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Items: 30

1.

Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks.

Lyashenko E, Niepel M, Dixit PD, Lim SK, Sorger PK, Vitkup D.

Elife. 2020 Jan 21;9. pii: e50342. doi: 10.7554/eLife.50342. [Epub ahead of print]

2.

Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks.

Dixit PD, Lyashenko E, Niepel M, Vitkup D.

Cell Syst. 2019 Dec 13. pii: S2405-4712(19)30430-2. doi: 10.1016/j.cels.2019.11.010. [Epub ahead of print]

PMID:
31864963
3.

Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling.

Ji BW, Sheth RU, Dixit PD, Huang Y, Kaufman A, Wang HH, Vitkup D.

Nat Methods. 2019 Aug;16(8):731-736. doi: 10.1038/s41592-019-0467-y. Epub 2019 Jul 15.

PMID:
31308552
4.

Introducing User-Prescribed Constraints in Markov Chains for Nonlinear Dimensionality Reduction.

Dixit PD.

Neural Comput. 2019 May;31(5):980-997. doi: 10.1162/neco_a_01184. Epub 2019 Mar 18.

PMID:
30883279
5.

Building Markov state models using optimal transport theory.

Dixit PD, Dill KA.

J Chem Phys. 2019 Feb 7;150(5):054105. doi: 10.1063/1.5086681.

PMID:
30736685
6.

Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models.

Dixit PD, Dill KA.

J Chem Theory Comput. 2018 Feb 13;14(2):1111-1119. doi: 10.1021/acs.jctc.7b01126. Epub 2018 Jan 26.

PMID:
29323898
7.

Perspective: Maximum caliber is a general variational principle for dynamical systems.

Dixit PD, Wagoner J, Weistuch C, Pressé S, Ghosh K, Dill KA.

J Chem Phys. 2018 Jan 7;148(1):010901. doi: 10.1063/1.5012990.

PMID:
29306272
8.

Mini-grand canonical ensemble: Chemical potential in the solvation shell.

Dixit PD, Bansal A, Chapman WG, Asthagiri D.

J Chem Phys. 2017 Oct 28;147(16):164901. doi: 10.1063/1.4993178.

PMID:
29096517
9.

Recombination-Driven Genome Evolution and Stability of Bacterial Species.

Dixit PD, Pang TY, Maslov S.

Genetics. 2017 Sep;207(1):281-295. doi: 10.1534/genetics.117.300061. Epub 2017 Jul 27.

10.

Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers.

Mayers JR, Torrence ME, Danai LV, Papagiannakopoulos T, Davidson SM, Bauer MR, Lau AN, Ji BW, Dixit PD, Hosios AM, Muir A, Chin CR, Freinkman E, Jacks T, Wolpin BM, Vitkup D, Vander Heiden MG.

Science. 2016 Sep 9;353(6304):1161-5. doi: 10.1126/science.aaf5171.

11.

Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes.

Dixit PD, Jain A, Stock G, Dill KA.

J Chem Theory Comput. 2015 Nov 10;11(11):5464-72. doi: 10.1021/acs.jctc.5b00537. Epub 2015 Oct 2.

PMID:
26574334
12.

Stationary properties of maximum-entropy random walks.

Dixit PD.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Oct;92(4):042149. doi: 10.1103/PhysRevE.92.042149. Epub 2015 Oct 23.

PMID:
26565210
13.

Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics.

Hazoglou MJ, Walther V, Dixit PD, Dill KA.

J Chem Phys. 2015 Aug 7;143(5):051104. doi: 10.1063/1.4928193.

PMID:
26254635
14.

Recombinant transfer in the basic genome of Escherichia coli.

Dixit PD, Pang TY, Studier FW, Maslov S.

Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):9070-5. doi: 10.1073/pnas.1510839112. Epub 2015 Jul 7.

15.

Detecting temperature fluctuations at equilibrium.

Dixit PD.

