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; et al. (Nucleic Acids Res., 1997)

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; et al. (Nucleic Acids Res., 1998)

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; et al. (Nucleic Acids Res., 1999)

Finding an Optimal Inversion Median: Experimental Results. - Adam C. Siepel; Bernard M. E. Moret (WABI, 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 001; William D. Beavis; Bruno W. S. Sobral (Bioinform., 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)

An algorithm to enumerate all sorting reversals. - Adam C. Siepel (RECOMB, 2002)

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

An Algorithm to Enumerate Sorting Reversals for Signed Permutations. - Adam C. Siepel (J. Comput. Biol., 2003)

Efficient approximations for learning phylogenetic HMM models from data. - Vladimir Jojic; Nebojsa Jojic; Christopher Meek; Dan Geiger; Adam C. Siepel; David Haussler; David Heckerman (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Computational identification of evolutionarily conserved exons. - Adam C. Siepel; David Haussler (RECOMB, 2004)

Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis. - Adam C. Siepel; David Haussler (J. Comput. Biol., 2004)

New Methods for Detecting Lineage-Specific Selection. - Adam C. Siepel; Katherine S. Pollard; David Haussler (RECOMB, 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; et al. (Nucleic Acids Res., 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 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; et al. (Nucleic Acids Res., 2007)

Reconstructing the Evolutionary History of Complex Human Gene Clusters. - Yu Zhang 002; Giltae Song; Tomás Vinar; Eric D. Green; Adam C. Siepel; Webb Miller (RECOMB, 2008)

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

Evolutionary History Reconstruction for Mammalian Complex Gene Clusters. - Yu Zhang 002; Giltae Song; Tomás Vinar; Eric D. Green; Adam C. Siepel; Webb Miller (J. Comput. Biol., 2009)

Reconstructing Histories of Complex Gene Clusters on a Phylogeny. - Tomás Vinar; Brona Brejová; Giltae Song; Adam C. Siepel (J. Comput. Biol., 2010)

PHAST and RPHAST: phylogenetic analysis with space/time models. - Melissa J. Hubisz; Katherine S. Pollard; Adam C. Siepel (Briefings Bioinform., 2011)

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)

PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP. - Ritika Ramani; Katie Krumholz; Yi-Fei Huang 004; Adam C. Siepel (Bioinform., 2019)

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)