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Daniel R Caffrey PHD

TitleAssociate Professor
InstitutionUMass Chan Medical School
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DivisionInfectious Diseases

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBioinformatics and Computational Biology

    Collapse Biography 
    Collapse education and training
    Maynooth University, Maynooth, , IrelandBSBiology & Computer Science
    Trinity College, Dublin, , IrelandPHDBiochemistry

    Collapse Overview 
    Collapse overview

    Daniel Caffrey received his BSc in Biology and Computer Science from Maynooth University in 1997.  He received his PhD from Trinity College Dublin in 2002 where he conducted his research in the laboratories of Professor Denis Shields (RCSI) and Professor Luke O’Neill (TCD).  During his PhD studies, he leveraged both computational and experimental methods to study the evolution and function of the MAP kinase pathways in IL1-activated cells. He joined Pfizer in 2002, where he developed various methods to discover and optimize drugs for different gene families.  During this period, he was also an adjunct faculty member at Brandeis University and subsequently the chair of the Brandeis Bioinformatics Program from 2008 to 2014.  Since joining the University of Massachusetts Medical School in 2010, his research has focused on the use of genomic and computational methods to investigate various aspects of the immune response and host-pathogen interactions.

    Research Interests

    • The evolution and function of host-virus interactions.
    • The structural principles associated with the evolution of host-virus interactions. 
    • The evolution and function of innate immune genes.



    Pfaat (pronounced Pea-fat) was developed to analyze the evolution, structure, and function of proteins.







    Complete List of Publications (Google Scholar)



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    Pleas e-mail Daniel Caffrey if you are interested in rotations.

