Casey M. Bergman

17 papers Journal 16Unranked 1
YearRankTypeTitle / Venue / Authors
2012 J jnl
BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events.
Bioinform.
Martin Gerner, Farzaneh Sarafraz, Casey M. Bergman, Goran Nenadic
2011 J jnl
Annotating genes and genomes with DNA sequences extracted from biomedical articles.
Bioinform.
Maximilian Haeussler, Martin Gerner, Casey M. Bergman
2011 J jnl
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in
Nucleic Acids Res.
Steven M. Gallo, Dave T. Gerrard, David Miner, Michael Simich, Benjamin Des Soye, Casey M. Bergman, Marc S. Halfon
2011 J jnl
The GNAT library for local and remote gene mention normalization.
Bioinform.
Jörg Hakenberg, Martin Gerner, Maximilian Haeussler, Illés Solt, Conrad Plake, Michael Schroeder, Graciela Gonzalez, Goran Nenadic, Casey M. Bergman
2010 — conf
An Exploration of Mining Gene Expression Mentions and Their Anatomical Locations from Biomedical Text.
BioNLP@ACL
Martin Gerner, Goran Nenadic, Casey M. Bergman
2010 J jnl
LINNAEUS: A species name identification system for biomedical literature.
BMC Bioinform.
Martin Gerner, Goran Nenadic, Casey M. Bergman
2009 J jnl
Assigning roles to protein mentions: The case of transcription factors.
J. Biomed. Informatics
Hui Yang, John A. Keane, Casey M. Bergman, Goran Nenadic
2008 J jnl
ORegAnno: an open-access community-driven resource for regulatory annotation.
Nucleic Acids Res.
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
2008 J jnl
REDfly 2.0: an integrated database of
Nucleic Acids Res.
Marc S. Halfon, Steven M. Gallo, Casey M. Bergman
2007 J jnl
Discovering and detecting transposable elements in genome sequences.
Briefings Bioinform.
Casey M. Bergman, Hadi Quesneville
2007 J jnl
Large-Scale Discovery of Promoter Motifs in
PLoS Comput. Biol.
Thomas A. Down, Casey M. Bergman, Jing Su, Tim J. P. Hubbard
2006 J jnl
Identifying
Bioinform.
Nora Pierstorff, Casey M. Bergman, Thomas Wiehe
2006 J jnl
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.
Bioinform.
Stephen B. Montgomery, Obi L. Griffith, Monica C. Sleumer, Casey M. Bergman, Misha Bilenky, Erin Pleasance, Y. Prychyna, X. Zhang, Steven J. M. Jones
2005 J jnl
Combined Evidence Annotation of Transposable Elements in Genome Sequences.
PLoS Comput. Biol.
Hadi Quesneville, Casey M. Bergman, Olivier Andrieu, Delphine Autard, Danielle Nouaud, Michael Ashburner, Dominique Anxolabéhère
2005 J jnl
Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.
Bioinform.
Casey M. Bergman, Joseph W. Carlson, Susan E. Celniker
2004 J jnl
Benchmarking tools for the alignment of functional noncoding DNA.
BMC Bioinform.
Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen
2004 J jnl
Correction: Benchmarking tools for the alignment of functional noncodingDNA.
BMC Bioinform.
Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen