The linear framework II: using graph theory to analyse the transient regime of Markov processes

Cells use molecular working memory to navigate in changing chemoattractant fields

(2022) Akhilesh Nandan et al.   eLife

Allosteric conformational ensembles have unlimited capacity for integrating information

(2021) John W Biddle et al.   eLife

Gene Regulation in and out of Equilibrium

(2020) Felix Wong et al.   Annual Review of Biophysics

Robustness and parameter geography in post-translational modification systems

(2020) Kee-Myoung Nam et al.   PLoS Computational Biology

A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting

(2020) Nicholas C. Lammers et al.   CURRENT OPINION IN CELL BIOLOGY

Trade-Offs between Error, Speed, Noise, and Energy Dissipation in Biological Processes with Proofreading

(2019) Joel D. Mallory et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Negative reciprocity, not ordered assembly, underlies the interaction of Sox2 and Oct4 on DNA

(2019) John W Biddle et al.   eLife

Steady-State Differential Dose Response in Biological Systems

(2018) Pencho Yordanov et al.   BIOPHYSICAL JOURNAL

tRNA tracking for direct measurements of protein synthesis kinetics in live cells

(2018) Ivan L. Volkov et al.   Nature Chemical Biology

Temporal precision of regulated gene expression

(2018) Shivam Gupta et al.   PLoS Computational Biology

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Identifying feasible operating regimes for early T-cell recognition: The speed, energy, accuracy trade-off in kinetic proofreading and adaptive sorting

(2018) Wenping Cui et al.   PLoS One

Structural conditions on complex networks for the Michaelis–Menten input–output response

(2018) Felix Wong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs

(2018) Jeremy Dufourt et al.   Nature Communications

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos

(2018) Mustafa Mir et al.   eLife

Elucidating interplay of speed and accuracy in biological error correction

(2017) Kinshuk Banerjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

First-passage time approach to controlling noise in the timing of intracellular events

(2017) Khem Raj Ghusinga et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinetics of dCas9 target search inEscherichia coli

(2017) Daniel Lawson Jones et al.   SCIENCE

Live-cell p53 single-molecule binding is modulated by C-terminal acetylation and correlates with transcriptional activity

(2017) Alessia Loffreda et al.   Nature Communications

Information Integration and Energy Expenditure in Gene Regulation

(2016) Javier Estrada et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Stochastic timing in gene expression for simple regulatory strategies

(2016) Alma Dal Co et al.   NUCLEIC ACIDS RESEARCH

Single-molecule motions and interactions in live cells reveal target search dynamics in mismatch repair

(2015) Yi Liao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reliable cell cycle commitment in budding yeast is ensured by signal integration

(2015) Xili Liu et al.   eLife

A Fundamental Trade-off in Covalent Switching and Its Circumvention by Enzyme Bifunctionality in Glucose Homeostasis

(2014) Tathagata Dasgupta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Laplacian Dynamics on General Graphs

(2013) Inomzhon Mirzaev et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Time-scale separation - Michaelis and Menten's old idea, still bearing fruit

(2013) Jeremy Gunawardena   FEBS Journal

Extracting signal from noise: kinetic mechanisms from a Michaelis-Menten-like expression for enzymatic fluctuations

(2013) Jeffrey R. Moffitt et al.   FEBS Journal

The Bacterial SMC Complex Displays Two Distinct Modes of Interaction with the Chromosome

(2013) Luise A.K. Kleine Borgmann et al.   Cell Reports

A Linear Framework for Time-Scale Separation in Nonlinear Biochemical Systems

(2012) Jeremy Gunawardena   PLoS One

Michaelis−Menten Equation and Detailed Balance in Enzymatic Networks

(2011) Jianshu Cao   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations

(2010) J. R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Holin triggering in real time

(2010) R. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The rational parameterisation theorem for multisite post-translational modification systems

(2009) Matthew Thomson et al.   JOURNAL OF THEORETICAL BIOLOGY

Stochastic kinetics of ribosomes: Single motor properties and collective behavior

(2009) Ashok Garai et al.   PHYSICAL REVIEW E

Exact Solutions for Kinetic Models of Macromolecular Dynamics†

(2008) Yann R. Chemla et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Self-organization in cell biology: a brief history

(2008) Eric Karsenti   NATURE REVIEWS MOLECULAR CELL BIOLOGY