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 …

What are the forces that shape the structure of prokaryotic genomes: the order of genes, their
proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are …

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 …

Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they
regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion …

Transcription factors (TFs) are the key elements responsible for controlling the expression of
genes in bacterial genomes and when visualized on a genomic scale form a dense network …

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 …

The proteins associated with gene regulation are often shared between multiple pathways
simultaneously. By way of contrast, models in regulatory biology often assume these …

Coordinated regulation of gene expression relies on transcription factors (TFs) binding to
specific DNA sites. Our large-scale information–theoretical analysis of> 950 TF-binding …

The quantitative relation between transcription factor concentrations and the rate of protein
production from downstream genes is central to the function of genetic networks. Here we …

We introduce macromolecular crowding quantitatively into the model for kinetics of gene
regulation in Escherichia coli. We analyse and compute the specific-site searching time for …