Adam C. Siepel

Melissa J. Hubisz, Katherine S. Pollard, Adam C. Siepel: PHAST and RPHAST: phylogenetic analysis with space/time models. Briefings in Bioinformatics 12(1): 41-51 (2011)

Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel: Reconstructing Histories of Complex Gene Clusters on a Phylogeny. Journal of Computational Biology 17(9): 1267-1279 (2010)

Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller: Evolutionary History Reconstruction for Mammalian Complex Gene Clusters. Journal of Computational Biology 16(8): 1051-1070 (2009)

Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel: Reconstructing Histories of Complex Gene Clusters on a Phylogeny. RECOMB-CG 2009: 150-163

Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel: Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny. CoRR abs/0906.2635 (2009)

Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller: Reconstructing the Evolutionary History of Complex Human Gene Clusters. RECOMB 2008: 29-49

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)

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)

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 Computational Biology 2(4) (2006)

Adam C. Siepel, Katherine S. Pollard, David Haussler: New Methods for Detecting Lineage-Specific Selection. RECOMB 2006: 190-205

Adam C. Siepel, David Haussler: Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis. Journal of Computational Biology 11(2/3): 413-428 (2004)

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

Adam C. Siepel, David Haussler: Computational identification of evolutionarily conserved exons. RECOMB 2004: 177-186

Adam C. Siepel: An Algorithm to Enumerate Sorting Reversals for Signed Permutations. Journal of Computational Biology 10(3/4): 575-597 (2003)

Adam C. Siepel, David Haussler: Combining phylogenetic and hidden Markov models in biosequence analysis. RECOMB 2003: 277-286

Adam C. Siepel: An algorithm to enumerate all sorting reversals. RECOMB 2002: 281-290

Bernard M. E. Moret, Adam C. Siepel, Jijun Tang, Tao Liu: Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data. WABI 2002: 521-536

Adam C. Siepel, Andrew D. Farmer, Andrew N. Tolopko, Mingzhe Zhuang, Pedro Mendes, William D. Beavis, Bruno W. S. Sobral: ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics 17(1): 83-94 (2001)

Adam C. Siepel, Andrew N. Tolopko, Andrew D. Farmer, Peter A. Steadman, Faye D. Schilkey, B. Dawn Perry, William D. Beavis: An integration platform for heterogeneous bioinformatics software components. IBM Systems Journal 40(2): 570-591 (2001)

Adam C. Siepel, Bernard M. E. Moret: Finding an Optimal Inversion Median: Experimental Results. WABI 2001: 189-203

M. P. Skupski, M. Booker, Andrew D. Farmer, M. Harpold, Wen Huang, Jeff T. Inman, Donald Kiphart, C. Kodira, S. Root, Faye D. Schilkey, Jolene Schwertfeger, Adam C. Siepel, D. Stamper, Nina Thayer, R. Thompson, J. Wortman, J. J. Zhuang, Carol Harger: The Genome Sequence DataBase: towards an integrated functional genomics resource. Nucleic Acids Research 27(1): 35-38 (1999)

Carol Harger, M. P. Skupski, J. Bingham, Andrew D. Farmer, S. Hoisie, Peter Hraber, Donald Kiphart, L. Krakowski, Mia McLeod, Jolene Schwertfeger, G. A. Seluja, Adam C. Siepel, G. Singh, D. Stamper, Peter A. Steadman, Nina Thayer, R. Thompson, P. Wargo, Mark E. Waugh, J. J. Zhuang, P. A. Schad: The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Research 26(1): 21-26 (1998)

Carol Harger, M. P. Skupski, E. Allen, C. Clark, David Crowley, Emily Dickinson, D. Easley, Ada Espinosa-Lujan, Andrew D. Farmer, Chris A. Fields, L. Flores, L. Harris, Gifford Keen, Mo Manning, Michael P. McLeod, John O'Neill, Maria Pumilia, Rhonda Reinert, David Rider, John Rohrlich, Y. Romero, Jolene Schwertfeger, G. A. Seluja, Adam C. Siepel, P. A. Schad: The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes. Nucleic Acids Research 25(1): 18-23 (1997)