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 evolution, lncRNAs, and host-pathogen interactions.

Profile

Daniel Caffrey, PhD, is an Assistant Professor at the University of Massachusetts Medical School. His current research interests include: Evolution - Host-pathogen interactions - lncRNA - Systems Biology of the immune Response

Courses Taught

RBIF	101	Structural Bioinformatics
RBIF	109	Biological Sequence Analysis

Scholarship

Bossaller L, Rathinam VAK, Bonegio R, Chiang PI, Busto P, Wespiser AR, Caffrey DR, Li QZ, Mohan , Fitzgerald KA, Latz E, Marshak-Rothstein A. "Overexpression of Membrane-Bound Fas Ligand (CD95L) Exacerbates Autoimmune Disease and Renal Pathology in Pristane-Induced Lupus." The Journal of Immunology 191. 5 (2013): 2104-2114.

Carpenter S, Aiello D, Atianand M, Ricci E, Gandhi P , Halli LL, Byron M, Monks B, Henry-Bezy M, O'Neill LAJ, Lawrence JB, Moore MJ, Caffrey DR, Fitzgerald KA. "A long noncoding RNA mediates both activation and repression of immune response genes." Science 341. 6147 (2013): 789-792.

Ermler ME, Yerukhim E, Schriewer J, Schattgen S, Traylor Z, Wespiser AR, Caffrey DR, Chen ZJ, King CH, Gale M Jr, Colonna M, Fitzgerald KA, Buller RM, Hise AG.. "RNA helicase signaling is critical for type I interferon production and protection against Rift Valley fever virus during mucosal challenge." JVI 87. 9 (2013): 4846.

Marinotti O, Cerqueira GC, de Almeida LG, Ferro MI, Loreto EL, Zaha A, Teixeira SM, Wespiser AR, Almeida E Silva A, Schlindwein AD, Pacheco AC, Silva AL, Graveley BR, Walenz BP, Lima BD, Ribeiro CA, Nunes-Silva CG, de Carvalho CR, Soares CM, de Menezes C. "The Genome of Anopheles darlingi, the main neotropical malaria vector." NAR 41. 15 (2013): 7387-7400.

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.