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

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

(2014) Jeremy Gunawardena   BMC BIOLOGY

The Secret Garden--Epigenetic Alleles Underlie Complex Traits

(2014) R. J. Schmitz   SCIENCE

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

Epigenetic programming and reprogramming during development

(2013) Irene Cantone et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Effect of an Intervening Promoter Nucleosome on Gene Expression

(2013) Rasesh Y. Parikh et al.   PLoS One

Genetic Determinants and Cellular Constraints in Noisy Gene Expression

(2013) A. Sanchez et al.   SCIENCE

Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression

(2013) Christopher R. Brown et al.   PLOS BIOLOGY

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

(2012) Colin R. Lickwar et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

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

(2012) Jeremy Gunawardena   PLoS One

Dynamics of inherently bounded histone modification domains

(2012) C. Hodges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speed, dissipation, and error in kinetic proofreading

(2012) Arvind Murugan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamic State Ensemble Models of cis-Regulation

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

Kinetic Proofreading in Chromatin Remodeling: The Case of ISWI/ACF

(2011) Ralf Blossey et al.   BIOPHYSICAL JOURNAL

Mechanism of transcriptional repression at a bacterial promoter by analysis of single molecules

(2011) Alvaro Sanchez et al.   EMBO JOURNAL

Europe to map the human epigenome

(2011) Alison Abbott   NATURE

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity

(2011) D. S. Parker et al.   Science Signaling

Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression

(2011) Alvaro Sanchez et al.   PLoS Computational Biology

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

A proposal for kinetic proof reading by ISWI family chromatin remodeling motors

(2010) Geeta J Narlikar   CURRENT OPINION IN CHEMICAL BIOLOGY

Noncooperative Interactions between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses to Environmental Inputs

(2010) Luca Giorgetti et al.   MOLECULAR CELL

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo

(2010) Walid D Fakhouri et al.   Molecular Systems Biology

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

A theoretical framework for gene induction and experimental comparisons

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

Nucleosome-mediated cooperativity between transcription factors

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

Molecular Signals of Epigenetic States

(2010) Roberto Bonasio et al.   SCIENCE

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression

(2010) Xin He et al.   PLoS Computational Biology

Direct Measurement of Association and Dissociation Rates of DNA Binding in Live Cells by Fluorescence Correlation Spectroscopy

(2009) Ariel Michelman-Ribeiro et al.   BIOPHYSICAL JOURNAL

Fidelity at the Molecular Level: Lessons from Protein Synthesis

(2009) Hani S. Zaher et al.   CELL

Incorporating nucleosomes into thermodynamic models of transcription regulation

(2009) T. Raveh-Sadka et al.   GENOME RESEARCH

The rational parameterisation theorem for multisite post-translational modification systems

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

Unlimited multistability in multisite phosphorylation systems

(2009) Matthew Thomson et al.   NATURE

From DNA sequence to transcriptional behaviour: a quantitative approach

(2009) Eran Segal et al.   NATURE REVIEWS GENETICS

How transcription factors can adjust the gene expression floodgates

(2009) Denis Michel   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

What goes on behind closed doors: physiological versus pharmacological steroid hormone actions

(2008) S. Stoney Simons   BIOESSAYS

Kinetic proofreading of gene activation by chromatin remodeling

(2008) R. Blossey et al.   HFSP Journal

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Chromatin decouples promoter threshold from dynamic range

(2008) Felix H. Lam et al.   NATURE

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

A quantitative model of transcription factor–activated gene expression

(2008) Harold D Kim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY