Casey M. Bergman

Martin Gerner, Farzaneh Sarafraz, Casey M. Bergman, Goran Nenadic: BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events. Bioinformatics 28(16): 2154-2161 (2012)

Maximilian Haeussler, Martin Gerner, Casey M. Bergman: Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics 27(7): 980-986 (2011)

Jörg Hakenberg, Martin Gerner, Maximilian Haeussler, Illés Solt, Conrad Plake, Michael Schroeder, Graciela Gonzalez, Goran Nenadic, Casey M. Bergman: The GNAT library for local and remote gene mention normalization. Bioinformatics 27(19): 2769-2771 (2011)

Steven M. Gallo, Dave T. Gerrard, David Miner, Michael Simich, Benjamin Des Soye, Casey M. Bergman, Marc S. Halfon: REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Research 39(Database-Issue): 118-123 (2011)

Martin Gerner, Goran Nenadic, Casey M. Bergman: LINNAEUS: A species name identification system for biomedical literature. BMC Bioinformatics 11: 85 (2010)

Hui Yang, John A. Keane, Casey M. Bergman, Goran Nenadic: Assigning roles to protein mentions: The case of transcription factors. Journal of Biomedical Informatics 42(5): 887-894 (2009)

Obi L. Griffith, Stephen 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: ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research 36(Database-Issue): 107-113 (2008)

Marc S. Halfon, Steven M. Gallo, Casey M. Bergman: REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Research 36(Database-Issue): 594-598 (2008)

Casey M. Bergman, Hadi Quesneville: Discovering and detecting transposable elements in genome sequences. Briefings in Bioinformatics 8(6): 382-392 (2007)

Thomas A. Down, Casey M. Bergman, Jing Su, Tim J. P. Hubbard: Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster. PLoS Computational Biology 3(1) (2007)

Stephen Montgomery, Obi L. Griffith, Monica C. Sleumer, Casey M. Bergman, Misha Bilenky, Erin Pleasance, Y. Prychyna, X. Zhang, Steven J. M. Jones: ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics 22(5): 637-640 (2006)

Nora Pierstorff, Casey M. Bergman, Thomas Wiehe: Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. Bioinformatics 22(23): 2858-2864 (2006)

Casey M. Bergman, Joseph W. Carlson, Susan E. Celniker: Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics 21(8): 1747-1749 (2005)

Hadi Quesneville, Casey M. Bergman, Olivier Andrieu, Delphine Autard, Danielle Nouaud, Michael Ashburner, Dominique Anxolabéhère: Combined Evidence Annotation of Transposable Elements in Genome Sequences. PLoS Computational Biology 1(2) (2005)

Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 5: 6 (2004)

Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen: Correction: Benchmarking tools for the alignment of functional noncodingDNA. BMC Bioinformatics 5: 73 (2004)