Genomics Browse, NIH, 2008-2011

Publications (275)

Top publication keywords:
Information DisseminationDatabases, Nucleic AcidGenome, HumanDatabases, GeneticConserved SequencePhylogenyGenomicsComputational BiologySequence AlignmentSequence Analysis, RNAOrganoidsSequence Analysis, DNAGenomeEvolution, MolecularSoftware

• SpikeLab: Agentic tools for spike data analysis.
  bioRxiv : the preprint server for biology 2026 Van der Molen T, Cheney L, Hussain K, Brahme O, Robbins A, Lim M, Spaeth A, Geng J, Parks D, Kosik K, Teodorescu M, Haussler D, Sharf T
• Microfluidic Control of Dorsal-Ventral Patterning Within a Single Forebrain Organoid.
  bioRxiv : the preprint server for biology 2026 Torres-Montoya S, Vera-Choqqueccota S, Seiler ST, Haussler D, Salama SR, Mostajo-Radji MA, Teodorescu M
• A Modular In-Incubator Microscope for Longitudinal Live Cell Microscopy.
  bioRxiv : the preprint server for biology 2026 Ehrlich D, Rosen Y, Arul S, Minnick J, Nicholson S, Voitiuk K, Seiler S, Toledo A, Vera-Choqqueccota S, Doherty N, Sevetson J, McGlynn M, Doganyigit K, Moarefian M, Kurniawan S, Mostajo-Radji MA, …
• Establishing mouse forebrain organoids as models of intrinsic cortical network assembly.
  Stem cell reports 2026 Hernandez S, Schweiger HE, Cline I, Kaurala GA, Robbins A, Solis D, Vera-Choqqueccota S, Geng J, van der Molen T, Reyes F, Asogwa CN, Voitiuk K, Chini M, Rolandi M, Salama SR, Colquitt BM, Sharf T, …
• Goal-directed learning in cortical organoids.
  Cell reports 2026 Robbins A, Schweiger HE, Hernandez S, Spaeth A, Voitiuk K, Parks DF, van der Molen T, Geng J, Cline I, Kosik KS, Salama SR, Sharf T, Mostajo-Radji MA, Haussler D, Teodorescu M

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• A modular platform for automated organoid culture and longitudinal imaging.
  Scientific reports 2026 Torres-Montoya S, Hernandez S, Seiler ST, Schweiger HE, Vera-Choqqueccota S, Kaurala G, Sharf T, Haussler D, Mostajo-Radji MA, Teodorescu M
• CytoVerse: Single-Cell AI Foundation Models in the Browser.
  bioRxiv : the preprint server for biology 2026 Currie R, Gonzalez-Ferrer J, Mostajo-Radji MA, Haussler D
• Cloud-Connected Pluripotent Stem Cell Platform Enhances Scientific Identity in Underrepresented Students.
  bioRxiv : the preprint server for biology 2026 Vera-Choqqueccota S, Ehrlich D, Luna-Gomez V, Hernandez S, Gonzalez-Ferrer J, Schweiger HE, Voitiuk K, Rosen Y, Doganyigit K, Cline I, Ward R, Yeh E, Miga KH, Rochers BD, Kurniawan S, Haussler D, …
• The UCSC Genome Browser database: 2026 update.
  Nucleic acids research 2026 Casper J, Speir ML, Raney BJ, Perez G, Nassar LR, Lee CM, Hinrichs AS, Gonzalez JN, Fischer C, Diekhans M, Clawson H, Benet-Pages A, Barber GP, Vaske CJ, van Baren MJ, Wang K, Rodriguez YJP, Jenkins-…
• Microscale maps of bursting dynamics across human hippocampal slices from patients with epilepsy.
  Journal of neurophysiology 2025 Elliott MAT, Andrews JP, van der Molen T, Geng J, Spaeth A, Toledo A, Voitiuk K, Core C, Gillespie T, Sinervo A, Parks DF, Robbins A, Solís D, Chang EF, Nowakowski TJ, Teodorescu M, Haussler D, Sharf …
• Single molecule nanopore counting assay targeting small extracellular vesicle cargo for non-invasive monitoring of cerebral organoid development and health.
  Scientific reports 2025 Saiduzzaman SM, Xu R, Sampad MJN, Hoffman RN, Seiler ST, Brail Q, Yurevych V, Walker ZJ, Wells TN, Ong EM, Yuzvinsky TD, Hawkins AR, Salama SR, Teodorescu M, Haussler D, Schmidt H
• Incubator-Free Organoid Culture in a Sealed Recirculatory System.
  bioRxiv : the preprint server for biology 2025 Rosen Y, Doganyigit K, Arul S, Wachtel E, Ehrlich D, Venuturimilli V, Mouzaya M, Oriaku S, Ndiforchu B, Kaurala G, Hernandez S, Moarefian M, Schweiger H, Cisneros A, Zeraatkar M, Geng J, Mostajo-Radji…
• A feedback-driven brain organoid platform enables automated maintenance and high-resolution neural activity monitoring.
  Internet of things (Amsterdam, Netherlands) 2025 Voitiuk K, Seiler ST, de Melo MP, Geng J, van der Molen T, Hernandez S, Schweiger HE, Sevetson JL, Parks DF, Robbins A, Torres-Montoya S, Ehrlich D, Elliott MAT, Sharf T, Haussler D, Mostajo-Radji MA,…
• Consistently processed RNA sequencing data from 50 sources enriched for pediatric data.
  Scientific data 2025 Beale HC, Learned K, Kephart ET, Lyle AG, van den Bout A, McCabe M, Echandia-Monroe K, Khare MJ, Huang EY, Jariwala S, Antilla R, Cheney A, Lee AG, Sayles LC, Leung SG, Vasquez YA, Sanders L, Haussler…
• Highly accurate assembly polishing with DeepPolisher.
  Genome research 2025 Mastoras M, Asri M, Brambrink L, Hebbar P, Kolesnikov A, Cook DE, Nattestad M, Lucas J, Won TS, Chang PC, Carroll A, Paten B, Shafin K, and the Human Pangenome Reference Consortium
• Microfluidic Topography Biases Neural Organoid Morphogenesis.
  Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference 2025 Minnick J, Ehrlich D, Moarefian M, Sevetson J, Geng J, Voitiuk K, Rosen Y, Salama SR, Haussler D, Teodorescu M
• Weighted Graph for Longitudinal Tracking of Neurons in Cortical Organoids on a High-Density Microelectrode Array.
  Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference 2025 Geng J, Gonzalez-Ferrer J, Voitiuk K, Seiler ST, Schweiger HE, Hernandez S, Salama SR, Haussler D, Mostajo-Radji MA, Teodorescu M
• Comparative analysis of RNA expression identifies effective targeted drug in myoepithelial carcinoma.
  NPJ precision oncology 2025 Vasquez YA, Sanders L, Beale HC, Lyle AG, Kephart ET, Learned K, Peralez J, Li A, Huang M, Pyke-Grimm KA, Tan SY, Salama SR, Haussler D, Bjork I, Vaske OM, Spunt SL
• Self-Organizing Neural Networks in Organoids Reveal Principles of Forebrain Circuit Assembly.
  bioRxiv : the preprint server for biology 2025 Hernandez S, Schweiger HE, Cline I, Kaurala GA, Robbins A, Solis D, Geng J, van der Molen T, Reyes F, Asogwa CN, Voitiuk K, Chini M, Rolandi M, Salama SR, Colquitt BM, Sharf T, Haussler D, Teodorescu …
• Protocol for deep-learning-driven cell type label transfer in single-cell RNA sequencing data.
  STAR protocols 2025 Zabetian Z, Gonzalez-Ferrer J, Lehrer J, Jonsson VD, Teodorescu M, Haussler D, Mostajo-Radji MA
• Comparative analysis of RNA expression in a single institution cohort of pediatric cancer patients.
  NPJ precision oncology 2025 Vasquez YA, Beale HC, Sanders L, Lyle AG, Kephart ET, Learned K, Thompson D, Peralez J, Li A, Huang M, Pyke-Grimm KA, Salama SR, Haussler D, Bjork I, Sheri LS, Vaske OM
• Microscope Upcycling: Transforming legacy microscopes into automated cloud-integrated imaging systems.
  HardwareX 2025 Ehrlich D, Rosen Y, Parks DF, Doganyigit K, Fenimore R, Vera-Choqqueccota S, Hernandez S, Toledo A, Haussler D, Kurniawan S, Teodorescu M
• Pathological microcircuits and epileptiform events in patient hippocampal slices.
  bioRxiv : the preprint server for biology 2025 Elliott MAT, Andrews JP, van der Molen T, Geng J, Spaeth A, Toledo A, Voitiuk K, Core C, Gillespie T, Sinervo A, Parks DF, Robbins A, Solís D, Chang EF, Nowakowski TJ, Teodorescu M, Haussler D, Sharf …
• HIPPIE: A Multimodal Deep Learning Model for Electrophysiological Classification of Neurons.
  bioRxiv : the preprint server for biology 2025 Gonzalez-Ferrer J, Lehrer J, Schweiger HE, Geng J, Hernandez S, Reyes F, Sevetson JL, Salama SR, Teodorescu M, Haussler D, Mostajo-Radji MA
• The UCSC Genome Browser database: 2025 update.
  Nucleic acids research 2025 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
• Multiscale Cloud-Based Pipeline for Neuronal Electrophysiology Analysis and Visualization.
  bioRxiv : the preprint server for biology 2024 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, …
• Goal-Directed Learning in Cortical Organoids.
  bioRxiv : the preprint server for biology 2024 Robbins A, Schweiger HE, Hernandez S, Spaeth A, Voitiuk K, Parks DF, van der Molen T, Geng J, Sharf T, Mostajo-Radji MA, Haussler D, Teodorescu M
• A feedback-driven brain organoid platform enables automated maintenance and high-resolution neural activity monitoring.
  bioRxiv : the preprint server for biology 2024 Voitiuk K, Seiler ST, Pessoa de Melo M, Geng J, van der Molen T, Hernandez S, Schweiger HE, Sevetson JL, Parks DF, Robbins A, Torres-Montoya S, Ehrlich D, Elliott MAT, Sharf T, Haussler D, Mostajo-…
• RT-Sort: An action potential propagation-based algorithm for real time spike detection and sorting with millisecond latencies.
  PloS one 2024 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
• Multimodal evaluation of network activity and optogenetic interventions in human hippocampal slices.
  Nature neuroscience 2024 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…
• Model-agnostic neural mean field with a data-driven transfer function.
  Neuromorphic computing and engineering 2024 Spaeth A, Haussler D, Teodorescu M
• Reducing education inequalities through cloud-enabled live-cell biotechnology.
  Trends in biotechnology 2024 Vera-Choqqueccota S, Belmekki BEY, Alouini MS, Teodorescu M, Haussler D, Mostajo-Radji MA
• A nonoscillatory, millisecond-scale embedding of brain state provides insight into behavior.
  Nature neuroscience 2024 Parks DF, Schneider AM, Xu Y, Brunwasser SJ, Funderburk S, Thurber D, Blanche T, Dyer EL, Haussler D, Hengen KB
• Internet-enabled lab-on-a-chip technology for education.
  Scientific reports 2024 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
• SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis.
  Cell genomics 2024 Gonzalez-Ferrer J, Lehrer J, O'Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA
• Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders.
  Cell stem cell 2024 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, …
• Model-Agnostic Neural Mean Field With The Refractory SoftPlus Transfer Function.
  bioRxiv : the preprint server for biology 2024 Spaeth A, Haussler D, Teodorescu M
• The UCSC Genome Browser database: 2024 update.
  Nucleic acids research 2024 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,…
• Internet-Connected Cortical Organoids for Project-Based Stem Cell and Neuroscience Education.
  eNeuro 2023 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
• Unraveling Neuronal Identities Using SIMS: A Deep Learning Label Transfer Tool for Single-Cell RNA Sequencing Analysis.
  bioRxiv : the preprint server for biology 2023 Gonzalez-Ferrer J, Lehrer J, O'Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA
• GenArk: towards a million UCSC genome browsers.
  Genome biology 2023 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 …
• Internet-connected cortical organoids for project-based stem cell and neuroscience education.
  bioRxiv : the preprint server for biology 2023 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
• A non-oscillatory, millisecond-scale embedding of brain state provides insight into behavior.
  bioRxiv : the preprint server for biology 2023 Parks DF, Schneider AM, Xu Y, Brunwasser SJ, Funderburk S, Thurber D, Blanche T, Dyer EL, Haussler D, Hengen KB
• A draft human pangenome reference.
  Nature 2023 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…
• Isoform-specific translational control is evolutionarily conserved in primates.
  bioRxiv : the preprint server for biology 2023 Draper JM, Philipp J, Neeb ZT, Thomas R, Katzman S, Salama S, Haussler D, Sanford J
• Open-loop lab-on-a-chip technology enables remote computer science training in Latinx life sciences students.
  bioRxiv : the preprint server for biology 2023 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
• GenArk: Towards a million UCSC Genome Browsers.
  Research square 2023 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 …
• The UCSC Genome Browser database: 2023 update.
  Nucleic acids research 2023 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, …
• Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors.
  Communications biology 2022 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
• Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids.
  Scientific reports 2022 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
• Cloud-controlled microscopy enables remote project-based biology education in underserved Latinx communities.
  Heliyon 2022 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 …
• The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science.
  Neoplasia (New York, N.Y.) 2022 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, …
• Semi-automated assembly of high-quality diploid human reference genomes.
  Nature 2022 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, …
• IoT cloud laboratory: Internet of Things architecture for cellular biology.
  Internet of things (Amsterdam, Netherlands) 2022 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…
• Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape.
  Nature 2022 Turakhia Y, Thornlow B, Hinrichs A, McBroome J, Ayala N, Ye C, Smith K, De Maio N, Haussler D, Lanfear R, Corbett-Detig R
• Author Correction: Comparative and demographic analysis of orang-utan genomes.
  Nature 2022 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, …
• A complete pedigree-based graph workflow for rare candidate variant analysis.
  Genome research 2022 Markello C, Huang C, Rodriguez A, Carroll A, Chang PC, Eizenga J, Markello T, Haussler D, Paten B
• The Human Pangenome Project: a global resource to map genomic diversity.
  Nature 2022 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-…
• A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci.
  Genome research 2022 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 …
• The Earth BioGenome Project 2020: Starting the clock.
  Proceedings of the National Academy of Sciences of the United States of America 2022 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, …
• The UCSC Genome Browser database: 2022 update.
  Nucleic acids research 2022 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 …
• Pangenomics enables genotyping of known structural variants in 5202 diverse genomes.
  Science (New York, N.Y.) 2021 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, …
• A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees.
  Molecular biology and evolution 2021 McBroome J, Thornlow B, Hinrichs AS, Kramer A, De Maio N, Goldman N, Haussler D, Corbett-Detig R, Turakhia Y
• Light-weight electrophysiology hardware and software platform for cloud-based neural recording experiments.
