Transcription factors (TFs) with regulatory action at multiple promoter targets is the rule
rather than the exception, with examples ranging from the cAMP receptor protein (CRP) in E …

Transcription factors (TFs) interact with a multitude of binding sites on DNA and partner
proteins inside cells. We investigate how nonspecific binding/unbinding to such decoy …

We present three models of how transcription factors (TFs) bind to their specific binding sites
on the DNA: a model based on statistical physics, a Markov-chain model and a …

The capacity of transcription factors to activate gene expression is encoded in the promoter
sequences, which are composed of short regulatory motifs that function as transcription …

Following recent discoveries of colocalization of downstream-regulating genes in living
cells, the impact of the spatial distance between such genes on the kinetics of gene product …

In the present work we extend and analyze the scope of our recently proposed stochastic
model for transcriptional regulation, which considers an arbitrarily complex cis-regulatory …

A crucial step in the regulation of gene expression is binding of transcription factor (TF)
proteins to regulatory sites along the DNA. But transcription factors act at nanomolar …

We study theoretical “design principles” for transcription factor (TF)–DNA interaction in
bacteria, focusing particularly on the statistical interaction of the TFs with the genomic …

Models of transcription are often built around a picture of RNA polymerase and transcription
factors (TFs) acting on a single copy of a promoter. However, most TFs are shared between …

Transcription factors (TFs) control gene expression, often acting synergistically. Classical
thermodynamic models offer a biophysical explanation for synergy based on binding …