A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1

Surviving the host: Microbial metabolic genes required for growth of Pseudomonas aeruginosa in physiologically-relevant conditions

(2022) Corrie R. Belanger et al.   Frontiers in Microbiology

Azithromycin Exhibits Activity Against Pseudomonas aeruginosa in Chronic Rat Lung Infection Model

(2021) Manoj Kumar et al.   Frontiers in Microbiology

Could Azithromycin Be Part of Pseudomonas aeruginosa Acute Pneumonia Treatment?

(2021) Anne-Gaëlle Leroy et al.   Frontiers in Microbiology

A first perturbome of Pseudomonas aeruginosa: Identification of core genes related to multiple perturbations by a machine learning approach

(2021) Jose Arturo Molina Mora et al.   BIOSYSTEMS

Phosphorus stress induces the synthesis of novel glycolipids in Pseudomonas aeruginosa that confer protection against a last-resort antibiotic

(2021) Rebekah A. Jones et al.   ISME Journal

Transcriptome Analysis and Weighted Gene Co-expression Network Reveal Multitarget-Directed Antibacterial Mechanisms of Benzyl Isothiocyanate against Staphylococcus aureus

(2021) Hongbo Li et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Pseudomonas aeruginosa transcriptome adaptations from colonization to biofilm infection of skin wounds

(2021) Peter D’Arpa et al.   Scientific Reports

Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach

(2020) José Arturo Molina-Mora et al.   Scientific Reports

A Comprehensive Coexpression Network Analysis in Vibrio cholerae

(2020) Cory D. DuPai et al.   mSystems

Identification of novel targets of azithromycin activity against Pseudomonas aeruginosa grown in physiologically relevant media

(2020) Corrie R. Belanger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial fitness in chronic wounds appears to be mediated by the capacity for high-density growth,not virulence or biofilm functions

(2019) Sarah J. Morgan et al.   PLoS Pathogens

Integrative meta-analysis of transcriptomic responses to abiotic stress in cotton

(2019) Ahmad Tahmasebi et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Pseudomonas aeruginosa requires the DNA-specific endonuclease EndA to degrade eDNA to disperse from the biofilm

(2019) Kathryn E. Cherny et al.   JOURNAL OF BACTERIOLOGY

Distinct Roles of Outer Membrane Porins in Antibiotic Resistance and Membrane Integrity in Escherichia coli

(2019) Umji Choi et al.   Frontiers in Microbiology

Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung

(2019) Adrian Kordes et al.   Nature Communications

Gene expression in Pseudomonas aeruginosa exposed to hydroxyl-radicals

(2018) Noa Aharoni et al.   CHEMOSPHERE

Comparison of gene co-expression networks in Pseudomonas aeruginosa and Staphylococcus aureus reveals conservation in some aspects of virulence

(2018) Nazanin Hosseinkhan et al.   GENE

Intergenic evolution during host adaptation increases expression of the metallophore pseudopaline in Pseudomonas aeruginosa

(2018) Grith Miriam Maigaard Hermansen et al.   MICROBIOLOGY-SGM

Construction and Analysis of Gene Co-Expression Networks in Escherichia coli

(2018) Wei Liu et al.   Cells

The Pseudomonas aeruginosa Orphan Quorum Sensing Signal Receptor QscR Regulates Global Quorum Sensing Gene Expression by Activating a Single Linked Operon

(2018) Fengming Ding et al.   mBio

Biofilms: Survival and defense strategy for pathogens

(2017) Ashutosh Kumar et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data

(2017) Ji Huang et al.   PLANT PHYSIOLOGY

Bacteriocin-Antimicrobial Synergy: A Medical and Food Perspective

(2017) Harsh Mathur et al.   Frontiers in Microbiology

Pseudomonas aeruginosa zinc uptake in chelating environment is primarily mediated by the metallophore pseudopaline

(2017) Sébastien Lhospice et al.   Scientific Reports

Protein Network of the Pseudomonas aeruginosa Denitrification Apparatus

(2016) José Manuel Borrero-de Acuña et al.   JOURNAL OF BACTERIOLOGY

Bacterial Strategies to Maintain Zinc Metallostasis at the Host-Pathogen Interface

(2016) Daiana A. Capdevila et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Sparse factor model for co-expression networks with an application using prior biological knowledge

(2016) Yuna Blum et al.   Statistical Applications in Genetics and Molecular Biology

Sparse factor model for co-expression networks with an application using prior biological knowledge

(2016) Yuna Blum et al.   Statistical Applications in Genetics and Molecular Biology

Gene Co-Expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Type 1 Diabetes

(2016) Ignacio Riquelme Medina et al.   PLoS One

Construction and application of a co-expression network in Mycobacterium tuberculosis

(2016) Jun Jiang et al.   Scientific Reports

50 years of Arabidopsis research: highlights and future directions

(2015) Nicholas J. Provart et al.   NEW PHYTOLOGIST

Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways

(2015) Karima Righetti et al.   PLANT CELL

Structural and mechanistic insights on nitrate reductases

(2015) Catarina Coelho et al.   PROTEIN SCIENCE

Phenazine virulence factor binding to extracellular DNA is important for Pseudomonas aeruginosa biofilm formation