  Journal of neural engineering 2021 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
• GA4GH: International policies and standards for data sharing across genomic research and healthcare.
  Cell genomics 2021 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,…
• Picroscope: low-cost system for simultaneous longitudinal biological imaging.
  Communications biology 2021 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, …
• Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans.
  Genome research 2021 Cahill JA, Armstrong J, Deran A, Khoury CJ, Paten B, Haussler D, Jarvis ED
• A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees.
  bioRxiv : the preprint server for biology 2021 McBroome J, Thornlow B, Hinrichs AS, De Maio N, Goldman N, Haussler D, Corbett-Detig R, Turakhia Y
• Cancer microenvironment and genomics: evolution in process.
  Clinical & experimental metastasis 2021 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
• Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic.
  Nature genetics 2021 Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, Corbett-Detig R
• Towards complete and error-free genome assemblies of all vertebrate species.
  Nature 2021 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, …
• A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control.
  bioRxiv : the preprint server for biology 2021 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, …
• Author Correction: Dense sampling of bird diversity increases power of comparative genomics.
  Nature 2021 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, …
• The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets.
  GigaScience 2021 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
• Share pandemic sequences openly and fast.
  Nature 2021 Haussler D, Haeussler M, Hinrichs A, Corbett-Detig R, Bjork I
• The UCSC Genome Browser database: 2021 update.
  Nucleic acids research 2021 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, …
• Identification of a differentiation stall in epithelial mesenchymal transition in histone H3-mutant diffuse midline glioma.
  GigaScience 2020 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
• Stability of SARS-CoV-2 phylogenies.
  PLoS genetics 2020 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
• Dense sampling of bird diversity increases power of comparative genomics.
  Nature 2020 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, …
• Progressive Cactus is a multiple-genome aligner for the thousand-genome era.
  Nature 2020 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, …
• ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy.
  Frontiers in immunology 2020 Rao AA, Madejska AA, Pfeil J, Paten B, Salama SR, Haussler D
• Spiking neural state machine for gait frequency entrainment in a flexible modular robot.
  PloS one 2020 Spaeth A, Tebyani M, Haussler D, Teodorescu M
• The UCSC SARS-CoV-2 Genome Browser.
  Nature genetics 2020 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, …
• Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic.
  bioRxiv : the preprint server for biology 2020 Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, Corbett-Detig R
• A user guide for the online exploration and visualization of PCAWG data.
  Nature communications 2020 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, …
• Visualizing and interpreting cancer genomics data via the Xena platform.
  Nature biotechnology 2020 Goldman MJ, Craft B, Hastie M, Repecka K, McDade F, Kamath A, Banerjee A, Luo Y, Rogers D, Brooks AN, Zhu J, Haussler D
• Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
  Nature biotechnology 2020 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, …
• Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures.
  PLoS computational biology 2020 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 …
• The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families.
  Mobile DNA 2020 Fernandes JD, Zamudio-Hurtado A, Clawson H, Kent WJ, Haussler D, Salama SR, Haeussler M
• Blockchain-Authenticated Sharing of Genomic and Clinical Outcomes Data of Patients With Cancer: A Prospective Cohort Study.
  Journal of medical Internet research 2020 Glicksberg BS, Burns S, Currie R, Griffin A, Wang ZJ, Haussler D, Goldstein T, Collisson E
• UCSC Genome Browser enters 20th year.
  Nucleic acids research 2020 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, …
• Erratum: Data sharing for clinical utility.
  Cold Spring Harbor molecular case studies 2019 Bjork I, Peralez J, Haussler D, Spunt SL, Morozova Vaske O
• Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.
  Cell reports 2019 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, …
• Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor.
  Cold Spring Harbor molecular case studies 2019 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, …
• Data sharing for clinical utility.
  Cold Spring Harbor molecular case studies 2019 Bjork I, Peralez J, Haussler D, Spunt SL, Vaske OM
• Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer.
  JAMA network open 2019 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, …
• Barriers to accessing public cancer genomic data.
  Scientific data 2019 Learned K, Durbin A, Currie R, Kephart ET, Beale HC, Sanders LM, Pfeil J, Goldstein TC, Salama SR, Haussler D, Vaske OM, Bjork IM
• Publisher Correction: Federated discovery and sharing of genomic data using Beacons.
  Nature biotechnology 2019 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…
• Data sharing for pediatric cancers.
  Science (New York, N.Y.) 2019 Vaske OM, Haussler D
• Federated discovery and sharing of genomic data using Beacons.
  Nature biotechnology 2019 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…
• Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution.
  Cell 2019 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, …
• Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes.
  Stem cell reports 2019 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
• The UCSC Genome Browser database: 2019 update.
  Nucleic acids research 2019 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
• BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2.
  PLoS genetics 2018 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, …
• Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.
  Genome biology 2018 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, …
• The ESCRT-III Protein CHMP1A Mediates Secretion of Sonic Hedgehog on a Distinctive Subtype of Extracellular Vesicles.
  Cell reports 2018 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, …
• Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.
  Genome research 2018 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
• High-resolution comparative analysis of great ape genomes.
  Science (New York, N.Y.) 2018 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, …
• Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis.
  Cell 2018 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, …
• A Flow Procedure for Linearization of Genome Sequence Graphs.
  Journal of computational biology : a journal of computational molecular cell biology 2018 Haussler D, Smuga-Otto M, Eizenga JM, Paten B, Novak AM, Nikitin S, Zueva M, Miagkov D
• Earth BioGenome Project: Sequencing life for the future of life.
  Proceedings of the National Academy of Sciences of the United States of America 2018 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…
• Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer.
  JCO precision oncology 2018 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, …
• Linear assembly of a human centromere on the Y chromosome.
  Nature biotechnology 2018 Jain M, Olsen HE, Turner DJ, Stoddart D, Bulazel KV, Paten B, Haussler D, Willard HF, Akeson M, Miga KH
• A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations.
  Frontiers in immunology 2018 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
• The UCSC Genome Browser database: 2018 update.
  Nucleic acids research 2018 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, …
• TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.
  Cancer research 2017 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
• Sharing Clinical and Genomic Data on Cancer - The Need for Global Solutions.
  The New England journal of medicine 2017 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…
• Consistency of BRCA1 and BRCA2 Variant Classifications Among Clinical Diagnostic Laboratories.
  JCO precision oncology 2017 Lincoln SE, Yang S, Cline MS, Kobayashi Y, Zhang C, Topper S, Haussler D, Paten B, Nussbaum RL
• Toil enables reproducible, open source, big biomedical data analyses.
  Nature biotechnology 2017 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, …
• The UCSC Genome Browser database: 2017 update.
  Nucleic acids research 2016 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, …
• Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.
  BMC bioinformatics 2016 Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D
• Facilitating a culture of responsible and effective sharing of cancer genome data.
  Nature medicine 2016 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 …
• Long-read sequence assembly of the gorilla genome.
  Science (New York, N.Y.) 2016 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, …
• Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.
  Genome research 2016 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
• Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.
  Cell 2016 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, …
• UCSC Data Integrator and Variant Annotation Integrator.
  Bioinformatics (Oxford, England) 2016 Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ
• A Distributed Network for Intensive Longitudinal Monitoring in Metastatic Triple-Negative Breast Cancer.
  Journal of the National Comprehensive Cancer Network : JNCCN 2016 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…
• The UCSC Genome Browser database: 2016 update.
  Nucleic acids research 2015 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…
• Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.
  The New England journal of medicine 2015 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 …
• Canonical, stable, general mapping using context schemes.
  Bioinformatics (Oxford, England) 2015 Novak AM, Rosen Y, Haussler D, Paten B
• The NIH BD2K center for big data in translational genomics.
  Journal of the American Medical Informatics Association : JAMIA 2015 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,…
• Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.
  The New England journal of medicine 2015 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, …
• Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.
  Nature methods 2015 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, …
• Integrative analysis of 111 reference human epigenomes.
  Nature 2015 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 …
• Building a pan-genome reference for a population.
  Journal of computational biology : a journal of computational molecular cell biology 2015 Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B
• Whole-genome analyses resolve early branches in the tree of life of modern birds.
  Science (New York, N.Y.) 2014 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, …
• Comparative genomics reveals insights into avian genome evolution and adaptation.
  Science (New York, N.Y.) 2014 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…
• The birds of Genome10K.
  GigaScience 2014 OBrien SJ, Haussler D, Ryder O
• Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.
  Science (New York, N.Y.) 2014 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,…
• The UCSC Genome Browser database: 2015 update.
  Nucleic acids research 2014 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, …
• Feather development genes and associated regulatory innovation predate the origin of Dinosauria.
  Molecular biology and evolution 2014 Lowe CB, Clarke JA, Baker AJ, Haussler D, Edwards SV
• RADIA: RNA and DNA integrated analysis for somatic mutation detection.
  PloS one 2014 Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D
• The UCSC Cancer Genomics Browser: update 2015.
  Nucleic acids research 2014 Goldman M, Craft B, Swatloski T, Cline M, Morozova O, Diekhans M, Haussler D, Zhu J
• The UCSC Ebola Genome Portal.
  PLoS currents 2014 Haeussler M, Karolchik D, Clawson H, Raney BJ, Rosenbloom KR, Fujita PA, Hinrichs AS, Speir ML, Eisenhart C, Zweig AS, Haussler D, Kent WJ
• Navigating protected genomics data with UCSC Genome Browser in a Box.
  Bioinformatics (Oxford, England) 2014 Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ
• Alignathon: a competitive assessment of whole-genome alignment methods.
  Genome research 2014 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…
• The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data.
  Database : the journal of biological databases and curation 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, …
• An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.
  Nature 2014 Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D
• Comparative assembly hubs: web-accessible browsers for comparative genomics.
  Bioinformatics (Oxford, England) 2014 Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B
• A unifying model of genome evolution under parsimony.
  BMC bioinformatics 2014 Paten B, Zerbino DR, Hickey G, Haussler D
• The UCSC Genome Browser database: 2014 update.
  Nucleic acids research 2013 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, …
• Current status and new features of the Consensus Coding Sequence database.
  Nucleic acids research 2013 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…
• The somatic genomic landscape of glioblastoma.
  Cell 2013 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, …
• Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser.
  Scientific reports 2013 Cline MS, Craft B, Swatloski T, Goldman M, Ma S, Haussler D, Zhu J
• Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).
  Bioinformatics (Oxford, England) 2013 Paull EO, Carlin DE, Niepel M, Sorger PK, Haussler D, Stuart JM
• Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.
  Cancer research 2013 Sanborn JZ, Salama SR, Grifford M, Brennan CW, Mikkelsen T, Jhanwar S, Katzman S, Chin L, Haussler D
• Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
  GigaScience 2013 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, …
• The UCSC Interaction Browser: multidimensional data views in pathway context.
  Nucleic acids research 2013 Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D, Stuart JM
• HAL: a hierarchical format for storing and analyzing multiple genome alignments.
  Bioinformatics (Oxford, England) 2013 Hickey G, Paten B, Earl D, Zerbino D, Haussler D
• Retrotransposition of gene transcripts leads to structural variation in mammalian genomes.
  Genome biology 2013 Ewing AD, Ballinger TJ, Earl D, Broad Institute Genome Sequencing and Analysis Program and Platform, Harris CC, Ding L, Wilson RK, Haussler D
• Life, the universe, and everything: an interview with David Haussler. Interviewed by Jane Gitschier.
  PLoS genetics 2013 Haussler D
• ENCODE data in the UCSC Genome Browser: year 5 update.
  Nucleic acids research 2012 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 …
• The UCSC Genome Browser database: extensions and updates 2013.
  Nucleic acids research 2012 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, …
• The UCSC Cancer Genomics Browser: update 2013.
  Nucleic acids research 2012 Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M, Ma S, Wilks C, Stuart J, Haussler D, Zhu J
• PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.
  Bioinformatics (Oxford, England) 2012 Ng S, Collisson EA, Sokolov A, Goldstein T, Gonzalez-Perez A, Lopez-Bigas N, Benz C, Haussler D, Stuart JM
• GENCODE: the reference human genome annotation for The ENCODE Project.
  Genome research 2012 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 …
• 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome.
  PloS one 2012 Lowe CB, Haussler D
• Gene isoform specificity through enhancer-associated antisense transcription.
  PloS one 2012 Onodera CS, Underwood JG, Katzman S, Jacobs F, Greenberg D, Salama SR, Haussler D
• The UCSC genome browser and associated tools.
  Briefings in bioinformatics 2012 Kuhn RM, Haussler D, Kent WJ
• Tissue sampling methods and standards for vertebrate genomics.
  GigaScience 2012 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
• The fishes of Genome 10K.
  Marine genomics 2012 Bernardi G, Wiley EO, Mansour H, Miller MR, Orti G, Haussler D, O'Brien SJ, Ryder OA, Venkatesh B
• The Human Epigenome Browser at Washington University.
  Nature methods 2011 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
• Human tRNA genes function as chromatin insulators.
  The EMBO journal 2011 Raab JR, Chiu J, Zhu J, Katzman S, Kurukuti S, Wade PA, Haussler D, Kamakaka RT
• The UCSC Genome Browser database: extensions and updates 2011.
  Nucleic acids research 2011 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…
• ENCODE whole-genome data in the UCSC Genome Browser: update 2012.
  Nucleic acids research 2011 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…
• Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma.
  Proceedings of the National Academy of Sciences of the United States of America 2011 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,…
• Subtype and pathway specific responses to anticancer compounds in breast cancer.
  Proceedings of the National Academy of Sciences of the United States of America 2011 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, …
• A high-resolution map of human evolutionary constraint using 29 mammals.
  Nature 2011 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, …
• Assemblathon 1: a competitive assessment of de novo short read assembly methods.
  Genome research 2011 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…
• Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.
  Proceedings of the National Academy of Sciences of the United States of America 2011 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
• The genome of the green anole lizard and a comparative analysis with birds and mammals.
  Nature 2011 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 …
• Three periods of regulatory innovation during vertebrate evolution.
  Science (New York, N.Y.) 2011 Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D
• Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots.
  Genome biology and evolution 2011 Katzman S, Capra JA, Haussler D, Pollard KS
• Cactus: Algorithms for genome multiple sequence alignment.
  Genome research 2011 Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D
• Meta-alignment with crumble and prune: partitioning very large alignment problems for performance and parallelization.
  BMC bioinformatics 2011 Roskin KM, Paten B, Haussler D
• Cactus graphs for genome comparisons.
  Journal of computational biology : a journal of computational molecular cell biology 2011 Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D
• David Haussler.
  Nature biotechnology 2011 Haussler D
• Comparative and demographic analysis of orang-utan genomes.
  Nature 2011 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, …
• The UCSC Cancer Genomics Browser: update 2011.
  Nucleic acids research 2010 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
• FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.
  Nature methods 2010 Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D
• ENCODE whole-genome data in the UCSC genome browser (2011 update).
