Markovian approaches to modeling intracellular reaction processes with molecular memory

Revisiting the Reduction of Stochastic Models of Genetic Feedback Loops with Fast Promoter Switching

(2019) James Holehouse et al.   BIOPHYSICAL JOURNAL

A Gillespie Algorithm for Non-Markovian Stochastic Processes

(2018) Naoki Masuda et al.   SIAM REVIEW

The Chemical Fluctuation Theorem governing gene expression

(2018) Seong Jun Park et al.   Nature Communications

Linear mapping approximation of gene regulatory networks with stochastic dynamics

(2018) Zhixing Cao et al.   Nature Communications

The continuous time random walk, still trendy: fifty-year history, state of art and outlook

(2017) Ryszard Kutner et al.   EUROPEAN PHYSICAL JOURNAL B

Approximation and inference methods for stochastic biochemical kinetics—a tutorial review

(2017) David Schnoerr et al.   Journal of Physics A-Mathematical and Theoretical

Equivalence between Non-Markovian and Markovian Dynamics in Epidemic Spreading Processes

(2017) Michele Starnini et al.   PHYSICAL REVIEW LETTERS

Chemical Continuous Time Random Walks

(2017) Tomás Aquino et al.   PHYSICAL REVIEW LETTERS

Random walks and diffusion on networks

(2017) Naoki Masuda et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Dynamics of non-Markovian open quantum systems

(2017) Inés de Vega et al.   REVIEWS OF MODERN PHYSICS

Stem Cell Differentiation as a Non-Markov Stochastic Process

(2017) Patrick S. Stumpf et al.   Cell Systems

Stochastic Simulation of Biomolecular Networks in Dynamic Environments

(2016) Margaritis Voliotis et al.   PLoS Computational Biology

Generalization of Pairwise Models to non-Markovian Epidemics on Networks

(2015) Istvan Z. Kiss et al.   PHYSICAL REVIEW LETTERS

Genetic Toggle Switch in the Absence of Cooperative Binding: Exact Results

(2015) Tommaso Biancalani et al.   PHYSICAL REVIEW LETTERS

Stochastic Phenotype Transition of a Single Cell in an Intermediate Region of Gene State Switching

(2015) Hao Ge et al.   PHYSICAL REVIEW LETTERS

Delay chemical master equation: direct and closed-form solutions

(2015) Andre Leier et al.   PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Generalized Continuous Time Random Walks, Master Equations, and Fractional Fokker--Planck Equations

(2015) C. N. Angstmann et al.   SIAM JOURNAL ON APPLIED MATHEMATICS

Diffusion on networked systems is a question of time or structure

(2015) Jean-Charles Delvenne et al.   Nature Communications

Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models

(2015) Niraj Kumar et al.   PLoS Computational Biology

Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks

(2015) Christian L. Vestergaard et al.   PLoS Computational Biology

Simulating non-Markovian stochastic processes

(2014) Marian Boguñá et al.   PHYSICAL REVIEW E

Causality-driven slow-down and speed-up of diffusion in non-Markovian temporal networks

(2014) Ingo Scholtes et al.   Nature Communications

Reduction of chemical reaction networks through delay distributions

(2013) Manuel Barrio et al.   JOURNAL OF CHEMICAL PHYSICS

Non-Markovian Infection Spread Dramatically Alters the Susceptible-Infected-Susceptible Epidemic Threshold in Networks

(2013) P. Van Mieghem et al.   PHYSICAL REVIEW LETTERS

Stochastic Processes with Distributed Delays: Chemical Langevin Equation and Linear-Noise Approximation

(2013) Tobias Brett et al.   PHYSICAL REVIEW LETTERS

Complex dynamics of transcription regulation

(2012) Diana A. Stavreva et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Transcription Stochasticity of Complex Gene Regulation Models

(2012) Anne Schwabe et al.   BIOPHYSICAL JOURNAL

The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions

(2012) Philipp Thomas et al.   BMC Systems Biology

Noise-mean relationship in mutated promoters

(2012) G. Hornung et al.   GENOME RESEARCH

Steady-state fluctuations of a genetic feedback loop: An exact solution

(2012) R. Grima et al.   JOURNAL OF CHEMICAL PHYSICS

Expression Noise and Acetylation Profiles Distinguish HDAC Functions

(2012) Leehee Weinberger et al.   MOLECULAR CELL

Non-Markovian polymer reaction kinetics

(2012) T. Guérin et al.   Nature Chemistry

Intrinsic Noise in Stochastic Models of Gene Expression with Molecular Memory and Bursting

(2011) Tao Jia et al.   PHYSICAL REVIEW LETTERS

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Dynamic Analysis of Stochastic Transcription Cycles

(2011) Claire V. Harper et al.   PLOS BIOLOGY

CplexA: a Mathematica package to study macromolecular-assembly control of gene expression

(2010) Jose M.G. Vilar et al.   BIOINFORMATICS

A high-resolution human contact network for infectious disease transmission

(2010) M. Salathe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stochastic fluctuations in the susceptible-infective-recovered model with distributed infectious periods

(2009) Andrew J. Black et al.   PHYSICAL REVIEW E

Epigenetic and Conventional Regulation Is Distributed among Activators of FLO11 Allowing Tuning of Population-Level Heterogeneity in Its Expression

(2009) Leah M. Octavio et al.   PLoS Genetics

Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression

(2008) J. M. Pedraza et al.   SCIENCE