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Daniel Caffrey

Daniel Caffrey
Email: dcaffrey@brandeis.edu

Degrees:

Trinity College Dublin, Ph.D.
National University of Ireland, B.S.
Trinity College Dublin, Cert.

Courses:

  • RBIF 101
    Structural Bioinformatics

Publications:

  • 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.

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

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