Published/Accepted (As a faculty)

• GENERALIST: An efficient generative model for protein sequence families (to appear in PLoS Computational Biology), Akl H., Emison B., Mondal A., Perez A. Dixit P. D. 

• The ability to sense the environment is heterogeneously distributed in cell populations (to appear in eLife), Goetz A*, Hoda Akl H*, Dixit P. D. 

• EMBED: a low dimensional reconstruction of gut microbiome dynamics based on ecological normal modes (NPJ Sys Bio and App, 2023), Shahin M., Ji. B, and Dixit P. D., 

• Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited (Nature Metabolism, 2022). Li Z*, Ji B*, Dixit, PD*, Lien E, Tchourine K, Hoisos A, Abbott KL,  Westermark AM, Gorodetsky EF, Sullivan LB, Vander Heiden MG, and Vitkup D

• SiGMoiD: A superstatistical generative model for binary data (PLoS Computational Biology, 2021), Zhao X., Plata G., and Dixit P. D.  

• The biphasic and age-dependent impact of Klotho on hallmarks of aging and skeletal muscle function (eLife, 2021), Clemens Z,. Sivakumar S., Pius A., Sahu A., Shinde S., Mamiya. Luketich N., Cui, J., Dixit P. D., Hoeck J., Kreuz S., Franti M., Barchowsky A., Ambrosio F

• Reverse plasticity underlies rapid evolution by clonal selection within populations of fibroblasts propagated on a novel soft substrate (Molecular Biology and Evolution, 2021), Purkayastha P., Pendyala K., Saxena A., Hakimjavadi H., Chamala S., Dixit P. D., Baer C., and Lele T.

• Thermal behavior of small magnets (Journal of Statistical Mechanics: Theory and Experiments, 2021), Herron, L. and Dixit P. D. 

• TMI: Thermodynamic inference of data manifolds (Physical review research, 2020), Dixit PD.  

Published/Accepted (As a trainee)

• Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks (eLife, 2020), Lyashenko E*, Niepel M*, Dixit PD*, Lim SK, Sorger P, and Vitkup D

• Macroecological dynamics of gut bacteria (to appear in Nature Microbiology, 2020), Ji B*, Sheth R*, Dixit PD, Tchourine K, and Vitkup D. Featured on the cover! Featured on EurekAlert.org!

• The Maximum Caliber Variational Principle for Nonequilibria (Annual reviews of Physical Chemistry, 2020), Ghosh K*, Dixit PD*, Agozzino L, and Dill K 

• Maximum Entropy Framework For Inference Of Cell Population Heterogeneity In Signaling Networks (Cell Systems, 2020), Dixit PD*, Lyashenko E*, Niepel M, and Vitkup D.

• Quantifying spatiotemporal dynamics and noise in absolute microbiota abundances using replicate sampling (Nature Methods 2019), Ji B*, Sheth R*, Dixit PD*, Huang Y, Kaufman A, Wang H, and Vitkup D. Featured on the cover!

• Introducing user-prescribed constraints in Markov chains for nonlinear dimensionality reduction (Neural Computation 2019). Dixit PD

• Building Markov state models using optimal transport theory (Journal of Chemical Physics 2019), Dixit PD and Dill K

• Entropy production rate as a criterion for inconsistency in decision theory (Journal of Statistical Mechanics 2019), Dixit PD

• Communication: Introducing prescribed biases in out-of-equilibrium Markov models (Journal of Chemical Physics 2018), Dixit PD. Featured in the JCP editor's choice 2018 collection!

• Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models (Journal of Chemical Theory and Computation 2018), Dixit PD and Dill K

• Perspective: Maximum caliber is a general variational principle for dynamical systems (Journal of Chemical Physics 2018), Dixit PD, et al.

• Mini-grand canonical ensemble: Chemical potential in the solvation shell (Journal of Chemical Physics 2017), Dixit PD, Bansal A, Chapman G, and Asthagiri D. Editor's pick!

• Recombination-driven genome evolution and stability of bacterial species (Genetics 2017), Dixit PD, Pang TY, and Maslov S. Featured on EurekAlert.org and Phys.org 

• Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers (Science 2016), Mayers J et al.

• Stationary properties of maximum-entropy random walks (Physical Review E 2015), Dixit PD

• Recombinant transfer in the basic genome of Escherichia coli (PNAS 2015), Dixit PD*, Pang TY*, Studier FW, and Maslov S. Recommended in F1000Prime

• Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics (Journal of Chemical Physics 2015), Hazoglou M*, Walther V*, Dixit PD, and Dill K

• Inferring transition rates of networks from populations in continuous-time Markov processes (Journal of Chemical Theory and Computation 2015), Dixit PD, Jain A, Stock G, and Dill K

• Detecting temperature fluctuations at equilibrium (Physical Chemistry Chemical Physics 2015), Dixit PD

• Inferring microscopic kinetic rates from stationary state distributions (Journal of Chemical Theory and Computation 2014), Dixit PD, and Dill K

• A maximum entropy framework for nonexponential distributions (PNAS 2013), Peterson J, Dixit PD, and Dill K

• Evolutionary Capacitance and Control of Protein Stability in Protein-Protein Interaction Networks (PLoS Computational Biology 2013), Dixit PD and Maslov S

• Quantifying Extrinsic Noise in Gene Expression Using the Maximum Entropy Framework (Biophysical Journal 2013), Dixit PD 

• A maximum entropy thermodynamics of small systems (Journal of Chemical Physics 2013), Dixit PD

• Separating the Role of Protein Restraints and Local Metal-Site Interaction Chemistry in the Thermodynamics of a Zinc Finger Protein (Biophysical Journal 2011), Dixit PD and Asthagiri D

• Ion-water clusters, bulk medium effects, and ion hydration (Journal of Chemical Physics 2011), Merchant S, Dixit PD, Dean K, and Asthagiri D

• An Elastic-Network-Based Local Molecular Field Analysis of Zinc Finger Proteins (Journal of Physical Chemistry B 2011), Dixit PD and Asthagiri D

• 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 (Biophysical Journal 2011), Dixit PD and Asthagiri D

• Thermodynamics of ion selectivity in the KcsA K+ channel (Journal of General Physiology 2011), Dixit PD and Asthagiri D

• Molecular packing and chemical association in liquid water simulated using ab initio hybrid Monte Carlo and different exchange-correlation functionals (Journal of Chemical Physics 2010), Weber V, Merchant S, Dixit PD, and Asthagiri D

• Ion selectivity from local configurations of ligands in solutions and ion channels (Chemical Physics Letters 2010), Asthagiri D, Dixit PD, et al.

• Ion Selectivity in the KcsA Potassium Channel from the Perspective of the Ion Binding Site (Biophysical Journal 2009), Dixit PD, Merchant S, and Asthagiri D

• A simple measure of native‐state topology and chain connectivity predicts the folding rates of two‐state proteins with and without crosslinks (Proteins 2006), Dixit PD and Weikl T.