Eric Deeds
Publications:
Sparta B, Hamilton T, Natesan G, Aragones SD, Deeds EJ. Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing. PLoS Comput Biol. 2024 Sep; 20(9):e1012386. view on PubMed
Lagunes L, Briggs K, Martin-Holder P, Xu Z, Maurer D, Ghabra K, Deeds EJ. Modeling reveals the strength of weak interactions in stacked-ring assembly. Biophys J. 2024 Jul 02; 123(13):1763-1780. view on PubMed
Natesan G, Hamilton T, Deeds EJ, Shah PK. Novel metrics reveal new structure and unappreciated heterogeneity in Caenorhabditis elegans development. PLoS Comput Biol. 2023 Dec; 19(12):e1011733. view on PubMed
Natesan G, Hamilton T, Deeds EJ, Shah PK. Novel metrics reveal new structure and unappreciated heterogeneity in C. elegans development. bioRxiv. 2023 May 24. view on PubMed
Ly C, Ogana H, Kim HN, Hurwitz S, Deeds EJ, Kim YM, Rowat AC. Altered physical phenotypes of leukemia cells that survive chemotherapy treatment. Integr Biol (Camb). 2023 04 11; 15. view on PubMed
Vakser IA, Grudinin S, Jenkins NW, Kundrotas PJ, Deeds EJ. 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. view on PubMed
Itagi P, Kante A, Lagunes L, Deeds EJ. Understanding the separation of timescales in bacterial proteasome core particle assembly. Biophys J. 2022 10 18; 121(20):3975-3986. view on PubMed
Garfinkel A, Bennoun S, Deeds E, Van Valkenburgh B. Teaching Dynamics to Biology Undergraduates: the UCLA Experience. Bull Math Biol. 2022 02 12; 84(3):43. view on PubMed
Nariya MK, Mallela A, Shi JJ, Deeds EJ. Robustness and the evolution of length control strategies in the T3SS and flagellar hook. Biophys J. 2021 09 07; 120(17):3820-3830. view on PubMed
Tang Y, Adelaja A, Ye FX, Deeds E, Wollman R, Hoffmann A. Quantifying information accumulation encoded in the dynamics of biochemical signaling. Nat Commun. 2021 02 24; 12(1):1272. view on PubMed
Mallela A, Nariya MK, Deeds EJ. Crosstalk and ultrasensitivity in protein degradation pathways. PLoS Comput Biol. 2020 12; 16(12):e1008492. view on PubMed
Adeshina YO, Deeds EJ, Karanicolas J. 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. view on PubMed
Suppahia A, Itagi P, Burris A, Kim FMG, Vontz A, Kante A, Kim S, Im W, Deeds EJ, Roelofs J. Cooperativity in Proteasome Core Particle Maturation. iScience. 2020 May 22; 23(5):101090. view on PubMed
Nguyen AV, Trompetto B, Tan XHM, Scott MB, Hu KH, Deeds E, Butte MJ, Chiou PY, Rowat AC. 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. view on PubMed
Shockley EM, Rouzer CA, Marnett LJ, Deeds EJ, Lopez CF. Signal integration and information transfer in an allosterically regulated network. NPJ Syst Biol Appl. 2019; 5:23. view on PubMed
Vakser IA, Deeds EJ. Computational approaches to macromolecular interactions in the cell. Curr Opin Struct Biol. 2019 04; 55:59-65. view on PubMed
Suderman R, Deeds EJ. Intrinsic limits of information transmission in biochemical signalling motifs. Interface Focus. 2018 Dec 06; 8(6):20180039. view on PubMed
Nariya MK, Kim JH, Xiong J, Kleindl PA, Hewarathna A, Fisher AC, Joshi SB, Schöneich 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. J Pharm Sci. 2017 11; 106(11):3270-3279. view on PubMed
Kleindl PA, Xiong J, Hewarathna A, Mozziconacci O, Nariya MK, Fisher AC, Deeds EJ, Joshi SB, Middaugh CR, Schöneich C, Volkin DB, Forrest ML. 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. view on PubMed
Rowland MA, Greenbaum JM, Deeds EJ. Crosstalk and the evolvability of intracellular communication. Nat Commun. 2017 07 10; 8:16009. view on PubMed
Hewarathna A, Mozziconacci O, Nariya MK, Kleindl PA, Xiong J, Fisher AC, Joshi SB, Middaugh CR, Forrest ML, Volkin DB, Deeds EJ, Schöneich C. 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. view on PubMed
Suderman R, Bachman JA, Smith A, Sorger PK, Deeds EJ. 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. view on PubMed
