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1.
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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.
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2.
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Aiello D, Caffrey DR. Evolution of specific protein-protein interaction sites following gene duplication. J Mol Biol. 2012 Oct 19; 423(2):257-72.
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3.
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Caffrey DR, Fitzgerald KA. Immunology. Select inflammasome assembly. Science. 2012 Apr 27; 336(6080):420-1.
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4.
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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.
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5.
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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.
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6.
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Caffrey DR, Lunney EA, Moshinsky DJ. Prediction of specificity-determining residues for small-molecule kinase inhibitors. BMC Bioinformatics. 2008; 9:491.
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7.
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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; 8:381.
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8.
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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.
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9.
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Lauw FN, Caffrey DR, Golenbock DT. Of mice and man: TLR11 (finally) finds profilin. Trends Immunol. 2005 Oct; 26(10):509-11.
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10.
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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.
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11.
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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 6; 198(7):1043-55.
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12.
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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.
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13.
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Cotter PJ, Caffrey DR, Shields DC. Improved database searches for orthologous sequences by conditioning on outgroup sequences. Bioinformatics. 2002 Jan; 18(1):83-91.
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14.
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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.
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15.
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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.
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