Peter J. Thomas

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 54

Top Topics

Information Theory

Stochastic Simulation

Top Venues

IEEE Trans. Mol. Biol. Multi Scale Commun.

Living Machines

Publications

Casey O. Diekman, Peter J. Thomas, Christopher G. Wilson
COVID-19 and silent hypoxemia in a minimal closed-loop model of the respiratory rhythm generator. Biol. Cybern. 118 (3-4) (2024)
Chris Fietkiewicz, Robert A. McDougal, David Corrales Marco, Hillel J. Chiel, Peter J. Thomas
Tutorial: using NEURON for neuromechanical simulations. Frontiers Comput. Neurosci. 17 (2023)
Zhuojun Yu, Jonathan E. Rubin, Peter J. Thomas
Sensitivity to Control Signals in Triphasic Rhythmic Neural Systems: A Comparative Mechanistic Analysis via Infinitesimal Local Timing Response Curves. Neural Comput. 35 (6) (2023)
Tyler Barker, Peter J. Thomas, Massimiliano Pierobon
A Metric to Quantify Subjective Information in Biological Gradient Sensing. GLOBECOM (2023)
Daniel Chen, Alexander G. Strang, Andrew W. Eckford, Peter J. Thomas
Explicitly Solvable Continuous-time Inference for Partially Observed Markov Processes. CoRR (2023)
Shane Riddle, William Nourse, Zhuojun Yu, Peter J. Thomas, Roger D. Quinn
A Synthetic Nervous System with Coupled Oscillators Controls Peristaltic Locomotion. Living Machines (2022)
Wenhuan Sun, Mengdi Xu, Jeffrey P. Gill, Peter J. Thomas, Hillel J. Chiel, Victoria A. Webster-Wood
GymSlug: Deep Reinforcement Learning Toward Bio-inspired Control Based on Aplysia californica Feeding. Living Machines (2022)
Alexander S. Moffett, Peter J. Thomas, Michael Hinczewski, Andrew W. Eckford
Cheater suppression and stochastic clearance through quorum sensing. PLoS Comput. Biol. 18 (7) (2022)
Alberto Pérez-Cervera, Benjamin Lindner, Peter J. Thomas
Quantitative comparison of the mean-return-time phase and the stochastic asymptotic phase for noisy oscillators. Biol. Cybern. 116 (2) (2022)
J. MacLaurin, Jean-Marc Fellous, Peter J. Thomas, Benjamin Lindner
Stochastic oscillators in biology: introduction to the special issue. Biol. Cybern. 116 (2) (2022)
Daniel Chen, Alexander G. Strang, Andrew W. Eckford, Peter J. Thomas
Explicitly Solvable Continuous-Time Inference for Partially Observed Markov Processes. IEEE Trans. Signal Process. 70 (2022)
Yangyang Wang, Jeffrey P. Gill, Hillel J. Chiel, Peter J. Thomas
Variational and phase response analysis for limit cycles with hard boundaries, with applications to neuromechanical control problems. Biol. Cybern. 116 (5) (2022)
Alexander Strang, Karen C. Abbott, Peter J. Thomas
The Network HHD: Quantifying Cyclic Competition in Trait-Performance Models of Tournaments. SIAM Rev. 64 (2) (2022)
Konstantin Holzhausen, Lukas Ramlow, Shusen Pu, Peter J. Thomas, Benjamin Lindner
Mean-return-time phase of a stochastic oscillator provides an approximate renewal description for the associated point process. Biol. Cybern. 116 (2) (2022)
Tyler Barker, Massimiliano Pierobon, Peter J. Thomas
Subjective Information and Survival in a Simulated Biological System. Entropy 24 (5) (2022)
Shusen Pu, Peter J. Thomas
Correction to: Resolving molecular contributions of ion channel noise to interspike interval variability through stochastic shielding. Biol. Cybern. 115 (3) (2021)
Zhuojun Yu, Peter J. Thomas
Dynamical consequences of sensory feedback in a half-center oscillator coupled to a simple motor system. Biol. Cybern. 115 (2) (2021)
Yangyang Wang, Jeffrey P. Gill, Hillel J. Chiel, Peter J. Thomas
Shape versus Timing: Linear Responses of a Limit Cycle with Hard Boundaries under Instantaneous and Static Perturbation. SIAM J. Appl. Dyn. Syst. 20 (2) (2021)
Victoria A. Webster-Wood, Jeffrey P. Gill, Peter J. Thomas, Hillel J. Chiel
Correction to: Control for multifunctionality: bioinspired control based on feeding in Aplysia californica. Biol. Cybern. 115 (2) (2021)
Shusen Pu, Peter J. Thomas
Resolving molecular contributions of ion channel noise to interspike interval variability through stochastic shielding. Biol. Cybern. 115 (3) (2021)
Tyler Barker, Peter J. Thomas, Massimiliano Pierobon
Subjective Information in Life Processes: A Computational Case Study. NANOCOM (2021)
Benjamin Lindner, Peter J. Thomas, Jean-Marc Fellous, Paul H. E. Tiesinga
Biological Cybernetics: 60 years and more to come. Biol. Cybern. 115 (1) (2021)
Alexander Cao, Benjamin Lindner, Peter J. Thomas
A Partial Differential Equation for the Mean-Return-Time Phase of Planar Stochastic Oscillators. SIAM J. Appl. Math. 80 (1) (2020)
Marshaun N. Fitzpatrick, Yangyang Wang, Peter J. Thomas, Roger D. Quinn, Nicholas S. Szczecinski
Robotics Application of a Method for Analytically Computing Infinitesimal Phase Response Curves. Living Machines (2020)
Shusen Pu, Peter J. Thomas
Resolving Molecular Contributions of Ion Channel Noise to Interspike Interval Variability through Stochastic Shielding. CoRR (2020)
Victoria A. Webster-Wood, Jeffrey P. Gill, Peter J. Thomas, Hillel J. Chiel
Control for multifunctionality: bioinspired control based on feeding in Aplysia californica. Biol. Cybern. 114 (6) (2020)
Shusen Pu, Peter J. Thomas
Fast and Accurate Langevin Simulations of Stochastic Hodgkin-Huxley Dynamics. Neural Comput. 32 (10) (2020)
Shusen Pu, Peter J. Thomas
Fast and Accurate Langevin Simulations of Stochastic Hodgkin-Huxley Dynamics. CoRR (2020)
Benjamin Lindner, Peter J. Thomas, Jean-Marc Fellous
A Renewed Vision for Biological Cybernetics. Biol. Cybern. 114 (3) (2020)
Victoria A. Webster-Wood, Jeffrey P. Gill, Peter J. Thomas, Hillel J. Chiel
Control for Multifunctionality: Bioinspired Control Based on Feeding in Aplysia californica. CoRR (2020)
Alexander Cao, Benjamin Lindner, Peter J. Thomas
A Partial Differential Equation for the Mean-Return-Time Phase of Planar Stochastic Oscillators. CoRR (2019)
Gregory R. Hessler, Andrew W. Eckford, Peter J. Thomas
Linear Noise Approximation of Intensity-Driven Signal Transduction Channels. GLOBECOM (2019)
Gregory R. Hessler, Andrew W. Eckford, Peter J. Thomas
Linear Noise Approximation of Intensity-Driven Signal Transduction Channels. CoRR (2019)
Peter J. Thomas, Mette Sofie Olufsen, Rodolphe Sepulchre, Pablo A. Iglesias, Auke Jan Ijspeert, Manoj Srinivasan
Control theory in biology and medicine - Introduction to the special issue. Biol. Cybern. 113 (1-2) (2019)
Casey O. Diekman, Peter J. Thomas, Christopher G. Wilson
Experimental Validation of a Closed-Loop Respiratory Control Model using Dynamic Clamp. EMBC (2018)
Benjamin Lindner, Peter J. Thomas, Jean-Marc Fellous
Welcome from the new Editor(s)-in-Chief. Biol. Cybern. 112 (3) (2018)
Andrew W. Eckford, Peter J. Thomas
The Channel Capacity of Channelrhodopsin and Other Intensity-Driven Signal Transduction Receptors. IEEE Trans. Mol. Biol. Multi Scale Commun. 4 (1) (2018)
Andrew W. Eckford, Peter J. Thomas
The Channel Capacity of Channelrhodopsin and Other Intensity-Driven Signal Transduction Receptors. CoRR (2018)
Andrew W. Eckford, Benjamin Kuznets-Speck, Michael Hinczewski, Peter J. Thomas
Thermodynamic Properties of Molecular Communication. ISIT (2018)
Andrew W. Eckford, Benjamin Kuznets-Speck, Michael Hinczewski, Peter J. Thomas
Thermodynamic Properties of Molecular Communication. CoRR (2018)
Deena R. Schmidt, Roberto F. Galán, Peter J. Thomas
Stochastic shielding and edge importance for Markov chains with timescale separation. PLoS Comput. Biol. 14 (6) (2018)
David N. Lyttle, Jeffrey P. Gill, Kendrick M. Shaw, Peter J. Thomas, Hillel J. Chiel
Robustness, flexibility, and sensitivity in a multifunctional motor control model. Biol. Cybern. 111 (1) (2017)
Andrew W. Eckford, Peter J. Thomas
Entropy of the Sum of Two Independent, Non-Identically-Distributed Exponential Random Variables. CoRR (2016)
Andrew W. Eckford, Kenneth A. Loparo, Peter J. Thomas
Finite-state channel models for signal transduction in neural systems. ICASSP (2016)
Peter J. Thomas, Andrew W. Eckford
Capacity of a Simple Intercellular Signal Transduction Channel. IEEE Trans. Inf. Theory 62 (12) (2016)
Alexander G. Dimitrov, Faramarz Fekri, Aurel A. Lazar, Stefan M. Moser, Peter J. Thomas
Guest Editorial Biological Applications of Information Theory in Honor of Claude Shannon's Centennial - Part 1. IEEE Trans. Mol. Biol. Multi Scale Commun. 2 (1) (2016)
Andrew W. Eckford, Kenneth A. Loparo, Peter J. Thomas
Finite-State Channel Models for Signal Transduction in Neural Systems. CoRR (2016)
Peter J. Thomas, Andrew W. Eckford
Shannon capacity of signal transduction for multiple independent receptors. ISIT (2016)
Alexander G. Dimitrov, Faramarz Fekri, Aurel A. Lazar, Stefan M. Moser, Peter J. Thomas
Guest Editorial Biological Applications of Information Theory in Honor of Claude Shannon's Centennial - Part II. IEEE Trans. Mol. Biol. Multi Scale Commun. 2 (2) (2016)
Peter J. Thomas, Andrew W. Eckford
Shannon Capacity of Signal Transduction for Multiple Independent Receptors. CoRR (2016)
Kendrick M. Shaw, David N. Lyttle, Jeffrey P. Gill, Miranda J. Cullins, Jeffrey M. McManus, Hui Lu, Peter J. Thomas, Hillel J. Chiel
The significance of dynamical architecture for adaptive responses to mechanical loads during rhythmic behavior. J. Comput. Neurosci. 38 (1) (2015)
Andrew W. Eckford, Peter J. Thomas
Information theory of intercellular signal transduction. ACSSC (2015)
Peter J. Thomas
Commentary on Structured chaos shapes spike-response noise entropy in balanced neural networks, by Lajoie, Thivierge, and Shea-Brown. Frontiers Comput. Neurosci. 9 (2015)
David F. Anderson, Bard Ermentrout, Peter J. Thomas
Stochastic representations of ion channel kinetics and exact stochastic simulation of neuronal dynamics. J. Comput. Neurosci. 38 (1) (2015)
Andrew W. Eckford, Peter J. Thomas
Capacity of a Simple Intercellular Signal Transduction Channel CoRR (2013)
Andrew W. Eckford, Peter J. Thomas
Capacity of a simple intercellular signal transduction channel. ISIT (2013)
David J. Meyer, Jason Messer, Tanya Singh, Peter J. Thomas, Wojbor A. Woyczynski, Jeffrey A. Kaye, Alan J. Lerner
Random local temporal structure of category fluency responses. J. Comput. Neurosci. 32 (2) (2012)
Kendrick M. Shaw, Youngmin Park, Hillel J. Chiel, Peter J. Thomas
Phase Resetting in an Asymptotically Phaseless System: On the Phase Response of Limit Cycles Verging on a Heteroclinic Orbit. SIAM J. Appl. Dyn. Syst. 11 (1) (2012)
Casey O. Diekman, Christopher G. Wilson, Peter J. Thomas
Spontaneous autoresuscitation in a model of respiratory control. EMBC (2012)
J. Vincent Toups, Jean-Marc Fellous, Peter J. Thomas, Terrence J. Sejnowski, Paul H. E. Tiesinga
Multiple Spike Time Patterns Occur at Bifurcation Points of Membrane Potential Dynamics. PLoS Comput. Biol. 8 (10) (2012)
J. Vincent Toups, Jean-Marc Fellous, Peter J. Thomas, Terrence J. Sejnowski, Paul H. E. Tiesinga
Finding the Event Structure of Neuronal Spike Trains. Neural Comput. 23 (9) (2011)
Edward K. Agarwala, Hillel J. Chiel, Peter J. Thomas
Information Maximization Fails to Maximize Expected Utility in a Simple Foraging Model CoRR (2010)
Joseph M. Kimmel, Richard M. Salter, Peter J. Thomas
An Information Theoretic Framework for Eukaryotic Gradient Sensing. NIPS (2006)
Peter J. Thomas, Donald J. Spencer, Sierra K. Hampton, Peter Park, Joseph P. Zurkus
The Diffusion-Limited Biochemical Signal-Relay Channel. NIPS (2003)
Peter J. Thomas, Paul H. E. Tiesinga, Jean-Marc Fellous, Terrence J. Sejnowski
Reliability and bifurcation in neurons driven by multiple sinusoids. Neurocomputing (2003)
Paul C. Bressloff, Jack D. Cowan, Martin Golubitsky, Peter J. Thomas, Matthew C. Wiener
What Geometric Visual Hallucinations Tell Us about the Visual Cortex. Neural Comput. 14 (3) (2002)