RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12

A Santos-Zavaleta, H Salgado… - Nucleic acids …, 2019 - academic.oup.com
RegulonDB, first published 20 years ago, is a comprehensive electronic resource about
regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from …

Systems‐level transcriptional regulation of Caenorhabditis elegans metabolism

S Nanda, MA Jacques, W Wang, CL Myers… - Molecular systems …, 2023 - embopress.org
Metabolism is controlled to ensure organismal development and homeostasis. Several
mechanisms regulate metabolism, including allosteric control and transcriptional regulation …

[HTML][HTML] Metabolism as a signal generator in bacteria

D Ledezma-Tejeida, E Schastnaya, U Sauer - Current Opinion in Systems …, 2021 - Elsevier
Bacteria constantly monitor their environment to adapt their inner makeup. Beyond providing
chemical sustenance, metabolism provides most of the feedback on the cellular environment …

Sensory Systems and Transcriptional Regulation in Escherichia coli

G Femerling, S Gama-Castro, P Lara… - … in Bioengineering and …, 2022 - frontiersin.org
In free-living bacteria, the ability to regulate gene expression is at the core of adapting and
interacting with the environment. For these systems to have a logic, a signal must trigger a …

Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes

JC Higareda-Almaraz, M Karbiener, M Giroud… - BMC genomics, 2018 - Springer
Background Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT)
functions, including lipolysis, free fatty acid liberation and, under certain conditions …

Using RegulonDB, the Escherichia coli K‐12 Gene Regulatory Transcriptional Network Database

H Salgado, I Martínez‐Flores… - Current protocols in …, 2018 - Wiley Online Library
In RegulonDB, for over 25 years, we have been gathering knowledge by manual curation
from original scientific literature on the regulation of transcription initiation and genome …

Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes

D Ledezma-Tejeida, L Altamirano-Pacheco… - Nucleic Acids …, 2019 - academic.oup.com
Transcription factors (TFs) are important drivers of cellular decision-making. When bacteria
encounter a change in the environment, TFs alter the expression of a defined set of genes in …

Programmatic access to bacterial regulatory networks with regutools

J Chávez, C Barberena-Jonas… - …, 2020 - academic.oup.com
RegulonDB has collected, harmonized and centralized data from hundreds of experiments
for nearly two decades and is considered a point of reference for transcriptional regulation in …

Dynamic heterogeneity in an E. coli stress response regulon mediates gene activation and antimicrobial peptide tolerance

CM Blassick, JB Lugagne, MJ Dunlop - bioRxiv, 2024 - biorxiv.org
The bacterial stress response is an intricately regulated system that plays a critical role in
cellular resistance to drug treatment. The complexity of this response is further complicated …

[PDF][PDF] RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in

A Santos-Zavaleta, H Salgado, S Gama-Castro… - E. coli - academia.edu
RegulonDB, first published 20 years ago, is a comprehensive electronic resource about
regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from …