Thermodynamic State Ensemble Models of cis-Regulation

Simplified Models of Biological Networks

(2010) Kim Sneppen et al.   Annual Review of Biophysics

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

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

A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription

(2010) S. Kuttykrishnan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions

(2009) Jason Gertz et al.   THEORETICAL POPULATION BIOLOGY

Two Modes of Transcriptional Activation at Native Promoters by NF-κB p65

(2009) Dominic van Essen et al.   PLOS BIOLOGY

Modulation of RNA Polymerase Assembly Dynamics in Transcriptional Regulation

(2008) Stanislaw A. Gorski et al.   MOLECULAR CELL

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE