Adam C. Siepel

26 papers B 5C 2Journal 17Unranked 2
YearRankTypeTitle / Venue / Authors
2021 J jnl
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells.
Bioinform.
Yixin Zhao, Noah Dukler, Gilad Barshad, Shushan Toneyan, Charles G. Danko, Adam C. Siepel
2019 J jnl
PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP.
Bioinform.
Ritika Ramani, Katie Krumholz, Yi-Fei Huang, Adam C. Siepel
2014 J jnl
Enabling large-scale next-generation sequence assembly with Blacklight.
Concurr. Comput. Pract. Exp.
M. Brian Couger, Lenore Pipes, Fabio Squina, Rolf Prade, Adam C. Siepel, Robert Palermo, Michael G. Katze, Christopher E. Mason, Philip D. Blood
2011 J jnl
PHAST and RPHAST: phylogenetic analysis with space/time models.
Briefings Bioinform.
Melissa J. Hubisz, Katherine S. Pollard, Adam C. Siepel
2010 J jnl
Reconstructing Histories of Complex Gene Clusters on a Phylogeny.
J. Comput. Biol.
Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
2009 J jnl
Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny
CoRR
Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
2009 J jnl
Evolutionary History Reconstruction for Mammalian Complex Gene Clusters.
J. Comput. Biol.
Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller
2009 — conf
Reconstructing Histories of Complex Gene Clusters on a Phylogeny.
RECOMB-CG
Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
2008 B conf
Reconstructing the Evolutionary History of Complex Human Gene Clusters.
RECOMB
Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller
2007 J jnl
The UCSC genome browser database: update 2007.
Nucleic Acids Res.
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
2006 J jnl
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome.
PLoS Comput. Biol.
Jakob Skou Pedersen, Gill Bejerano, Adam C. Siepel, Kate R. Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, Jim Kent, Webb Miller, David Haussler
2006 B conf
New Methods for Detecting Lineage-Specific Selection.
RECOMB
Adam C. Siepel, Katherine S. Pollard, David Haussler
2006 J jnl
The UCSC Genome Browser Database: update 2006.
Nucleic Acids Res.
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
2004 J jnl
Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis.
J. Comput. Biol.
Adam C. Siepel, David Haussler
2004 B conf
Computational identification of evolutionarily conserved exons.
RECOMB
Adam C. Siepel, David Haussler
2004 — conf
Efficient approximations for learning phylogenetic HMM models from data.
ISMB/ECCB (Supplement of Bioinformatics)
Vladimir Jojic, Nebojsa Jojic, Christopher Meek, Dan Geiger, Adam C. Siepel, David Haussler, David Heckerman
2003 J jnl
An Algorithm to Enumerate Sorting Reversals for Signed Permutations.
J. Comput. Biol.
Adam C. Siepel
2003 B conf
Combining phylogenetic and hidden Markov models in biosequence analysis.
RECOMB
Adam C. Siepel, David Haussler
2002 B conf
An algorithm to enumerate all sorting reversals.
RECOMB
Adam C. Siepel
2002 C conf
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data.
WABI
Bernard M. E. Moret, Adam C. Siepel, Jijun Tang, Tao Liu
2001 J jnl
An integration platform for heterogeneous bioinformatics software components.
IBM Syst. J.
Adam C. Siepel, Andrew N. Tolopko, Andrew D. Farmer, Peter A. Steadman, Faye D. Schilkey, B. Dawn Perry, William D. Beavis
2001 C conf
Finding an Optimal Inversion Median: Experimental Results.
WABI
Adam C. Siepel, Bernard M. E. Moret
2001 J jnl
ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources.
Bioinform.
Adam C. Siepel, Andrew D. Farmer, Andrew N. Tolopko, Mingzhe Zhuang, Pedro Mendes, William D. Beavis, Bruno W. S. Sobral
1999 J jnl
The Genome Sequence DataBase: towards an integrated functional genomics resource.
Nucleic Acids Res.
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
1998 J jnl
The Genome Sequence DataBase (GSDB): improving data quality and data access.
Nucleic Acids Res.
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
1997 J jnl
The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes.
Nucleic Acids Res.
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