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ORCIDDavid Haussler
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- affiliation: University of California, Santa Cruz, USA
- award (2003): ACM - AAAI Allen Newell Award
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2020 – today
- 2023
[j110]Luis R. Nassar
, Galt P. Barber, Anna Benet-Pagès, Jonathan Casper, Hiram Clawson, Mark Diekhans, Clayton M. Fischer, Jairo Navarro Gonzalez, Angie S. Hinrichs, Brian T. Lee, Christopher M. Lee, Pranav Muthuraman, Beagan Nguy, Tiana Pereira, Parisa Nejad, Gerardo Perez, Brian J. Raney, Daniel Schmelter, Matthew L. Speir, Brittney D. Wick, Ann S. Zweig, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent:
The UCSC Genome Browser database: 2023 update. Nucleic Acids Res. 51(D1): 1188-1195 (2023)- 2022
- [j109]Pierre V. Baudin, Victoria T. Ly, Pattawong Pansodtee, Erik A. Jung, Robert Currie, Ryan Hoffman, Helen Rankin Willsey, Alex A. Pollen, Tomasz J. Nowakowski, David Haussler, Mohammed Andres Mostajo-Radji, Sofie R. Salama, Mircea Teodorescu:
Low cost cloud based remote microscopy for biological sciences. Internet Things 18: 100454 (2022) - [j108]David F. Parks, Kateryna Voitiuk, Jinghui Geng, Matthew A. T. Elliott, Matthew G. Keefe, Erik A. Jung, Ash Robbins, Pierre V. Baudin, Victoria T. Ly, Nico Hawthorne, Dylan Yong, Sebastian E. Sanso, Nick Rezaee, Jess L. Sevetson, Spencer T. Seiler, Robert Currie, Alex A. Pollen, Keith B. Hengen, Tomasz J. Nowakowski, Mohammed Andres Mostajo-Radji, Sofie R. Salama, Mircea Teodorescu, David Haussler:
IoT cloud laboratory: Internet of Things architecture for cellular biology. Internet Things 20: 100618 (2022) - [j107]Brian T. Lee, Galt P. Barber, Anna Benet-Pagès, Jonathan Casper, Hiram Clawson, Mark Diekhans, Clayton M. Fischer, Jairo Navarro Gonzalez, Angie S. Hinrichs, Christopher M. Lee, Pranav Muthuraman, Luis R. Nassar, Beagan Nguy, Tiana Pereira, Gerardo Perez, Brian J. Raney, Kate R. Rosenbloom, Daniel Schmelter, Matthew L. Speir, Brittney D. Wick, Ann S. Zweig, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent:
The UCSC Genome Browser database: 2022 update. Nucleic Acids Res. 50(D1): 1115-1122 (2022) - 2021
- [j106]Jairo Navarro Gonzalez, Ann S. Zweig, Matthew L. Speir, Daniel Schmelter, Kate R. Rosenbloom, Brian J. Raney, Conner C. Powell, Luis R. Nassar, Nathan D. Maulding, Christopher M. Lee, Brian T. Lee, Angie S. Hinrichs, Alastair C. Fyfe, Jason D. Fernandes, Mark Diekhans, Hiram Clawson, Jonathan Casper, Anna Benet-Pagès, Galt P. Barber, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent:
The UCSC Genome Browser database: 2021 update. Nucleic Acids Res. 49(Database-Issue): D1046-D1057 (2021) - [c65]Maxim Kuznetsov, Aviv Elor, Sri Kurniawan, Colleen M. Bosworth, Yohei Rosen, Nicholas Heyer, Mircea Teodorescu, Benedict Paten, David Haussler:
The Immersive Graph Genome Explorer: Navigating Genomics in Immersive Virtual Reality. SEGAH 2021: 1-8 - [i2]Pierre V. Baudin, Victoria T. Ly, Pattawong Pansodtee, Erik A. Jung, Robert Currie, Ryan Hoffman, Helen Rankin Willsey, Alex A. Pollen, Tomasz J. Nowakowski, David Haussler, Mohammed Andres Mostajo-Radji, Sofie R. Salama, Mircea Teodorescu:
Low cost cloud based remote microscopy for biological sciences. CoRR abs/2106.07419 (2021) - 2020
- [j105]Christopher M. Lee, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Jairo Navarro Gonzalez, Angie S. Hinrichs, Brian T. Lee, Luis R. Nassar, Conner C. Powell, Brian J. Raney, Kate R. Rosenbloom, Daniel Schmelter, Matthew L. Speir, Ann S. Zweig, David Haussler, Maximilian Haeussler, Robert M. Kuhn, W. James Kent:
UCSC Genome Browser enters 20th year. Nucleic Acids Res. 48(Database-Issue): D756-D761 (2020) - [j104]Jacob Pfeil, Lauren M. Sanders, Ioannis N. Anastopoulos, A. Geoffrey Lyle, Alana S. Weinstein, Yuanqing Xue, Andrew Blair, Holly C. Beale, Alex Lee, Stanley G. Leung, Phuong T. Dinh, Avanthi Tayi Shah, Marcus R. Breese, W. Patrick Devine, Isabel Bjork, Sofie R. Salama, E. Alejandro Sweet-Cordero, David Haussler, Olena Morozova Vaske:
Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. PLoS Comput. Biol. 16(4) (2020) - [c64]Alex Spaeth, Maryam Tebyani, David Haussler, Mircea Teodorescu:
Neuromorphic Closed-Loop Control of a Flexible Modular Robot by a Simulated Spiking Central Pattern Generator. RoboSoft 2020: 46-51 - [i1]Alex Spaeth, Maryam Tebyani, David Haussler, Mircea Teodorescu:
Spiking neural state machine for gait frequency entrainment in a flexible modular robot. CoRR abs/2007.07346 (2020)
2010 – 2019
- 2019
- [j103]Maximilian Haeussler, Ann S. Zweig, Cath Tyner, Matthew L. Speir, Kate R. Rosenbloom, Brian J. Raney, Christopher M. Lee, Brian T. Lee, Angie S. Hinrichs, Jairo Navarro Gonzalez, David Gibson, Mark Diekhans, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent:
The UCSC Genome Browser database: 2019 update. Nucleic Acids Res. 47(Database-Issue): D853-D858 (2019) - 2018
- [j102]David Haussler, Maciej Smuga-Otto, Jordan M. Eizenga, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov:
A Flow Procedure for Linearization of Genome Sequence Graphs. J. Comput. Biol. 25(7): 664-676 (2018) - [j101]Jonathan Casper, Ann S. Zweig, Chris Villarreal, Cath Tyner, Matthew L. Speir, Kate R. Rosenbloom, Brian J. Raney, Christopher M. Lee, Brian T. Lee, Donna Karolchik, Angie S. Hinrichs, Maximilian Haeussler, Luvina Guruvadoo, Jairo Navarro Gonzalez, David Gibson, Ian T. Fiddes, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Galt P. Barber, Joel Armstrong, David Haussler, Robert M. Kuhn, W. James Kent:
The UCSC Genome Browser database: 2018 update. Nucleic Acids Res. 46(Database-Issue): D762-D769 (2018) - 2017
- [j100]Cath Tyner, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Christopher Eisenhart, Clayton M. Fischer, David Gibson, Jairo Navarro Gonzalez, Luvina Guruvadoo, Maximilian Haeussler, Steven G. Heitner, Angie S. Hinrichs, Donna Karolchik, Brian T. Lee, Christopher M. Lee, Parisa Nejad, Brian J. Raney, Kate R. Rosenbloom, Matthew L. Speir, Chris Villarreal, John Vivian, Ann S. Zweig, David Haussler, Michael Kuhn, W. James Kent:
The UCSC Genome Browser database: 2017 update. Nucleic Acids Res. 45(Database-Issue): D626-D634 (2017) - [c63]Xiaoqian Jiang, Claudiu Farcas, Benedict Paten, Mark Diekhans, Paul Avillach, Wallace Wadge, David Haussler, Lucila Ohno-Machado, Ida Sim:
Count Everything: Secure Count Query Framework Across Big Data Centers. CRI 2017 - [c62]David Haussler, Maciej Smuga-Otto, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov:
A Flow Procedure for the Linearization of Genome Sequence Graphs. RECOMB 2017: 34-49 - 2016
