Adam C. Siepel

Publication Activity (10 Years)

Years Active: 1997-2021
Publications (10 Years): 1

Top Topics

Assembly Process

Top Venues

Concurr. Comput. Pract. Exp.

Publications

Yixin Zhao, Noah Dukler, Gilad Barshad, Shushan Toneyan, Charles G. Danko, Adam C. Siepel
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinform. 37 (24) (2021)
M. Brian Couger, Lenore Pipes, Fabio Squina, Rolf Prade, Adam C. Siepel, Robert Palermo, Michael G. Katze, Christopher E. Mason, Philip D. Blood
Enabling large-scale next-generation sequence assembly with Blacklight. Concurr. Comput. Pract. Exp. 26 (13) (2014)
Melissa J. Hubisz, Katherine S. Pollard, Adam C. Siepel
PHAST and RPHAST: phylogenetic analysis with space/time models. Briefings Bioinform. 12 (1) (2011)
Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
Reconstructing Histories of Complex Gene Clusters on a Phylogeny. J. Comput. Biol. 17 (9) (2010)
Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny CoRR (2009)
Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller
Evolutionary History Reconstruction for Mammalian Complex Gene Clusters. J. Comput. Biol. 16 (8) (2009)
Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
Reconstructing Histories of Complex Gene Clusters on a Phylogeny. RECOMB-CG (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)
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) (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, 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) (2006)
Adam C. Siepel, Katherine S. Pollard, David Haussler
New Methods for Detecting Lineage-Specific Selection. RECOMB (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 Comput. Biol. 2 (4) (2006)
Adam C. Siepel, David Haussler
Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis. J. Comput. Biol. 11 (2/3) (2004)
Adam C. Siepel, David Haussler
Computational identification of evolutionarily conserved exons. RECOMB (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)
Adam C. Siepel
An Algorithm to Enumerate Sorting Reversals for Signed Permutations. J. Comput. Biol. 10 (3/4) (2003)
Adam C. Siepel, David Haussler
Combining phylogenetic and hidden Markov models in biosequence analysis. RECOMB (2003)
Adam C. Siepel
An algorithm to enumerate all sorting reversals. RECOMB (2002)
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)
Adam C. Siepel, Bernard M. E. Moret
Finding an Optimal Inversion Median: Experimental Results. WABI (2001)
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. Bioinform. 17 (1) (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 Syst. J. 40 (2) (2001)
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, David Stamper, Nina Thayer, R. Thompson, Jennifer R. Wortman, J. J. Zhuang, Carol Harger
The Genome Sequence DataBase: towards an integrated functional genomics resource. Nucleic Acids Res. 27 (1) (1999)
Carol Harger, M. P. Skupski, J. Bingham, Andrew D. Farmer, S. Hoisie, Peter T. Hraber, Donald Kiphart, L. Krakowski, Mia McLeod, Jolene Schwertfeger, G. A. Seluja, Adam C. Siepel, Gautam Singh, David Stamper, Peter A. Steadman, Nina Thayer, R. Thompson, P. Wargo, Mark E. Waugh, J. J. Zhuang, Peter A. Schad
The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Res. 26 (1) (1998)
Carol Harger, Marian Skupski, Ethan Allen, Christopher Clark, David Crowley, Emily Dickinson, David Easley, Ada Espinosa-Lujan, Andrew D. Farmer, Chris A. Fields, Leandrita Flores, Lynn Harris, Gifford Keen, Maurice Manning, Michael P. McLeod, John O'Neill, Maria Pumilia, Rhonda Reinert, David Rider, John Rohrlich, Yolanda Romero, Jolene Schwertfeger, Gustavo Seluja, Adam C. Siepel, Gautam Singh, Linda Smyth, David Stamper, Judy Stein, Randy Suggs, Rajini Takkallapalli, Nina Thayer, Gary Thompson, Colleen Walsh, Frederick Wedgeworth III, Peter A. Schad
The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes. Nucleic Acids Res. 25 (1) (1997)