David Henry Haussler - Publications

Affiliations: 
Center for Biomolecular Science & Engineering University of California, Santa Cruz, Santa Cruz, CA, United States 
Website:
http://www.cbse.ucsc.edu/people/hausslerlab

254 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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, ... ... Haussler D, et al. The UCSC SARS-CoV-2 Genome Browser. Nature Genetics. PMID 32908258 DOI: 10.1038/S41588-020-0700-8  0.72
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, ... ... Haussler D, et al. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology. PMID 32686750 DOI: 10.1038/S41587-020-0503-6  0.4
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, et al. A user guide for the online exploration and visualization of PCAWG data. Nature Communications. 11: 3400. PMID 32636365 DOI: 10.1038/S41467-020-16785-6  0.56
2020 Goldman MJ, Craft B, Hastie M, Repečka K, McDade F, Kamath A, Banerjee A, Luo Y, Rogers D, Brooks AN, Zhu J, Haussler D. Visualizing and interpreting cancer genomics data via the Xena platform. Nature Biotechnology. PMID 32444850 DOI: 10.1038/S41587-020-0546-8  0.56
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, ... ... Haussler D, et al. Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. Plos Computational Biology. 16: e1007753. PMID 32275708 DOI: 10.1371/Journal.Pcbi.1007753  0.64
2020 Fernandes JD, Zamudio-Hurtado A, Clawson H, Kent WJ, Haussler D, Salama SR, Haeussler M. The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. Mobile Dna. 11: 13. PMID 32266012 DOI: 10.1186/S13100-020-00208-W  0.72
2020 Haussler D. Abstract IA02: The Treehouse Childhood Cancer Initiative Clinical Cancer Research. 26. DOI: 10.1158/1557-3265.Advprecmed20-Ia02  0.48
2020 Cheney AR, Sanders LM, Seninge L, Beale HC, Kephart ET, Pfeil J, Learned K, Lyle AG, Bjork I, Haussler D, Salama SR, Vaske OM. Abstract B06: Candidate differentiation stall in epithelial mesenchymal transition in H3K27M diffuse midline glioma Cancer Research. 80. DOI: 10.1158/1538-7445.Pedca19-B06  0.64
2020 Sanders LM, Lyle AG, Beale HC, Kephart ET, Learned K, Peralez J, Lacayo N, Rangaswami A, Spunt SL, Bjork I, Haussler D, Salama SR, Vaske OM. Abstract A44: Comparative gene expression analysis for identification and prioritization of therapeutic targets in a cohort of childhood cancers Cancer Research. 80. DOI: 10.1158/1538-7445.Pedca19-A44  0.64
2020 Cheney AR, Sanders LM, Seninge L, Beale HC, Kephart ET, Pfeil J, Learned K, Lyle AG, Bjork I, Haussler D, Salama SR, Vaske OM. Abstract 6154: H3K27M gliomas are characterized by a stall in the epithelial-mesenchymal transition Tumor Biology. DOI: 10.1158/1538-7445.Am2020-6154  0.64
2019 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, et al. UCSC Genome Browser enters 20th year. Nucleic Acids Research. PMID 31691824 DOI: 10.1093/Nar/Gkz1012  0.72
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. Barriers to accessing public cancer genomic data. Scientific Data. 6: 98. PMID 31222016 DOI: 10.1038/S41597-019-0096-4  0.64
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, ... ... Haussler D, et al. Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. Cell. 176: 743-756.e17. PMID 30735633 DOI: 10.1016/J.Cell.2019.01.017  0.72
2019 Sanders L, Cheney A, Beale H, Kephart E, Bjork I, Pfeil JJ, Salama SR, Haussler D, Morozova O. Shared dysregulation of long non-coding RNA and developmental gene networks in histone H3 K27M gliomas and PF-A ependymomas. Journal of Clinical Oncology. 37. DOI: 10.1200/Jco.2019.37.15_Suppl.E21523  0.64
2019 Goldman M, Craft B, Zhu J, Haussler D. Abstract 911: UCSC Xena for cancer genomics visualization and interpretation Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-911  0.56
2019 Allegakoen HR, Goldman M, Caughey B, Consunji M, Benz CC, Haussler D, Zhu J, Collisson EA. Abstract 2466: Designing an intuitive visualization of BRCAness scores for clinicians Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-2466  0.56
2019 Sanders L, Cheney A, Field A, Beale H, Kephart E, Learned K, Bjork I, Durbin A, Lyle G, Pfeil J, Salama S, Haussler D, Vaske O. Gene-11. Shared Long Non-Coding Rna Dysregulation In Histone H3 K27M Gliomas And Pf-A Ependymomas Neuro-Oncology. 21. DOI: 10.1093/Neuonc/Noz036.082  0.48
2018 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. Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes. Stem Cell Reports. PMID 30639214 DOI: 10.1016/J.Stemcr.2018.12.006  0.64
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, ... ... Haussler D, et al. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. Plos Genetics. 14: e1007752. PMID 30586411 DOI: 10.1371/Journal.Pgen.1007752  0.32
2018 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, et al. The UCSC Genome Browser database: 2019 update. Nucleic Acids Research. PMID 30407534 DOI: 10.1093/Nar/Gky1095  0.72
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, Kellen MR, Chen K, ... ... Haussler D, et al. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biology. 19: 188. PMID 30400818 DOI: 10.1186/S13059-018-1539-5  0.48
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. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Research. PMID 29884752 DOI: 10.1101/Gr.233460.117  0.56
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, ... ... Haussler D, et al. High-resolution comparative analysis of great ape genomes. Science (New York, N.Y.). 360. PMID 29880660 DOI: 10.1126/Science.Aar6343  0.56
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, ... ... Haussler D, et al. Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis. Cell. 173: 1356-1369.e22. PMID 29856954 DOI: 10.1016/J.Cell.2018.03.051  0.64
2018 Jain M, Olsen HE, Turner DJ, Stoddart D, Bulazel KV, Paten B, Haussler D, Willard HF, Akeson M, Miga KH. Linear assembly of a human centromere on the Y chromosome. Nature Biotechnology. PMID 29553574 DOI: 10.1038/Nbt.4109  0.4
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. A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations. Frontiers in Immunology. 9: 99. PMID 29441070 DOI: 10.3389/Fimmu.2018.00099  0.64
2018 Beale H, Kephart E, Sanders L, Pfeil J, Bjork I, Salama SR, Haussler D, Morozova O. Getting consistent results from comparative analysis of RNA_Seq data from single patients. Journal of Clinical Oncology. 36. DOI: 10.1200/Jco.2018.36.15_Suppl.E24194  0.64
2018 Sanders L, Rose-Dey B, Beale H, Kephart E, Pfeil J, Morozova O, Agnihotri S, Salama SR, Haussler D. Comparative gene expression analysis for identifying clinically relevant overexpressed genes in childhood brain tumors. Journal of Clinical Oncology. 36. DOI: 10.1200/Jco.2018.36.15_Suppl.E14033  0.64
2018 Pfeil J, Thornton A, Durbin A, Kephart E, Beale H, Sanders L, Bjork I, Morozova O, Salama SR, Haussler D. Gene expression analysis for improved subtyping of high-risk neuroblastoma. Journal of Clinical Oncology. 36: 10559-10559. DOI: 10.1200/Jco.2018.36.15_Suppl.10559  0.64
2018 Goldman M, Craft B, Zhu J, Haussler D. Abstract 2274: Cancer genomics visualization and interpretation using UCSC Xena Cancer Research. 78: 2274-2274. DOI: 10.1158/1538-7445.Am2018-2274  0.56
2018 Sanders L, Rose-Dey B, Beale H, Pfeil J, Kephart E, Learned K, Durbin A, Bjork I, Currie R, Morozova O, Agnihotri S, Salama S, Haussler D. Dipg-07. Genomic Analysis Methods For Identification Of Cancer Driver Pathways In Childhood Brain Tumors Neuro-Oncology. 20. DOI: 10.1093/Neuonc/Noy059.101  0.48
2017 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, ... ... Haussler D, et al. The UCSC Genome Browser database: 2018 update. Nucleic Acids Research. PMID 29106570 DOI: 10.1093/Nar/Gkx1020  0.72
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. TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal. Cancer Research. 77: e111-e114. PMID 29092953 DOI: 10.1158/0008-5472.Can-17-0580  0.64
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, ... ... Haussler D, et al. Toil enables reproducible, open source, big biomedical data analyses. Nature Biotechnology. 35: 314-316. PMID 28398314 DOI: 10.1038/Nbt.3772  0.72
2017 Morozova O, Salama SR, Bjork I, Goldstein TC, Mueller S, Sender LS, Sweet-Cordero A, Haussler D, Team CKCC. Comparative genomic analysis for pediatric cancer patients evaluated in a California Initiative to Advance Precision Medicine Demonstration Project. Journal of Clinical Oncology. 35. DOI: 10.1200/Jco.2017.35.15_Suppl.Tps10578  0.64
2017 Learned K, Durbin A, Currie R, Beale H, Lam DL, Goldstein T, Salama SR, Haussler D, Morozova O, Bjork I. Abstract LB-338: A critical evaluation of genomic data sharing: Barriers to accessing pediatric cancer genomic datasets: a Treehouse Childhood Cancer Initiative experience Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Lb-338  0.64
2017 Rao AA, Toor J, Tripathi S, Pfeil J, Sgourakis N, Salama S, Haussler D. Abstract 4891: Identification of recurrent high-affinity MHC class I restricted neo-epitopes in neuroblastoma using ProTECT Cancer Research. 77: 4891-4891. DOI: 10.1158/1538-7445.Am2017-4891  0.48
2017 Morozova O, Newton Y, Shah AT, Beale H, Lam DL, Vivian J, Bjork I, Goldstein T, Stuart J, Salama S, Sweet-Cordero EA, Haussler D. Abstract 4890: A pan-cancer analysis framework for incorporating gene expression information into clinical interpretation of pediatric cancer genomic data Cancer Research. 77: 4890-4890. DOI: 10.1158/1538-7445.Am2017-4890  0.48
2017 Goldman M, Craft B, Zhu J, Haussler D. Abstract 2584: The UCSC Xena system for cancer genomics data visualization and interpretation Cancer Research. 77: 2584-2584. DOI: 10.1158/1538-7445.Am2017-2584  0.56
2017 Beale H, Lam DL, Vivian J, Newton Y, Shah AT, Bjork I, Goldstein T, Brooks AN, Stuart J, Salama S, Sweet-Cordero EA, Haussler D, Morozova O. Abstract 2466: Identifying confidently measured genes in single pediatric cancer patient samples using RNA sequencing Cancer Research. 77: 2466-2466. DOI: 10.1158/1538-7445.Am2017-2466  0.48
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, ... ... Haussler D, et al. The UCSC Genome Browser database: 2017 update. Nucleic Acids Research. PMID 27899642 DOI: 10.1093/Nar/Gkw1134  0.72
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, et al. Facilitating a culture of responsible and effective sharing of cancer genome data. Nature Medicine. 22: 464-71. PMID 27149219 DOI: 10.1038/Nm.4089  0.72
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, ... ... Haussler D, et al. Long-read sequence assembly of the gorilla genome. Science (New York, N.Y.). 352: aae0344. PMID 27034376 DOI: 10.1126/Science.Aae0344  0.72
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. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Research. PMID 26848124 DOI: 10.1101/Gr.193474.115  0.72
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, ... ... Haussler D, et al. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell. 164: 550-563. PMID 26824661 DOI: 10.1016/J.Cell.2015.12.028  0.72
2016 Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics (Oxford, England). PMID 26740527 DOI: 10.1093/Bioinformatics/Btv766  0.72
2016 Morozova O, Newton Y, Cline M, Yip S, Rao A, Stuart J, Goldstein T, Salama S, Deyell R, Rassekh SR, Haussler D. Abstract PR14: Harnessing the power of big data to advance pediatric cancer care Cancer Research. 76. DOI: 10.1158/1538-7445.Pedca15-Pr14  0.48
2016 Newton Y, Novak A, Swatlowski T, Chopra S, Salama S, Morozova O, Haussler D, Stuart J. Abstract LB-290: UCSC TumorMap: Exploring cancer signatures on an interactive dynamic landscape Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Lb-290  0.48
2016 Goldman M, Craft B, Zhu J, Swatloski T, Cline M, Haussler D. Abstract 5270: The UCSC Xena system for integrating and visualizing functional genomics Cancer Research. 76: 5270-5270. DOI: 10.1158/1538-7445.Am2016-5270  0.56
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, ... ... Haussler D, et al. The UCSC Genome Browser database: 2016 update. Nucleic Acids Research. PMID 26590259 DOI: 10.1093/Nar/Gkv1275  0.72
2015 Novak AM, Rosen Y, Haussler D, Paten B. Canonical, stable, general mapping using context schemes. Bioinformatics (Oxford, England). 31: 3569-76. PMID 26220960 DOI: 10.1093/Bioinformatics/Btv435  0.72
2015 Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, James Kent W, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, ... ... Haussler D, et al. The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association : Jamia. PMID 26174866 DOI: 10.1093/Jamia/Ocv047  0.72
2015 Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY, Kellen MR, Norman TC, Haussler D, Friend SH, et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nature Methods. PMID 25984700 DOI: 10.1038/Nmeth.3407  0.72
2015 Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Building a pan-genome reference for a population. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 387-401. PMID 25565268 DOI: 10.1089/Cmb.2014.0146  0.72
2015 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, ... ... Haussler D, et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Research. 43: D670-81. PMID 25428374 DOI: 10.1093/Nar/Gku1177  0.72