- [j99]Angie S. Hinrichs, Brian J. Raney, Matthew L. Speir, Brooke L. Rhead, Jonathan Casper, Donna Karolchik, Robert M. Kuhn, Kate R. Rosenbloom, Ann S. Zweig, David Haussler, W. James Kent:
UCSC Data Integrator and Variant Annotation Integrator. Bioinform. 32(9): 1430-1432 (2016) - [j98]Daniel R. Zerbino, Tracy Ballinger, Benedict Paten, Glenn Hickey, David Haussler:
Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs. BMC Bioinform. 17: 400 (2016) - [j97]Matthew L. Speir, Ann S. Zweig, Kate R. Rosenbloom, Brian J. Raney, Benedict Paten, Parisa Nejad, Brian T. Lee, Katrina Learned, Donna Karolchik, Angie S. Hinrichs, Steven G. Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Pauline A. Fujita, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent:
The UCSC Genome Browser database: 2016 update. Nucleic Acids Res. 44(Database-Issue): 717-725 (2016) - 2015
- [j96]Maximilian Haeussler, Brian J. Raney, Angie S. Hinrichs, Hiram Clawson, Ann S. Zweig, Donna Karolchik, Jonathan Casper, Matthew L. Speir, David Haussler, W. James Kent:
Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinform. 31(5): 764-766 (2015) - [j95]Adam M. Novak, Yohei Rosen, David Haussler, Benedict Paten:
Canonical, stable, general mapping using context schemes. Bioinform. 31(22): 3569-3576 (2015) - [j94]Benedict Paten, Mark Diekhans, Brian J. Druker, Stephen H. Friend, Justin Guinney, Nadine Gassner, Mitchell Guttman, W. James Kent, Patrick Mantey, Adam A. Margolin, Matt Massie, Adam M. Novak, Frank A. Nothaft, Lior Pachter, David A. Patterson, Maciej Smuga-Otto, Joshua M. Stuart, Laura J. van't Veer, Barbara J. Wold, David Haussler:
The NIH BD2K center for big data in translational genomics. J. Am. Medical Informatics Assoc. 22(6): 1143-1147 (2015) - [j93]Ngan Nguyen, Glenn Hickey, Daniel R. Zerbino, Brian J. Raney, Dent Earl, Joel Armstrong, W. James Kent, David Haussler, Benedict Paten:
Building a Pan-Genome Reference for a Population. J. Comput. Biol. 22(5): 387-401 (2015) - [j92]Kate R. Rosenbloom, Joel Armstrong, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler, Rachel A. Harte, Steven G. Heitner, Glenn Hickey, Angie S. Hinrichs, Robert Hubley, Donna Karolchik, Katrina Learned, Brian T. Lee, Chin H. Li, Karen H. Miga, Ngan Nguyen, Benedict Paten, Brian J. Raney, Arian F. A. Smit, Matthew L. Speir, Ann S. Zweig, David Haussler, Robert M. Kuhn, W. James Kent:
The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 43(Database-Issue): 670-681 (2015) - [j91]Mary Goldman, Brian Craft, Teresa Swatloski, Melissa S. Cline, Olena Morozova, Mark Diekhans, David Haussler, Jingchun Zhu:
The UCSC Cancer Genomics Browser: update 2015. Nucleic Acids Res. 43(Database-Issue): 812-817 (2015) - [j90]Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi Moussavi, Pouya Kheradpour, ZhiZhuo Zhang, Jianrong Wang, Michael J. Ziller, Viren Amin, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald T. Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kyle Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca F. Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil R. Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis:
Integrative analysis of 111 reference human epigenomes Open. Nat. 518(7539): 317-330 (2015) - 2014