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Chen Y, Lei X, Jiang Z, Humphries F, Parsi KM, Mustone NJ, Ramos I, Mutetwa T, Fernandez-Sesma A, Maehr R, Caffrey DR, Fitzgerald KA. Cellular nucleic acid-binding protein restricts SARS-CoV-2 by regulating interferon and disrupting RNA-protein condensates. Proc Natl Acad Sci U S A. 2023 Nov 21; 120(47):e2308355120. PMID: 37963251.
      Citations:    Fields:    Translation:AnimalsCells
    2. Crabtree JN, Caffrey DR, de Souza Silva L, Kurt-Jones EA, Dobbs K, Dent A, Fitzgerald KA, Golenbock DT. Lymphocyte crosstalk is required for monocyte-intrinsic trained immunity to Plasmodium falciparum. J Clin Invest. 2022 06 01; 132(11). PMID: 35642634.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    3. Sciabola S, Xi H, Cruz D, Cao Q, Lawrence C, Zhang T, Rotstein S, Hughes JD, Caffrey DR, Stanton RV. PFRED: A computational platform for siRNA and antisense oligonucleotides design. PLoS One. 2021; 16(1):e0238753. PMID: 33481821.
      Citations: 12     Fields:    
    4. Tzeng TC, Hasegawa Y, Iguchi R, Cheung A, Caffrey DR, Thatcher EJ, Mao W, Germain G, Tamburro ND, Okabe S, Heneka MT, Latz E, Futai K, Golenbock DT. Inflammasome-derived cytokine IL18 suppresses amyloid-induced seizures in Alzheimer-prone mice. Proc Natl Acad Sci U S A. 2018 09 04; 115(36):9002-9007. PMID: 30127003.
      Citations: 26     Fields:    Translation:AnimalsCells
    5. Canale AS, Venev SV, Whitfield TW, Caffrey DR, Marasco WA, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Zeldovich KB, Wang JP, Bolon DNA. Synonymous Mutations at the Beginning of the Influenza A Virus Hemagglutinin Gene Impact Experimental Fitness. J Mol Biol. 2018 04 13; 430(8):1098-1115. PMID: 29466705.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    6. Paik D, Monahan A, Caffrey DR, Elling R, Goldman WE, Silverman N. SLC46 Family Transporters Facilitate Cytosolic Innate Immune Recognition of Monomeric Peptidoglycans. J Immunol. 2017 07 01; 199(1):263-270. PMID: 28539433.
      Citations: 22     Fields:    Translation:HumansAnimalsCells
    7. Kalantari P, Harandi OF, Agarwal S, Rus F, Kurt-Jones EA, Fitzgerald KA, Caffrey DR, Golenbock DT. miR-718 represses proinflammatory cytokine production through targeting phosphatase and tensin homolog (PTEN). J Biol Chem. 2017 04 07; 292(14):5634-5644. PMID: 28209713.
      Citations: 24     Fields:    Translation:HumansAnimalsCells
    8. Atianand MK, Caffrey DR, Fitzgerald KA. Immunobiology of Long Noncoding RNAs. Annu Rev Immunol. 2017 04 26; 35:177-198. PMID: 28125358.
      Citations: 238     Fields:    Translation:HumansAnimals
    9. Atianand MK, Hu W, Satpathy AT, Shen Y, Ricci EP, Alvarez-Dominguez JR, Bhatta A, Schattgen SA, McGowan JD, Blin J, Braun JE, Gandhi P, Moore MJ, Chang HY, Lodish HF, Caffrey DR, Fitzgerald KA. A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation. Cell. 2016 Jun 16; 165(7):1672-1685. PMID: 27315481.
      Citations: 235     Fields:    Translation:HumansAnimalsCells
    10. Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayll?n N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calder?n GI, Grabowski JM, Jiang D, Khalil SMS, Kim D, Kocan KM, Koci J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, S?nchez-Gracia A, Severo MS, Silverman N, ?imo L, Tojo M, Tornador C, Van Zee JP, V?zquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJP, Park Y, Rozas J, Benton R, Pedra JHF, Nelson DR, Unger MF, Tubio JMC, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA. Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nat Commun. 2016 Feb 09; 7:10507. PMID: 26856261.
      Citations: 225     Fields:    Translation:AnimalsCellsPHPublic Health
    11. Kim EZ, Wespiser AR, Caffrey DR. The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs. RNA. 2016 Feb; 22(2):254-64. PMID: 26654912.
      Citations: 16     Fields:    Translation:HumansCells
    12. Jiang L, Liu P, Bank C, Renzette N, Prachanronarong K, Yilmaz LS, Caffrey DR, Zeldovich KB, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Bolon DNA. A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance. J Mol Biol. 2016 Feb 13; 428(3):538-553. PMID: 26656922.
      Citations: 20     Fields:    Translation:HumansAnimalsCells
    13. Chan J, Atianand M, Jiang Z, Carpenter S, Aiello D, Elling R, Fitzgerald KA, Caffrey DR. Cutting Edge: A Natural Antisense Transcript, AS-IL1a, Controls Inducible Transcription of the Proinflammatory Cytokine IL-1a. J Immunol. 2015 Aug 15; 195(4):1359-63. PMID: 26179904.
      Citations: 58     Fields:    Translation:AnimalsCells
    14. Zeldovich KB, Liu P, Renzette N, Foll M, Pham ST, Venev SV, Gallagher GR, Bolon DN, Kurt-Jones EA, Jensen JD, Caffrey DR, Schiffer CA, Kowalik TF, Wang JP, Finberg RW. Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment. Mol Biol Evol. 2015 Jun; 32(6):1519-32. PMID: 25713211.
      Citations: 10     Fields:    Translation:AnimalsCells
    15. Foll M, Poh YP, Renzette N, Ferrer-Admetlla A, Bank C, Shim H, Malaspinas AS, Ewing G, Liu P, Wegmann D, Caffrey DR, Zeldovich KB, Bolon DN, Wang JP, Kowalik TF, Schiffer CA, Finberg RW, Jensen JD. Influenza virus drug resistance: a time-sampled population genetics perspective. PLoS Genet. 2014 Feb; 10(2):e1004185. PMID: 24586206.
      Citations: 70     Fields:    Translation:HumansCells
    16. Severa M, Islam SA, Waggoner SN, Jiang Z, Kim ND, Ryan G, Kurt-Jones E, Charo I, Caffrey DR, Boyartchuk VL, Luster AD, Fitzgerald KA. The transcriptional repressor BLIMP1 curbs host defenses by suppressing expression of the chemokine CCL8. J Immunol. 2014 Mar 01; 192(5):2291-304. PMID: 24477914.
      Citations: 19     Fields:    Translation:AnimalsCells
    17. Fitzgerald KA, Caffrey DR. Long noncoding RNAs in innate and adaptive immunity. Curr Opin Immunol. 2014 Feb; 26:140-6. PMID: 24556411.
      Citations: 108     Fields:    Translation:HumansAnimalsCells
    18. Li HJ, Johnston B, Aiello D, Caffrey DR, Giel-Moloney M, Rindi G, Leiter AB. Distinct cellular origins for serotonin-expressing and enterochromaffin-like cells in the gastric corpus. Gastroenterology. 2014 Mar; 146(3):754-764.e3. PMID: 24316261.
      Citations: 24     Fields:    Translation:AnimalsCells
    19. Renzette N, Caffrey DR, Zeldovich KB, Liu P, Gallagher GR, Aiello D, Porter AJ, Kurt-Jones EA, Bolon DN, Poh YP, Jensen JD, Schiffer CA, Kowalik TF, Finberg RW, Wang JP. Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. J Virol. 2014 Jan; 88(1):272-81. PMID: 24155392.
      Citations: 27     Fields:    Translation:AnimalsCells
    20. Bossaller L, Rathinam VA, Bonegio R, Chiang PI, Busto P, Wespiser AR, Caffrey DR, Li QZ, Mohan C, Fitzgerald KA, Latz E, Marshak-Rothstein A. Overexpression of membrane-bound fas ligand (CD95L) exacerbates autoimmune disease and renal pathology in pristane-induced lupus. J Immunol. 2013 Sep 01; 191(5):2104-14. PMID: 23918976.
      Citations: 12     Fields:    Translation:AnimalsCells
    21. Marinotti O et al. The genome of Anopheles darlingi, the main neotropical malaria vector. Nucleic Acids Res. 2013; 41(15):7387-400.
    22. Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL, Byron M, Monks B, Henry-Bezy M, Lawrence JB, O'Neill LA, Moore MJ, Caffrey DR, Fitzgerald KA. A long noncoding RNA mediates both activation and repression of immune response genes. Science. 2013 Aug 16; 341(6147):789-92. PMID: 23907535.
      Citations: 514     Fields:    Translation:AnimalsCells
    23. 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 Bde A, Ribeiro CA, Nunes-Silva CG, de Carvalho CR, Soares CM, de Menezes CB, Matiolli C, Caffrey D, Ara?jo DA, de Oliveira DM, Golenbock D, Grisard EC, Fantinatti-Garboggini F, de Carvalho FM, Barcellos FG, Prosdocimi F, May G, Azevedo Junior GM, Guimar?es GM, Goldman GH, Padilha IQ, Batista Jda S, Ferro JA, Ribeiro JM, Fietto JL, Dabbas KM, Cerdeira L, Agnez-Lima LF, Brocchi M, de Carvalho MO, Teixeira Mde M, Diniz Maia Mde M, Goldman MH, Cruz Schneider MP, Felipe MS, Hungria M, Nicol?s MF, Pereira M, Montes MA, Cant?o ME, Vincentz M, Rafael MS, Silverman N, Stoco PH, Souza RC, Vicentini R, Gazzinelli RT, Neves Rde O, Silva R, Astolfi-Filho S, Maciel TE, Urm?nyi TP, Tadei WP, Camargo EP, de Vasconcelos AT. The genome of Anopheles darlingi, the main neotropical malaria vector. Nucleic Acids Res. 2013 Aug; 41(15):7387-400. PMID: 23761445.
      Citations: 62     Fields:    Translation:AnimalsCellsPHPublic Health
    24. Ermler ME, Yerukhim E, Schriewer J, Schattgen S, Traylor Z, Wespiser AR, Caffrey DR, Chen ZJ, King CH, Gale M, 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. J Virol. 2013 May; 87(9):4846-60. PMID: 23408632.
      Citations: 17     Fields:    Translation:HumansAnimalsCells
    25. Aiello D, Caffrey DR. Evolution of specific protein-protein interaction sites following gene duplication. J Mol Biol. 2012 Oct 19; 423(2):257-72. PMID: 22789570.
      Citations: 5     Fields:    Translation:Cells
    26. Caffrey DR, Fitzgerald KA. Immunology. Select inflammasome assembly. Science. 2012 Apr 27; 336(6080):420-1. PMID: 22539706.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    27. Caffrey DR, Zhao J, Song Z, Schaffer ME, Haney SA, Subramanian RR, Seymour AB, Hughes JD. siRNA off-target effects can be reduced at concentrations that match their individual potency. PLoS One. 2011; 6(7):e21503. PMID: 21750714.
      Citations: 43     Fields:    Translation:HumansCells
    28. 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. 2009 Mar 26; 458(7237):514-8. PMID: 19158675.
      Citations: 1229     Fields:    Translation:HumansAnimalsCells
    29. Caffrey DR, Lunney EA, Moshinsky DJ. Prediction of specificity-determining residues for small-molecule kinase inhibitors. BMC Bioinformatics. 2008 Nov 25; 9:491. PMID: 19032760.
      Citations: 7     Fields:    Translation:HumansCells
    30. 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. 2007 Oct 11; 8:381. PMID: 17931421.
      Citations: 37     Fields:    Translation:Cells
    31. 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. 2007 Jan; 25(1):71-5. PMID: 17211405.
      Citations: 217     Fields:    Translation:Cells
    32. Lauw FN, Caffrey DR, Golenbock DT. Of mice and man: TLR11 (finally) finds profilin. Trends Immunol. 2005 Oct; 26(10):509-11. PMID: 16111920.
      Citations: 38     Fields:    Translation:HumansAnimalsCells
    33. Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci. 2004 Jan; 13(1):190-202. PMID: 14691234.
      Citations: 136     Fields:    Translation:Cells
    34. Fitzgerald KA, Rowe DC, Barnes BJ, Caffrey DR, Visintin A, Latz E, Monks B, Pitha PM, Golenbock DT. LPS-TLR4 signaling to IRF-3/7 and NF-kappaB involves the toll adapters TRAM and TRIF. J Exp Med. 2003 Oct 06; 198(7):1043-55. PMID: 14517278.
      Citations: 425     Fields:    Translation:HumansAnimalsCells
    35. Hokamp K, Shields DC, Wolfe KH, Caffrey DR. Wrapping up BLAST and other applications for use on Unix clusters. Bioinformatics. 2003 Feb 12; 19(3):441-2. PMID: 12584141.
      Citations: 2     Fields:    
    36. Caffrey DR, O'Neill LA, Shields DC. A method to predict residues conferring functional differences between related proteins: application to MAP kinase pathways. Protein Sci. 2000 Apr; 9(4):655-70. PMID: 10794408.
      Citations: 4     Fields:    Translation:Cells
    37. Caffrey DR, O'Neill LA, Shields DC. The evolution of the MAP kinase pathways: coduplication of interacting proteins leads to new signaling cascades. J Mol Evol. 1999 Nov; 49(5):567-82. PMID: 10552038.
      Citations: 39     Fields:    Translation:AnimalsCells
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