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

Non-equilibrium coupling of protein structure and function to translation–elongation kinetics

(2018) Ajeet K Sharma et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Are theoretical results ‘Results’?

(2018) Raymond E Goldstein   eLife

Core Concept: How nonequilibrium thermodynamics speaks to the mystery of life

(2017) Stephen Ornes   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle

(2017) Clarissa Scholes et al.   Cell Systems

Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: A new perspective

(2016) Erin E. Swinstead et al.   BIOESSAYS

Information Integration and Energy Expenditure in Gene Regulation

(2016) Javier Estrada et al.   CELL

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

Chromatin Scanning by Dynamic Binding of Pioneer Factors

(2016) Kenneth S. Zaret et al.   MOLECULAR CELL

Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq

(2016) Yiming K. Chang et al.   NUCLEIC ACIDS RESEARCH

Broken detailed balance at mesoscopic scales in active biological systems

(2016) Christopher Battle et al.   SCIENCE

Theory in Biology: Figure 1 or Figure 7?

(2015) Rob Phillips   TRENDS IN CELL BIOLOGY

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

A framework for modelling gene regulation which accommodates non-equilibrium mechanisms

(2014) Tobias Ahsendorf et al.   BMC BIOLOGY

Models in biology: ‘accurate descriptions of our pathetic thinking’

(2014) Jeremy Gunawardena   BMC BIOLOGY

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Single-molecule analysis of transcription factor binding at transcription sites in live cells

(2014) Tatsuya Morisaki et al.   Nature Communications

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

Eukaryotic transcriptional dynamics: from single molecules to cell populations

(2013) Antoine Coulon et al.   NATURE REVIEWS GENETICS

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements

(2012) Calista K. L. Ng et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Jeremy Gunawardena   PLoS One

Thermodynamic State Ensemble Models of cis-Regulation

(2012) Marc S. Sherman et al.   PLoS Computational Biology

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

(2011) Ty C. Voss et al.   CELL

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From DNA sequence to transcriptional behaviour: a quantitative approach

(2009) Eran Segal et al.   NATURE REVIEWS GENETICS