- [j89]Christopher Wilks, Melissa S. Cline, Erich Weiler, Mark Diekhans, Brian Craft, Christy Martin, Daniel Murphy, Howdy Pierce, John Black, Donavan Nelson, Brian Litzinger, Thomas Hatton, Lori Maltbie, Michael Ainsworth, Patrick Allen, Linda Rosewood, Elizabeth Mitchell, Bradley Smith, Jim Warner, John Groboske, Haifang Telc, Daniel Wilson, Brian Sanford, Hannes Schmidt, David Haussler, Daniel Maltbie:
The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Database J. Biol. Databases Curation 2014 (2014) - [j88]Ngan Nguyen, Glenn Hickey, Brian J. Raney, Joel Armstrong, Hiram Clawson, Ann S. Zweig, Donna Karolchik, William James Kent, David Haussler, Benedict Paten:
Comparative assembly hubs: Web-accessible browsers for comparative genomics. Bioinform. 30(23): 3293-3301 (2014) - [j87]Benedict Paten, Daniel R. Zerbino, Glenn Hickey, David Haussler:
A unifying model of genome evolution under parsimony. BMC Bioinform. 15: 206 (2014) - [j86]Donna Karolchik, Galt P. Barber, Jonathan Casper, Hiram Clawson, Melissa S. Cline, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler, Rachel A. Harte, Steven G. Heitner, Angie S. Hinrichs, Katrina Learned, Brian T. Lee, Chin H. Li, Brian J. Raney, Brooke L. Rhead, Kate R. Rosenbloom, Cricket A. Sloan, Matthew L. Speir, Ann S. Zweig, David Haussler, Robert M. Kuhn, W. James Kent:
The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 42(Database-Issue): 764-770 (2014) - [j85]Catherine M. Farrell, Nuala A. O'Leary, Rachel A. Harte, Jane E. Loveland, Laurens G. Wilming, Craig Wallin, Mark Diekhans, Daniel Barrell, Stephen M. J. Searle, Bronwen L. Aken, Susan M. Hiatt, Adam Frankish, Marie-Marthe Suner, Bhanu Rajput, Charles A. Steward, Garth R. Brown, Ruth Bennett, Michael R. Murphy, Wendy Wu, Mike P. Kay, Jennifer Hart, Jeena Rajan, Janet Weber, Catherine Snow, Lillian D. Riddick, Toby Hunt, David Webb, Mark Thomas, Pamela Tamez, Sanjida H. Rangwala, Kelly M. McGarvey, Shashikant Pujar, Andrei Shkeda, Jonathan M. Mudge, Jose M. Gonzalez, James G. R. Gilbert, Stephen J. Trevanion, Robert Baertsch, Jennifer L. Harrow, Tim J. P. Hubbard, James M. Ostell, David Haussler, Kim D. Pruitt:
Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res. 42(Database-Issue): 865-872 (2014) - [c61]Ngan Nguyen, Glenn Hickey, Daniel R. Zerbino, Brian J. Raney, Dent Earl, Joel Armstrong, David Haussler, Benedict Paten:
Building a Pangenome Reference for a Population. RECOMB 2014: 207-221 - 2013
- [j84]Robert M. Kuhn, David Haussler, W. James Kent:
The UCSC genome browser and associated tools. Briefings Bioinform. 14(2): 144-161 (2013) - [j83]Glenn Hickey, Benedict Paten, Dent Earl, Daniel R. Zerbino, David Haussler:
HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinform. 29(10): 1341-1342 (2013) - [j82]Evan O. Paull, Daniel E. Carlin, Mario Niepel, Peter K. Sorger, David Haussler, Joshua M. Stuart:
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinform. 29(21): 2757-2764 (2013) - [j81]Kate R. Rosenbloom, Cricket A. Sloan, Venkat S. Malladi, Timothy R. Dreszer, Katrina Learned, Vanessa Kirkup, Matthew C. Wong, Morgan Maddren, Ruihua Fang, Steven G. Heitner, Brian T. Lee, Galt P. Barber, Rachel A. Harte, Mark Diekhans, Jeffrey C. Long, Steven P. Wilder, Ann S. Zweig, Donna Karolchik, Robert M. Kuhn, David Haussler, W. James Kent:
ENCODE Data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 41(Database-Issue): 56-63 (2013) - [j80]Laurence R. Meyer, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Robert M. Kuhn, Matthew C. Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke L. Rhead, Brian J. Raney, Andy Pohl, Venkat S. Malladi, Chin H. Li, Brian T. Lee, Katrina Learned, Vanessa Kirkup, Fan Hsu, Steven G. Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Mary Goldman, Belinda Giardine, Pauline A. Fujita, Timothy R. Dreszer, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent:
The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 41(Database-Issue): 64-69 (2013) - [j79]Mary Goldman, Brian Craft, Teresa Swatloski, Kyle Ellrott, Melissa S. Cline, Mark Diekhans, Singer Ma, Chris Wilks, Joshua M. Stuart, David Haussler, Jingchun Zhu:
The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Res. 41(Database-Issue): 949-954 (2013) - [j78]Christopher K. Wong, Charles J. Vaske, Sam Ng, J. Zachary Sanborn, Stephen C. Benz, David Haussler, Joshua M. Stuart:
The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Res. 41(Webserver-Issue): 218-224 (2013) - 2012
- [j77]Sam Ng, Eric A. Collisson, Artem Sokolov, Theodore Goldstein, Abel Gonzalez-Perez, Núria López-Bigas, Christopher Benz, David Haussler, Joshua M. Stuart:
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinform. 28(18): 640-646 (2012) - [j76]Kate R. Rosenbloom, Timothy R. Dreszer, Jeffrey C. Long, Venkat S. Malladi, Cricket A. Sloan, Brian J. Raney, Melissa S. Cline, Donna Karolchik, Galt P. Barber, Hiram Clawson, Mark Diekhans, Pauline A. Fujita, Mary Goldman, Robert C. Gravell, Rachel A. Harte, Angie S. Hinrichs, Vanessa Kirkup, Robert M. Kuhn, Katrina Learned, Morgan Maddren, Laurence R. Meyer, Andy Pohl, Brooke L. Rhead, Matthew C. Wong, Ann S. Zweig, David Haussler, W. James Kent:
ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res. 40(Database-Issue): 912-917 (2012) - [j75]Timothy R. Dreszer, Donna Karolchik, Ann S. Zweig, Angie S. Hinrichs, Brian J. Raney, Robert M. Kuhn, Laurence R. Meyer, Matthew C. Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke L. Rhead, Andy Pohl, Venkat S. Malladi, Chin H. Li, Katrina Learned, Vanessa Kirkup, Fan Hsu, Rachel A. Harte, Luvina Guruvadoo, Mary Goldman, Belinda Giardine, Pauline A. Fujita, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent:
The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 40(Database-Issue): 918-923 (2012) - 2011
- [j74]Krishna M. Roskin, Benedict Paten, David Haussler:
Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization. BMC Bioinform. 12: 144 (2011) - [j73]Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler:
Cactus Graphs for Genome Comparisons. J. Comput. Biol. 18(3): 469-481 (2011) - [j72]Brian J. Raney, Melissa S. Cline, Kate R. Rosenbloom, Timothy R. Dreszer, Katrina Learned, Galt P. Barber, Laurence R. Meyer, Cricket A. Sloan, Venkat S. Malladi, Krishna M. Roskin, Bernard B. Suh, Angie S. Hinrichs, Hiram Clawson, Ann S. Zweig, Vanessa Kirkup, Pauline A. Fujita, Brooke L. Rhead, Kayla E. Smith, Andy Pohl, Robert M. Kuhn, Donna Karolchik, David Haussler, W. James Kent:
ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 39(Database-Issue): 871-875 (2011) - [j71]Pauline A. Fujita, Brooke L. Rhead, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Melissa S. Cline, Mary Goldman, Galt P. Barber, Hiram Clawson, António Coelho, Mark Diekhans, Timothy R. Dreszer, Belinda Giardine, Rachel A. Harte, Jennifer Hillman-Jackson, Fan Hsu, Vanessa Kirkup, Robert M. Kuhn, Katrina Learned, Chin H. Li, Laurence R. Meyer, Andy Pohl, Brian J. Raney, Kate R. Rosenbloom, Kayla E. Smith, David Haussler, W. James Kent:
