Lawrence Hunter, Ph.D.
Bada M, Hunter L. Enrichment of OBO Ontologies.
J Biomed Inform. 2006 Jul 26; [Epub ahead of print]
http://dx.doi.org/10.1016/j.jbi.2006.07.003

Hunter L, Cohen KB. Biomedical language processing: what's beyond PubMed?
Mol Cell. 2006 Mar 3;21(5):589-94.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1702322

Lawrence Hunter, Zhiyong Lu, James Firby, William A Baumgartner Jr., Helen L Johnson, Philip V Ogren and K Brettonel Cohen. OpenDMAP: An open-source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-specific gene expression. BMC Bioinformatics 2008, 9:78

http://www.biomedcentral.com/1471-2105/9/78

http://www.ncbi.nlm.nih.gov/pubmed/18237434

Harvell DM, Spoelstra NS, Singh M, McManaman JL, Finlayson C, Phang T, Trapp S, Hunter L, Dye WW, Borges VF, Elias A, Horwitz KB, Richer JK.  Molecular signatures of neoadjuvant endocrine therapy for breast cancer:  Chacterisitics of response or intrinsic resistance.  Breast Cancer Res Treat. 2008 Mar 9  PMID:18327671

Baumgartner, WA Jr, Cohen KB, Hunter L. An Open-Source Framework for large-scale, flexible evaluation of biomedical text mining systems.  J Biomed Discov Collab.  2008 Jan 29;3(1):1   PMID:18230184

Caporaso JG, Deshpande N, Fink JL, Bourne PE, Cohen KB, Hunter L.  Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Synp Biocomputi.  2008;:640-51. PMID: 18229722

Cohen, KB, Hunter L.  Getting started in text mining.  PLoS Comput Biol.  2008 Jan;4(1):e20.  PMID:  18225946

Caporaso JG, Baumgartner WA, Randolph DA, Cohen KB, Hunter L.  Rapid pattern development for concept recognition systems:  application to point mutations.  J Bioinfomr Comput Biol.  2007 Dec;5(6): 1233-59.  PMID:  18172927

David Pollock, Ph.D.
Williams PD, Pollock DD, Blackburne BP, Goldstein RA.
Related Articles, Links (Free in PubMedCentral)
Assessing the accuracy of ancestral protein reconstruction methods.
PLoS Comput Biol. 2006 Jun 23;2(6):e69. Epub 2006 Jun 23.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1480538

Raina SZ, Faith JJ, Disotell TR, Seligmann H, Stewart CB, Pollock DD.
Related Articles, Links (Free in PMC)
Evolution of base-substitution gradients in primate mitochondrial genomes.
Genome Res. 2005 May;15(5):665-73.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1088294

Pollock DD, Larkin JC.
Related Articles, Links (Free in PMC)
Estimating the degree of saturation in mutant screens.
Genetics. 2004 Sep;168(1):489-502.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1448089
 

Debra Goldberg, Ph.D.
DS Goldberg and FP Roth. Assessing experimentally derived interactions in a
small world, Proceedings of the National Academy of Sciences 100(8): 4372-4376
(2003).
http://www.cs.colorado.edu/~debra/papers/DSGoldberg_PNAS_2003.pdf

KC Gunsalus*, H Ge*, AJ Schetter*, DS Goldberg*, J-DJ Han, T Hao, N Bertin, N
Li, J Huang, L-S Chuang, R Mani, GF Berriz, AA Hyman, B Sönnichsen, CJ
Echeverri, FP Roth, M Vidal and F Piano. Predictive models of molecular
machines involved in C. elegans early embryogenesis. Nature 436(7052):861-865
(2005).
*These authors contributed equally to this work.
http://www.cs.colorado.edu/~debra/papers/nature_molecular_machines_05.pdf
Supplement: http://llama.med.harvard.edu/supplements/Gunsalus_Nature_2005/

Daniel Dvorkin, CBP Student

Li Ma, Daniel Dvorkin, John R. Garbe, and Yang Da. Genome-wide analysis of single-locus and epistasis single-nucleotide polymorphism effects on anti-cyclic citrullinated peptide as a measure of rheumatoid arthritis. BMC Proceedings, 1(Suppl 1):S127, 18 December 2007. http://www.biomedcentral.com/1753-6561/1/S1/S127