Eric Jameson Deeds

Title(s)Professor, Integrative Biology And Physiology
SchoolCollege of Letters and Science
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    Collapse Research 
    Collapse Research Activities and Funding
    Developing tools for the unbiased analysis and visualization of scRNA-seq data
    NIH R01GM143378Sep 1, 2021 - Aug 31, 2025
    Role: Principal Investigator
    Structural and Dynamical Specificity on Intracellular Signaling Networks
    NIH F32GM080123Feb 6, 2006 - Jul 31, 2009
    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. Modeling reveals the strength of weak interactions in stacked-ring assembly. Biophys J. 2024 May 18. Lagunes L, Briggs K, Martin-Holder P, Xu Z, Maurer D, Ghabra K, Deeds EJ. PMID: 38762753.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    2. Novel metrics reveal new structure and unappreciated heterogeneity in Caenorhabditis elegans development. PLoS Comput Biol. 2023 Dec; 19(12):e1011733. Natesan G, Hamilton T, Deeds EJ, Shah PK. PMID: 38113280; PMCID: PMC10763962.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    3. Novel metrics reveal new structure and unappreciated heterogeneity in C. elegans development. bioRxiv. 2023 May 24. Natesan G, Hamilton T, Deeds EJ, Shah PK. PMID: 37292606; PMCID: PMC10245744.
      View in: PubMed   Mentions:
    4. Altered physical phenotypes of leukemia cells that survive chemotherapy treatment. Integr Biol (Camb). 2023 04 11; 15. Ly C, Ogana H, Kim HN, Hurwitz S, Deeds EJ, Kim YM, Rowat AC. PMID: 37247849.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    5. Docking-based long timescale simulation of cell-size protein systems at atomic resolution. Proc Natl Acad Sci U S A. 2022 10 11; 119(41):e2210249119. Vakser IA, Grudinin S, Jenkins NW, Kundrotas PJ, Deeds EJ. PMID: 36191203; PMCID: PMC9565162.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    6. Understanding the separation of timescales in bacterial proteasome core particle assembly. Biophys J. 2022 10 18; 121(20):3975-3986. Itagi P, Kante A, Lagunes L, Deeds EJ. PMID: 36016496; PMCID: PMC9674962.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    7. Teaching Dynamics to Biology Undergraduates: the UCLA Experience. Bull Math Biol. 2022 02 12; 84(3):43. Garfinkel A, Bennoun S, Deeds E, Van Valkenburgh B. PMID: 35150346; PMCID: PMC8840928.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    8. Robustness and the evolution of length control strategies in the T3SS and flagellar hook. Biophys J. 2021 09 07; 120(17):3820-3830. Nariya MK, Mallela A, Shi JJ, Deeds EJ. PMID: 34246629; PMCID: PMC8456370.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    9. Quantifying information accumulation encoded in the dynamics of biochemical signaling. Nat Commun. 2021 02 24; 12(1):1272. Tang Y, Adelaja A, Ye FX, Deeds E, Wollman R, Hoffmann A. PMID: 33627672; PMCID: PMC7904837.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    10. Crosstalk and ultrasensitivity in protein degradation pathways. PLoS Comput Biol. 2020 12; 16(12):e1008492. Mallela A, Nariya MK, Deeds EJ. PMID: 33370258; PMCID: PMC7793289.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    11. Machine learning classification can reduce false positives in structure-based virtual screening. Proc Natl Acad Sci U S A. 2020 08 04; 117(31):18477-18488. Adeshina YO, Deeds EJ, Karanicolas J. PMID: 32669436; PMCID: PMC7414157.
      View in: PubMed   Mentions: 51     Fields:    Translation:Humans
    12. Cooperativity in Proteasome Core Particle Maturation. iScience. 2020 May 22; 23(5):101090. Suppahia A, Itagi P, Burris A, Kim FMG, Vontz A, Kante A, Kim S, Im W, Deeds EJ, Roelofs J. PMID: 32380419; PMCID: PMC7210456.
      View in: PubMed   Mentions: 1  
    13. Differential Contributions of Actin and Myosin to the Physical Phenotypes and Invasion of Pancreatic Cancer Cells. Cell Mol Bioeng. 2020 Feb; 13(1):27-44. Nguyen AV, Trompetto B, Tan XHM, Scott MB, Hu KH, Deeds E, Butte MJ, Chiou PY, Rowat AC. PMID: 32030106; PMCID: PMC6981337.
