Casey M. Bergman

According to our database, Casey M. Bergman authored at least 17 papers between 2004 and 2012.

Collaborative distances:

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

2012

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

2011

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in <i>Drosophila</i>.

Steven M. Gallo, Dave T. Gerrard, David Miner, Michael Simich, Benjamin Des Soye, Casey M. Bergman, Marc S. Halfon

Nucleic Acids Res., 2011

The GNAT library for local and remote gene mention normalization.

Jörg Hakenberg, Martin Gerner, Maximilian Haeussler, Illés Solt, Conrad Plake, Michael Schroeder, Graciela Gonzalez, Goran Nenadic, Casey M. Bergman

Bioinform., 2011

Annotating genes and genomes with DNA sequences extracted from biomedical articles.

Maximilian Haeussler, Martin Gerner, Casey M. Bergman

Bioinform., 2011

2010

LINNAEUS: A species name identification system for biomedical literature.

Martin Gerner, Goran Nenadic, Casey M. Bergman

BMC Bioinform., 2010

An Exploration of Mining Gene Expression Mentions and Their Anatomical Locations from Biomedical Text.

Martin Gerner, Goran Nenadic, Casey M. Bergman

Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, 2010

2009

Assigning roles to protein mentions: The case of transcription factors.

Hui Yang, John A. Keane, Casey M. Bergman, Goran Nenadic

J. Biomed. Informatics, 2009

2008

REDfly 2.0: an integrated database of <i>cis</i>-regulatory modules and transcription factor binding sites in <i>Drosophila</i>.

Marc S. Halfon, Steven M. Gallo, Casey M. Bergman

Nucleic Acids Res., 2008

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, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter J. De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth W. Wasserman, Ross C. Hardison, Casey M. Bergman, Steven J. M. Jones

Nucleic Acids Res., 2008

2007

Large-Scale Discovery of Promoter Motifs in <i>Drosophila melanogaster</i>.

Thomas A. Down, Casey M. Bergman, Jing Su, Tim J. P. Hubbard

PLoS Comput. Biol., 2007

Discovering and detecting transposable elements in genome sequences.

Casey M. Bergman, Hadi Quesneville

Briefings Bioinform., 2007

2006

Identifying <i>cis</i>-regulatory modules by combining comparative and compositional analysis of DNA.

Nora Pierstorff, Casey M. Bergman, Thomas Wiehe

Bioinform., 2006

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

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

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

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

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