Nariya MK, Israeli J, Shi JJ, Deeds EJ. 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. view on PubMed
Wani PS, Rowland MA, Ondracek A, Deeds EJ, Roelofs J. Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association. Nat Commun. 2015 Mar 16; 6:6384. view on PubMed
Rowland MA, Harrison B, Deeds EJ. Phosphatase specificity and pathway insulation in signaling networks. Biophys J. 2015 Feb 17; 108(4):986-996. view on PubMed
Rowland MA, Deeds EJ. Crosstalk and the evolution of specificity in two-component signaling. Proc Natl Acad Sci U S A. 2014 Apr 15; 111(15):5550-5. view on PubMed
Suderman R, Deeds EJ. Machines vs. ensembles: effective MAPK signaling through heterogeneous sets of protein complexes. PLoS Comput Biol. 2013; 9(10):e1003278. view on PubMed
Gowthaman R, Deeds EJ, Karanicolas J. Structural properties of non-traditional drug targets present new challenges for virtual screening. J Chem Inf Model. 2013 Aug 26; 53(8):2073-81. view on PubMed
Rowland MA, Fontana W, Deeds EJ. Crosstalk and competition in signaling networks. Biophys J. 2012 Dec 05; 103(11):2389-98. view on PubMed
Deeds EJ, Krivine J, Feret J, Danos V, Fontana W. Combinatorial complexity and compositional drift in protein interaction networks. PLoS One. 2012; 7(3):e32032. view on PubMed
Deeds EJ, Bachman JA, Fontana W. Optimizing ring assembly reveals the strength of weak interactions. Proc Natl Acad Sci U S A. 2012 Feb 14; 109(7):2348-53. view on PubMed
Deeds EJ, Savage V, Fontana W. Curvature in metabolic scaling: a reply to MacKay. J Theor Biol. 2011 Jul 07; 280(1):197-8. view on PubMed
Kolokotrones T, Deeds EJ, Fontana W. Curvature in metabolic scaling. Nature. 2010 Apr 01; 464(7289):753-6. view on PubMed
Savage VM, Deeds EJ, Fontana W. Sizing up allometric scaling theory. PLoS Comput Biol. 2008 Sep 12; 4(9):e1000171. view on PubMed
Deeds EJ, Ashenberg O, Gerardin J, Shakhnovich EI. Robust protein protein interactions in crowded cellular environments. Proc Natl Acad Sci U S A. 2007 Sep 18; 104(38):14952-7. view on PubMed
Perlstein EO, Deeds EJ, Ashenberg O, Shakhnovich EI, Schreiber SL. Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations. Proc Natl Acad Sci U S A. 2007 Jun 19; 104(25):10553-8. view on PubMed
Deeds EJ, Shakhnovich EI. A structure-centric view of protein evolution, design, and adaptation. Adv Enzymol Relat Areas Mol Biol. 2007; 75:133-91, xi-xii. view on PubMed
Hubner IA, Deeds EJ, Shakhnovich EI. Understanding ensemble protein folding at atomic detail. Proc Natl Acad Sci U S A. 2006 Nov 21; 103(47):17747-52. view on PubMed
Deeds EJ, Ashenberg O, Shakhnovich EI. 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. view on PubMed
Hubner IA, Deeds EJ, Shakhnovich EI. High-resolution protein folding with a transferable potential. Proc Natl Acad Sci U S A. 2005 Dec 27; 102(52):18914-9. view on PubMed
Deeds EJ, Shakhnovich EI. The emergence of scaling in sequence-based physical models of protein evolution. Biophys J. 2005 Jun; 88(6):3905-11. view on PubMed
Deeds EJ, Hennessey H, Shakhnovich EI. Prokaryotic phylogenies inferred from protein structural domains. Genome Res. 2005 Mar; 15(3):393-402. view on PubMed
Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Res. 2005 Mar; 15(3):385-92. view on PubMed
Tannenbaum E, Deeds EJ, Shakhnovich EI. Semiconservative replication in the quasispecies model. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Jun; 69(6 Pt 1):061916. view on PubMed
Deeds EJ, Shakhnovich B, Shakhnovich EI. Proteomic traces of speciation. J Mol Biol. 2004 Feb 20; 336(3):695-706. view on PubMed
Deeds EJ, Dokholyan NV, Shakhnovich EI. Protein evolution within a structural space. Biophys J. 2003 Nov; 85(5):2962-72. view on PubMed
Tannenbaum E, Deeds EJ, Shakhnovich EI. Equilibrium distribution of mutators in the single fitness peak model. Phys Rev Lett. 2003 Sep 26; 91(13):138105. view on PubMed
