Distance Matters: The Impact of Gene Proximity in Bacterial Gene Regulation

In Vivo Facilitated Diffusion Model

(2013) Maximilian Bauer et al.   PLoS One

Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19

(2013) Marco Di Stefano et al.   PLoS Computational Biology

Generalized Facilitated Diffusion Model for DNA-Binding Proteins with Search and Recognition States

(2012) Maximilian Bauer et al.   BIOPHYSICAL JOURNAL

Gene location and DNA density determine transcription factor distributions in Escherichia coli

(2012) Thomas E Kuhlman et al.   Molecular Systems Biology

Facilitated diffusion on confined DNA

(2012) G. Foffano et al.   PHYSICAL REVIEW E

Universal Protein Fluctuations in Populations of Microorganisms

(2012) Hanna Salman et al.   PHYSICAL REVIEW LETTERS

Facilitated Diffusion on Mobile DNA: Configurational Traps and Sequence Heterogeneity

(2012) C. A. Brackley et al.   PHYSICAL REVIEW LETTERS

Classes of fast and specific search mechanisms for proteins on DNA

(2012) M Sheinman et al.   REPORTS ON PROGRESS IN PHYSICS

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

Theoretical and Computational Modeling of Target-Site Search Kinetics In Vitro and In Vivo

(2011) Elena F. Koslover et al.   BIOPHYSICAL JOURNAL

Transition probabilities for general birth–death processes with applications in ecology, genetics, and evolution

(2011) Forrest W. Crawford et al.   JOURNAL OF MATHEMATICAL BIOLOGY

General properties of transcriptional time series in Escherichia coli

(2011) Lok-hang So et al.   NATURE GENETICS

Transcription factor search for a DNA promoter in a three-state model

(2011) Jürgen Reingruber et al.   PHYSICAL REVIEW E

Spatial organization of the flow of genetic information in bacteria

(2010) Paula Montero Llopis et al.   NATURE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Identification of influential spreaders in complex networks

(2010) Maksim Kitsak et al.   Nature Physics

Physics of protein–DNA interactions: mechanisms of facilitated target search

(2010) Anatoly B. Kolomeisky   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Facilitated diffusion in a crowded environment: from kinetics to stochastics

(2009) Yasmine Meroz et al.   Journal of Physics A-Mathematical and Theoretical

How a protein searches for its site on DNA: the mechanism of facilitated diffusion

(2009) Leonid Mirny et al.   Journal of Physics A-Mathematical and Theoretical

Transcriptional regulation shapes the organization of genes on bacterial chromosomes

(2009) Sarath Chandra Janga et al.   NUCLEIC ACIDS RESEARCH

Quantifying Hopping and Jumping in Facilitated Diffusion of DNA-Binding Proteins

(2009) C. Loverdo et al.   PHYSICAL REVIEW LETTERS

Facilitated diffusion with DNA coiling

(2009) M. A. Lomholt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistical physics of social dynamics

(2009) Claudio Castellano et al.   REVIEWS OF MODERN PHYSICS

Single-Molecule Approach to Molecular Biology in Living Bacterial Cells

(2008) X. Sunney Xie et al.   Annual Review of Biophysics

The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks

(2008) Irma Lozada-Chávez et al.   JOURNAL OF MOLECULAR BIOLOGY

Spatial effects on the speed and reliability of protein–DNA search

(2008) Zeba Wunderlich et al.   NUCLEIC ACIDS RESEARCH

How DNA coiling enhances target localization by proteins

(2008) B. van den Broek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analytical distributions for stochastic gene expression

(2008) V. Shahrezaei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell

(2008) P. J. Choi et al.   SCIENCE