2015 Lowe CB, Clarke JA, Baker AJ, Haussler D, Edwards SV. Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Molecular Biology and Evolution. 32: 23-8. PMID 25415961 DOI: 10.1093/Molbev/Msu309  0.72
2015 Goldman M, Craft B, Swatloski T, Cline M, Morozova O, Diekhans M, Haussler D, Zhu J. The UCSC Cancer Genomics Browser: update 2015. Nucleic Acids Research. 43: D812-7. PMID 25392408 DOI: 10.1093/Nar/Gku1073  0.72
2015 Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ. Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics (Oxford, England). 31: 764-6. PMID 25348212 DOI: 10.1093/Bioinformatics/Btu712  0.72
2015 Morozova O, Ng S, Rao A, Stuart J, Haussler D, Salama S. Abstract A2-52: Pan-cancer analysis reveals distinct effects of receptor tyrosine kinase mutations on downstream pathway activities Cancer Research. 75. DOI: 10.1158/1538-7445.Transcagen-A2-52  0.48
2015 Blau CA, Pritchard C, Dorschner MO, Blau S, Mecham B, Mahen E, Gadi V, Monsky W, Burton K, Ramirez A, Stilwell J, Kladjian E, Collins C, McCune JS, Noble WS, ... ... Haussler D, et al. Abstract P4-08-01: Assessing the safety and feasibility of efficient hypothesis testing in patients with metastatic triple negative breast cancer Cancer Research. 75. DOI: 10.1158/1538-7445.Sabcs14-P4-08-01  0.56
2015 Ng S, Benz C, Haussler D, Stuart JM. Abstract B1-38: PARADIGM-SHIFT: Predicts the functional impact of ‘driver modules’ in multiple cancers using pathway impact analysis Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-38  0.48
2015 Ballinger TJ, Zerbino D, Paten B, Haussler D. Abstract B1-11: Application of the CN-AVG method to reconstruct the evolutionary history of glioblastoma multiforme Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-11  0.48
2015 Zhu J, Craft B, Goldman M, Cline M, Diekhans M, Haussler D. Abstract B1-07: Using the UCSC Xena Platform to integrate, visualize, and analyze your own data in the context of large external genomic datasets Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-07  0.56
2015 Morozova O, Newton Y, Cline M, Zhu J, Learned K, Stuart J, Salama S, Arceci R, Haussler D. Abstract LB-212: Treehouse Childhood Cancer Project: a resource for sharing and multiple cohort analysis of pediatric cancer genomics data Cancer Research. 75. DOI: 10.1158/1538-7445.Am2015-Lb-212  0.56
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. The UCSC Ebola Genome Portal. Plos Currents. 6. PMID 25685613 DOI: 10.1371/Currents.Outbreaks.386Ab0964Ab4D6C8Cb550Bfb6071D822  0.72
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, ... ... Haussler D, et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science (New York, N.Y.). 346: 1254449. PMID 25504731 DOI: 10.1126/Science.1254449  0.48
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, ... ... Haussler D, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science (New York, N.Y.). 346: 1311-20. PMID 25504712 DOI: 10.1126/Science.1251385  0.4
2014 Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D. RADIA: RNA and DNA integrated analysis for somatic mutation detection Plos One. 9. PMID 25405470 DOI: 10.1371/Journal.Pone.0111516  0.72
2014 Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature. 516: 242-5. PMID 25274305 DOI: 10.1038/Nature13760  0.72
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, ... ... Haussler D, et al. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Research. 24: 2077-89. PMID 25273068 DOI: 10.1101/Gr.174920.114  0.72
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, ... ... Haussler D, et al. The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Database : the Journal of Biological Databases and Curation. 2014. PMID 25267794 DOI: 10.1093/Database/Bau093  0.72
2014 Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. Comparative assembly hubs: web-accessible browsers for comparative genomics. Bioinformatics (Oxford, England). 30: 3293-301. PMID 25138168 DOI: 10.1093/Bioinformatics/Btu534  0.72
2014 Paten B, Zerbino DR, Hickey G, Haussler D. A unifying model of genome evolution under parsimony Bmc Bioinformatics. 15. PMID 24946830 DOI: 10.1186/1471-2105-15-206  0.72
2014 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, ... ... Haussler D, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Research. 42: D764-70. PMID 24270787 DOI: 10.1093/Nar/Gkt1168  0.72
2014 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, ... ... Haussler D, et al. Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Research. 42: D865-72. PMID 24217909 DOI: 10.1093/Nar/Gkt1059  0.72
2014 Cline M, Morozova O, Swatloski T, Craft B, Goldman M, Haussler D, Zhu J. Abstract A33: Exploring pediatric cancer genomics with the UCSC Cancer Genomics Browser Cancer Research. 74. DOI: 10.1158/1538-7445.Pedcan-A33  0.56
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, ... ... Haussler D, et al. The somatic genomic landscape of glioblastoma. Cell. 155: 462-77. PMID 24120142 DOI: 10.1016/J.Cell.2013.09.034  0.72
2013 Cline MS, Craft B, Swatloski T, Goldman M, Ma S, Haussler D, Zhu J. Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser. Scientific Reports. 3: 2652. PMID 24084870 DOI: 10.1038/Srep02652  0.72
2013 Paull EO, Carlin DE, Niepel M, Sorger PK, Haussler D, Stuart JM. Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinformatics (Oxford, England). 29: 2757-64. PMID 23986566 DOI: 10.1093/Bioinformatics/Btt471  0.72
2013 Sanborn JZ, Salama SR, Grifford M, Brennan CW, Mikkelsen T, Jhanwar S, Katzman S, Chin L, Haussler D. Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Cancer Research. 73: 6036-45. PMID 23940299 DOI: 10.1158/0008-5472.Can-13-0186  0.72
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, ... ... Haussler D, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2: 10. PMID 23870653 DOI: 10.1186/2047-217X-2-10  0.48
2013 Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D, Stuart JM. The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Research. 41: W218-24. PMID 23748957 DOI: 10.1093/Nar/Gkt473  0.72
2013 Hickey G, Paten B, Earl D, Zerbino D, Haussler D. HAL: A hierarchical format for storing and analyzing multiple genome alignments Bioinformatics. 29: 1341-1342. PMID 23505295 DOI: 10.1093/Bioinformatics/Btt128  0.72
2013 Ewing AD, Ballinger TJ, Earl D, Harris CC, Ding L, Wilson RK, Haussler D. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biology. 14: R22. PMID 23497673 DOI: 10.1186/Gb-2013-14-3-R22  0.72
2013 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, ... ... Haussler D, et al. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Research. 41: D56-63. PMID 23193274 DOI: 10.1093/Nar/Gks1172  0.72
