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Items: 32

1.

Signal integration and information transfer in an allosterically regulated network.

Shockley EM, Rouzer CA, Marnett LJ, Deeds EJ, Lopez CF.

NPJ Syst Biol Appl. 2019 Jul 18;5:23. doi: 10.1038/s41540-019-0100-9. eCollection 2019.

2.

Computational approaches to macromolecular interactions in the cell.

Vakser IA, Deeds EJ.

Curr Opin Struct Biol. 2019 Apr;55:59-65. doi: 10.1016/j.sbi.2019.03.012. Epub 2019 Apr 15. Review.

PMID:
30999240
3.

Intrinsic limits of information transmission in biochemical signalling motifs.

Suderman R, Deeds EJ.

Interface Focus. 2018 Dec 6;8(6):20180039. doi: 10.1098/rsfs.2018.0039. Epub 2018 Oct 19.

PMID:
30443336
4.

Comparative Characterization of Crofelemer Samples Using Data Mining and Machine Learning Approaches With Analytical Stability Data Sets.

Nariya MK, Kim JH, Xiong J, Kleindl PA, Hewarathna A, Fisher AC, Joshi SB, Schöneich C, Forrest ML, Middaugh CR, Volkin DB, Deeds EJ.

J Pharm Sci. 2017 Nov;106(11):3270-3279. doi: 10.1016/j.xphs.2017.07.013. Epub 2017 Jul 22.

5.

The Botanical Drug Substance Crofelemer as a Model System for Comparative Characterization of Complex Mixture Drugs.

Kleindl PA, Xiong J, Hewarathna A, Mozziconacci O, Nariya MK, Fisher AC, Deeds EJ, Joshi SB, Middaugh CR, Schöneich C, Volkin DB, Forrest ML.

J Pharm Sci. 2017 Nov;106(11):3242-3256. doi: 10.1016/j.xphs.2017.07.012. Epub 2017 Jul 22.

6.

Crosstalk and the evolvability of intracellular communication.

Rowland MA, Greenbaum JM, Deeds EJ.

Nat Commun. 2017 Jul 10;8:16009. doi: 10.1038/ncomms16009.

7.

Chemical Stability of the Botanical Drug Substance Crofelemer: A Model System for Comparative Characterization of Complex Mixture Drugs.

Hewarathna A, Mozziconacci O, Nariya MK, Kleindl PA, Xiong J, Fisher AC, Joshi SB, Middaugh CR, Forrest ML, Volkin DB, Deeds EJ, Schöneich C.

J Pharm Sci. 2017 Nov;106(11):3257-3269. doi: 10.1016/j.xphs.2017.06.022. Epub 2017 Jul 5.

8.

Fundamental trade-offs between information flow in single cells and cellular populations.

Suderman R, Bachman JA, Smith A, Sorger PK, Deeds EJ.

Proc Natl Acad Sci U S A. 2017 May 30;114(22):5755-5760. doi: 10.1073/pnas.1615660114. Epub 2017 May 12.

9.

Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System.

Nariya MK, Israeli J, Shi JJ, Deeds EJ.

PLoS Comput Biol. 2016 Apr 14;12(4):e1004851. doi: 10.1371/journal.pcbi.1004851. eCollection 2016 Apr.

10.

Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association.

Wani PS, Rowland MA, Ondracek A, Deeds EJ, Roelofs J.

Nat Commun. 2015 Mar 16;6:6384. doi: 10.1038/ncomms7384.

11.

Phosphatase specificity and pathway insulation in signaling networks.

Rowland MA, Harrison B, Deeds EJ.

Biophys J. 2015 Feb 17;108(4):986-996. doi: 10.1016/j.bpj.2014.12.011.

12.

Crosstalk and the evolution of specificity in two-component signaling.

Rowland MA, Deeds EJ.

Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):5550-5. doi: 10.1073/pnas.1317178111. Epub 2014 Mar 31.

13.

Machines vs. ensembles: effective MAPK signaling through heterogeneous sets of protein complexes.

Suderman R, Deeds EJ.

PLoS Comput Biol. 2013;9(10):e1003278. doi: 10.1371/journal.pcbi.1003278. Epub 2013 Oct 10.