  Nucleic acids research 2010 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…
• The UCSC Genome Browser database: update 2011.
  Nucleic acids research 2010 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,…
• Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
  Nature biotechnology 2010 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…
• Conserved role of intragenic DNA methylation in regulating alternative promoters.
  Nature 2010 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, …
• Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.
  Bioinformatics (Oxford, England) 2010 Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM
• GC-biased evolution near human accelerated regions.
  PLoS genetics 2010 Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D
• International network of cancer genome projects.
  Nature 2010 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, …
• Endangered species hold clues to human evolution.
  The Journal of heredity 2010 Lowe CB, Bejerano G, Salama SR, Haussler D
• A population genetic hidden Markov model for detecting genomic regions under selection.
  Molecular biology and evolution 2010 Kern AD, Haussler D
• ENCODE whole-genome data in the UCSC Genome Browser.
  Nucleic acids research 2009 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
• The UCSC Genome Browser database: update 2010.
  Nucleic acids research 2009 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,…
• The completion of the Mammalian Gene Collection (MGC).
  Genome research 2009 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 …
• The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
  Genome research 2009 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, …
• The UCSC Cancer Genomics Browser.
  Nature methods 2009 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
• Posttranscriptional crossregulation between Drosha and DGCR8.
  Cell 2009 Han J, Pedersen JS, Kwon SC, Belair CD, Kim YK, Yeom KH, Yang WY, Haussler D, Blelloch R, Kim VN
• Retrocopy contributions to the evolution of the human genome.
  BMC genomics 2008 Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J
• DUPCAR: reconstructing contiguous ancestral regions with duplications.
  Journal of computational biology : a journal of computational molecular cell biology 2008 Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D
• The infinite sites model of genome evolution.
  Proceedings of the National Academy of Sciences of the United States of America 2008 Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D
• UCSC genome browser tutorial.
  Genomics 2008 Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ
• Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
  Bioinformatics (Oxford, England) 2008 Stanke M, Diekhans M, Baertsch R, Haussler D
• Computational reconstruction of ancestral DNA sequences.
  Methods in molecular biology (Clifton, N.J.) 2008 Blanchette M, Diallo AB, Green ED, Miller W, Haussler D
• Phylogenomic resources at the UCSC Genome Browser.
  Methods in molecular biology (Clifton, N.J.) 2008 Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W
• Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins.
  Nucleic acids research 2007 Zeng J, Yan J, Wang T, Mosbrook-Davis D, Dolan KT, Christensen R, Stormo GD, Haussler D, Lathrop RH, Brachmann RK, Burgess SM
• Comparative genomics search for losses of long-established genes on the human lineage.
  PLoS computational biology 2007 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D
• Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53.
  Proceedings of the National Academy of Sciences of the United States of America 2007 Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D
• Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
  Nature 2007 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…
• Targeted discovery of novel human exons by comparative genomics.
  Genome research 2007 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
• 28-way vertebrate alignment and conservation track in the UCSC Genome Browser.
  Genome research 2007 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…
• Detecting coevolution in and among protein domains.
  PLoS computational biology 2007 Yeang CH, Haussler D
• Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion.
  Genome research 2007 Dreszer TR, Wall GD, Haussler D, Pollard KS
• Human genome ultraconserved elements are ultraselected.
  Science (New York, N.Y.) 2007 Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D
• Detecting the coevolution of biosequences--an example of RNA interaction prediction.
  Molecular biology and evolution 2007 Yeang CH, Darot JF, Noller HF, Haussler D
• Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
  Nature 2007 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, …
• Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
  Genome research 2007 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 …
• Thousands of human mobile element fragments undergo strong purifying selection near developmental genes.
  Proceedings of the National Academy of Sciences of the United States of America 2007 Lowe CB, Bejerano G, Haussler D
• Evolutionary and biomedical insights from the rhesus macaque genome.
  Science (New York, N.Y.) 2007 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 …
• Editing modifies the GABA(A) receptor subunit alpha3.
  RNA (New York, N.Y.) 2007 Ohlson J, Pedersen JS, Haussler D, Ohman M
• Comparative genomic analysis using the UCSC genome browser.
  Methods in molecular biology (Clifton, N.J.) 2007 Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ
• The ENCODE Project at UC Santa Cruz.
  Nucleic acids research 2006 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 …
• Variation resources at UC Santa Cruz.
  Nucleic acids research 2006 Thomas DJ, Trumbower H, Kern AD, Rhead BL, Kuhn RM, Haussler D, Kent WJ
• Reconstructing contiguous regions of an ancestral genome.
  Genome research 2006 Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W
• Forces shaping the fastest evolving regions in the human genome.
  PLoS genetics 2006 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
• An RNA gene expressed during cortical development evolved rapidly in humans.
  Nature 2006 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
• Coding exon detection using comparative sequences.
  Journal of computational biology : a journal of computational molecular cell biology 2006 Wu J, Haussler D
• Identification and classification of conserved RNA secondary structures in the human genome.
  PLoS computational biology 2006 Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D
• A distal enhancer and an ultraconserved exon are derived from a novel retroposon.
