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

  • Sparta, B.*, Hamilton, T.*, Hughes, S. and Deeds, E. J. (2024) “A lack of distinct cell identities in single-cell measurements: revisiting Waddington’s landscape” In submission, bioRχiv preprint: https://www.biorxiv.org/content/10.1101/2022.06.03.494765v1?rss=1
  • Sparta, B., Hamilton, T., Aragones, S. D. and Deeds, E. J. (2024) “Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing” In revision, bioRχiv preprint: https://www.biorxiv.org/content/10.1101/2021.07.11.451989v1
  • Lagunes, L., Briggs, K., Martin-Holder, P., Xu, Z., Maurer, D., Ghabra, K. and Deeds, E.J. (2024) “Modeling reveals the strength of weak interactions in stacked ring assembly” In revision, bioRχiv preprint: https://www.biorxiv.org/content/10.1101/2024.02.02.578706v1
  • Cooley, S. M.*, Hamilton, T.*, Aaragones, S. D. Ray, J. C. J. † and Deeds, E. J. † (2024) “A novel metric reveals previously unrecognized distortion in dimensionality reduction of scRNA-seq data” In revision, bioRχiv preprint: https://www.biorxiv.org/content/10.1101/689851v6
  • Natesan, T., Hamilton, T., Deeds, E. J. † and Shah, P. K. (2023) “Novel metrics reveal new structure and unappreciated heterogeneity in C. elegans development.” PLoS Comput Biol 19(12), e1011733
  • Itagi, P., Kante, A., Lagunes, L. and Deeds, E. J.† (2022) “Understanding the Separation of Timescales in Rhodococcus erythropolis Proteasome Core Particle Assembly” Biophys J 121(20), 3975
  • Vakser, I. A., Grudinin, S., Jenkins, N. W., Kundrotas, P. J. and Deeds, E. J. (2022) “Docking-based long timescale simulation of cell-size protein systems at atomic resolution” Proc Natl Acad Sci USA 119(41), e2210249119
  • Garfinkel, A., Bennoun, S., Deeds, E. J. and Van Valkenburgh, B. (2022) “Teaching Dynamics to Biology Undergraduates: the UCLA Experience” Bull Math Bio 84(3), 83
  • Nariya, M., Mallela, A., Shi, J., and Deeds, E. J. (2021) “Robustness and the evolution of length control mechanisms in the type III secretion system and flagellar hook” Biophys J 120(17), 3820
  • Tang, Y., Adelaja, A., Ye, F. X.-F., Deeds, E. J., Wollman, R. and Hoffmann, A. (2021) “Quantifying information accumulation encoded in the dynamics of biochemical signaling” Nat Commun 12(1), 1272
  • Mallela, A., Nariya, M. and Deeds, E. J. (2020). “Crosstalk and ultrasensitivity in protein degradation pathways” PLoS Comp Bio 16(12), e1008492
  • Adeshina, Y. O., Deeds, E. J. and Karanicolas, J. K. (2020) “Machine learning classification can reduce false positives in structure-based virtual screening” Proc Natl Acad Sci USA 117, 18477
  • Suppahia, A., Itagi, P., Burris, A., Kim, M. F., Vontz, A., Kante, A., Kim, S., Im, W., Deeds, E. J. † and Roelofs, J. † (2020) “Cooperativity in proteasome core particle autocatalytic processing” iScience 23(5), 101090
  • Nguyen, A. V., Trompetto, B., Tan, M., Hu, K. H., Deeds, E. J., Butte, M., Chiou, E. and Rowat, A. C. (2019) “Differential contributions of actin and myosin to the physical phenotypes and invasion of pancreatic cancer cells” Cell Mol Bioeng https://doi.org/10.1007/s12195-019-00603-1
  • Vakser, I. A. and Deeds, E. J., “Computational Approaches to Macromolecular Interactions in the Cell”, Curr Opin Struct Biol, 55 : 59-65 (2019).
  • Shockley, E. M., Rouzer, C. A., Marnett, L. J., Deeds, E. J. and Lopez, C. F., “Signal integration and information transfer in an allosterically regulated network”, npc Syst Biol Appl, 5 (1): 324-333 (2019).
  • Suderman, R. and Deeds, E. J., “Intrinsic limits on information transfer in cellular signaling networks”, Interface Focus, 8 (6): 20180039- (2018).
  • Nariya MK, Kim JH, Xiong J, Kleindl PA, Hewarathna A, Fisher AC, Joshi SB, Schneich C, Forrest ML, Middaugh CR, Volkin DB, Deeds EJ, “Comparative Characterization of Crofelemer Samples Using Data Mining and Machine Learning Approaches With Analytical Stability Data Sets”, Journal of pharmaceutical sciences, 106 (11): 3270-3279 (2017).
  • Rowland, M. A., Greenbaum, J. M. and Deeds, E. J. (2017) “Crosstalk and the evolvability of intracellular communication” Nat Commun In press
  • Suderman, R., Bachman, J. A., Smith, A., Sorger, P. K. and Deeds, E. J. (2017) “Fundamental trade-offs between information flow in single cells and cellular populations” Proc Natl Acad Sci USA 114(22), 575
  • Nariya, M. K., Israeli, J., Shi, J. J. and Deeds, E. J. (2016) “Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System” PLoS Comput Biol 12(4), e1004851
  • 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(7), 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), e32032
  • Kolokotrones, T., Savage, V., Deeds, E. J. and Fontana, W. (2010) “Curvature in metabolic scaling” Nature 464(7289), 753
  • Savage, V. M.*, Deeds, E. J.* and Fontana, W. (2008) “Sizing up Allometric Scaling Theory” PLoS Comput Biol 4(9), 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 USA 104(38), 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 USA 104 (25), 10553
  • Hubner, I. A.*, Deeds, E. J.* and Shakhnovich, E. I. (2006) “Understanding Ensemble Protein Folding at Atomic Detail” Proc Natl Acad Sci USA 103(47), 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 USA 103(2), 311
  • Hubner, I. A., Deeds, E. J. and Shakhnovich, E. I. (2005) “High-Resolution Protein Folding with a Transferable Potential” Proc Natl Acad Sci USA 102(52), 18914
  • Deeds, E. J. and Shakhnovich, E. I. (2005) “The Emergence of Scaling in Sequence-Based Models of Protein Evolution” Biophys J 88(6), 3905
  • Deeds, E. J., Hennessey, H. and Shakhnovich, E. I. (2005) “Prokaryotic Phylogenies Inferred from Protein Structural Domains” Genome Res 15(3), 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(3), 385
  • Deeds, E. J., Shakhnovich, B. and Shakhnovich, E. I. (2004) “Proteomic Traces of Speciation” J Mol Biol 336(3), 695
  • Tannenbaum, E., Deeds, E. J. and Shakhnovich, E. I. (2004) “Semiconservative Replication in the Quasispecies Model” Phys Rev E 69(6), 061916
  • Deeds, E. J., Dokholyan, N. V. and Shakhnovich, E. I. (2003) “Protein Evolution within a Structural Space” Biophys J 85(5), 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(13), 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
© COPYRIGHT - ERIC DEEDS LAB