Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

Genomic encyclopedia of sugar utilization pathways in the Shewanella genus

(2010) Dmitry A Rodionov et al.   BMC GENOMICS

Characterization of the Pseudomonas aeruginosa Transcriptional Response to Phenylalanine and Tyrosine

(2010) G. C. Palmer et al.   JOURNAL OF BACTERIOLOGY

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

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

Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation

(2010) Grigoriy E. Pinchuk et al.   PLoS Computational Biology

Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria

(2009) Abel D González Pérez et al.   BMC GENOMICS

Direct methods for studying transcription regulatory proteins and RNA polymerase in bacteria

(2009) David C Grainger et al.   CURRENT OPINION IN MICROBIOLOGY

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

(2009) Pavel S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

MicrobesOnline: an integrated portal for comparative and functional genomics

(2009) P. S. Dehal et al.   NUCLEIC ACIDS RESEARCH

Genomic reconstruction ofShewanella oneidensisMR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization

(2009) Grigory E. Pinchuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative systems biology across an evolutionary gradient within the Shewanella genus

(2009) K. T. Konstantinidis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response

(2008) Yunfeng Yang et al.   BMC GENOMICS

Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses

(2008) Haichun Gao et al.   BMC GENOMICS

Comparative Genomics of Regulation of Fatty Acid and Branched-Chain Amino Acid Utilization in Proteobacteria

(2008) A. E. Kazakov et al.   JOURNAL OF BACTERIOLOGY

Analysis of mechanisms of activation and repression at bacterial promoters

(2008) Stephen D. Minchin et al.   METHODS

Towards environmental systems biology of Shewanella

(2008) James K. Fredrickson et al.   NATURE REVIEWS MICROBIOLOGY

A protein-DNA docking benchmark

(2008) M. van Dijk et al.   NUCLEIC ACIDS RESEARCH

The cis-regulatory map of Shewanella genomes

(2008) J. Liu et al.   NUCLEIC ACIDS RESEARCH

Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators

(2008) Dmitry A. Rodionov et al.   NUCLEIC ACIDS RESEARCH

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH