Publications

  1. Holliday G, Brown SD, Akiva E, Mischel D, Hicks MA, Morris J, Huang C, Meng E, Pegg S, Ferrin T and Babbitt PC. Biocuration in the Structure-Function Linkage Database: The Anatomy of a Superfamily, Accepted for publication in DATABASE - The Journal of Biological Databases and Curation.

  2. Akiva E, Babbitt PC. Evolutionary Reprograming of Protein-Protein Interaction Specificity, Cell, 2015 (a preview paper).(link)

  3. Holliday GL, Davidson R, Akiva E, Babbitt PC. Evaluating functional annotations of enzymes using the Gene Ontology. In Dessimoz C & Škunca N (Eds.), The Gene Ontology Handbook (pp. 111-132). New York, NY: Springer (Humana Press), 2016, DOI 10.1007/978-1-4939-3743-1. (link)

  4. 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, 2014.(link)

  5. 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.(link)

  6. 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 and Babbitt PC. Large-Scale Determination of Sequence, Structure, and Function Relationships in Cytosolic Glutathione Transferases across the Biosphere, PLoS Biology, 12(4):e1001843., 2014 (link).

  7. Akiva E*, Brown SD*, Almonacid DE, Barber AE 2nd, 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 and Babbitt PC. The Structure-Function Linkage Database, Nucleic Acid Research, DOI: 10.1093/nar/gkt1130, 2013 (*equal contribution). (link)

  8. Humphris EL*, Akiva E*, Varela R, O’Connor S and Kortemme T. Prediction of viral mutational tolerance using flexible backbone protein design, PLoS Computational Biology, 8:e1002639, 2012. (*equal contribution). (link)

  9. Akiva E, Friedlander G, Itzhaki Z and Margalit H. A dynamic view of domain-motif interactions, PLoS Computational Biology, 8:e1002341, 2012.(link)

  10. Jäger S, Cimermancic P, Gulbahce N , Johnson J, Clarke S, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang G, Roth S, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, ODonoghue A, Todorovic A, Morris J, Maltby D, Alber T, Cagney G, Bushman F, Young J, Chanda S, Sundquist W, Kortemme T, Hernandez R, Craik C, Burlingame A, Sali A, Frankel A, and Krogan NJ. Global Landscape of HIV-Human Protein Complexes, Nature, 481(7381):365-70, 2011. (link)

  11. Itzhaki Z, Akiva E and Margalit H. Preferential use of protein domain-pairs as interaction mediators: order and transitivity, Bioinformatics, 26(20):2564-70, 2010. (link)

  12. Akiva E, Itzhaki Z and Margalit H. Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains, Proc Natl Acad Sci U S A., 105:36(13292-7), 2008. (link)

  13. Itzhaki Z, Akiva E, Altuvia Y and Margalit H. Evolutionary conservation of domain-domain interactions, Genome Biol. 7(12):R125, 2006. (link)