2013 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, ... ... Haussler D, et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Research. 41: D64-9. PMID 23155063 DOI: 10.1093/Nar/Gks1048  0.72
2013 Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M, Ma S, Wilks C, Stuart J, Haussler D, Zhu J. The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Research. 41: D949-54. PMID 23109555 DOI: 10.1093/Nar/Gks1008  0.72
2013 Kuhn RM, Haussler D, Kent WJ. The UCSC genome browser and associated tools. Briefings in Bioinformatics. 14: 144-61. PMID 22908213 DOI: 10.1093/Bib/Bbs038  0.72
2013 Goldstein TC, Baertsch R, Febbo PG, Stuart J, Haussler D. Abstract 60: The MedBook network for cancer precision medical care. Cancer Research. 73: 60-60. DOI: 10.1158/1538-7445.Am2013-60  0.48
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. Tissue sampling methods and standards for vertebrate genomics. Gigascience. 1: 8. PMID 23587255 DOI: 10.1186/2047-217X-1-8  0.72
2012 Ng S, Collisson EA, Sokolov A, Goldstein T, Gonzalez-Perez A, Lopez-Bigas N, Benz C, Haussler D, Stuart JM. PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinformatics (Oxford, England). 28: i640-i646. PMID 22962493 DOI: 10.1093/Bioinformatics/Bts402  0.72
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, ... ... Haussler D, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Research. 22: 1760-74. PMID 22955987 DOI: 10.1101/Gr.135350.111  0.72
2012 Lowe CB, Haussler D. 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. Plos One. 7: e43128. PMID 22952639 DOI: 10.1371/Journal.Pone.0043128  0.72
2012 Onodera CS, Underwood JG, Katzman S, Jacobs F, Greenberg D, Salama SR, Haussler D. Gene isoform specificity through enhancer-associated antisense transcription. Plos One. 7: e43511. PMID 22937057 DOI: 10.1371/Journal.Pone.0043511  0.72
2012 Bernardi G, Wiley EO, Mansour H, Miller MR, Orti G, Haussler D, O'Brien SJ, Ryder OA, Venkatesh B. The fishes of Genome 10K. Marine Genomics. 7: 3-6. PMID 22897955 DOI: 10.1016/J.Margen.2012.02.002  0.72
2012 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, ... ... Haussler D, et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Research. 40: D918-23. PMID 22086951 DOI: 10.1093/Nar/Gkr1055  0.72
2012 Raab JR, Chiu J, Zhu J, Katzman S, Kurukuti S, Wade PA, Haussler D, Kamakaka RT. Human tRNA genes function as chromatin insulators. The Embo Journal. 31: 330-50. PMID 22085927 DOI: 10.1038/Emboj.2011.406  0.72
2012 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, ... ... Haussler D, et al. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Research. 40: D912-7. PMID 22075998 DOI: 10.1093/Nar/Gkr1012  0.72
2012 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, ... ... Haussler D, et al. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 109: 2724-9. PMID 22003129 DOI: 10.1073/Pnas.1018854108  0.72
2012 Kristensen VN, Vaske CJ, Ursini-Siegel J, Van Loo P, Nordgard SH, Sachidanandam R, Sørlie T, Wärnberg F, Haakensen VD, Helland Å, Naume B, Perou CM, Haussler D, Troyanskaya OG, Børresen-Dale AL. Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proceedings of the National Academy of Sciences of the United States of America. 109: 2802-7. PMID 21908711 DOI: 10.1073/Pnas.1108781108  0.72
2012 Zhu J, Craft B, Swatloski T, Ellrott K, Goldman M, Wilks C, Ma S, Szeto C, Collisson E, Haussler D. Abstract 5087: UCSC Cancer Genomics Browser 2.0 Cancer Research. 72: 5087-5087. DOI: 10.1158/1538-7445.Am2012-5087  0.56
2012 Szeto CW, Sokolov A, Benz S, Stuart J, Haussler D. Abstract 5085: TopModel: An online resource for predictive models in cancer Cancer Research. 72: 5085-5085. DOI: 10.1158/1538-7445.Am2012-5085  0.48
2012 Ng S, Thusberg J, Benz S, Vaske C, Ellrott K, Zhu J, Yau C, Collisson E, Mooney S, Benz C, Haussler D, Stuart J. Abstract 2985: Predicting the impact of mutations in cancer using an integrated pathway approach Cancer Research. 72: 2985-2985. DOI: 10.1158/1538-7445.Am2012-2985  0.56
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, et al. The Human Epigenome Browser at Washington University. Nature Methods. 8: 989-90. PMID 22127213 DOI: 10.1038/Nmeth.1772  0.72
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, ... ... Haussler D, et al. 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. 108: 17761-6. PMID 22006338 DOI: 10.1073/Pnas.1114669108  0.72
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, ... ... Haussler D, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530  0.72
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, ... ... Haussler D, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21: 2224-41. PMID 21926179 DOI: 10.1101/Gr.126599.111  0.72
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, ... ... Haussler D, et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 477: 587-91. PMID 21881562 DOI: 10.1038/Nature10390  0.72
2011 Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. Three periods of regulatory innovation during vertebrate evolution. Science (New York, N.Y.). 333: 1019-24. PMID 21852499 DOI: 10.1126/Science.1202702  0.72
2011 Katzman S, Capra JA, Haussler D, Pollard KS. Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots Genome Biology and Evolution. 3: 614-626. PMID 21697099 DOI: 10.1093/Gbe/Evr058  0.72
2011 Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: Algorithms for genome multiple sequence alignment Genome Research. 21: 1512-1528. PMID 21665927 DOI: 10.1101/Gr.123356.111  0.72
2011 Roskin KM, Paten B, Haussler D. Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization Bmc Bioinformatics. 12. PMID 21569267 DOI: 10.1186/1471-2105-12-144  0.72
2011 Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D. Cactus graphs for genome comparisons Journal of Computational Biology. 18: 469-481. PMID 21385048 DOI: 10.1089/Cmb.2010.0252  0.72
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, ... ... Haussler D, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 469: 529-33. PMID 21270892 DOI: 10.1038/Nature09687  0.72
2011 Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J. The UCSC Cancer Genomics Browser: update 2011. Nucleic Acids Research. 39: D951-9. PMID 21059681 DOI: 10.1093/Nar/Gkq1113  0.72
2011 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, ... ... Haussler D, et al. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Research. 39: D871-5. PMID 21037257 DOI: 10.1093/Nar/Gkq1017  0.72
2011 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, ... ... Haussler D, et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Research. 39: D876-82. PMID 20959295 DOI: 10.1093/Nar/Gkq963  0.72
