Eric Deeds • UCLA Profiles (original) (raw)

  1. Life in the fast lane: Functional consequences of male-female dynamic differences in the renal auto-regulation of flow. bioRxiv. 2025 Oct 22. Xiong LI, Garfinkel A, Bennett KM, Baldelomar EJ, Brown L, Barrows K, Vallon V, Edwards A, McDonough AA, Porat-Shliom N, Deeds EJ. PMID: 41000627; PMCID: PMC12458117.
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  2. DeepAtlas: a tool for effective manifold learning. bioRxiv. 2025 Aug 31. Hughes S, Hamilton T, Kolokotrones T, Deeds EJ. PMID: 40909682; PMCID: PMC12407865.
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  3. DeepAtlas: a tool for effective manifold learning. ArXiv. 2025 Aug 26. Hughes S, Hamilton T, Kolokotrones T, Deeds EJ. PMID: 40909155; PMCID: PMC12407675.
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  4. Sarcospan protects against LGMD R5 via remodeling of the sarcoglycan complex composition in dystrophic mice. J Clin Invest. 2025 Sep 02; 135(17). Mokhonova EI, Helzer D, Malik R, Mamsa H, Walker J, Maslanka M, Fleser TS, Afsharinia MH, Liu S, Holmberg J, Zhou ZH, Deeds EJ, Hansen KC, McNally EM, Crosbie RH. PMID: 40549548; PMCID: PMC12404760.
    View in: PubMed Mentions: Fields:
    Translation:HumansAnimals
  5. Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing. PLoS Comput Biol. 2024 Sep; 20(9):e1012386. Sparta B, Hamilton T, Natesan G, Aragones SD, Deeds EJ. PMID: 39241106; PMCID: PMC11410258.
    View in: PubMed Mentions: 2 Fields:
    Translation:HumansAnimals
  6. Modeling reveals the strength of weak interactions in stacked-ring assembly. Biophys J. 2024 07 02; 123(13):1763-1780. Lagunes L, Briggs K, Martin-Holder P, Xu Z, Maurer D, Ghabra K, Deeds EJ. PMID: 38762753; PMCID: PMC11267433.
    View in: PubMed Mentions: Fields:
    Translation:Cells
  7. Novel metrics reveal new structure and unappreciated heterogeneity in Caenorhabditis elegans development. PLoS Comput Biol. 2023 12; 19(12):e1011733. Natesan G, Hamilton T, Deeds EJ, Shah PK. PMID: 38113280; PMCID: PMC10763962.
    View in: PubMed Mentions: 6 Fields:
    Translation:Animals
  8. 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.
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  9. 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: 2 Fields:
    Translation:Humans
  10. 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: 12 Fields:
    Translation:Cells
  11. 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
  12. 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
  13. 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.
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    Translation:Cells
  14. 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: 16 Fields:
    Translation:HumansCells
  15. 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
  16. 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: 76 Fields:
    Translation:Humans
  17. 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: 2
  18. 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: 10
  19. 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: 9 Fields:
    Translation:Cells
  20. 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: 11 Fields:
    Translation:Cells
  21. 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
  22. 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
  23. 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
  24. 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: 20 Fields:
    Translation:HumansCells
  25. 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
  26. 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: 57 Fields:
    Translation:HumansCells
  27. 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: 5 Fields:
    Translation:Cells
  28. 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: 33 Fields:
    Translation:Cells
  29. 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: 15 Fields:
    Translation:AnimalsCells
  30. 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: 58 Fields:
    Translation:Cells
  31. 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: 26 Fields:
    Translation:AnimalsCells
  32. 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: 17 Fields:
    Translation:Cells
  33. 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: 34 Fields:
    Translation:HumansAnimalsCells
  34. 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: 23 Fields:
    Translation:Cells
  35. 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: 28 Fields:
    Translation:Cells
  36. 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:
  37. Curvature in metabolic scaling. Nature. 2010 Apr 01; 464(7289):753-6. Kolokotrones T, Deeds EJ, Fontana W. PMID: 20360740.
    View in: PubMed Mentions: 97 Fields:
    Translation:Animals
  38. 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: 72 Fields:
    Translation:Animals
  39. 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: 43 Fields:
    Translation:Cells
  40. 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
  41. 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
  42. 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: 26 Fields:
    Translation:Cells
  43. 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: 49 Fields:
    Translation:Cells
  44. 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
  45. 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
  46. 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: 37 Fields:
    Translation:Cells
  47. 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
  48. 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
  49. 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
  50. 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: 12 Fields:
    Translation:Cells
  51. 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: 4 Fields:
    Translation:Cells

This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.

This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.

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