Faculty Guide

Title

Program Chair for the Bioinformatics Program and Instructor in the Rabb School of Continuing Studies, Division of Graduate Professional Studies

Rabb School of Continuing Studies, Division of Graduate Professional Studies

Expertise

Daniel Caffrey, Ph.D. specializes in genome and protein evolution.

Profile

Daniel Caffrey, PhD, is an Assistant Professor at the University of Massachusetts Medical School. His research interests include protein evolution, genome analysis, protein-drug interactions, protein-protein interactions, and systems biology of the immune response. He is the project leader for PFAAT, a popular bioinformatics application. He is the Academic
Chair of the Bioinformatics program.

Courses Taught

RBIF	101	Structural Bioinformatics
RBIF	109	Biological Sequence Analysis

Scholarship

Aiello Daniel Caffrey, Daniel. "Evolution of Specific Protein-Protein Interaction Sites Following Gene Duplication." JMB 423. 2 (2012): 257-272.

Caffrey DR, Zhao J, Song Z, Schaffer ME, Haney S, Subramanian RR, Seymour AB, Hughes JD. "siRNA off-target effects can be reduced at concentrations that match their individual potency." PLoS one 6. 7 (2012): e21503.

Caffrey, Daniel. "Select inflammasome assembly." Science 336. 6080 (2012): 420-421.

Hornung V, Ablasser A, Charrel-Dennis M, Bauernfeind F, Horvath G, Caffrey DR, Latz E, Fitzgerald KA. "AIM2 recognizes cytosolic dsDNA and forms a caspase-1-activating inflammasome with ASC." Nature 458. 7237 (2009): 514-8.

Caffrey DR, Lunney EA, Moshinsky DJ.. "Prediction of specificity-determining residues for small-molecule kinase inhibitors.." BMC Bioinformatics 9. (2008): 491.

Caffrey DR, Dana PH, Mathur V, Ocano M, Hong EJ, Wang YE, Somaroo S, Caffrey BE, Potluri S, Huang ES.. "PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments.." BMC Bioinformatics 8. (2007): 381.

Cheng AC, Coleman RG, Smyth KT, Cao Q, Soulard P, Caffrey DR, Salzberg AC, Huang ES.. "Structure-based maximal affinity model predicts small-molecule druggability.." Nat Biotechnol 25. 1 (2007): 71-5.

Lauw FN, Caffrey DR, Golenbock DT. "Of mice and man: TLR11 (finally) finds profilin.." Trends Immunol (2005).

Caffrey, DR., Somaroo, S., Hughes, JH., Mintseris, J., and Huang ES, D.R. Caffrey S.Somaroo, J. Hughes, J.Mintseris, and E.Huang. "Are Protein-Protein Interfaces More Conserved in Sequence than the Rest of the Protein Surface?." Protein Science 13. 1 (2004): 190-189.

Fitzgerald, KA., Rowe DC., Branes BJ., Caffrey, DR., Visintin A., Latz E., Monks, B., Pitha, PM., and Golenbock, DT, K. Fitzgerald, D.Rowe , B. Barnes, A. Visintin, E. Latz, B. Monks, P.Pitha and D.Golenbock. "LPS-TLR-4 Signaling to IRF-3/7 and NF-kB Involves the Toll Adapters TRAM and TRIF." Journal of Experimental Medicine 198. 7 (2003): 1043-1055.

Hokamp K., Shields DC., Wolfe KH., and Caffrey, DR. "Wrapping Up BLAST and Other Applicaitions for Use on Unix Clusters." Bionformatics 19. 3 (2003): 441-2.

Cotter, PJ., Caffrey DR., and Shields, DC. "Improved Database Searches for Orthoglogous Sequences by Conditioning on Outgroup Sequences." Bionformatics 18. 1 (2002): 83-91.

Caffrey, DR., O'Neill, LAJ., and Shields, DC. "A Method to Predict Residues Conferring Functional Differences Between Related Proteins: Applications to MAP Kinase Pathways." Protein Science 9. 4 (2000): 655-70.

Caffrey, DR., O'Neill, LAJ, and Shields DC. "The Evolution of the MAP Kinase Pathways: Coduplication of Interacting Proteins Leads to New Signaling Cascades.." Journal of Molecular Evolution 49. 5 (1996): 567-82.