2011 Listerman I, Gazzaniga FS, Heiser LM, Lukas JJ, Goldstein T, Haussler D, Gray JW, Blackburn EH. Abstract A58: Wnt signaling pathway components are associated with telomerase activity in breast cancer Cancer Research. 71. DOI: 10.1158/1538-7445.Fbcr11-A58  0.48
2011 Radenbaugh A, Sanborn JZ, Zerbino D, Wilks C, Stuart JM, Haussler D. Abstract 59: Identification of RNA editing events in cancer using high-throughput sequencing data Cancer Research. 71: 59-59. DOI: 10.1158/1538-7445.Am2011-59  0.56
2011 Zhu J, Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Goldman M, Meyer L, Vaske C, Collisson E, Stuart J, Haussler D. Abstract 4985: The UCSC Cancer Genomics Browser Cancer Research. 71: 4985-4985. DOI: 10.1158/1538-7445.Am2011-4985  0.56
2011 Ng S, Vaske C, Benz S, Durbin J, Szeto C, Heiser L, Wang N, Korkola J, Bayani N, Spellman P, Gray JW, Haussler D, Stuart J. Abstract 49: Constructing pathway based predictors of cancer clinical outcome Cancer Research. 71: 49-49. DOI: 10.1158/1538-7445.Am2011-49  0.48
2011 Szeto CW, Zhu J, Durbin J, Benz S, Vaske C, Stuart J, Haussler D. Abstract 43: Using matrix factorization to discover clinically-relevant molecular signatures across cancers Cancer Research. 71: 43-43. DOI: 10.1158/1538-7445.Am2011-43  0.56
2011 Haussler D. SR2-6: Genome Data for the Masses: Presentation of TCGA and IGC Breast Tumor Data. Cancer Research. 71. DOI: 10.1158/0008-5472.Sabcs11-Sr2-6  0.48
2011 Yau C, Benz S, Sanborn J, Stuart J, Haussler D, Benz C. PD03-04: SuperPathway Analyses of Luminal and Basaloid Breast Cancers from the Cancer Genome Atlas (TCGA) Program. Cancer Research. 71. DOI: 10.1158/0008-5472.Sabcs11-Pd03-04  0.48
2011 Wolf D, Yau C, Benz S, Vaske C, Stuart J, Roy R, Olshen A, Boudreau A, Haussler D, Gray J, Spellman P, Davis S, Hylton N, Veer LV, Esserman L. P1-06-09: Patient-Specific Integrative Pathway Analysis Using PARADIGM Identifies Key Activities in I-SPY 1 Breast Cancer Patients (CALGB 150007/150012; ACRIN 6657). Cancer Research. 71. DOI: 10.1158/0008-5472.Sabcs11-P1-06-09  0.48
2010 Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nature Methods. 7: 995-1001. PMID 21057495 DOI: 10.1038/Nmeth.1529  0.72
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, ... ... Haussler D, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/Nbt.1682  0.72
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, ... ... Haussler D, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 466: 253-7. PMID 20613842 DOI: 10.1038/Nature09165  0.72
2010 Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics (Oxford, England). 26: i237-45. PMID 20529912 DOI: 10.1093/Bioinformatics/Btq182  0.72
2010 Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. GC-biased evolution near human accelerated regions. Plos Genetics. 6: e1000960. PMID 20502635 DOI: 10.1371/Journal.Pgen.1000960  0.72
2010 Lowe CB, Bejerano G, Salama SR, Haussler D. Endangered species hold clues to human evolution. The Journal of Heredity. 101: 437-47. PMID 20332163 DOI: 10.1093/Jhered/Esq016  0.72
2010 Kern AD, Haussler D. A population genetic hidden Markov model for detecting genomic regions under selection. Molecular Biology and Evolution. 27: 1673-85. PMID 20185453 DOI: 10.1093/Molbev/Msq053  0.72
2010 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, ... ... Haussler D, et al. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Research. 38: D620-5. PMID 19920125 DOI: 10.1093/Nar/Gkp961  0.72
2010 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, ... ... Haussler D, et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Research. 38: D613-9. PMID 19906737 DOI: 10.1093/Nar/Gkp939  0.72
2010 Haussler D. Cancer genomics and the TCGA project Clinical Cancer Research. 16. DOI: 10.1158/Diag-10-Ed3B-1  0.48
2010 Benz SC, Vaske C, Ng S, Sanborn JZ, Zhu J, Haussler D, Stuart J. Abstract 4905: Patient-specific pathway analysis using PARADIGM identifies key activities in multiple cancers Cancer Research. 71: 4905-4905. DOI: 10.1158/1538-7445.Am2011-4905  0.56
2010 Sanborn JZ, Haussler D. Abstract 89: BamBam: Simultaneous processing of tumor and germline sequencing data Cellular and Molecular Biology. 70: 89-89. DOI: 10.1158/1538-7445.Am10-89  0.56
2010 Christopher S, Benz S, Vaske C, Sanborn JZ, Zhu J, Stuart J, Haussler D. Abstract 2001: Non-negative matrix factorization (NMF) as a clinical classifier: An example with chemotherapy response in ovarian cancer Cancer Research. 70: 2001-2001. DOI: 10.1158/1538-7445.Am10-2001  0.56
2010 Yau C, Meyer L, Labhart P, Haussler D, Benz CC. Abstract 106: Metastatic outcome of early-stage estrogen receptor-positive (ER+) primary breast cancers predicted by differential expression of a subset of wild-type p53 target genes Cancer Research. 70: 106-106. DOI: 10.1158/1538-7445.Am10-106  0.48
2009 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, ... ... Haussler D, et al. The completion of the Mammalian Gene Collection (MGC). Genome Research. 19: 2324-33. PMID 19767417 DOI: 10.1101/Gr.095976.109  0.72
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, ... ... Haussler D, et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Research. 19: 1316-23. PMID 19498102 DOI: 10.1101/Gr.080531.108  0.72
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. The UCSC Cancer Genomics Browser. Nature Methods. 6: 239-40. PMID 19333237 DOI: 10.1038/Nmeth0409-239  0.72
2009 Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, ... ... Haussler D, et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Research. 37: D755-61. PMID 18996895 DOI: 10.1093/Nar/Gkn875  0.72
2009 Zhu J, Sanborn J, Wang T, Hsu F, Benz S, Szeto C, Esserman L, Haussler D. UCSC cancer genomics browser. Cancer Research. 69: 2022. DOI: 10.1158/0008-5472.Sabcs-2022  0.56
2009 Haussler D, O'Brien SJ, Ryder OA, Keith Barker F, Clamp M, Crawford AJ, Hanner R, Hanotte O, Johnson WE, McGuire JA, Miller W, Murphy RW, Murphy WJ, Sheldon FH, Sinervo B, et al. Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species Journal of Heredity. 100: 659-674. DOI: 10.1093/Jhered/Esp086  0.72
2008 Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. Bmc Genomics. 9: 466. PMID 18842134 DOI: 10.1186/1471-2164-9-466  0.72
2008 Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D. The infinite sites model of genome evolution. Proceedings of the National Academy of Sciences of the United States of America. 105: 14254-61. PMID 18787111 DOI: 10.1073/Pnas.0805217105  0.72
2008 Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D. DUPCAR: reconstructing contiguous ancestral regions with duplications. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 1007-27. PMID 18774902 DOI: 10.1089/Cmb.2008.0069  0.72
