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

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

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

Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers

(2010) Richard W. Lusk et al.   PLoS Genetics

Optimizing static thermodynamic models of transcriptional regulation

(2009) Denis C. Bauer et al.   BIOINFORMATICS

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

(2009) T. Wasson et al.   GENOME RESEARCH

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Using DNA mechanics to predict in vitro nucleosome positions and formation energies

(2009) Alexandre V. Morozov et al.   NUCLEIC ACIDS RESEARCH

Modeling the Quantitative Specificity of DNA-Binding Proteins from Example Binding Sites

(2009) Dana S. F. Homsi et al.   PLoS One

Dynamical Analysis on Gene Activity in the Presence of Repressors and an Interfering Promoter

(2008) Hiizu Nakanishi et al.   BIOPHYSICAL JOURNAL

A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm

(2008) Charless C. Fowlkes et al.   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

Single-RNA counting reveals alternative modes of gene expression in yeast

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

(2008) Marcus B. Noyes et al.   NUCLEIC ACIDS RESEARCH

CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing

(2008) Pradipta Ray et al.   PLoS Computational Biology