Recent experiments have shown that in addition to control by cis regulatory elements, the
local chromosomal context of a gene also has a profound impact on its transcription …

We present a theory of pluralistic and stochastic gene regulation. To bridge the gap between
empirical studies and mathematical models, we integrate pre-existing observations with our …

Transcription in bacteria is controlled by multiple molecular mechanisms that precisely
regulate gene expression. It has been recently shown that initial RNA synthesis by the …

Feed-forward loops are hierarchical three-node transcriptional subnetworks, wherein a top-
level protein regulates the activity of a target gene via two paths: a direct-regulatory path …

Most genes change expression levels across conditions, but it is unclear which of these
changes represents specific regulation and what determines their quantitative degree. Here …

Cell fate changes during development, differentiation, and reprogramming are largely
controlled at the transcription level. The DNA-binding transcription factors (TFs) often act in a …

In this work, we study the behavior of a time-delayed mutually repressive auto-activating
three-gene system. Delays are introduced to account for the location difference between …

Bacterial gene expression depends on the allocation of limited transcriptional resources
provided a particular growth rate and growth condition. Early studies in a few genes …

Closely spaced promoters are ubiquitous in prokaryotic and eukaryotic genomes. How their
structure and dynamics relate remains unclear, particularly for tandem formations. To study …

Two prokaryotic organisms for which transcriptional regulatory interactions have been well
elucidated by experimental means are Escherichia coli and Bacillus subtilis. Here we show …