RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

The functional landscape bound to the transcription factors of Escherichia coli K-12

(2015) Ernesto Pérez-Rueda et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

RSAT 2015: Regulatory Sequence Analysis Tools

(2015) Alejandra Medina-Rivera et al.   NUCLEIC ACIDS RESEARCH

Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli

(2015) Sang Woo Seo et al.   Nature Communications

Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655

(2015) Sang Woo Seo et al.   Cell Reports

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

(2014) Maureen K. Thomason et al.   JOURNAL OF BACTERIOLOGY

The SUPERFAMILY 1.75 database in 2014: a doubling of data

(2014) Matt E. Oates et al.   NUCLEIC ACIDS RESEARCH

HAMAP in 2015: updates to the protein family classification and annotation system

(2014) Ivo Pedruzzi et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia: Table 1.

(2013) Pieter Meysman et al.   NUCLEIC ACIDS RESEARCH

CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria

(2013) Sefa Kılıç et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Prokaryotic genome regulation: A revolutionary paradigm

(2012) Akira ISHIHAMA   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

Improved similarity scores for comparing motifs

(2011) Emi Tanaka et al.   BIOINFORMATICS

Novel roles of LeuO in transcription regulation of E. coli genome: antagonistic interplay with the universal silencer H-NS

(2011) Tomohiro Shimada et al.   MOLECULAR MICROBIOLOGY

Theoretical and empirical quality assessment of transcription factor-binding motifs

(2011) Alejandra Medina-Rivera et al.   NUCLEIC ACIDS RESEARCH

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon Sources

(2011) Tomohiro Shimada et al.   PLoS One

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

TB database 2010: Overview and update

(2010) James E. Galagan et al.   TUBERCULOSIS

Evolvability and hierarchy in rewired bacterial gene networks

(2008) Mark Isalan et al.   NATURE

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

(2008) A. Funahashi et al.   PROCEEDINGS OF THE IEEE