Adam C. Siepel

According to our database, Adam C. Siepel authored at least 24 papers between 1997 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2021

Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells.

Yixin Zhao, Noah Dukler, Gilad Barshad, Shushan Toneyan, Charles G. Danko, Adam C. Siepel

Bioinform., 2021

2019

PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP.

Ritika Ramani, Katie Krumholz, Yi-Fei Huang, Adam C. Siepel

Bioinform., 2019

2014

Enabling large-scale next-generation sequence assembly with Blacklight.

M. Brian Couger, Lenore Pipes, Fabio Squina, Rolf Prade, Adam C. Siepel, Robert Palermo, Michael G. Katze, Christopher E. Mason, Philip D. Blood

Concurr. Comput. Pract. Exp., 2014

2011

PHAST and RPHAST: phylogenetic analysis with space/time models.

Melissa J. Hubisz, Katherine S. Pollard, Adam C. Siepel

Briefings Bioinform., 2011

2010

Reconstructing Histories of Complex Gene Clusters on a Phylogeny.

Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel

J. Comput. Biol., 2010

2009

Evolutionary History Reconstruction for Mammalian Complex Gene Clusters.

Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller

J. Comput. Biol., 2009

Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny

Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel

CoRR, 2009

2008

Reconstructing the Evolutionary History of Complex Human Gene Clusters.

Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller

Proceedings of the Research in Computational Molecular Biology, 2008

2007

The UCSC genome browser database: update 2007.

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

Nucleic Acids Res., 2007

2006

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome.

Jakob Skou Pedersen, Gill Bejerano, Adam C. Siepel, Kate R. Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, Jim Kent, Webb Miller, David Haussler

PLoS Comput. Biol., 2006

The UCSC Genome Browser Database: update 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, Ryan J. Weber, M. Weirauch, Ann S. Zweig, David Haussler, W. James Kent

Nucleic Acids Res., 2006

New Methods for Detecting Lineage-Specific Selection.

Adam C. Siepel, Katherine S. Pollard, David Haussler

Proceedings of the Research in Computational Molecular Biology, 2006

2004

Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis.

Adam C. Siepel, David Haussler

J. Comput. Biol., 2004

Computational identification of evolutionarily conserved exons.

Adam C. Siepel, David Haussler

Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

Efficient approximations for learning phylogenetic HMM models from data.

Vladimir Jojic, Nebojsa Jojic, Christopher Meek, Dan Geiger, Adam C. Siepel, David Haussler, David Heckerman

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2003

An Algorithm to Enumerate Sorting Reversals for Signed Permutations.

Adam C. Siepel

J. Comput. Biol., 2003

2002

Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data.

Bernard M. E. Moret, Adam C. Siepel, Jijun Tang, Tao Liu

Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

An algorithm to enumerate all sorting reversals.

Adam C. Siepel

Proceedings of the Sixth Annual International Conference on Computational Biology, 2002

2001

An integration platform for heterogeneous bioinformatics software components.

Adam C. Siepel, Andrew N. Tolopko, Andrew D. Farmer, Peter A. Steadman, Faye D. Schilkey, B. Dawn Perry, William D. Beavis

IBM Syst. J., 2001

ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources.

Adam C. Siepel, Andrew D. Farmer, Andrew N. Tolopko, Mingzhe Zhuang, Pedro Mendes, William D. Beavis, Bruno W. S. Sobral

Bioinform., 2001

Finding an Optimal Inversion Median: Experimental Results.

Adam C. Siepel, Bernard M. E. Moret

Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

1999

The Genome Sequence DataBase: towards an integrated functional genomics resource.

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

Nucleic Acids Res., 1999

1998

The Genome Sequence DataBase (GSDB): improving data quality and data access.

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

Nucleic Acids Res., 1998

1997

The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes.

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

Nucleic Acids Res., 1997