Nature Search

Regulatory promoter architectures in the hands of thermodynamic modelling

Julio Collado-Vides recalls two 2005 publications that provide a conceptual framework based on a statistical thermodynamics approach to quantitatively model the regulatory activity at promoters subject to regulation by multiple transcription factors.

Julio Collado-Vides
Research Highlights06 Feb 2023
Nature Reviews Genetics

Volume: 24, P: 349
Information on Transcriptional Regulation and Signal Transduction of Escherichia coli K-12 Integrated in the Database RegulonDB.

Socorro Gama-Castro
Alberto Santos-Zavaleta
Julio Collado-Vides
MultimediaOpen Access17 Nov 2010
Nature Precedings

P: 1
Information on Transcriptional Regulation and Signal Transduction of Escherichia coli K-12 Integrated in the Database RegulonDB.

Socorro Gama-Castro
Alberto Santos-Zavaleta
Julio Collado-Vides
MultimediaOpen Access19 Nov 2010
Nature Precedings

P: 1
Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli

The authors describe BoltzNet, a neural network that learns the energy of transcription factor (TF)-DNA binding from genomic data and can be used to design new binding sites. They report the in vivo mapping and BoltzNet modeling of 139 E. coli TFs.

Patrick Lally
Laura Gómez-Romero
James E. Galagan
ResearchOpen Access07 May 2025
Nature Communications

Volume: 16, P: 1-16
Correction: Corrigendum: The BioPAX community standard for pathway data sharing

Emek Demir
Michael P Cary
Gary D Bader
Amendments and Corrections07 Dec 2010
Nature Biotechnology

Volume: 28, P: 1308
Correction: Corrigendum: The BioPAX community standard for pathway data sharing

Emek Demir
Michael P Cary
Gary D Bader
Amendments and Corrections10 Apr 2012
Nature Biotechnology

Volume: 30, P: 365
Morphological and community changes of turf algae in competition with corals

Neidy P. Cetz-Navarro
Lizette I. Quan-Young
Julio Espinoza-Avalos
ResearchOpen Access05 Aug 2015
Scientific Reports

Volume: 5, P: 1-12
The BioPAX community standard for pathway data sharing

Incompatible data storage formats have hindered the sharing and analyses of digital representations of biological pathways. BioPAX is a standardized language supported by >40 databases and software tools for exchanging pathway data.

Emek Demir
Michael P Cary
Gary D Bader
Reviews09 Sept 2010
Nature Biotechnology

Volume: 28, P: 935-942
Minimum information requested in the annotation of biochemical models (MIRIAM)

Nicolas Le Novère
Andrew Finney
Barry L Wanner
Reviews06 Dec 2005
Nature Biotechnology

Volume: 23, P: 1509-1515
Redefining fundamental concepts of transcription initiation in bacteria

In this Expert Recommendation, the authors review the definitions of classic concepts relating to bacterial gene regulation, with a focus on transcription initiation, and suggest up-to-date, precise definitions to provide a reference for knowledge representation, modelling and future research on bacterial gene regulation.

Citlalli Mejía-Almonte
Stephen J. W. Busby
Julio Collado-Vides
Reviews14 Jul 2020
Nature Reviews Genetics

Volume: 21, P: 699-714
PulmonDB: a curated lung disease gene expression database

Ana B. Villaseñor-Altamirano
Marco Moretto
Alejandra Medina-Rivera
ResearchOpen Access16 Jan 2020
Scientific Reports

Volume: 10, P: 1-9
In silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD

Irma Martínez-Flores
Deyanira Pérez-Morales
Víctor H. Bustamante
ResearchOpen Access25 Nov 2016
Scientific Reports

Volume: 6, P: 1-12

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Regulatory promoter architectures in the hands of thermodynamic modelling

Information on Transcriptional Regulation and Signal Transduction of Escherichia coli K-12 Integrated in the Database RegulonDB.

Information on Transcriptional Regulation and Signal Transduction of Escherichia coli K-12 Integrated in the Database RegulonDB.

Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli

Correction: Corrigendum: The BioPAX community standard for pathway data sharing

Correction: Corrigendum: The BioPAX community standard for pathway data sharing

Morphological and community changes of turf algae in competition with corals

The BioPAX community standard for pathway data sharing

Minimum information requested in the annotation of biochemical models (MIRIAM)

Redefining fundamental concepts of transcription initiation in bacteria

PulmonDB: a curated lung disease gene expression database

In silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD

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