  Nature 2006 Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D
• The UCSC Known Genes.
  Bioinformatics (Oxford, England) 2006 Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D
• Unusual intron conservation near tissue-regulated exons found by splicing microarrays.
  PLoS computational biology 2006 Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D, Ares M
• Counterexample to a claim about the reconstruction of ancestral character states.
  Systematic biology 2005 Lucena B, Haussler D
• Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
  Genome research 2005 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
• Computational screening of conserved genomic DNA in search of functional noncoding elements.
  Nature methods 2005 Bejerano G, Siepel AC, Kent WJ, Haussler D
• Exploring relationships and mining data with the UCSC Gene Sorter.
  Genome research 2005 Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D
• LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
  Bioinformatics (Oxford, England) 2005 Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A
• The UCSC Proteome Browser.
  Nucleic acids research 2005 Hsu F, Pringle TH, Kuhn RM, Karolchik D, Diekhans M, Haussler D, Kent WJ
• The structure of a rigorously conserved RNA element within the SARS virus genome.
  PLoS biology 2004 Robertson MP, Igel H, Baertsch R, Haussler D, Ares M, Scott WG
• Reconstructing large regions of an ancestral mammalian genome in silico.
  Genome research 2004 Blanchette M, Green ED, Miller W, Haussler D
• Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing.
  Genome research 2004 Furey TS, Diekhans M, Lu Y, Graves TA, Oddy L, Randall-Maher J, Hillier LW, Wilson RK, Haussler D
• The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
  Genome research 2004 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…
• The structure and evolution of centromeric transition regions within the human genome.
  Nature 2004 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
• Efficient approximations for learning phylogenetic HMM models from data.
  Bioinformatics (Oxford, England) 2004 Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D
• Into the heart of darkness: large-scale clustering of human non-coding DNA.
  Bioinformatics (Oxford, England) 2004 Bejerano G, Haussler D, Blanchette M
• Ultraconserved elements in the human genome.
  Science (New York, N.Y.) 2004 Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D
• Aligning multiple genomic sequences with the threaded blockset aligner.
  Genome research 2004 Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W
• Comparative recombination rates in the rat, mouse, and human genomes.
  Genome research 2004 Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ
• Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
  Nature 2004 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, …
• Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.
  Genome research 2004 Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC
• Hotspots of mammalian chromosomal evolution.
  Genome biology 2004 Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE
• Combining phylogenetic and hidden Markov models in biosequence analysis.
  Journal of computational biology : a journal of computational molecular cell biology 2004 Siepel A, Haussler D
• Score functions for determining regional conservation in two-species local alignments.
  Journal of computational biology : a journal of computational molecular cell biology 2004 Roskin KM, Diekhans M, Haussler D
• The UCSC Table Browser data retrieval tool.
  Nucleic acids research 2004 Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ
• Phylogenetic estimation of context-dependent substitution rates by maximum likelihood.
  Molecular biology and evolution 2003 Siepel A, Haussler D
• Identification and characterization of multi-species conserved sequences.
  Genome research 2003 Margulies EH, Blanchette M, NISC Comparative Sequencing Program, Haussler D, Green ED
• Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.
  Proceedings of the National Academy of Sciences of the United States of America 2003 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D
• Integration of the cytogenetic map with the draft human genome sequence.
  Human molecular genetics 2003 Furey TS, Haussler D
• Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules.
  Biophysical journal 2003 Winters-Hilt S, Vercoutere W, DeGuzman VS, Deamer D, Akeson M, Haussler D
• Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.
  Genome research 2003 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
• Gene structure-based splice variant deconvolution using a microarray platform.
  Bioinformatics (Oxford, England) 2003 Wang H, Hubbell E, Hu JS, Mei G, Cline M, Lu G, Clark T, Siani-Rose MA, Ares M, Kulp DC, Haussler D
• Human-mouse alignments with BLASTZ.
  Genome research 2003 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W
• Initial sequencing and comparative analysis of the mouse genome.
  Nature 2002 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…
• Information-theoretic dissection of pairwise contact potentials.
  Proteins 2002 Cline MS, Karplus K, Lathrop RH, Smith TF, Rogers RG, Haussler D
• The human genome browser at UCSC.
  Genome research 2002 Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D
• Classifying G-protein coupled receptors with support vector machines.
  Bioinformatics (Oxford, England) 2002 Karchin R, Karplus K, Haussler D
• 1Alpha-hydroxyvitamin D3. An analog of vitamin D which apparently acts by metabolism to 1alpha, 25-dihydroxyvitamin D3.
  Biochemistry 1974 Zerwekh JE, Brumbaugh PF, Haussler DH, Cork DJ, Haussler MR
• Filter assay for 1alpha, 25-dihydroxyvitamin D3. Utilization of the hormone's target tissue chromatin receptor.
  Biochemistry 1974 Brumbaugh PF, Haussler DH, Bursac KM, Haussler MR
• Radioreceptor assay for 1 alpha,25-dihydroxyvitamin D3.
  Science (New York, N.Y.) 1974 Brumbaugh PF, Haussler DH, Bressler R, Haussler MR