      View in: PubMed   Mentions: 8  
    14. Signal integration and information transfer in an allosterically regulated network. NPJ Syst Biol Appl. 2019; 5:23. Shockley EM, Rouzer CA, Marnett LJ, Deeds EJ, Lopez CF. PMID: 31341635; PMCID: PMC6639376.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    15. Computational approaches to macromolecular interactions in the cell. Curr Opin Struct Biol. 2019 04; 55:59-65. Vakser IA, Deeds EJ. PMID: 30999240; PMCID: PMC6692245.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    16. Intrinsic limits of information transmission in biochemical signalling motifs. Interface Focus. 2018 Dec 06; 8(6):20180039. Suderman R, Deeds EJ. PMID: 30443336; PMCID: PMC6227803.
      View in: PubMed   Mentions: 3  
    17. Comparative Characterization of Crofelemer Samples Using Data Mining and Machine Learning Approaches With Analytical Stability Data Sets. J Pharm Sci. 2017 11; 106(11):3270-3279. Nariya MK, Kim JH, Xiong J, Kleindl PA, Hewarathna A, Fisher AC, Joshi SB, Schöneich C, Forrest ML, Middaugh CR, Volkin DB, Deeds EJ. PMID: 28743607; PMCID: PMC6588356.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    18. The Botanical Drug Substance Crofelemer as a Model System for Comparative Characterization of Complex Mixture Drugs. J Pharm Sci. 2017 11; 106(11):3242-3256. Kleindl PA, Xiong J, Hewarathna A, Mozziconacci O, Nariya MK, Fisher AC, Deeds EJ, Joshi SB, Middaugh CR, Schöneich C, Volkin DB, Forrest ML. PMID: 28743606; PMCID: PMC5643239.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    19. Crosstalk and the evolvability of intracellular communication. Nat Commun. 2017 07 10; 8:16009. Rowland MA, Greenbaum JM, Deeds EJ. PMID: 28691706; PMCID: PMC5508131.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    20. Chemical Stability of the Botanical Drug Substance Crofelemer: A Model System for Comparative Characterization of Complex Mixture Drugs. J Pharm Sci. 2017 11; 106(11):3257-3269. Hewarathna A, Mozziconacci O, Nariya MK, Kleindl PA, Xiong J, Fisher AC, Joshi SB, Middaugh CR, Forrest ML, Volkin DB, Deeds EJ, Schöneich C. PMID: 28688843; PMCID: PMC6644711.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    21. Fundamental trade-offs between information flow in single cells and cellular populations. Proc Natl Acad Sci U S A. 2017 05 30; 114(22):5755-5760. Suderman R, Bachman JA, Smith A, Sorger PK, Deeds EJ. PMID: 28500273; PMCID: PMC5465904.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    22. Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System. PLoS Comput Biol. 2016 Apr; 12(4):e1004851. Nariya MK, Israeli J, Shi JJ, Deeds EJ. PMID: 27078235; PMCID: PMC4831731.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    23. Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association. Nat Commun. 2015 Mar 16; 6:6384. Wani PS, Rowland MA, Ondracek A, Deeds EJ, Roelofs J. PMID: 25812915; PMCID: PMC4380239.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    24. Phosphatase specificity and pathway insulation in signaling networks. Biophys J. 2015 Feb 17; 108(4):986-996. Rowland MA, Harrison B, Deeds EJ. PMID: 25692603; PMCID: PMC4336360.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    25. Crosstalk and the evolution of specificity in two-component signaling. Proc Natl Acad Sci U S A. 2014 Apr 15; 111(15):5550-5. Rowland MA, Deeds EJ. PMID: 24706803; PMCID: PMC3992699.
      View in: PubMed   Mentions: 50     Fields:    Translation:Cells
    26. Machines vs. ensembles: effective MAPK signaling through heterogeneous sets of protein complexes. PLoS Comput Biol. 2013; 9(10):e1003278. Suderman R, Deeds EJ. PMID: 24130475; PMCID: PMC3794900.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    27. Structural properties of non-traditional drug targets present new challenges for virtual screening. J Chem Inf Model. 2013 Aug 26; 53(8):2073-81. Gowthaman R, Deeds EJ, Karanicolas J. PMID: 23879197; PMCID: PMC3819422.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    28. Crosstalk and competition in signaling networks. Biophys J. 2012 Dec 05; 103(11):2389-98. Rowland MA, Fontana W, Deeds EJ. PMID: 23283238; PMCID: PMC3514525.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansAnimalsCells
    29. Combinatorial complexity and compositional drift in protein interaction networks. PLoS One. 2012; 7(3):e32032. Deeds EJ, Krivine J, Feret J, Danos V, Fontana W. PMID: 22412851; PMCID: PMC3297590.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    30. Optimizing ring assembly reveals the strength of weak interactions. Proc Natl Acad Sci U S A. 2012 Feb 14; 109(7):2348-53. Deeds EJ, Bachman JA, Fontana W. PMID: 22308356; PMCID: PMC3289332.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    31. Curvature in metabolic scaling: a reply to MacKay. J Theor Biol. 2011 Jul 07; 280(1):197-8. Deeds EJ, Savage V, Fontana W. PMID: 21497609.
