Benchmarking tools for the alignment of functional noncoding DNA. - Daniel A. Pollard; Casey M. Bergman; Jens Stoye; Susan E. Celniker; Michael B. Eisen (BMC Bioinform., 2004)

Correction: Benchmarking tools for the alignment of functional noncodingDNA. - Daniel A. Pollard; Casey M. Bergman; Jens Stoye; Susan E. Celniker; Michael B. Eisen (BMC Bioinform., 2004)

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. - Casey M. Bergman; Joseph W. Carlson; Susan E. Celniker (Bioinform., 2005)

Combined Evidence Annotation of Transposable Elements in Genome Sequences. - Hadi Quesneville; Casey M. Bergman; Olivier Andrieu; Delphine Autard; Danielle Nouaud; Michael Ashburner; Dominique Anxolabéhère (PLoS Comput. Biol., 2005)

ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. - Stephen B. Montgomery; Obi L. Griffith; Monica C. Sleumer; Casey M. Bergman; Misha Bilenky; Erin Pleasance; Y. Prychyna; X. Zhang; Steven J. M. Jones (Bioinform., 2006)

Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. - Nora Pierstorff; Casey M. Bergman; Thomas Wiehe (Bioinform., 2006)

Discovering and detecting transposable elements in genome sequences. - Casey M. Bergman; Hadi Quesneville (Briefings Bioinform., 2007)

Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster. - Thomas A. Down; Casey M. Bergman; Jing Su; Tim J. P. Hubbard (PLoS Comput. Biol., 2007)

ORegAnno: an open-access community-driven resource for regulatory annotation. - Obi L. Griffith; Stephen B. Montgomery; Bridget Bernier; Bryan Chu; Katayoon Kasaian; Stein Aerts; Shaun Mahony; Monica C. Sleumer; Mikhail Bilenky; Maximilian Haeussler; Malachi Griffith; Steven M. Gallo; et al. (Nucleic Acids Res., 2008)

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. - Marc S. Halfon; Steven M. Gallo; Casey M. Bergman (Nucleic Acids Res., 2008)

Assigning roles to protein mentions: The case of transcription factors. - Hui Yang 004; John A. Keane; Casey M. Bergman; Goran Nenadic (J. Biomed. Informatics, 2009)

An Exploration of Mining Gene Expression Mentions and Their Anatomical Locations from Biomedical Text. - Martin Gerner; Goran Nenadic; Casey M. Bergman (BioNLP@ACL, 2010)

LINNAEUS: A species name identification system for biomedical literature. - Martin Gerner; Goran Nenadic; Casey M. Bergman (BMC Bioinform., 2010)

Annotating genes and genomes with DNA sequences extracted from biomedical articles. - Maximilian Haeussler; Martin Gerner; Casey M. Bergman (Bioinform., 2011)

The GNAT library for local and remote gene mention normalization. - Jörg Hakenberg; Martin Gerner; Maximilian Haeussler; Illés Solt; Conrad Plake; Michael Schroeder 001; Graciela Gonzalez 001; Goran Nenadic; Casey M. Bergman (Bioinform., 2011)

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. - Steven M. Gallo; Dave T. Gerrard; David Miner; Michael Simich; Benjamin Des Soye; Casey M. Bergman; Marc S. Halfon (Nucleic Acids Res., 2011)

BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events. - Martin Gerner; Farzaneh Sarafraz; Casey M. Bergman; Goran Nenadic (Bioinform., 2012)