A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data

Metagenomic sequencing reveals altered metabolic pathways in the oral microbiota of sailors during a long sea voyage

(2015) Weiwei Zheng et al.   Scientific Reports

Characterization of the SOS meta-regulon in the human gut microbiome

(2014) Joseph P. Cornish et al.   BIOINFORMATICS

Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities

(2014) Leyden Fernandez et al.   BMC GENOMICS

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

DNA Looping in Prokaryotes: Experimental and Theoretical Approaches

(2013) A. Cournac et al.   JOURNAL OF BACTERIOLOGY

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell 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

Exploration of Noncoding Sequences in Metagenomes

(2013) Fabián Tobar-Tosse et al.   PLoS One

Mechanisms of copper homeostasis in bacteria

(2013) José M. Argüello et al.   Frontiers in Cellular and Infection Microbiology

Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community

(2012) Laura A Hug et al.   BMC GENOMICS

Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes

(2012) Neus Sanchez-Alberola et al.   BMC GENOMICS

Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli

(2012) Tom Kormelink et al.   BMC GENOMICS

Bioinformatic approaches for functional annotation and pathway inference in metagenomics data

(2012) C. De Filippo et al.   BRIEFINGS IN BIOINFORMATICS

Response to Copper Stress inStreptomyces lividansExtends beyond Genes under Direct Control of a Copper-sensitive Operon Repressor Protein (CsoR)

(2012) Srivatsa Dwarakanath et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Copper-responsive gene regulation in bacteria

(2012) C. Rademacher et al.   MICROBIOLOGY-SGM

The Transcription Factor AmrZ Utilizes Multiple DNA Binding Modes to Recognize Activator and Repressor Sequences of Pseudomonas aeruginosa Virulence Genes

(2012) Edward E. Pryor et al.   PLoS Pathogens

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

(2012) Nicola Segata et al.   GENOME BIOLOGY

The Staphylococcus aureus CsoR regulates both chromosomal and plasmid-encoded copper resistance mechanisms

(2011) Jonathan Baker et al.   ENVIRONMENTAL MICROBIOLOGY

The combined actions of the copper-responsive repressor CsoR and copper-metallochaperone CopZ modulate CopA-mediated copper efflux in the intracellular pathogen Listeria monocytogenes

(2011) David Corbett et al.   MOLECULAR MICROBIOLOGY

Structural and functional characterization of the transcriptional repressor CsoR from Thermus thermophilus HB8

(2010) K. Sakamoto et al.   MICROBIOLOGY-SGM

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Molecular Insights into the Metal Selectivity of the Copper(I)-Sensing Repressor CsoR fromBacillus subtilis†

(2009) Zhen Ma et al.   BIOCHEMISTRY

Response of Gram-positive bacteria to copper stress

(2009) Marc Solioz et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

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

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

A CuI-Sensing ArsR Family Metal Sensor Protein with a Relaxed Metal Selectivity Profile†

(2008) Tong Liu et al.   BIOCHEMISTRY

Metagenomics

(2008) R.D. Sleator et al.   LETTERS IN APPLIED MICROBIOLOGY

Analysis of mechanisms of activation and repression at bacterial promoters

(2008) Stephen D. Minchin et al.   METHODS

Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins

(2008) S. E. Maddocks et al.   MICROBIOLOGY-SGM

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE