J. Gregory Caporaso

Search for my publications on PubMed.

Peer-reviewed articles

1. Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics. J. Gregory Caporaso, Sandra Smit, Brett C. Easton, Lawrence Hunter, Gavin A. Huttley, and Rob Knight. BMC Evolutionary Biology, December, 2008. PDF
2. Concept recognition for extracting protein interaction relations from biomedical text; William A. Baumgartner, Jr., Zhiyong Lu, Helen L. Johnson, J. Gregory Caporaso, Jesse Paquette, Anna Lindemann, Elizabeth K. White, Olga Medvedeva, K. Bretonnel Cohen, and Lawrence Hunter; Genome Biology 2008, 9(Suppl 2):S9 doi:10.1186/gb-2008-9-s2-s9. Open Access Text
3. Intrinsic evaluation of text mining tools may not predict performance on realistic tasks; J. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, and Lawrence Hunter; Pacific Symposium on Biocomputing 13:640-651(2008). PDF
4. PyCogent: a toolkit for making sense from sequence; Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J. Gregory Caporaso, Brett C. Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymon Sammut, Sandra Smit, Matthew J. Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying, and Gavin A. Huttley; Genome Biology 2007, 8:R171; doi:10.1186/gb-2007-8-8-r171. Abstract Open Access Text PyCogent downloads
5. Rapid pattern development for concept recognition systems: application to point mutations; J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter; J Bioinform Comput Biol. 2007 Dec;5(6):1233-59. doi:10.1142/S0219720007003144. PDF
6. MutationFinder: A high-performance system for extracting point mutation mentions from text; J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter; Bioinformatics, 2007 23(14):1862-1865; doi: 10.1093/bioinformatics/btm235; Abstract Open Access Text MutationFinder downloads
7. Error Minimization and Coding Triplet/Binding Site Associations are Independent Features of the Canonical Genetic Code; J. Gregory Caporaso, Michael Yarus, and Rob Knight; Journal of Molecular Evolution, 2005; Abstract
8. Origins of the Genetic Code: The Escaped Triplet Theory; Michael Yarus, J. Gregory Caporaso, Rob Knight; Annual Reviews of Biochemistry, 2005; Abstract

Non-peer-reviewed articles

1. Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question Answering; J. Gregory Caporaso, William A. Baumgartner Jr., Hyun-min Kim, Zhiyong Lu, Helen L. Johnson, Olga Medvedeva, Anna Lindemann, Lynne M. Fox, Elizabeth K. White, K. Bretonnel Cohen, and Lawrence Hunter; In TREC 2006 Proceedings, 2006; PDF
2. Concept recognition and the TREC Genomics tasks; J. Gregory Caporaso, William A. Baumgartner Jr., K. Bretonnel Cohen, Helen L. Johnson, Jesse Paquette, and Lawrence Hunter; In The Fourteenth Text REtrieval Conference (TREC 2005) Proceedings, 2005; PDF