Mark Diekhans

Christopher Douville, Hannah Carter, Rick Kim, Noushin Niknafs, Mark Diekhans, Peter D. Stenson, David N. Cooper, Michael C. Ryan, Rachel Karchin: CRAVAT: cancer-related analysis of variants toolkit. Bioinformatics 29(5): 647-648 (2013)

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 Research 41(Database-Issue): 56-63 (2013)

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 Research 41(Database-Issue): 64-69 (2013)

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 Research 41(Database-Issue): 949-954 (2013)

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 Research 40(Database-Issue): 912-917 (2012)

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 Research 40(Database-Issue): 918-923 (2012)

Wing Chung Wong, Dewey Kim, Hannah Carter, Mark Diekhans, Michael C. Ryan, Rachel Karchin: CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics 27(15): 2147-2148 (2011)

Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler: Cactus Graphs for Genome Comparisons. Journal of Computational Biology 18(3): 469-481 (2011)

Pauline A. Fujita, Brooke L. Rhead, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Melissa S. Cline, Mary Goldman, Galt P. Barber, Hiram Clawson, Antonio 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 Research 39(Database-Issue): 876-882 (2011)

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 Research 38(Database-Issue): 613-619 (2010)

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

Michael C. Ryan, Mark Diekhans, Stephanie Lien, Yun Liu, Rachel Karchin: LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics 25(11): 1431-1432 (2009)

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 Research 37(Database-Issue): 755-761 (2009)

Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler: Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24(5): 637-644 (2008)

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 Research 36(Database-Issue): 773-779 (2008)

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 Research 35(Database-Issue): 668-673 (2007)

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 Computational Biology 3(12) (2007)

Fan Hsu, W. James Kent, Hiram Clawson, Robert M. Kuhn, Mark Diekhans, David Haussler: The UCSC Known Genes. Bioinformatics 22(9): 1036-1046 (2006)

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, R. J. Weber, M. Weirauch, Ann S. Zweig, David Haussler, W. James Kent: The UCSC Genome Browser Database: update 2006. Nucleic Acids Research 34(Database-Issue): 590-598 (2006)

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. Bioinformatics 21(12): 2814-2820 (2005)

Fan Hsu, Tom H. Pringle, Robert M. Kuhn, Donna Karolchik, Mark Diekhans, David Haussler, W. James Kent: The UCSC Proteome Browser. Nucleic Acids Research 33(Database-Issue): 454-458 (2005)

Andrea Di Blas, David M. Dahle, Mark Diekhans, Leslie Grate, Jeffrey D. Hirschberg, Kevin Karplus, Hansjörg Keller, Mark Kendrick, Francisco J. Mesa-Martinez, David Pease, Eric Rice, Angela Schultz, Don Speck, Richard Hughey: The UCSC Kestrel Parallel Processor. IEEE Trans. Parallel Distrib. Syst. 16(1): 80-92 (2005)

Krishna M. Roskin, Mark Diekhans, David Haussler: Score Functions for Determining Regional Conservation in Two-Species Local Alignments. Journal of Computational Biology 11(2/3): 395-411 (2004)

Donna Karolchik, Robert Baertsch, Mark Diekhans, Terrence S. Furey, Angela S. Hinrichs, Y. T. Lu, Krishna M. Roskin, M. Schwartz, Charles W. Sugnet, Daryl J. Thomas, R. J. Weber, David Haussler, W. James Kent: The UCSC Genome Browser Database. Nucleic Acids Research 31(1): 51-54 (2003)

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

Leslie Grate, Mark Diekhans, David M. Dahle, Richard Hughey: Sequence Analysis With the Kestrel SIMD Parallel Processor. Pacific Symposium on Biocomputing 2001: 263-274

Tommi Jaakkola, Mark Diekhans, David Haussler: A Discriminative Framework for Detecting Remote Protein Homologies. Journal of Computational Biology 7(1-2): 95-114 (2000)

Tommi Jaakkola, Mark Diekhans, David Haussler: Using the Fisher Kernel Method to Detect Remote Protein Homologies. ISMB 1999: 149-158