The Influence of Transcription Factor Competition on the Relationship between Occupancy and Affinity

A comprehensive computational model of facilitated diffusion in prokaryotes

(2012) Nicolae Radu Zabet et al.   BIOINFORMATICS

GRiP: a computational tool to simulate transcription factor binding in prokaryotes

(2012) Nicolae Radu Zabet et al.   BIOINFORMATICS

System size reduction in stochastic simulations of the facilitated diffusion mechanism

(2012) Nicolae Radu Zabet   BMC Systems Biology

Computational models for large-scale simulations of facilitated diffusion

(2012) Nicolae Radu Zabet et al.   Molecular BioSystems

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Frustration in protein-DNA binding influences conformational switching and target search kinetics

(2011) A. Marcovitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

(2011) Tommy Kaplan et al.   PLoS Genetics

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

(2011) Sean Thomas et al.   GENOME BIOLOGY

Hopping Enables a DNA Repair Glycosylase To Search Both Strands and Bypass a Bound Protein

(2010) Mark Hedglin et al.   ACS Chemical Biology

An ensemble model of competitive multi-factor binding of the genome

(2009) T. Wasson et al.   GENOME RESEARCH

Incorporating nucleosomes into thermodynamic models of transcription regulation

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

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

From DNA sequence to transcriptional behaviour: a quantitative approach

(2009) Eran Segal et al.   NATURE REVIEWS GENETICS

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

Inferring Binding Energies from Selected Binding Sites

(2009) Yue Zhao et al.   PLoS Computational Biology

A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm

(2008) Charless C. Fowlkes et al.   CELL

Models of transcription factor binding: Sensitivity of activation functions to model assumptions

(2008) Dominique Chu et al.   JOURNAL OF THEORETICAL BIOLOGY