Matthew Daugherty

Title(s)Associate Professor, Molecular Biology
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research 
    Collapse Research Activities and Funding
    Pathogen-driven evolution of innate antiviral defense mechanisms
    NIH R35GM133633Aug 1, 2019 - Jun 30, 2024
    Role: Principal Investigator
    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. to make corrections and additions.
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    Altmetrics Details 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. Running With Scissors: Evolutionary Conflicts Between Viral Proteases and the Host Immune System. Front Immunol. 2021; 12:769543. Tsu BV, Fay EJ, Nguyen KT, Corley MR, Hosuru B, Dominguez VA, Daugherty MD. PMID: 34790204; PMCID: PMC8591160.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    2. ADP-ribosyltransferases, an update on function and nomenclature. FEBS J. 2022 Dec; 289(23):7399-7410. Lüscher B, Ahel I, Altmeyer M, Ashworth A, Bai P, Chang P, Cohen M, Corda D, Dantzer F, Daugherty MD, Dawson TM, Dawson VL, Deindl S, Fehr AR, Feijs KLH, Filippov DV, Gagné JP, Grimaldi G, Guettler S, Hoch NC, Hottiger MO, Korn P, Kraus WL, Ladurner A, Lehtiö L, Leung AKL, Lord CJ, Mangerich A, Matic I, Matthews J, Moldovan GL, Moss J, Natoli G, Nielsen ML, Niepel M, Nolte F, Pascal J, Paschal BM, Pawlowski K, Poirier GG, Smith S, Timinszky G, Wang ZQ, Yélamos J, Yu X, Zaja R, Ziegler M. PMID: 34323016; PMCID: PMC9027952.
      View in: PubMed   Mentions: 25     Fields:    
    3. Ribosome quality control activity potentiates vaccinia virus protein synthesis during infection. J Cell Sci. 2021 04 15; 134(8). Sundaramoorthy E, Ryan AP, Fulzele A, Leonard M, Daugherty MD, Bennett EJ. PMID: 33912921; PMCID: PMC8106952.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    4. Diverse viral proteases activate the NLRP1 inflammasome. Elife. 2021 01 07; 10. Tsu BV, Beierschmitt C, Ryan AP, Agarwal R, Mitchell PS, Daugherty MD. PMID: 33410748; PMCID: PMC7857732.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    5. Cell-cycle-gated feedback control mediates desensitization to interferon stimulation. Elife. 2020 09 18; 9. Mudla A, Jiang Y, Arimoto KI, Xu B, Rajesh A, Ryan AP, Wang W, Daugherty MD, Zhang DE, Hao N. PMID: 32945770; PMCID: PMC7500952.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    6. Diversification of the Caenorhabditis heat shock response by Helitron transposable elements. Elife. 2019 12 11; 8. Garrigues JM, Tsu BV, Daugherty MD, Pasquinelli AE. PMID: 31825311; PMCID: PMC6927752.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    7. RNA-binding protein isoforms ZAP-S and ZAP-L have distinct antiviral and immune resolution functions. Nat Immunol. 2019 12; 20(12):1610-1620. Schwerk J, Soveg FW, Ryan AP, Thomas KR, Hatfield LD, Ozarkar S, Forero A, Kell AM, Roby JA, So L, Hyde JL, Gale M, Daugherty MD, Savan R. PMID: 31740798; PMCID: PMC7240801.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    8. Gene conversion generates evolutionary novelty that fuels genetic conflicts. Curr Opin Genet Dev. 2019 10; 58-59:49-54. Daugherty MD, Zanders SE. PMID: 31466040; PMCID: PMC6889005.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    9. ICTV Virus Taxonomy Profile: Polyomaviridae. J Gen Virol. 2017 Jun; 98(6):1159-1160. Moens U, Calvignac-Spencer S, Lauber C, Ramqvist T, Feltkamp MCW, Daugherty MD, Verschoor EJ, Ehlers B. PMID: 28640744; PMCID: PMC5656788.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansAnimalsCells
    10. Functional and Evolutionary Analyses Identify Proteolysis as a General Mechanism for NLRP1 Inflammasome Activation. PLoS Pathog. 2016 Dec; 12(12):e1006052. Chavarría-Smith J, Mitchell PS, Ho AM, Daugherty MD, Vance RE. PMID: 27926929; PMCID: PMC5142783.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansAnimalsCells
    11. Evolution-guided functional analyses reveal diverse antiviral specificities encoded by IFIT1 genes in mammals. Elife. 2016 05 31; 5. Daugherty MD, Schaller AM, Geballe AP, Malik HS. PMID: 27240734; PMCID: PMC4887208.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    12. A taxonomy update for the family Polyomaviridae. Arch Virol. 2016 Jun; 161(6):1739-50. Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses, Calvignac-Spencer S, Feltkamp MC, Daugherty MD, Moens U, Ramqvist T, Johne R, Ehlers B. PMID: 26923930.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansAnimalsCells
    13. Transferred interbacterial antagonism genes augment eukaryotic innate immune function. Nature. 2015 Feb 05; 518(7537):98-101. Chou S, Daugherty MD, 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. PMID: 25470067; PMCID: PMC4713192.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    14. How a virus blocks a cellular emergency access lane to the nucleus, STAT! Cell Host Microbe. 2014 Aug 13; 16(2):150-152. Daugherty MD, Malik HS. PMID: 25121743.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    15. Rapid evolution of PARP genes suggests a broad role for ADP-ribosylation in host-virus conflicts. PLoS Genet. 2014; 10(5):e1004403. Daugherty MD, Young JM, Kerns JA, Malik HS. PMID: 24875882; PMCID: PMC4038475.
      View in: PubMed   Mentions: 83     Fields:    Translation:HumansCells
    16. Molecular basis for specific recognition of bacterial ligands by NAIP/NLRC4 inflammasomes. Mol Cell. 2014 Apr 10; 54(1):17-29. Tenthorey JL, Kofoed EM, Daugherty MD, Malik HS, Vance RE. PMID: 24657167; PMCID: PMC3988258.
      View in: PubMed   Mentions: 88     Fields:    Translation:HumansAnimalsCells
    17. 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. Carter JJ, Daugherty MD, Qi X, Bheda-Malge A, Wipf GC, Robinson K, Roman A, Malik HS, Galloway DA. PMID: 23847207; PMCID: PMC3732942.
      View in: PubMed   Mentions: 74     Fields:    Translation:Cells
    18. Rules of engagement: molecular insights from host-virus arms races. Annu Rev Genet. 2012; 46:677-700. Daugherty MD, Malik HS. PMID: 23145935.
      View in: PubMed   Mentions: 222     Fields:    Translation:HumansAnimalsCells
    19. 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. Wang H, Ma X, Yeh YS, Zhu Y, Daugherty MD, Frankel AD, Musier-Forsyth K, Barbara PF. PMID: 21081095; PMCID: PMC2980704.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    20. Structural basis for cooperative RNA binding and export complex assembly by HIV Rev. Nat Struct Mol Biol. 2010 Nov; 17(11):1337-42. Daugherty MD, Liu B, Frankel AD. PMID: 20953181; PMCID: PMC2988976.
      View in: PubMed   Mentions: 98     Fields:    Translation:Cells
    21. 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. Daugherty MD, Booth DS, Jayaraman B, Cheng Y, Frankel AD. PMID: 20616058; PMCID: PMC2906596.
      View in: PubMed   Mentions: 51     Fields:    Translation:Cells
    22. 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. Daugherty MD, D'Orso I, Frankel AD. PMID: 18922466; PMCID: PMC2651398.
      View in: PubMed   Mentions: 72     Fields:    Translation:Cells
    23. 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. Fuhrmann CN, Daugherty MD, Agard DA. PMID: 16834383.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    24. An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction. J Am Chem Soc. 2006 Mar 22; 128(11):3496-7. Mills NL, Daugherty MD, Frankel AD, Guy RK. PMID: 16536504; PMCID: PMC2566309.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    25. A simple motif for protein recognition in DNA secondary structures. J Mol Biol. 2005 Sep 02; 351(5):982-94. Landt SG, Ramirez A, Daugherty MD, Frankel AD. PMID: 16055152.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    26. Should we expect population thresholds for wildlife disease? Trends Ecol Evol. 2005 Sep; 20(9):511-9. Lloyd-Smith JO, Cross PC, Briggs CJ, Daugherty M, Getz WM, Latto J, Sanchez MS, Smith AB, Swei A. PMID: 16701428.
      View in: PubMed   Mentions: 155     Fields:    
    27. 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. Calabro V, Daugherty MD, Frankel AD. PMID: 15857951; PMCID: PMC1100766.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    28. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol. 2003 Oct; 185(19):5673-84. Gerdes SY, Scholle MD, Campbell JW, Balázsi G, Ravasz E, Daugherty MD, 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. PMID: 13129938; PMCID: PMC193955.
      View in: PubMed   Mentions: 328     Fields:    Translation:Cells
    29. From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J Bacteriol. 2002 Aug; 184(16):4555-72. Gerdes SY, Scholle MD, D'Souza M, Bernal A, Baev MV, Farrell M, Kurnasov OV, Daugherty MD, Mseeh F, Polanuyer BM, Campbell JW, Anantha S, Shatalin KY, Chowdhury SA, Fonstein MY, Osterman AL. PMID: 12142426; PMCID: PMC135229.
      View in: PubMed   Mentions: 103     Fields:    Translation:Cells
    30. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. J Biol Chem. 2002 Jun 14; 277(24):21431-9. Daugherty M, Polanuyer B, Farrell M, Scholle M, Lykidis A, de Crécy-Lagard V, Osterman A. PMID: 11923312.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansCells
    31. Structural basis for the catalysis and substrate specificity of homoserine kinase. Biochemistry. 2001 Sep 11; 40(36):10810-8. Krishna SS, Zhou T, Daugherty M, Osterman A, Zhang H. PMID: 11535056.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimalsCells
    32. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J Bacteriol. 2001 Jan; 183(1):292-300. Daugherty M, Vonstein V, Overbeek R, Osterman A. PMID: 11114929; PMCID: PMC94878.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    33. Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily. Structure. 2000 Dec 15; 8(12):1247-57. Zhou T, Daugherty M, Grishin NV, Osterman AL, Zhang H. PMID: 11188689.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
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