The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39(Database-Issue): 876-882 (2011) - [j70]J. Zachary Sanborn, Stephen C. Benz, Brian Craft, Christopher Szeto, Kord M. Kober, Laurence R. Meyer, Charles J. Vaske, Mary Goldman, Kayla E. Smith, Robert M. Kuhn, Donna Karolchik, W. James Kent, Joshua M. Stuart, David Haussler, Jingchun Zhu:
The UCSC cancer genomics browser: update 2011. Nucleic Acids Res. 39(Database-Issue): 951-959 (2011) - [c60]David Haussler:
Cancer genomics. KDD 2011: 3-4 - 2010
- [j69]Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, Joshua M. Stuart:
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinform. 26(12): 237-245 (2010) - [j68]Brooke L. Rhead, Donna Karolchik, Robert M. Kuhn, Angie S. Hinrichs, Ann S. Zweig, Pauline A. Fujita, Mark Diekhans, Kayla E. Smith, Kate R. Rosenbloom, Brian J. Raney, Andy Pohl, Michael Pheasant, Laurence R. Meyer, Katrina Learned, Fan Hsu, Jennifer Hillman-Jackson, Rachel A. Harte, Belinda Giardine, Timothy R. Dreszer, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent:
The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 38(Database-Issue): 613-619 (2010) - [j67]Kate R. Rosenbloom, Timothy R. Dreszer, Michael Pheasant, Galt P. Barber, Laurence R. Meyer, Andy Pohl, Brian J. Raney, Ting Wang, Angie S. Hinrichs, Ann S. Zweig, Pauline A. Fujita, Katrina Learned, Brooke L. Rhead, Kayla E. Smith, Robert M. Kuhn, Donna Karolchik, David Haussler, W. James Kent:
ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 38(Database-Issue): 620-625 (2010) - [c59]Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler:
Cactus Graphs for Genome Comparisons. RECOMB 2010: 410-425
2000 – 2009
- 2009
- [j66]Robert M. Kuhn, Donna Karolchik, Ann S. Zweig, Ting Wang, Kayla E. Smith, Kate R. Rosenbloom, Brooke L. Rhead, Brian J. Raney, Andy Pohl, Michael Pheasant, Laurence R. Meyer, Fan Hsu, Angela S. Hinrichs, Rachel A. Harte, Belinda Giardine, Pauline A. Fujita, Mark Diekhans, Timothy R. Dreszer, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent:
The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 37(Database-Issue): 755-761 (2009) - 2008
- [j65]Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler:
Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinform. 24(5): 637-644 (2008) - [j64]Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Louxin Zhang, Webb Miller, David Haussler:
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications. J. Comput. Biol. 15(8): 1007-1027 (2008) - [j63]Donna Karolchik, Robert M. Kuhn, Robert Baertsch, Galt P. Barber, Hiram Clawson, Mark Diekhans, Belinda Giardine, Rachel A. Harte, Angela S. Hinrichs, Fan Hsu, Kord M. Kober, Webb Miller, Jakob Skou Pedersen, Andy Pohl, Brian J. Raney, Brooke L. Rhead, Kate R. Rosenbloom, Kayla E. Smith, Mario Stanke, Archana Thakkapallayil, Heather Trumbower, Ting Wang, Ann S. Zweig, David Haussler, W. James Kent:
The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 36(Database-Issue): 773-779 (2008) - [j62]Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Webb Miller, David Haussler:
