Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis

ENNET: inferring large gene regulatory networks from expression data using gradient boosting

(2013) Janusz Sławek et al.   BMC Systems Biology

The Mycobacterium tuberculosis regulatory network and hypoxia

(2013) James E. Galagan et al.   NATURE

hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests

(2013) I. S. Jang et al.   Interface Focus

Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors

(2013) Frank Emmert-Streib   PeerJ

Global Analysis of the Regulon of the Transcriptional Repressor LexA, a Key Component of SOS Response inMycobacterium tuberculosis

(2012) Katherine L. Smollett et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

(2012) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

Annotation of the M. tuberculosis Hypothetical Orfeome: Adding Functional Information to More than Half of the Uncharacterized Proteins

(2012) Tobias Doerks et al.   PLoS One

DDN: a caBIG® analytical tool for differential network analysis

(2011) Bai Zhang et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Differential C3NET reveals disease networks of direct physical interactions

(2011) Gökmen Altay et al.   BMC BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Comparative Genomics of the Dormancy Regulons in Mycobacteria

(2011) A. Gerasimova et al.   JOURNAL OF BACTERIOLOGY

ClpR Protein-like Regulator Specifically Recognizes RecA Protein-independent Promoter Motif and Broadly Regulates Expression of DNA Damage-inducible Genes in Mycobacteria

(2011) Yi Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function

(2011) Vincenzo Belcastro et al.   NUCLEIC ACIDS RESEARCH

The UniProt-GO Annotation database in 2011

(2011) E. C. Dimmer et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Comprehensive insights into Mycobacterium tuberculosis DevR (DosR) regulon activation switch

(2011) Santosh Chauhan et al.   NUCLEIC ACIDS RESEARCH

The Transcriptional Regulatory Network of Mycobacterium tuberculosis

(2011) Joaquín Sanz et al.   PLoS One

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

Letting Sleeping dos Lie: Does Dormancy Play a Role in Tuberculosis?

(2010) Michael C. Chao et al.   Annual Review of Microbiology

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

A statistical framework for differential network analysis from microarray data

(2010) Ryan Gill et al.   BMC BIOINFORMATICS

Inferring the conservative causal core of gene regulatory networks

(2010) Gökmen Altay et al.   BMC Systems Biology

SigG Does Not Control Gene Expression in Response to DNA Damage in Mycobacterium tuberculosis H37Rv

(2010) K. L. Smollett et al.   JOURNAL OF BACTERIOLOGY

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Nitrate Respiration Protects Hypoxic Mycobacterium tuberculosis Against Acid- and Reactive Nitrogen Species Stresses

(2010) Mai Ping Tan et al.   PLoS One

Essential roles for imuA'- and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis

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

TubercuList – 10 years after

(2010) Jocelyne M. Lew et al.   TUBERCULOSIS

Lessons from the DREAM2 Challenges

(2009) Gustavo Stolovitzky et al.   Annals of the New York Academy of Sciences

DIYA: a bacterial annotation pipeline for any genomics lab

(2009) Andrew C. Stewart et al.   BIOINFORMATICS

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

The sigma factors of Mycobacterium tuberculosis: regulation of the regulators

(2009) Preeti Sachdeva et al.   FEBS Journal

Unique Roles of DosT and DosS in DosR Regulon Induction and Mycobacterium tuberculosis Dormancy

(2009) R. W. Honaker et al.   INFECTION AND IMMUNITY

Network inference and network response identification: moving genome-scale data to the next level of biological discovery

(2009) Diogo F. T. Veiga et al.   Molecular BioSystems

A Novel In Vitro Multiple-Stress Dormancy Model for Mycobacterium tuberculosis Generates a Lipid-Loaded, Drug-Tolerant, Dormant Pathogen

(2009) Chirajyoti Deb et al.   PLoS One

Mycobacterial Esx-3 is required for mycobactin-mediated iron acquisition

(2009) M. S. Siegrist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The DosR regulon of M. tuberculosis and antibacterial tolerance

(2009) I.L. Bartek et al.   TUBERCULOSIS

The Sleipnir library for computational functional genomics

(2008) C. Huttenhower et al.   BIOINFORMATICS

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information

(2008) Patrick E Meyer et al.   BMC BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

The bacterial LexA transcriptional repressor

(2008) M. Butala et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Function and Regulation of Class I Ribonucleotide Reductase-Encoding Genes in Mycobacteria

(2008) Mohube B. Mowa et al.   JOURNAL OF BACTERIOLOGY

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest

(2008) Gábor Balázsi et al.   Molecular Systems Biology

RSAT: regulatory sequence analysis tools

(2008) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

TB database: an integrated platform for tuberculosis research

(2008) T. B. K. Reddy et al.   NUCLEIC ACIDS RESEARCH

Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis

(2008) K. Horan et al.   PLANT PHYSIOLOGY