      View in: PubMed   Mentions: 2     Fields:    
    32. Curvature in metabolic scaling. Nature. 2010 Apr 01; 464(7289):753-6. Kolokotrones T, Deeds EJ, Fontana W. PMID: 20360740.
      View in: PubMed   Mentions: 89     Fields:    Translation:Animals
    33. Sizing up allometric scaling theory. PLoS Comput Biol. 2008 Sep 12; 4(9):e1000171. Savage VM, Deeds EJ, Fontana W. PMID: 18787686; PMCID: PMC2518954.
      View in: PubMed   Mentions: 65     Fields:    Translation:Animals
    34. Robust protein protein interactions in crowded cellular environments. Proc Natl Acad Sci U S A. 2007 Sep 18; 104(38):14952-7. Deeds EJ, Ashenberg O, Gerardin J, Shakhnovich EI. PMID: 17848524; PMCID: PMC1986594.
      View in: PubMed   Mentions: 39     Fields:    Translation:Cells
    35. Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations. Proc Natl Acad Sci U S A. 2007 Jun 19; 104(25):10553-8. Perlstein EO, Deeds EJ, Ashenberg O, Shakhnovich EI, Schreiber SL. PMID: 17566105; PMCID: PMC1965551.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    36. A structure-centric view of protein evolution, design, and adaptation. Adv Enzymol Relat Areas Mol Biol. 2007; 75:133-91, xi-xii. Deeds EJ, Shakhnovich EI. PMID: 17124867.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    37. Understanding ensemble protein folding at atomic detail. Proc Natl Acad Sci U S A. 2006 Nov 21; 103(47):17747-52. Hubner IA, Deeds EJ, Shakhnovich EI. PMID: 17095606; PMCID: PMC1635542.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    38. A simple physical model for scaling in protein-protein interaction networks. Proc Natl Acad Sci U S A. 2006 Jan 10; 103(2):311-6. Deeds EJ, Ashenberg O, Shakhnovich EI. PMID: 16384916; PMCID: PMC1326177.
      View in: PubMed   Mentions: 46     Fields:    Translation:Cells
    39. High-resolution protein folding with a transferable potential. Proc Natl Acad Sci U S A. 2005 Dec 27; 102(52):18914-9. Hubner IA, Deeds EJ, Shakhnovich EI. PMID: 16365306; PMCID: PMC1323145.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    40. The emergence of scaling in sequence-based physical models of protein evolution. Biophys J. 2005 Jun; 88(6):3905-11. Deeds EJ, Shakhnovich EI. PMID: 15805176; PMCID: PMC1305622.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    41. Prokaryotic phylogenies inferred from protein structural domains. Genome Res. 2005 Mar; 15(3):393-402. Deeds EJ, Hennessey H, Shakhnovich EI. PMID: 15741510; PMCID: PMC551566.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    42. Protein structure and evolutionary history determine sequence space topology. Genome Res. 2005 Mar; 15(3):385-92. Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. PMID: 15741509; PMCID: PMC551565.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    43. Semiconservative replication in the quasispecies model. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Jun; 69(6 Pt 1):061916. Tannenbaum E, Deeds EJ, Shakhnovich EI. PMID: 15244626.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    44. Proteomic traces of speciation. J Mol Biol. 2004 Feb 20; 336(3):695-706. Deeds EJ, Shakhnovich B, Shakhnovich EI. PMID: 15095981.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    45. Protein evolution within a structural space. Biophys J. 2003 Nov; 85(5):2962-72. Deeds EJ, Dokholyan NV, Shakhnovich EI. PMID: 14581198; PMCID: PMC1303574.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    46. Equilibrium distribution of mutators in the single fitness peak model. Phys Rev Lett. 2003 Sep 26; 91(13):138105. Tannenbaum E, Deeds EJ, Shakhnovich EI. PMID: 14525341.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
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