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Geometry of gene regulatory dynamics

Proceedings of the National Academy of Sciences - PNAS, 2021-09, Vol.118 (38)

2021

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Quantifying cell transitions in C. elegans with data-fitted landscape models

PLoS computational biology, 2021-06, Vol.17 (6), p.e1009034-e1009034

2021

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Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions

Cell systems, 2022-01, Vol.13 (1), p.12-28.e3

2022

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Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference

PLoS computational biology, 2017-07, Vol.13 (7), p.e1005676-e1005676

2017

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Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle

Proceedings of the National Academy of Sciences - PNAS, 2014-07, Vol.111 (27), p.9828-9833

2014

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Coupling between the Circadian Clock and Cell Cycle Oscillators: Implication for Healthy Cells and Malignant Growth

Frontiers in neurology, 2015-05, Vol.6, p.96-96

2015

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Sensitivity, robustness, and identifiability in stochastic chemical kinetics models

Proceedings of the National Academy of Sciences - PNAS, 2011-05, Vol.108 (21), p.8645-8650

2011

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TimeTeller: A tool to probe the circadian clock as a multigene dynamical system

PLoS computational biology, 2024-02, Vol.20 (2), p.e1011779-e1011779

2024

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Dynamic analysis of stochastic transcription cycles

PLoS biology, 2011-04, Vol.9 (4), p.e1000607-e1000607

2011

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Population robustness arising from cellular heterogeneity

Proceedings of the National Academy of Sciences - PNAS, 2010-06, Vol.107 (25), p.11644-11649

2010

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Signal transduction controls heterogeneous NF-κB dynamics and target gene expression through cytokine-specific refractory states

Nature communications, 2016-07, Vol.7 (1), p.12057-12057, Article 12057

2016

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Frequency Modulated Translocational Oscillations of Nrf2 Mediate the Antioxidant Response Element Cytoprotective Transcriptional Response

Antioxidants & redox signaling, 2015-09, Vol.23 (7), p.613-629

2015

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Parameter sensitivity analysis for biochemical reaction networks

Mathematical biosciences and engineering : MBE, 2019-01, Vol.16 (5), p.3965-3987

2019

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Bayesian inference of biochemical kinetic parameters using the linear noise approximation

BMC bioinformatics, 2009-10, Vol.10 (1), p.343-343, Article 343

2009

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Multiplexing information flow through dynamic signalling systems

PLoS computational biology, 2020-08, Vol.16 (8), p.e1008076-e1008076

2020

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Designing lead–acid batteries to meet energy and power requirements of future automobiles

Journal of power sources, 2012-12, Vol.219, p.75-79

2012

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Frequency modulated translocational oscillations of Nrf2, a transcription factor functioning like a wireless sensor

Biochemical Society transactions, 2015-08, Vol.43 (4), p.669-673

2015

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Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells

PLoS computational biology, 2016-04, Vol.12 (4), p.e1004828-e1004828

2016

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Fuel Cell Systems Explained (3rd Edition)

Third edition, 2018

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Systems Chronotherapeutics

Pharmacological reviews, 2017-04, Vol.69 (2), p.161-199

2017

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Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures

Molecular systems biology, 2013, Vol.9 (1), p.650-n/a

2013

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ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data

BMC bioinformatics, 2017-06, Vol.18 (1), p.316-316, Article 316

2017

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Spatially coordinated dynamic gene transcription in living pituitary tissue

eLife, 2016-02, Vol.5, p.e08494-e08494

2016

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Prediction of Photoperiodic Regulators from Quantitative Gene Circuit Models

Cell, 2009-12, Vol.139 (6), p.1170-1179

2009

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Geometry of gene regulatory dynamics

Quantifying cell transitions in C. elegans with data-fitted landscape models

Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions

Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference

Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle

Coupling between the Circadian Clock and Cell Cycle Oscillators: Implication for Healthy Cells and Malignant Growth

Sensitivity, robustness, and identifiability in stochastic chemical kinetics models

TimeTeller: A tool to probe the circadian clock as a multigene dynamical system

Dynamic analysis of stochastic transcription cycles

Population robustness arising from cellular heterogeneity

Signal transduction controls heterogeneous NF-κB dynamics and target gene expression through cytokine-specific refractory states

Frequency Modulated Translocational Oscillations of Nrf2 Mediate the Antioxidant Response Element Cytoprotective Transcriptional Response

Parameter sensitivity analysis for biochemical reaction networks

Bayesian inference of biochemical kinetic parameters using the linear noise approximation

Multiplexing information flow through dynamic signalling systems

Designing lead–acid batteries to meet energy and power requirements of future automobiles

Frequency modulated translocational oscillations of Nrf2, a transcription factor functioning like a wireless sensor

Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells

Fuel Cell Systems Explained (3rd Edition)

The dynamic architecture of the metabolic switch in Streptomyces coelicolor

Systems Chronotherapeutics

Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures

ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data

Spatially coordinated dynamic gene transcription in living pituitary tissue

Prediction of Photoperiodic Regulators from Quantitative Gene Circuit Models

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