2008 Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Computational reconstruction of ancestral DNA sequences. Methods in Molecular Biology (Clifton, N.J.). 422: 171-84. PMID 18629667 DOI: 10.1007/978-1-59745-581-7_11  0.72
2008 Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W. Phylogenomic resources at the UCSC Genome Browser. Methods in Molecular Biology (Clifton, N.J.). 422: 133-44. PMID 18629665 DOI: 10.1007/978-1-59745-581-7_9  0.72
2008 Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. UCSC genome browser tutorial. Genomics. 92: 75-84. PMID 18514479 DOI: 10.1016/J.Ygeno.2008.02.003  0.72
2008 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding Bioinformatics. 24: 637-644. PMID 18218656 DOI: 10.1093/Bioinformatics/Btn013  0.56
2008 Zeng J, Yan J, Wang T, Mosbrook-Davis D, Dolan KT, Christensen R, Stormo GD, Haussler D, Lathrop RH, Brachmann RK, Burgess SM. Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins. Nucleic Acids Research. 36: e8. PMID 18086703 DOI: 10.1093/Nar/Gkm1117  0.72
2008 Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, ... ... Haussler D, et al. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Research. 36: D773-9. PMID 18086701 DOI: 10.1093/Nar/Gkm966  0.72
2007 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. Plos Computational Biology. 3: e247. PMID 18085818 DOI: 10.1371/Journal.Pcbi.0030247  0.72
2007 Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proceedings of the National Academy of Sciences of the United States of America. 104: 18613-8. PMID 18003932 DOI: 10.1073/Pnas.0703637104  0.72
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, Hodges E, ... ... Haussler D, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/Nature06340  0.72
2007 Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. Comparative genomic analysis using the UCSC genome browser. Methods in Molecular Biology (Clifton, N.J.). 395: 17-34. PMID 17993665 DOI: 10.1007/978-1-59745-514-5_2  0.36
2007 Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CLG, Davis C, Ewing B, Oommen S, Lau C, Yu HC, Li J, Roe BA, Green P, Gerhard DS, ... ... Haussler D, et al. Targeted discovery of novel human exons by comparative genomics Genome Research. 17: 1763-1773. PMID 17989246 DOI: 10.1101/Gr.7128207  0.72
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, ... ... Haussler D, et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research. 17: 1797-808. PMID 17984227 DOI: 10.1101/Gr.6761107  0.72
2007 Yeang CH, Haussler D. Detecting coevolution in and among protein domains. Plos Computational Biology. 3: e211. PMID 17983264 DOI: 10.1371/Journal.Pcbi.0030211  0.72
2007 Dreszer TR, Wall GD, Haussler D, Pollard KS. Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion Genome Research. 17: 1420-1430. PMID 17785536 DOI: 10.1101/Gr.6395807  0.72
2007 Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D. Human genome ultraconserved elements are ultraselected. Science (New York, N.Y.). 317: 915. PMID 17702936 DOI: 10.1126/Science.1142430  0.72
2007 Yeang CH, Darot JFJ, Noller HF, Haussler D. Detecting the coevolution of biosequences - An example of RNA interaction prediction Molecular Biology and Evolution. 24: 2119-2131. PMID 17636042 DOI: 10.1093/Molbev/Msm142  0.72
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, ... ... Haussler D, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307  0.72
2007 Lowe CB, Bejerano G, Haussler D. 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. 104: 8005-10. PMID 17463089 DOI: 10.1073/Pnas.0611223104  0.72
2007 Ohlson J, Pedersen JS, Haussler D, Ohman M. Editing modifies the GABA(A) receptor subunit alpha3. Rna (New York, N.Y.). 13: 698-703. PMID 17369310 DOI: 10.1261/Rna.349107  0.72
2007 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, ... ... Haussler D, et al. The ENCODE Project at UC Santa Cruz. Nucleic Acids Research. 35: D663-7. PMID 17166863 DOI: 10.1093/Nar/Gkl1017  0.72
2007 Thomas DJ, Trumbower H, Kern AD, Rhead BL, Kuhn RM, Haussler D, Kent WJ. Variation resources at UC Santa Cruz. Nucleic Acids Research. 35: D716-20. PMID 17151077 DOI: 10.1093/Nar/Gkl953  0.72
2007 Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, ... ... Haussler D, et al. The UCSC genome browser database: update 2007. Nucleic Acids Research. 35: D668-73. PMID 17142222 DOI: 10.1093/Nar/Gkl928  0.72
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. Forces shaping the fastest evolving regions in the human genome. Plos Genetics. 2: e168. PMID 17040131 DOI: 10.1371/Journal.Pgen.0020168  0.72
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, et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 443: 167-72. PMID 16915236 DOI: 10.1038/Nature05113  0.72
2006 Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. Plos Computational Biology. 2: e33. PMID 16628248 DOI: 10.1371/Journal.Pcbi.0020033  0.72
2006 Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 441: 87-90. PMID 16625209 DOI: 10.1038/Nature04696  0.72
2006 Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC Known Genes. Bioinformatics (Oxford, England). 22: 1036-46. PMID 16500937 DOI: 10.1093/Bioinformatics/Btl048  0.72
2006 Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D, Ares M. Unusual intron conservation near tissue-regulated exons found by splicing microarrays. Plos Computational Biology. 2: e4. PMID 16424921 DOI: 10.1371/Journal.Pcbi.0020004  0.72
2006 Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, ... ... Haussler D, et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Research. 34: D590-8. PMID 16381938 DOI: 10.1093/Nar/Gkj144  0.72
2005 Bejerano G, Siepel AC, Kent WJ, Haussler D. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nature Methods. 2: 535-45. PMID 16170870 DOI: 10.1038/Nmeth0705-535  0.72
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, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research. 15: 1034-50. PMID 16024819 DOI: 10.1101/Gr.3715005  0.72
2005 Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Research. 15: 737-41. PMID 15867434 DOI: 10.1101/Gr.3694705  0.72
2005 Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics (Oxford, England). 21: 2814-20. PMID 15827081 DOI: 10.1093/Bioinformatics/Bti442  0.72
2005 Robertson MP, Igel H, Baertsch R, Haussler D, Ares M, Scott WG. The structure of a rigorously conserved RNA element within the SARS virus genome. Plos Biology. 3: e5. PMID 15630477 DOI: 10.1371/Journal.Pbio.0030005  0.72
2005 Hsu F, Pringle TH, Kuhn RM, Karolchik D, Diekhans M, Haussler D, Kent WJ. The UCSC Proteome Browser. Nucleic Acids Research. 33: D454-8. PMID 15608236 DOI: 10.1093/Nar/Gki100  0.72
2004 Blanchette M, Green ED, Miller W, Haussler D. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Research. 14: 2412-23. PMID 15574820 DOI: 10.1101/Gr.2800104  0.4
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, ... ... Haussler D, et al. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Research. 14: 2121-7. PMID 15489334 DOI: 10.1101/Gr.2596504  0.72
2004 Furey TS, Diekhans M, Lu Y, Graves TA, Oddy L, Randall-Maher J, Hillier LW, Wilson RK, Haussler D. Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. Genome Research. 14: 2034-40. PMID 15489323 DOI: 10.1101/Gr.2467904  0.72
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, et al. The structure and evolution of centromeric transition regions within the human genome. Nature. 430: 857-64. PMID 15318213 DOI: 10.1038/Nature02806  0.72
2004 Siepel AC, Haussler D. Combining phylogenetic and hidden Markov models in biosequence analysis. Journal of Computational Biology. 11: 413-428. PMID 15285899 DOI: 10.1089/1066527041410472  0.72
2004 Roskin KM, Diekhans M, Haussler D. Score functions for determining regional conservation in two-species local alignments. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 395-411. PMID 15285898 DOI: 10.1089/1066527041410328  0.72
2004 Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved elements in the human genome. Science (New York, N.Y.). 304: 1321-5. PMID 15131266 DOI: 10.1126/Science.1098119  0.72
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. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Research. 14: 708-15. PMID 15060014 DOI: 10.1101/Gr.1933104  0.72
2004 Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ. Comparative recombination rates in the rat, mouse, and human genomes. Genome Research. 14: 528-38. PMID 15059993 DOI: 10.1101/Gr.1970304  0.72
2004 Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC. Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Research. 14: 517-27. PMID 15059992 DOI: 10.1101/Gr.1984404  0.72
2004 Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. Hotspots of mammalian chromosomal evolution. Genome Biology. 5: R23. PMID 15059256 DOI: 10.1186/Gb-2004-5-4-R23  0.72
2004 Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Research. 32: D493-6. PMID 14681465 DOI: 10.1093/Nar/Gkh103  0.72
2003 Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang S, Giardine B, Zhang Y, Riemer C, Schwartz S, Haussler D, Roskin KM, Weber RJ, Diekhans M, et al. Global predictions and tests of erythroid regulatory regions. Cold Spring Harbor Symposia On Quantitative Biology. 68: 335-44. PMID 15338635 DOI: 10.1101/Sqb.2003.68.335  0.72
2003 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. 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. 100: 11484-9. PMID 14500911 DOI: 10.1073/Pnas.1932072100  0.72
2003 Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, ... ... Haussler D, et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 424: 788-93. PMID 12917688 DOI: 10.1038/Nature01858  0.72
2003 Wang H, Hubbell E, Hu JS, Mei G, Cline M, Lu G, Clark T, Siani-Rose MA, Ares M, Kulp DC, Haussler D. Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics (Oxford, England). 19: i315-22. PMID 12855476 DOI: 10.1093/Bioinformatics/Btg1044  0.72
2003 Furey TS, Haussler D. Integration of the cytogenetic map with the draft human genome sequence. Human Molecular Genetics. 12: 1037-44. PMID 12700172 DOI: 10.1093/Hmg/Ddg113  0.72
2003 Winters-Hilt S, Vercoutere W, DeGuzman VS, Deamer D, Akeson M, Haussler D. Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules. Biophysical Journal. 84: 967-76. PMID 12547778 DOI: 10.1016/S0006-3495(03)74913-3  0.72
2003 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Research. 13: 103-7. PMID 12529312 DOI: 10.1101/Gr.809403  0.72
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, ... ... Haussler D, et al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Research. 13: 13-26. PMID 12529302 DOI: 10.1101/Gr.844103  0.72
2003 Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ. The UCSC Genome Browser Database. Nucleic Acids Research. 31: 51-4. PMID 12519945 DOI: 10.1093/Nar/Gkg129  0.72
2002 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, ... ... Haussler D, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  0.72
2002 Cline MS, Karplus K, Lathrop RH, Smith TF, Rogers RG, Haussler D. Information-theoretic dissection of pairwise contact potentials. Proteins. 49: 7-14. PMID 12211011 DOI: 10.1002/Prot.10198  0.72
2002 Karchin R, Karplus K, Haussler D. Classifying G-protein coupled receptors with support vector machines. Bioinformatics (Oxford, England). 18: 147-59. PMID 11836223 DOI: 10.1093/Bioinformatics/18.1.147  0.72
2001 Kent WJ, Haussler D. Assembly of the working draft of the human genome with GigAssembler. Genome Research. 11: 1541-8. PMID 11544197 DOI: 10.1101/Gr.183201  0.72
2001 Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, ... ... Haussler D, et al. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 409: 953-8. PMID 11237021 DOI: 10.1038/35057192  0.72
2001 McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, ... ... Haussler D, et al. A physical map of the human genome. Nature. 409: 934-41. PMID 11237014 DOI: 10.1038/35057157  0.72
2001 Vercoutere W, Winters-Hilt S, Olsen H, Deamer D, Haussler D, Akeson M. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nature Biotechnology. 19: 248-52. PMID 11231558 DOI: 10.1038/85696  0.72
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Haussler D, et al. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature. 412: 565-566. DOI: 10.1038/35087627  0.72
2000 Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M, Haussler D. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics (Oxford, England). 16: 906-14. PMID 11120680 DOI: 10.1093/Bioinformatics/16.10.906  0.72
2000 Jaakkola T, Diekhans M, Haussler D. A discriminative framework for detecting remote protein homologies Journal of Computational Biology. 7: 95-114. PMID 10890390 DOI: 10.1089/10665270050081405  0.72
2000 Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M, Haussler D. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proceedings of the National Academy of Sciences of the United States of America. 97: 262-7. PMID 10618406 DOI: 10.1073/Pnas.97.1.262  0.72
1999 Haussler D. Computational Analysis of High-throughput Genomics Data Using Hidden Markov Models and Support Vector Machines Genome Informatics. 10: 199-199. DOI: 10.11234/Gi1990.10.199  0.48
