Ilya Nemenman, PhD, MS

Research Program

Cell and Molecular Biology
Phone Number

404-727-9286
Email Address

ilya.nemenman@emory.edu

Biography

Ilya Nemenman, PhD, MS, is an associate professor in the Department of Biology and in the Department of Physics at Emory University. Dr. Nemenman is a member of the Cell and Molecular Biology Research Program at Winship.

Education

Dr. Nemenman earned his PhD in Physics from Princeton University and his MS in Physics from San Francisco State University.

Titles & Roles

Associate Professor, Department of Biology

Emory University
Associate Professor, Department of Physics

Emory University

Research

Dr. Nemenman's research focuses on working to understand how biological systems, such as cells, organisms, and populations, learn from their surrounding environment and respond to it.

Publications

Title/Journal	Authors	Publication Date
Randomness with constraints: constructing minimal models for high-dimensional biology. ArXiv	I Nemenman, P Mehta	09/03/2025
Physics-tailored machine learning reveals unexpected physics in dusty plasmas. Proceedings of the National Academy of Sciences of the United States of America	W Yu, E Abdelaleem, I Nemenman, JC Burton	08/05/2025
A mathematical model for ketosis-prone diabetes suggests the existence of multiple pancreatic β-cell inactivation mechanisms. eLife	SA Ridout, P Vellanki, I Nemenman	07/15/2025
Variance in C. elegans gut bacterial load suggests complex host-microbe dynamics. PLoS computational biology	SS Boddu, KM Martini, I Nemenman, NM Vega	06/01/2025
A mathematical model for ketosis-prone diabetes suggests the existence of multiple pancreatic β-cell inactivation mechanisms. bioRxiv : the preprint server for biology	SA Ridout, P Vellanki, I Nemenman	04/28/2025
Millisecond-scale motor coding precedes sensorimotor learning in songbirds. bioRxiv : the preprint server for biology	LMM Pascual, A Vusirikala, IM Nemenman, SJ Sober, M Pasek	12/22/2024
Maximum likelihood estimators for colony-forming units. Microbiology spectrum	KM Martini, SS Boddu, I Nemenman, NM Vega	09/03/2024
Data Efficiency, Dimensionality Reduction, and the Generalized Symmetric Information Bottleneck. Neural computation	KM Martini, I Nemenman	06/07/2024
Neural criticality from effective latent variables. eLife	MC Morrell, I Nemenman, A Sederberg	03/12/2024
Bayesian estimation of the Kullback-Leibler divergence for categorical systems using mixtures of Dirichlet priors. Physical review. E	F Camaglia, I Nemenman, T Mora, AM Walczak	02/01/2024
Neural criticality from effective latent variables. ArXiv	M Morrell, I Nemenman, AJ Sederberg	10/13/2023
Extrinsic vs Intrinsic Criticality in Systems with Many Components. ArXiv	V Ngampruetikorn, I Nemenman, DJ Schwab	09/25/2023
Inferring local structure from pairwise correlations. Physical review. E	M Rahman, I Nemenman	09/01/2023
Low-probability states, data statistics, and entropy estimation. Physical review. E	DG Hernández, A Roman, I Nemenman	07/01/2023
A dynamical model of C. elegans thermal preference reveals independent excitatory and inhibitory learning pathways. Proceedings of the National Academy of Sciences of the United States of America	A Roman, K Palanski, I Nemenman, WS Ryu	03/28/2023
Statistical properties of large data sets with linear latent features. Physical review. E	P Fleig, I Nemenman	07/01/2022
Unsupervised Bayesian Ising Approximation for decoding neural activity and other biological dictionaries. eLife	DG Hernández, SJ Sober, I Nemenman	03/22/2022
Constrained brain volume in an efficient coding model explains the fraction of excitatory and inhibitory neurons in sensory cortices. PLoS computational biology	A Alreja, I Nemenman, CJ Rozell	01/01/2022
Latent Dynamical Variables Produce Signatures of Spatiotemporal Criticality in Large Biological Systems. Physical review letters	MC Morrell, AJ Sederberg, I Nemenman	03/19/2021
Inferring phenomenological models of first passage processes. PLoS computational biology	C Rivera, D Hofmann, I Nemenman	03/01/2021
Precise spatial memory in local random networks. Physical review. E	JL Natale, HGE Hentschel, I Nemenman	08/01/2020
Randomly connected networks generate emergent selectivity and predict decoding properties of large populations of neurons. PLoS computational biology	A Sederberg, I Nemenman	05/01/2020
Universal Properties of Concentration Sensing in Large Ligand-Receptor Networks. Physical review letters	V Singh, I Nemenman	01/17/2020
Physical Limit to Concentration Sensing in a Changing Environment. Physical review letters	T Mora, I Nemenman	11/08/2019
Estimation of mutual information for real-valued data with error bars and controlled bias. Physical review. E	CM Holmes, I Nemenman	08/01/2019
Automated, predictive, and interpretable inference of Caenorhabditis elegans escape dynamics. Proceedings of the National Academy of Sciences of the United States of America	BC Daniels, WS Ryu, I Nemenman	04/09/2019
Receptor crosstalk improves concentration sensing of multiple ligands. Physical review. E	M Carballo-Pacheco, J Desponds, T Gavrilchenko, A Mayer, R Prizak, G Reddy, I Nemenman, T Mora	02/01/2019
Millisecond Spike Timing Codes for Motor Control. Trends in neurosciences	SJ Sober, S Sponberg, I Nemenman, LH Ting	10/01/2018
Chance, long tails, and inference in a non-Gaussian, Bayesian theory of vocal learning in songbirds. Proceedings of the National Academy of Sciences of the United States of America	B Zhou, D Hofmann, I Pinkoviezky, SJ Sober, I Nemenman	09/04/2018
Luria-Delbrück, revisited: the classic experiment does not rule out Lamarckian evolution. Physical biology	CM Holmes, M Ghafari, A Abbas, V Saravanan, I Nemenman	08/21/2017
Growth of bacteria in 3-d colonies. PLoS computational biology	X Shao, A Mugler, J Kim, HJ Jeong, BR Levin, I Nemenman	07/01/2017
Single variant bottleneck in the early dynamics of H. influenzae bacteremia in neonatal rats questions the theory of independent action. Physical biology	X Shao, B Levin, I Nemenman	06/15/2017
Simple biochemical networks allow accurate sensing of multiple ligands with a single receptor. PLoS computational biology	V Singh, I Nemenman	04/01/2017
Motor control by precisely timed spike patterns. Proceedings of the National Academy of Sciences of the United States of America	KH Srivastava, CM Holmes, M Vellema, AR Pack, CP Elemans, I Nemenman, SJ Sober	01/31/2017
Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level. PLoS computational biology	K Leung, A Mohammadi, WS Ryu, I Nemenman	12/01/2016
Effects of receptor correlations on molecular information transmission. Physical review. E	V Singh, M Tchernookov, I Nemenman	08/01/2016
Role of spatial averaging in multicellular gradient sensing. Physical biology	T Smith, S Fancher, A Levchenko, I Nemenman, A Mugler	05/20/2016
Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis. Proceedings of the National Academy of Sciences of the United States of America	D Ellison, A Mugler, MD Brennan, SH Lee, RJ Huebner, ER Shamir, LA Woo, J Kim, P Amar, I Nemenman, AJ Ewald, A Levchenko	02/09/2016
Limits to the precision of gradient sensing with spatial communication and temporal integration. Proceedings of the National Academy of Sciences of the United States of America	A Mugler, A Levchenko, I Nemenman	02/09/2016
The eighth q-bio conference: meeting report and special issue preface. Physical biology	WS Hlavacek, S Gnanakaran, B Munsky, ME Wall, JR Faeder, Y Jiang, I Nemenman, O Resnekov	12/30/2015
Automated adaptive inference of phenomenological dynamical models. Nature communications	BC Daniels, I Nemenman	08/21/2015
Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression. PloS one	BC Daniels, I Nemenman	01/01/2015
Millisecond-scale motor encoding in a cortical vocal area. PLoS biology	C Tang, D Chehayeb, K Srivastava, I Nemenman, SJ Sober	12/01/2014
Zipf's law and criticality in multivariate data without fine-tuning. Physical review letters	DJ Schwab, I Nemenman, P Mehta	08/08/2014
Cellular noise and information transmission. Current opinion in biotechnology	A Levchenko, I Nemenman	08/01/2014
The Seventh q-bio Conference: meeting report and preface. Physical biology	I Nemenman, JR Faeder, S Gnanakaran, WS Hlavacek, B Munsky, ME Wall, Y Jiang	08/01/2014
Director field model of the primary visual cortex for contour detection. PloS one	V Singh, M Tchernookov, R Butterfield, I Nemenman	01/01/2014
A large number of receptors may reduce cellular response time variation. Physical biology	X Cheng, L Merchan, M Tchernookov, I Nemenman	06/01/2013
Population-expression models of immune response. Physical biology	SP Stromberg, R Antia, I Nemenman	06/01/2013
Special section dedicated to The Sixth q-bio Conference: meeting report and preface. Physical biology	I Nemenman, S Gnanakaran, B Munsky, ME Wall, Y Jiang, WS Hlavacek, JR Faeder	06/01/2013
Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter. PloS one	J Otwinowski, I Nemenman	01/01/2013
Fitness in time-dependent environments includes a geometric phase contribution. Journal of the Royal Society, Interface	S Tanase-Nicola, I Nemenman	06/07/2012
Gain control in molecular information processing: lessons from neuroscience. Physical biology	I Nemenman	01/01/2012
Information transduction capacity of noisy biochemical signaling networks. Science (New York, N.Y.)	R Cheong, A Rhee, CJ Wang, I Nemenman, A Levchenko	10/21/2011
Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing. Physical biology	I Nemenman, JR Faeder, WS Hlavacek, Y Jiang, ME Wall, A Zilman	10/01/2011
Model cortical association fields account for the time course and dependence on target complexity of human contour perception. PLoS computational biology	V Gintautas, MI Ham, B Kunsberg, S Barr, SP Brumby, C Rasmussen, JS George, I Nemenman, LM Bettencourt, GT Kenyon	10/01/2011
Speeding up Evolutionary Search by Small Fitness Fluctuations. Journal of statistical physics	J Otwinowski, S Tanase-Nicola, I Nemenman	07/01/2011
Mass conservation and inference of metabolic networks from high-throughput mass spectrometry data. Journal of computational biology : a journal of computational molecular cell biology	P Bandaru, M Bansal, I Nemenman	02/01/2011
Multivariate dependence and genetic networks inference. IET systems biology	AA Margolin, K Wang, A Califano, I Nemenman	11/01/2010
The Third q-bio Conference on Cellular Information Processing. IET systems biology	I Nemenman, WS Hlavacek, Y Jiang, ME Wall, A Zilman	11/01/2010
Time-dependent corrections to effective rate and event statistics in Michaelis-Menten kinetics. IET systems biology	NA Sinitsyn, I Nemenman	11/01/2010
The simplicity of completion time distributions for common complex biochemical processes. Physical biology	G Bel, B Munsky, I Nemenman	12/21/2009
Specificity and completion time distributions of biochemical processes. The Journal of chemical physics	B Munsky, I Nemenman, G Bel	12/21/2009
Mesoscopic statistical properties of multistep enzyme-mediated reactions. IET systems biology	WH de Ronde, BC Daniels, A Mugler, NA Sinitsyn, I Nemenman	09/01/2009
Quantifying evolvability in small biological networks. IET systems biology	A Mugler, E Ziv, I Nemenman, CH Wiggins	09/01/2009
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nature biotechnology	K Wang, M Saito, BC Bisikirska, MJ Alvarez, WK Lim, P Rajbhandari, Q Shen, I Nemenman, K Basso, AA Margolin, U Klein, R Dalla-Favera, A Califano	09/01/2009
Adiabatic coarse-graining and simulations of stochastic biochemical networks. Proceedings of the National Academy of Sciences of the United States of America	NA Sinitsyn, N Hengartner, I Nemenman	06/30/2009
Determinants of bistability in induction of the Escherichia coli lac operon. IET systems biology	DW Dreisigmeyer, J Stajic, I Nemenman, WS Hlavacek, ME Wall	09/01/2008
Serially regulated biological networks fully realise a constrained set of functions. IET systems biology	A Mugler, E Ziv, I Nemenman, CH Wiggins	09/01/2008
Neural coding of natural stimuli: information at sub-millisecond resolution. PLoS computational biology	I Nemenman, GD Lewen, W Bialek, RR de Ruyter van Steveninck	03/07/2008