14.

Structural properties of non-traditional drug targets present new challenges for virtual screening.

Gowthaman R, Deeds EJ, Karanicolas J.

J Chem Inf Model. 2013 Aug 26;53(8):2073-81. doi: 10.1021/ci4002316. Epub 2013 Aug 13.

15.

Crosstalk and competition in signaling networks.

Rowland MA, Fontana W, Deeds EJ.

Biophys J. 2012 Dec 5;103(11):2389-98. doi: 10.1016/j.bpj.2012.10.006.

16.

Combinatorial complexity and compositional drift in protein interaction networks.

Deeds EJ, Krivine J, Feret J, Danos V, Fontana W.

PLoS One. 2012;7(3):e32032. doi: 10.1371/journal.pone.0032032. Epub 2012 Mar 8.

17.

Optimizing ring assembly reveals the strength of weak interactions.

Deeds EJ, Bachman JA, Fontana W.

Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2348-53. doi: 10.1073/pnas.1113095109. Epub 2012 Jan 30.

18.

Curvature in metabolic scaling: a reply to MacKay.

Deeds EJ, Savage V, Fontana W.

J Theor Biol. 2011 Jul 7;280(1):197-8. doi: 10.1016/j.jtbi.2011.03.036. Epub 2011 Apr 9. No abstract available.

PMID:
21497609
19.

Curvature in metabolic scaling.

Kolokotrones T, Van Savage, Deeds EJ, Fontana W.

Nature. 2010 Apr 1;464(7289):753-6. doi: 10.1038/nature08920.

PMID:
20360740
20.

Sizing up allometric scaling theory.

Savage VM, Deeds EJ, Fontana W.

PLoS Comput Biol. 2008 Sep 12;4(9):e1000171. doi: 10.1371/journal.pcbi.1000171.

21.

Robust protein protein interactions in crowded cellular environments.

Deeds EJ, Ashenberg O, Gerardin J, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2007 Sep 18;104(38):14952-7. Epub 2007 Sep 11.

22.

Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations.

Perlstein EO, Deeds EJ, Ashenberg O, Shakhnovich EI, Schreiber SL.

Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10553-8. Epub 2007 Jun 12.

23.

A structure-centric view of protein evolution, design, and adaptation.

Deeds EJ, Shakhnovich EI.

Adv Enzymol Relat Areas Mol Biol. 2007;75:133-91, xi-xii. Review.

PMID:
17124867
24.

Understanding ensemble protein folding at atomic detail.

Hubner IA, Deeds EJ, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17747-52. Epub 2006 Nov 9.

25.

A simple physical model for scaling in protein-protein interaction networks.

Deeds EJ, Ashenberg O, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):311-6. Epub 2005 Dec 29.

26.

High-resolution protein folding with a transferable potential.

Hubner IA, Deeds EJ, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18914-9. Epub 2005 Dec 19.

27.

The emergence of scaling in sequence-based physical models of protein evolution.

Deeds EJ, Shakhnovich EI.

Biophys J. 2005 Jun;88(6):3905-11. Epub 2005 Apr 1.

28.

Prokaryotic phylogenies inferred from protein structural domains.

Deeds EJ, Hennessey H, Shakhnovich EI.

Genome Res. 2005 Mar;15(3):393-402.

29.

Semiconservative replication in the quasispecies model.

Tannenbaum E, Deeds EJ, Shakhnovich EI.

Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Jun;69(6 Pt 1):061916. Epub 2004 Jun 16.

PMID:
15244626
30.

Proteomic traces of speciation.

Deeds EJ, Shakhnovich B, Shakhnovich EI.

J Mol Biol. 2004 Feb 20;336(3):695-706.

PMID:
15095981
31.

Protein evolution within a structural space.

Deeds EJ, Dokholyan NV, Shakhnovich EI.

Biophys J. 2003 Nov;85(5):2962-72.

32.

Equilibrium distribution of mutators in the single fitness peak model.

Tannenbaum E, Deeds EJ, Shakhnovich EI.

Phys Rev Lett. 2003 Sep 26;91(13):138105. Epub 2003 Sep 26.

PMID:
14525341

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