The infinite sites model of genome evolution. Proc. Natl. Acad. Sci. USA 105(38): 14254-14261 (2008) - [c58]David Haussler:
Computing how we became human. STOC 2008: 639-640 - 2007
- [j61]Daryl J. Thomas, Kate R. Rosenbloom, Hiram Clawson, Angie S. Hinrichs, Heather Trumbower, Brian J. Raney, Donna Karolchik, Galt P. Barber, Rachel A. Harte, Jennifer Hillman-Jackson, Robert M. Kuhn, Brooke L. Rhead, Kayla E. Smith, Archana Thakkapallayil, Ann S. Zweig, David Haussler, W. James Kent:
The ENCODE Project at UC Santa Cruz. Nucleic Acids Res. 35(Database-Issue): 663-667 (2007) - [j60]Robert M. Kuhn, Donna Karolchik, Ann S. Zweig, Heather Trumbower, Daryl J. Thomas, Archana Thakkapallayil, Charles W. Sugnet, Mario Stanke, Kayla E. Smith, Adam C. Siepel, Kate R. Rosenbloom, Brooke L. Rhead, Brian J. Raney, Andy Pohl, Jakob Skou Pedersen, Fan Hsu, Angela S. Hinrichs, Rachel A. Harte, Mark Diekhans, Hiram Clawson, Gill Bejerano, Galt P. Barber, Robert Baertsch, David Haussler, W. James Kent:
The UCSC genome browser database: update 2007. Nucleic Acids Res. 35(Database-Issue): 668-673 (2007) - [j59]Daryl J. Thomas, Heather Trumbower, Andrew D. Kern, Brooke L. Rhead, Robert M. Kuhn, David Haussler, W. James Kent:
Variation resources at UC Santa Cruz. Nucleic Acids Res. 35(Database-Issue): 716-720 (2007) - [j58]Chen-Hsiang Yeang, David Haussler:
Detecting Coevolution in and among Protein Domains. PLoS Comput. Biol. 3(11) (2007) - [j57]Jingchun Zhu, J. Zachary Sanborn, Mark Diekhans, Craig B. Lowe, Tom H. Pringle, David Haussler:
Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage. PLoS Comput. Biol. 3(12) (2007) - [c57]Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler:
A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications. RECOMB-CG 2007: 122-135 - 2006
- [j56]Fan Hsu, W. James Kent, Hiram Clawson, Robert M. Kuhn, Mark Diekhans, David Haussler:
The UCSC Known Genes. Bioinform. 22(9): 1036-1046 (2006) - [j55]Jing Wu, David Haussler:
Coding Exon Detection Using Comparative Sequences. J. Comput. Biol. 13(6): 1148-1164 (2006) - [j54]Angela S. Hinrichs, Donna Karolchik, Robert Baertsch, Galt P. Barber, Gill Bejerano, Hiram Clawson, Mark Diekhans, Terrence S. Furey, Rachel A. Harte, Fan Hsu, Jennifer Hillman-Jackson, Robert M. Kuhn, Jakob Skou Pedersen, Andy Pohl, Brian J. Raney, Kate R. Rosenbloom, Adam C. Siepel, Kayla E. Smith, Charles W. Sugnet, A. Sultan-Qurraie, Daryl J. Thomas, Heather Trumbower, Ryan J. Weber, M. Weirauch, Ann S. Zweig, David Haussler, W. James Kent:
The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 34(Database-Issue): 590-598 (2006) - [j53]Charles W. Sugnet, Karpagam Srinivasan, Tyson Clark, Georgeann O'Brien, Melissa S. Cline, Hui Wang, Alan Williams, David Kulp, John Blume, David Haussler, Manuel Ares:
Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays. PLoS Comput. Biol. 2(1) (2006) - [j52]Jakob Skou Pedersen, Gill Bejerano, Adam C. Siepel, Kate R. Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, Jim Kent, Webb Miller, David Haussler:
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome. PLoS Comput. Biol. 2(4) (2006) - [c56]Adam C. Siepel, Katherine S. Pollard, David Haussler:
New Methods for Detecting Lineage-Specific Selection. RECOMB 2006: 190-205 - [c55]David Haussler:
Ultraconserved Elements, Living Fossil Transposons, and Rapid Bursts of Change: Reconstructing the Uneven Evolutionary History of the Human Genome. RECOMB 2006: 336-337 - [c54]Jeremy Darot, Chen-Hsiang Yeang, David Haussler:
Detecting the Dependent Evolution of Biosequences. RECOMB 2006: 595-609 - 2005
- [j51]Rachel Karchin, Mark Diekhans, Libusha Kelly, Daryl J. Thomas, Ursula Pieper, Narayanan Eswar, David Haussler, Andrej Sali:
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinform. 21(12): 2814-2820 (2005) - [j50]Fan Hsu, Tom H. Pringle, Robert M. Kuhn, Donna Karolchik, Mark Diekhans, David Haussler, W. James Kent:
The UCSC Proteome Browser. Nucleic Acids Res. 33(Database-Issue): 454-458 (2005) - 2004
- [j49]Krishna M. Roskin, Mark Diekhans, David Haussler:
Score Functions for Determining Regional Conservation in Two-Species Local Alignments. J. Comput. Biol. 11(2/3): 395-411 (2004) - [j48]Adam C. Siepel, David Haussler:
Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis. J. Comput. Biol. 11(2/3): 413-428 (2004) - [j47]Donna Karolchik, Angela S. Hinrichs, Terrence S. Furey, Krishna M. Roskin, Charles W. Sugnet, David Haussler, W. James Kent:
The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32(Database-Issue): 493-496 (2004) - [c53]Gill Bejerano, David Haussler, Mathieu Blanchette:
Into the heart of darkness: large-scale clustering of human non-coding DNA. ISMB/ECCB (Supplement of Bioinformatics) 2004: 40-48 - [c52]Vladimir Jojic, Nebojsa Jojic, Christopher Meek, Dan Geiger, Adam C. Siepel, David Haussler, David Heckerman:
Efficient approximations for learning phylogenetic HMM models from data. ISMB/ECCB (Supplement of Bioinformatics) 2004: 161-168 - [c51]Charles W. Sugnet, W. James Kent, Manuel Ares, David Haussler:
Transcriptome and Genome Conservation of Alternative Splicing Events in Humans and Mice. Pacific Symposium on Biocomputing 2004: 66-77 - [c50]Adam C. Siepel, David Haussler:
Computational identification of evolutionarily conserved exons. RECOMB 2004: 177-186 - 2003
- [j46]Donna Karolchik, Robert Baertsch, Mark Diekhans, Terrence S. Furey, Angela S. Hinrichs, Yontao Lu, Krishna M. Roskin, Matt Schwartz, Charles W. Sugnet, Daryl J. Thomas, Ryan J. Weber, David Haussler, W. James Kent:
The UCSC Genome Browser Database. Nucleic Acids Res. 31(1): 51-54 (2003) - [c49]Hui Wang, Earl Hubbell, Jing-Shan Hu, Gangwu Mei, Melissa S. Cline, Gang Lu, Tyson Clark, Michael A. Siani-Rose, Manuel Ares, David Kulp, David Haussler:
Gene structure-based splice variant deconvolution using a microarry platform. ISMB (Supplement of Bioinformatics) 2003: 315-322 - [c48]David Haussler:
Computational analysis of the human and other mammalian genomes. RECOMB 2003: 138-138 - [c47]Krishna M. Roskin, Mark Diekhans, David Haussler:
Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments. RECOMB 2003: 257-266 - [c46]Adam C. Siepel, David Haussler:
Combining phylogenetic and hidden Markov models in biosequence analysis. RECOMB 2003: 277-286 - 2002
- [j45]Rachel Karchin, Kevin Karplus, David Haussler:
Classifying G-protein coupled receptors with support vector machines. Bioinform. 18(1): 147-159 (2002) - 2001
- [c45]Paul Pavlidis, Terrence S. Furey, M. Liberto, David Haussler, William Noble Grundy:
Promoter Region-Based Classification of Genes. Pacific Symposium on Biocomputing 2001: 151-164 - 2000
- [j44]