1998 Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods Journal of Molecular Biology. 284: 1201-1210. PMID 9837738 DOI: 10.1006/Jmbi.1998.2221  0.72
1998 Haussler D, Kivinen J, Warmuth MK. Sequential prediction of individual sequences under general loss functions Ieee Transactions On Information Theory. 44: 1906-1925. DOI: 10.1109/18.705569  0.72
1998 Cesa-Bianchi N, Haussler D. A graph-theoretic generalization of the Sauer-Shelah lemma Discrete Applied Mathematics. 86: 27-35. DOI: 10.1016/S0166-218X(98)00012-2  0.48
1997 Haussler D, Opper M. Mutual Information, Metric Entropy And Cumulative Relative Entropy Risk Annals of Statistics. 25: 2451-2492. DOI: 10.1214/Aos/1030741081  0.48
1997 Alon N, Ben-David S, Cesa-Bianchi N, Haussler D. Scale-sensitive dimensions, uniform convergence, and learnability Journal of the Acm. 44: 615-631. DOI: 10.1145/263867.263927  0.48
1997 Cesa-Bianchi N, Freund Y, Haussler D, Helmbold DP, Schapire RE, Warmuth MK. How to use expert advice Journal of the Acm. 44: 427-485. DOI: 10.1145/258128.258179  0.48
1997 Haussler D. A general minimax result for relative entropy Ieee Transactions On Information Theory. 43: 1276-1280. DOI: 10.1109/18.605594  0.48
1997 Karplus K, Sjolander K, Barrett C, Cline M, Haussler D, Hughey R, Holm L. Predicting Protein Structure Using Hidden Markov Models Proteins. 29: 134-139. DOI: 10.1002/(Sici)1097-0134(1997)1+<134::Aid-Prot18>3.0.Co;2-P  0.48
1996 Sjölander K, Karplus K, Brown M, Hughey R, Krogh A, Mian IS, Haussler D. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Computer Applications in the Biosciences : Cabios. 12: 327-45. PMID 8902360 DOI: 10.1093/Bioinformatics/12.4.327  0.72
1996 Fayyad U, Haussler D, Stolorz P. Mining scientific data Communications of the Acm. 39: 51-57. DOI: 10.1145/240455.240471  0.48
1995 Haussler D. Sphere packing numbers for subsets of the Boolean n -cube with bounded Vapnik-Chervonenkis dimension Journal of Combinatorial Theory, Series A. 69: 217-232. DOI: 10.1016/0097-3165(95)90052-7  0.48
1995 Haussler D, Long PM. A generalization of Sauer's lemma Journal of Combinatorial Theory, Series A. 71: 219-240. DOI: 10.1016/0097-3165(95)90001-2  0.72
1995 Knill E, Ehrenfeucht A, Haussler D. The size of k-pseudotrees Discrete Mathematics. 141: 185-194. DOI: 10.1016/0012-365X(93)E0197-C  0.72
1995 Bendavid S, Cesabianchi N, Haussler D, Long PM. Characterizations of Learnability for Classes of {0, ..., n)-Valued Functions Journal of Computer and System Sciences. 50: 74-86. DOI: 10.1006/Jcss.1995.1008  0.48
1994 Haussler D, Littlestone N, Warmuth MK. Predicting {0, 1}-Functions on Randomly Drawn Points Information and Computation. 115: 248-292. DOI: 10.1006/Inco.1994.1097  0.72
1992 Haussler D. Decision theoretic generalizations of the PAC model for neural net and other learning applications Information & Computation. 100: 78-150. DOI: 10.1016/0890-5401(92)90010-D  0.48
1991 Haussler D, Kearns M, Littlestone N, Warmuth MK. Equivalence of models for polynomial learnability Information and Computation. 95: 129-161. DOI: 10.1016/0890-5401(91)90042-Z  0.72
1990 Pagallo G, Haussler D. Boolean Feature Discovery in Empirical Learning Machine Learning. 5: 71-99. DOI: 10.1023/A:1022611825350  0.48
1990 Haussler D. Applying valiant's learning framework to Al concept-learning problems Machine Learning. 641-669. DOI: 10.1016/B978-0-08-051055-2.50031-6  0.48
1989 Blumer A, Ehrenfeucht A, Haussler D, Warmuth MK. Learnability and the Vapnik-Chervonenkis dimension Journal of the Acm. 36: 929-965. DOI: 10.1145/76359.76371  0.72
1989 Haussler D. Learning Conjunctive Concepts in Structural Domains Machine Learning. 4: 7-40. DOI: 10.1023/A:1022601210986  0.48
1989 Ehrenfeucht A, Haussler D, Kearns M, Valiant L. A general lower bound on the number of examples needed for learning Information and Computation. 82: 247-261. DOI: 10.1016/0890-5401(89)90002-3  0.72
1989 Ehrenfeucht A, Haussler D. Learning decision trees from random examples Information and Computation. 82: 231-246. DOI: 10.1016/0890-5401(89)90001-1  0.72
1989 Blumer A, Ehrenfeucht A, Haussler D. Average sizes of suffix trees and DAWGs Discrete Applied Mathematics. 24: 37-45. DOI: 10.1016/0166-218X(92)90270-K  0.72
1988 Haussler D. New Theoretical Directions In Machine Learning Machine Learning. 2: 281-284. DOI: 10.1023/A:1022817027844  0.48
1988 Ehrenfeucht A, Haussler D. A new distance metric on strings computable in linear time Discrete Applied Mathematics. 20: 191-203. DOI: 10.1016/0166-218X(88)90076-5  0.72
1988 Haussler D. Quantifying inductive bias: AI learning algorithms and Valiant's learning framework Artificial Intelligence. 36: 177-221. DOI: 10.1016/0004-3702(88)90002-1  0.48
1987 Blumer A, Blumer J, Haussler D, McConnell R, Ehrenfeucht A. COMPLETE INVERTED FILES FOR EFFICIENT TEXT RETRIEVAL AND ANALYSIS. Journal of the Acm. 34: 578-595. DOI: 10.1145/28869.28873  0.72
1987 Main MG, Bucher W, Haussler D. Applications of an infinite square-free co-CFL Theoretical Computer Science. 49: 113-119. DOI: 10.1016/0304-3975(87)90003-X  0.48
1987 Blumer A, Ehrenfeucht A, Haussler D, Warmuth MK. Occam's Razor Information Processing Letters. 24: 377-380. DOI: 10.1016/0020-0190(87)90114-1  0.72
1987 Haussler D, Welzl E. ź-nets and simplex range queries Discrete and Computational Geometry. 2: 127-151. DOI: 10.1007/Bf02187876  0.48
1985 Bucher W, Ehrenfeucht A, Haussler D. On total regulators generated by derivation relations Theoretical Computer Science. 40: 131-148. DOI: 10.1016/0304-3975(85)90162-8  0.72
1985 Blumer A, Blumer J, Haussler D, Ehrenfeucht A, Chen MT, Seiferas J. The smallest automation recognizing the subwords of a text Theoretical Computer Science. 40: 31-55. DOI: 10.1016/0304-3975(85)90157-4  0.72
1985 Haussler D. Another generalization of Higman's well quasi order result on Σ∗ Discrete Mathematics. 57: 237-243. DOI: 10.1016/0012-365X(85)90176-1  0.48
1984 Warmuth MK, Haussler D. On the complexity of iterated shuffle Journal of Computer and System Sciences. 28: 345-358. DOI: 10.1016/0022-0000(84)90018-7  0.72
1984 Ehrenfeucht A, Haussler D, Rozenberg G, Zeiger P. On dos languages and dos mappings Semigroup Forum. 29: 123-148. DOI: 10.1007/Bf02573321  0.72
1983 Ehrenfeucht A, Haussler D, Rozenberg G. On regularity of context-free languages Theoretical Computer Science. 27: 311-332. DOI: 10.1016/0167-7136(83)90297-4  0.72
1980 Haussler D, Zeiger HP. Very special languages and representations of recursively enumerable languages via computation histories Information & Computation. 47: 201-212. DOI: 10.1016/S0019-9958(80)90537-9  0.48
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