Phys Chem Chem Phys. 2015 May 21;17(19):13000-5. doi: 10.1039/c5cp01423a.

PMID:
25912565
16.

Inferring Microscopic Kinetic Rates from Stationary State Distributions.

Dixit PD, Dill KA.

J Chem Theory Comput. 2014 Aug 12;10(8):3002-3005. Epub 2014 Jun 2.

17.

A maximum entropy framework for nonexponential distributions.

Peterson J, Dixit PD, Dill KA.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20380-5. doi: 10.1073/pnas.1320578110. Epub 2013 Dec 2.

18.

Quantifying extrinsic noise in gene expression using the maximum entropy framework.

Dixit PD.

Biophys J. 2013 Jun 18;104(12):2743-50. doi: 10.1016/j.bpj.2013.05.010.

19.

A maximum entropy thermodynamics of small systems.

Dixit PD.

J Chem Phys. 2013 May 14;138(18):184111. doi: 10.1063/1.4804549.

PMID:
23676033
20.

Evolutionary capacitance and control of protein stability in protein-protein interaction networks.

Dixit PD, Maslov S.

PLoS Comput Biol. 2013 Apr;9(4):e1003023. doi: 10.1371/journal.pcbi.1003023. Epub 2013 Apr 4.

21.

Separating the role of protein restraints and local metal-site interaction chemistry in the thermodynamics of a zinc finger protein.

Dixit PD, Asthagiri D.

Biophys J. 2011 Sep 21;101(6):1459-66. doi: 10.1016/j.bpj.2011.08.006. Epub 2011 Sep 20.

22.

Ion-water clusters, bulk medium effects, and ion hydration.

Merchant S, Dixit PD, Dean KR, Asthagiri D.

J Chem Phys. 2011 Aug 7;135(5):054505. doi: 10.1063/1.3620077.

PMID:
21823710
23.

An elastic-network-based local molecular field analysis of zinc finger proteins.

Dixit PD, Asthagiri D.

J Phys Chem B. 2011 Jun 9;115(22):7374-82. doi: 10.1021/jp200244r. Epub 2011 May 12. Erratum in: J Phys Chem B. 2011 Sep 8;115(35):10571.

PMID:
21563764
24.

Thermodynamics of ion selectivity in the KcsA K+ channel.

Dixit PD, Asthagiri D.

J Gen Physiol. 2011 May;137(5):427-33. doi: 10.1085/jgp.201010533. Review. No abstract available.

25.

The role of bulk protein in local models of ion-binding to proteins: comparative study of KcsA, its semisynthetic analog with a locked-in binding site, and valinomycin.

Dixit PD, Asthagiri D.

Biophys J. 2011 Mar 16;100(6):1542-9. doi: 10.1016/j.bpj.2011.01.044. Erratum in: Biophys J. 2011 Jun 8;100(11):2852.

26.

Molecular packing and chemical association in liquid water simulated using ab initio hybrid Monte Carlo and different exchange-correlation functionals.

Weber V, Merchant S, Dixit PD, Asthagiri D.

J Chem Phys. 2010 May 28;132(20):204509. doi: 10.1063/1.3437061.

27.

Ion selectivity from local configurations of ligands in solutions and ion channels.

Asthagiri D, Dixit PD, Merchant S, Paulaitis ME, Pratt LR, Rempe SB, Varma S.

Chem Phys Lett. 2010 Jan 18;485(1-3):1-7.

28.

Ion selectivity in the KcsA potassium channel from the perspective of the ion binding site.

Dixit PD, Merchant S, Asthagiri D.

Biophys J. 2009 Mar 18;96(6):2138-45. doi: 10.1016/j.bpj.2008.12.3917.

30.

Effect of 2-5 years of tobacco smoking on ventilatory function tests.

Bajentri AL, Veeranna N, Dixit PD, Kulkarni SB.

J Indian Med Assoc. 2003 Feb;101(2):96-7, 108.

PMID:
12841492

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