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ORCIDAdam C. Siepel
Person information
- affiliation: Cold Spring Harbor Laboratory, NY, USA
- affiliation (former): Cornell University, Ithaca, NY, USA
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Journal Articles
- 2021
[j16]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): 4727-4736 (2021)- 2019
- [j15]Ritika Ramani, Katie Krumholz, Yi-Fei Huang, Adam C. Siepel:
PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP. Bioinform. 35(13): 2320-2322 (2019) - 2014
- [j14]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): 2157-2166 (2014) - 2011
- [j13]Melissa J. Hubisz, Katherine S. Pollard, Adam C. Siepel:
PHAST and RPHAST: phylogenetic analysis with space/time models. Briefings Bioinform. 12(1): 41-51 (2011) - 2010
- [j12]Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel:
Reconstructing Histories of Complex Gene Clusters on a Phylogeny. J. Comput. Biol. 17(9): 1267-1279 (2010) - 2009
- [j11]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): 1051-1070 (2009) - 2007
- [j10]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): 668-673 (2007) - 2006
- [j9]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): 590-598 (2006) - [j8]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) - 2004
- [j7]Adam C. Siepel, David Haussler:
Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis. J. Comput. Biol. 11(2/3): 413-428 (2004) - 2003
- [j6]Adam C. Siepel:
An Algorithm to Enumerate Sorting Reversals for Signed Permutations. J. Comput. Biol. 10(3/4): 575-597 (2003) - 2001
- [j5]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): 83-94 (2001) - [j4]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): 570-591 (2001) - 1999
- [j3]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): 35-38 (1999) - 1998
- [j2]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): 21-26 (1998) - 1997
- [j1]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): 18-23 (1997)
Conference and Workshop Papers
- 2009
- [c9]Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel:
Reconstructing Histories of Complex Gene Clusters on a Phylogeny. RECOMB-CG 2009: 150-163 - 2008
- [c8]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 - 2006
- [c7]Adam C. Siepel, Katherine S. Pollard, David Haussler:
New Methods for Detecting Lineage-Specific Selection. RECOMB 2006: 190-205 - 2004
- [c6]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 - [c5]Adam C. Siepel, David Haussler:
Computational identification of evolutionarily conserved exons. RECOMB 2004: 177-186 - 2003
- [c4]Adam C. Siepel, David Haussler:
Combining phylogenetic and hidden Markov models in biosequence analysis. RECOMB 2003: 277-286 - 2002
- [c3]Adam C. Siepel:
An algorithm to enumerate all sorting reversals. RECOMB 2002: 281-290 - [c2]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 - 2001
- [c1]Adam C. Siepel, Bernard M. E. Moret:
Finding an Optimal Inversion Median: Experimental Results. WABI 2001: 189-203
Informal and Other Publications
- 2009
- [i1]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)
Coauthor Index
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