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Eyal Akiva, PhD

Address1700 4th Street
San Francisco CA 94158
Phone415-502-1248
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    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. Gorzalczany Y, Akiva E, Klein O, Merimsky O, Sagi-Eisenberg R. Mast cells are directly activated by contact with cancer cells by a mechanism involving autocrine formation of adenosine and autocrine/paracrine signaling of the adenosine A3 receptor. Cancer Lett. 2017 Jul 01; 397:23-32. PMID: 28342985.
      View in: PubMed
    2. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 Jan 01; 2017. PMID: 28605775.
      View in: PubMed
    3. Holliday GL, Davidson R, Akiva E, Babbitt PC. Evaluating Functional Annotations of Enzymes Using the Gene Ontology. Methods Mol Biol. 2017; 1446:111-132. PMID: 27812939.
      View in: PubMed
    4. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 Jan 01; 2017(1). PMID: 28365730.
      View in: PubMed
    5. Akiva E, Babbitt PC. Evolutionary reprograming of protein-protein interaction specificity. Cell. 2015 Oct 22; 163(3):535-7. PMID: 26496596.
      View in: PubMed
    6. Betz JN, Boswell NW, Fugate CJ, Holliday GL, Akiva E, Scott AG, Babbitt PC, Peters JW, Shepard EM, Broderick JB. [FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis. Biochemistry. 2015 Mar 10; 54(9):1807-18. PMID: 25654171; PMCID: PMC4839199.
    7. Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30; 3. PMID: 24980702; PMCID: PMC4113996.
    8. Mashiyama ST, Malabanan MM, Akiva E, Bhosle R, Branch MC, Hillerich B, Jagessar K, Kim J, Patskovsky Y, Seidel RD, Stead M, Toro R, Vetting MW, Almo SC, Armstrong RN, Babbitt PC. Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PLoS Biol. 2014 Apr; 12(4):e1001843. PMID: 24756107; PMCID: PMC3995644.
    9. Akiva E, Brown S, Almonacid DE, Barber AE, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC. The Structure-Function Linkage Database. Nucleic Acids Res. 2014 Jan; 42(Database issue):D521-30. PMID: 24271399; PMCID: PMC3965090.
    10. Humphris-Narayanan E, Akiva E, Varela R, Ó Conchúir S, Kortemme T. Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design. PLoS Comput Biol. 2012; 8(8):e1002639. PMID: 22927804; PMCID: PMC3426558.
    11. Akiva E, Friedlander G, Itzhaki Z, Margalit H. A dynamic view of domain-motif interactions. PLoS Comput Biol. 2012 Jan; 8(1):e1002341. PMID: 22253583; PMCID: PMC3257277.
    12. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70. PMID: 22190034; PMCID: PMC3310911.
    13. Itzhaki Z, Akiva E, Margalit H. Preferential use of protein domain pairs as interaction mediators: order and transitivity. Bioinformatics. 2010 Oct 15; 26(20):2564-70. PMID: 20802208.
      View in: PubMed
    14. Akiva E, Itzhaki Z, Margalit H. Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. Proc Natl Acad Sci U S A. 2008 Sep 09; 105(36):13292-7. PMID: 18757736; PMCID: PMC2533183.
    15. Itzhaki Z, Akiva E, Altuvia Y, Margalit H. Evolutionary conservation of domain-domain interactions. Genome Biol. 2006; 7(12):R125. PMID: 17184549; PMCID: PMC1794438.
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