An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks

Global Analysis of Photosynthesis Transcriptional Regulatory Networks

(2014) Saheed Imam et al.   PLoS Genetics

Global insights into energetic and metabolic networks in Rhodobacter sphaeroides

(2013) Saheed Imam et al.   BMC Systems Biology

Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity

(2013) Senapathy Rajagopalan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally

(2013) Dan M. Park et al.   PLoS Genetics

Inferring gene regulatory networks by ANOVA

(2012) Robert Küffner et al.   BIOINFORMATICS

Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network inThermotoga maritima

(2012) Irina A. Rodionova et al.   ENVIRONMENTAL MICROBIOLOGY

A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes

(2012) Yuri I. Wolf et al.   Genome Biology and Evolution

Revised Sequence and Annotation of the Rhodobacter sphaeroides 2.4.1 Genome

(2012) W. S. Kontur et al.   JOURNAL OF BACTERIOLOGY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ

(2012) N. N. Mank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergence of the Transcriptional Responses to Heat Shock and Singlet Oxygen Stresses

(2012) Yann S. Dufour et al.   PLoS Genetics

Pathways Involved in Reductant Distribution during Photobiological H2Production by Rhodobacter sphaeroides

(2011) Wayne S. Kontur et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network

(2011) Saheed Imam et al.   BMC Systems Biology

Control of Proteobacterial Central Carbon Metabolism by the HexR Transcriptional Regulator

(2011) Semen A. Leyn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Electron Partitioning During Light- and Nutrient-Powered Hydrogen Production by Rhodobacter sphaeroides

(2010) Luftu Safak Yilmaz et al.   BioEnergy Research

MochiView: versatile software for genome browsing and DNA motif analysis

(2010) Oliver R Homann et al.   BMC BIOLOGY

Coenzyme Q10 production in a 150-l reactor by a mutant strain of Rhodobacter sphaeroides

(2010) Nguyen Ba Kien et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

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

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

(2010) P. S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstruction of the Core and Extended Regulons of Global Transcription Factors

(2010) Yann S. Dufour et al.   PLoS Genetics

Module networks revisited: computational assessment and prioritization of model predictions

(2009) A. Joshi et al.   BIOINFORMATICS

Inferring the transcriptional network of Bacillus subtilis

(2009) Abeer Fadda et al.   Molecular BioSystems

Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde

(2009) Shota Atsumi et al.   NATURE BIOTECHNOLOGY

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

(2009) Karen Lemmens et al.   GENOME BIOLOGY

Visualization, documentation, analysis, and communication of large-scale gene regulatory networks

(2008) William J.R. Longabaugh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Role of the Global Transcriptional Regulator PrrA in Rhodobacter sphaeroides 2.4.1: Combined Transcriptome and Proteome Analysis

(2008) J. M. Eraso et al.   JOURNAL OF BACTERIOLOGY

The Use of Chromatin Immunoprecipitation to Define PpsR Binding Activity in Rhodobacter sphaeroides 2.4.1

(2008) P. Bruscella et al.   JOURNAL OF BACTERIOLOGY

Organization and Evolution of the Biological Response to Singlet Oxygen Stress

(2008) Yann S. Dufour et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein-protein interactions between CbbR and RegA (PrrA), transcriptional regulators of thecbboperons ofRhodobacter sphaeroides

(2008) Andrew W. Dangel et al.   MOLECULAR MICROBIOLOGY