Publications

A list of peer-reviewed journal articles and review articles may be found below. In this list, the * character indicates equal contribution of authors and the † character represents co-corresponding authors.

Journal Articles

  • Wani, P. S., Rowland, M. A., Odracek, A., Deeds, E. J.† and Roelofs, J.† (2015) “Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association” Nat Commun 6, 6384

  • Rowland M. A., Harrison B., Deeds E. J. (2015) “Phosphatase specificity and pathway insulation in signaling networks” Biophys J. 108(4):986-96

  • Rowland M. A. and Deeds E. J. (2014) “Crosstalk and the evolution of specificity in Two-Component Signaling” Proc Natl Acad Sci USA. 111(15):5550-5

  • Suderman R. and Deeds E. J. (2013) “Machines vs. ensembles: effective MAPK signaling through heterogeneous sets of protein complexes” PLoS Comp Bio 9(1), e1003278 PDF Model File Supporting Information

  • Rowland M. A., Fontana W., Deeds E. J. (2012) “Crosstalk and competition in signaling networks” Biophys J 103, 2389 Preprint PDF Supporting Material
      * Biophysical Journal Best of 2012

  • Deeds, E. J.*†, Bachman, J.* and Fontana, W.† (2012) “Optimizing ring assembly: the strength of weak bonds” Proc Natl Acad Sci 109, 109

  • Deeds, E. J., Krivine, J., Feret, J., Danos, V. and Fontana, W. (2012) “Combinatorial complexity and compositional drift in protein-protein interaction networks” PLoS ONE 7, 3

  • Kolokotrones, T., Savage, V., Deeds, E. J. and Fontana, W. (2010) “Curvature in metabolic scaling” Nature 464, 753

  • Savage, V. M.*, Deeds, E. J.* and Fontana, W. (2008) “Sizing up Allometric Scaling Theory” PLoS Comput Biol 4, e1000171

  • Deeds, E. J., Ashenberg, O., Gerardin, J. and Shakhnovich, E. I. (2007) “Robust protein-protein interactions in crowded cellular environments” Proc Natl Acad Sci 104, 14952

  • Perlstein, E. O.*, Deeds, E. J.*, Ashenberg, O., Ramachandran, G., Shakhnovich, E. I. and Schrieber, S. L. (2007) “Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations” Proc Natl Acad Sci 104, 10553

  • Hubner, I. A.*, Deeds, E. J.* and Shakhnovich, E. I. (2006) “Understanding Ensemble Protein Folding at Atomic Detail” Proc Natl Acad Sci 103, 17747

  • Deeds, E. J., Ashenberg, O. and Shakhnovich, E. I. (2006) “A simple physical model for scaling in protein-protein interaction networks” Proc Natl Acad Sci 103, 311

  • Hubner, I. A., Deeds, E. J. and Shakhnovich, E. I. (2005) “High-Resolution Protein Folding with a Transferable Potential” Proc Natl Acad Sci 102, 18914

  • Deeds, E. J. and Shakhnovich, E. I. (2005) “The Emergence of Scaling in Sequence-Based Models of Protein Evolution” Biophys J 88, 3905

  • Deeds, E. J., Hennessey, H. and Shakhnovich, E. I. (2005) “Prokaryotic Phylogenies Inferred from Protein Structural Domains” Genome Res 15, 393

  • Shakhnovich, B., Deeds, E. J., DeLisi, C. and Shakhnovich, E. I. (2005) “Protein Structure and Evolutionary History Determine Sequence Space Topology” Genome Res 15, 385

  • Deeds, E. J., Shakhnovich, B. and Shakhnovich, E. I. (2004) “Proteomic Traces of Speciation” J Mol Biol 336, 695

  • Tannenbaum, E., Deeds, E. J. and Shakhnovich, E. I. (2004) “Semiconservative Replication in the Quasispecies Model” Phys Rev E 69, 061916

  • Deeds, E. J., Dokholyan, N. V. and Shakhnovich, E. I. (2003) “Protein Evolution within a Structural Space” Biophys J 85, 2962

  • Tannenbaum, E., Deeds, E. J. and Shakhnovich, E. I. (2003) “Equilibrium Distribution of Mutators in the Single Fitness Peak Model” Phys Rev Lett 91, 138105

Review Articles

  • Deeds, E. J. and Shakhnovich, E. I. (2006) “A Structure-Centric View of Protein Evolution, Design and Adaptation” Adv Ezymol Relat Areas Mol Biol 75, 133