Publications

1. Natesan G, Hamilton T, Deeds EJ, Shah PK. Novel metrics reveal new structure and unappreciated heterogeneity in Caenorhabditis elegans development.. PLoS computational biology, 2023.
2. Natesan G, Hamilton T, Deeds EJ, Shah PK. Novel metrics reveal new structure and unappreciated heterogeneity in C. elegans development.. bioRxiv : the preprint server for biology, 2023.
3. Ly C, Ogana H, Kim HN, Hurwitz S, Deeds EJ, Kim YM, Rowat AC. Altered physical phenotypes of leukemia cells that survive chemotherapy treatment.. Integrative biology : quantitative biosciences from nano to macro, 2023.
4. Vakser IA, Grudinin S, Jenkins NW, Kundrotas PJ, Deeds EJ. Docking-based long timescale simulation of cell-size protein systems at atomic resolution.. Proceedings of the National Academy of Sciences of the United States of America, 2022.
5. Itagi P, Kante A, Lagunes L, Deeds EJ. Understanding the separation of timescales in bacterial proteasome core particle assembly.. Biophysical journal, 2022.
6. Garfinkel A, Bennoun S, Deeds E, Van Valkenburgh B. Teaching Dynamics to Biology Undergraduates: the UCLA Experience.. Bulletin of mathematical biology, 2022.
7. Nariya MK, Mallela A, Shi JJ, Deeds EJ. Robustness and the evolution of length control strategies in the T3SS and flagellar hook.. Biophysical journal, 2021.
8. Tang Y, Adelaja A, Ye FX, Deeds E, Wollman R, Hoffmann A. Quantifying information accumulation encoded in the dynamics of biochemical signaling.. Nature communications, 2021.
9. Mallela A, Nariya MK, Deeds EJ. Crosstalk and ultrasensitivity in protein degradation pathways.. PLoS computational biology, 2020.
10. Adeshina YO, Deeds EJ, Karanicolas J. Machine learning classification can reduce false positives in structure-based virtual screening.. Proceedings of the National Academy of Sciences of the United States of America, 2020.
11. 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.
12. 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.. Cellular and molecular bioengineering, 2019.
13. Shockley EM, Rouzer CA, Marnett LJ, Deeds EJ, Lopez CF. Signal integration and information transfer in an allosterically regulated network.. NPJ systems biology and applications, 2019.
14. Vakser IA, Deeds EJ. Computational approaches to macromolecular interactions in the cell.. Current opinion in structural biology, 2019.
15. Suderman R, Deeds EJ. Intrinsic limits of information transmission in biochemical signalling motifs.. Interface focus, 2018.
16. 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.. Journal of pharmaceutical sciences, 2017.
17. 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.. Journal of pharmaceutical sciences, 2017.
18. Rowland MA, Greenbaum JM, Deeds EJ. Crosstalk and the evolvability of intracellular communication.. Nature communications, 2017.
19. 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.. Journal of pharmaceutical sciences, 2017.
20. Suderman R, Bachman JA, Smith A, Sorger PK, Deeds EJ. Fundamental trade-offs between information flow in single cells and cellular populations.. Proceedings of the National Academy of Sciences of the United States of America, 2017.
21. 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 computational biology, 2016.
22. 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.. Nature communications, 2015.
23. Rowland MA, Harrison B, Deeds EJ. Phosphatase specificity and pathway insulation in signaling networks.. Biophysical journal, 2015.
24. Rowland MA, Deeds EJ. Crosstalk and the evolution of specificity in two-component signaling.. Proceedings of the National Academy of Sciences of the United States of America, 2014.
25. Suderman R, Deeds EJ. Machines vs. ensembles: effective MAPK signaling through heterogeneous sets of protein complexes.. PLoS computational biology, 2013.
26. Gowthaman R, Deeds EJ, Karanicolas J. Structural properties of non-traditional drug targets present new challenges for virtual screening.. Journal of chemical information and modeling, 2013.
27. Rowland MA, Fontana W, Deeds EJ. Crosstalk and competition in signaling networks.. Biophysical journal, 2012.
28. Deeds EJ, Krivine J, Feret J, Danos V, Fontana W. Combinatorial complexity and compositional drift in protein interaction networks.. PloS one, 2012.
29. Deeds EJ, Bachman JA, Fontana W. Optimizing ring assembly reveals the strength of weak interactions.. Proceedings of the National Academy of Sciences of the United States of America, 2012.
30. Deeds EJ, Savage V, Fontana W. Curvature in metabolic scaling: a reply to MacKay.. Journal of theoretical biology, 2011.
31. Kolokotrones T, Deeds EJ, Fontana W. Curvature in metabolic scaling.. Nature, 2010.
32. Savage VM, Deeds EJ, Fontana W. Sizing up allometric scaling theory.. PLoS computational biology, 2008.
33. Deeds EJ, Ashenberg O, Gerardin J, Shakhnovich EI. Robust protein protein interactions in crowded cellular environments.. Proceedings of the National Academy of Sciences of the United States of America, 2007.
34. Perlstein EO, Deeds EJ, Ashenberg O, Shakhnovich EI, Schreiber SL. Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations.. Proceedings of the National Academy of Sciences of the United States of America, 2007.
35. Deeds EJ, Shakhnovich EI. A structure-centric view of protein evolution, design, and adaptation.. Advances in enzymology and related areas of molecular biology, 2007.
36. Hubner IA, Deeds EJ, Shakhnovich EI. Understanding ensemble protein folding at atomic detail.. Proceedings of the National Academy of Sciences of the United States of America, 2006.
37. Deeds EJ, Ashenberg O, Shakhnovich EI. A simple physical model for scaling in protein-protein interaction networks.. Proceedings of the National Academy of Sciences of the United States of America, 2005.
38. Hubner IA, Deeds EJ, Shakhnovich EI. High-resolution protein folding with a transferable potential.. Proceedings of the National Academy of Sciences of the United States of America, 2005.
39. Deeds EJ, Shakhnovich EI. The emergence of scaling in sequence-based physical models of protein evolution.. Biophysical journal, 2005.
40. Deeds EJ, Hennessey H, Shakhnovich EI. Prokaryotic phylogenies inferred from protein structural domains.. Genome research, 2005.
41. Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. Protein structure and evolutionary history determine sequence space topology.. Genome research, 2005.
42. Tannenbaum E, Deeds EJ, Shakhnovich EI. Semiconservative replication in the quasispecies model.. Physical review. E, Statistical, nonlinear, and soft matter physics, 2004.
43. Deeds EJ, Shakhnovich B, Shakhnovich EI. Proteomic traces of speciation.. Journal of molecular biology, 2004.
44. Deeds EJ, Dokholyan NV, Shakhnovich EI. Protein evolution within a structural space.. Biophysical journal, 2003.
45. Tannenbaum E, Deeds EJ, Shakhnovich EI. Equilibrium distribution of mutators in the single fitness peak model.. Physical review letters, 2003.