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    Matthew Daugherty

    TitleAssistant Professor
    SchoolUniversity of California, San Diego
    DepartmentMolecular Biology
    Address9500 Gilman Drive #0377
    CA La Jolla 92093
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      Collapse Research 
      Collapse Research Activities and Funding
      Consequences of IFIT Gene Evolution on Species-Specific Antiviral Immunity
      NIH K22AI119017May 12, 2016 - Apr 30, 2018
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Moens U, Calvignac-Spencer S, Lauber C, Ramqvist T, Feltkamp MCW, Daugherty M, Verschoor EJ, Ehlers B. ICTV Virus Taxonomy Profile: Polyomaviridae. J Gen Virol. 2017 Jun; 98(6):1159-1160. PMID: 28640744.
        View in: PubMed
      2. Chavarría-Smith J, Mitchell PS, Ho AM, Daugherty M, Vance RE. Functional and Evolutionary Analyses Identify Proteolysis as a General Mechanism for NLRP1 Inflammasome Activation. PLoS Pathog. 2016 Dec; 12(12):e1006052. PMID: 27926929.
        View in: PubMed
      3. Daugherty M, Schaller AM, Geballe AP, Malik HS. Evolution-guided functional analyses reveal diverse antiviral specificities encoded by IFIT1 genes in mammals. Elife. 2016 May 31; 5. PMID: 27240734; PMCID: PMC4887208.
      4. Calvignac-Spencer S, Feltkamp MC, Daugherty M, Moens U, Ramqvist T, Johne R, Ehlers B. A taxonomy update for the family Polyomaviridae. Arch Virol. 2016 Jun; 161(6):1739-50. PMID: 26923930.
        View in: PubMed
      5. Chou S, Daugherty M, Peterson SB, Biboy J, Yang Y, Jutras BL, Fritz-Laylin LK, Ferrin MA, Harding BN, Jacobs-Wagner C, Yang XF, Vollmer W, Malik HS, Mougous JD. Transferred interbacterial antagonism genes augment eukaryotic innate immune function. Nature. 2015 Feb 05; 518(7537):98-101. PMID: 25470067; PMCID: PMC4713192.
      6. Daugherty M, Malik HS. How a virus blocks a cellular emergency access lane to the nucleus, STAT! Cell Host Microbe. 2014 Aug 13; 16(2):150-152. PMID: 25121743.
        View in: PubMed
      7. Daugherty M, Young JM, Kerns JA, Malik HS. Rapid evolution of PARP genes suggests a broad role for ADP-ribosylation in host-virus conflicts. PLoS Genet. 2014; 10(5):e1004403. PMID: 24875882; PMCID: PMC4038475.
      8. Tenthorey JL, Kofoed EM, Daugherty M, Malik HS, Vance RE. Molecular basis for specific recognition of bacterial ligands by NAIP/NLRC4 inflammasomes. Mol Cell. 2014 Apr 10; 54(1):17-29. PMID: 24657167; PMCID: PMC3988258.
      9. Carter JJ, Daugherty M, Qi X, Bheda-Malge A, Wipf GC, Robinson K, Roman A, Malik HS, Galloway DA. Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes. Proc Natl Acad Sci U S A. 2013 Jul 30; 110(31):12744-9. PMID: 23847207; PMCID: PMC3732942.
      10. Daugherty M, Malik HS. Rules of engagement: molecular insights from host-virus arms races. Annu Rev Genet. 2012; 46:677-700. PMID: 23145935.
        View in: PubMed
      11. Wang H, Ma X, Yeh YS, Zhu Y, Daugherty M, Frankel AD, Musier-Forsyth K, Barbara PF. Comparative analysis of RNA/protein dynamics for the arginine-rich-binding motif and zinc-finger-binding motif proteins encoded by HIV-1. Biophys J. 2010 Nov 17; 99(10):3454-62. PMID: 21081095; PMCID: PMC2980704.
      12. Daugherty M, Liu B, Frankel AD. Structural basis for cooperative RNA binding and export complex assembly by HIV Rev. Nat Struct Mol Biol. 2010 Nov; 17(11):1337-42. PMID: 20953181; PMCID: PMC2988976.
      13. Daugherty M, Booth DS, Jayaraman B, Cheng Y, Frankel AD. HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes. Proc Natl Acad Sci U S A. 2010 Jul 13; 107(28):12481-6. PMID: 20616058; PMCID: PMC2906596.
      14. Daugherty M, D'Orso I, Frankel AD. A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA. Mol Cell. 2008 Sep 26; 31(6):824-34. PMID: 18922466; PMCID: PMC2651398.
      15. Fuhrmann CN, Daugherty M, Agard DA. Subangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis. J Am Chem Soc. 2006 Jul 19; 128(28):9086-102. PMID: 16834383.
        View in: PubMed
      16. Mills NL, Daugherty M, Frankel AD, Guy RK. An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction. J Am Chem Soc. 2006 Mar 22; 128(11):3496-7. PMID: 16536504; PMCID: PMC2566309.
      17. Landt SG, Ramirez A, Daugherty M, Frankel AD. A simple motif for protein recognition in DNA secondary structures. J Mol Biol. 2005 Sep 02; 351(5):982-94. PMID: 16055152.
        View in: PubMed
      18. Lloyd-Smith JO, Cross PC, Briggs CJ, Daugherty M, Getz WM, Latto J, Sanchez MS, Smith AB, Swei A. Should we expect population thresholds for wildlife disease? Trends Ecol Evol. 2005 Sep; 20(9):511-9. PMID: 16701428.
        View in: PubMed
      19. Calabro V, Daugherty M, Frankel AD. A single intermolecular contact mediates intramolecular stabilization of both RNA and protein. Proc Natl Acad Sci U S A. 2005 May 10; 102(19):6849-54. PMID: 15857951; PMCID: PMC1100766.
      20. Gerdes SY, Scholle MD, Campbell JW, Balázsi G, Ravasz E, Daugherty M, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabási AL, Oltvai ZN, Osterman AL. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol. 2003 Oct; 185(19):5673-84. PMID: 13129938; PMCID: PMC193955.
      21. Gerdes SY, Scholle MD, D'Souza M, Bernal A, Baev MV, Farrell M, Kurnasov OV, Daugherty M, Mseeh F, Polanuyer BM, Campbell JW, Anantha S, Shatalin KY, Chowdhury SA, Fonstein MY, Osterman AL. From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J Bacteriol. 2002 Aug; 184(16):4555-72. PMID: 12142426; PMCID: PMC135229.
      22. Daugherty M, Polanuyer B, Farrell M, Scholle M, Lykidis A, de Crécy-Lagard V, Osterman A. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. J Biol Chem. 2002 Jun 14; 277(24):21431-9. PMID: 11923312.
        View in: PubMed
      23. Krishna SS, Zhou T, Daugherty M, Osterman A, Zhang H. Structural basis for the catalysis and substrate specificity of homoserine kinase. Biochemistry. 2001 Sep 11; 40(36):10810-8. PMID: 11535056.
        View in: PubMed
      24. Daugherty M, Vonstein V, Overbeek R, Osterman A. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J Bacteriol. 2001 Jan; 183(1):292-300. PMID: 11114929; PMCID: PMC94878.
      25. Zhou T, Daugherty M, Grishin NV, Osterman AL, Zhang H. Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily. Structure. 2000 Dec 15; 8(12):1247-57. PMID: 11188689.
        View in: PubMed