(2015) Theerthankar Das et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Annotation of gene function in citrus using gene expression information and co-expression networks

(2014) Darren CJ Wong et al.   BMC PLANT BIOLOGY

Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data

(2014) Polina Reshetova et al.   BMC Systems Biology

EsrC, an envelope stress-regulated repressor of themexCD-oprJmultidrug efflux operon inPseudomonas aeruginosa

(2014) Andrew Purssell et al.   ENVIRONMENTAL MICROBIOLOGY

Requirements for Pseudomonas aeruginosa Acute Burn and Chronic Surgical Wound Infection

(2014) Keith H. Turner et al.   PLoS Genetics

Genome-Wide Tissue-Specific Gene Expression, Co-expression and Regulation of Co-expressed Genes in Adult Nematode Ascaris suum

(2014) Bruce A. Rosa et al.   PLoS Neglected Tropical Diseases

Physiological levels of nitrate support anoxic growth by denitrification of Pseudomonas aeruginosa at growth rates reported in cystic fibrosis lungs and sputum

(2014) Laura Line et al.   Frontiers in Microbiology

Incorporating prior knowledge into Gene Network Study

(2013) Zixing Wang et al.   BIOINFORMATICS

Divergent Control of Two Type VI Secretion Systems by RpoN in Pseudomonas aeruginosa

(2013) Thibault G. Sana et al.   PLoS One

Towards revealing the functions of all genes in plants

(2013) Seung Yon Rhee et al.   TRENDS IN PLANT SCIENCE

Disentangling the Many Layers of Eukaryotic Transcriptional Regulation

(2012) Katherine M. Lelli et al.   Annual Review of Genetics

Phosphate Starvation Promotes Swarming Motility and Cytotoxicity of Pseudomonas aeruginosa

(2012) Manjeet Bains et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Second Type VI Secretion System ofPseudomonas aeruginosaStrain PAO1 Is Regulated by Quorum Sensing and Fur and Modulates Internalization in Epithelial Cells

(2012) Thibault G. Sana et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Co-expression Analysis Identifies CRC and AP1 the Regulator of Arabidopsis Fatty Acid Biosynthesis

(2012) Xinxin Han et al.   Journal of Integrative Plant Biology

Identification of Genes in the  22 Regulon of Pseudomonas aeruginosa Required for Cell Envelope Homeostasis in Either the Planktonic or the Sessile Mode of Growth

(2012) L. F. Wood et al.   mBio

Azithromycin Inhibits Expression of the GacA-Dependent Small RNAs RsmY and RsmZ in Pseudomonas aeruginosa

(2011) Isabel Pérez-Martínez et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach

(2011) Atsushi Fukushima et al.   Plant Biotechnology

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

(2011) M. Mutwil et al.   PLANT CELL

Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes

(2011) Kevin L. Childs et al.   PLoS One

Evolutionary dynamics of bacteria in a human host environment

(2011) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CoP: a database for characterizing co-expressed gene modules with biological information in plants

(2010) Y. Ogata et al.   BIOINFORMATICS

Recombinant human transferrin: Beyond iron binding and transport

(2010) Martin E. Brandsma et al.   BIOTECHNOLOGY ADVANCES

Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450 monooxygenases

(2010) Satish K Guttikonda et al.   BMC PLANT BIOLOGY

A general co-expression network-based approach to gene expression analysis: comparison and applications

(2010) Jianhua Ruan et al.   BMC Systems Biology

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice

(2010) Kazuki Hamada et al.   PLANT AND CELL PHYSIOLOGY

The Association of Multiple Interacting Genes with Specific Phenotypes in Rice Using Gene Coexpression Networks

(2010) Stephen P. Ficklin et al.   PLANT PHYSIOLOGY

Parallel Evolution in Pseudomonas aeruginosa over 39,000 Generations In Vivo

(2010) H. K. Huse et al.   mBio

Arabidopsis gene co-expression network and its functional modules

(2009) Linyong Mao et al.   BMC BIOINFORMATICS

The Pseudomonas aeruginosa Pyochelin-Iron Uptake Pathway and Its Metal Specificity

(2009) A. Braud et al.   JOURNAL OF BACTERIOLOGY

Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Articulation of three core metabolic processes in Arabidopsis: Fatty acid biosynthesis, leucine catabolism and starch metabolism

(2008) Wieslawa I Mentzen et al.   BMC PLANT BIOLOGY

Transcriptome Analysis of the Normal Human Mammary Cell Commitment and Differentiation Process

(2008) Afshin Raouf et al.   Cell Stem Cell

Signal integration in bacterial two-component regulatory systems

(2008) A. Y. Mitrophanov et al.   GENES & DEVELOPMENT

Reactive oxygen species: Current knowledge and applications in cancer research and therapeutic

(2008) Andy T.Y. Lau et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Functional and metabolic remodelling in GLUT4-deficient hearts confers hyper-responsiveness to substrate intervention

(2008) C.E. Huggins et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

ATTED-II provides coexpressed gene networks for Arabidopsis

(2008) T. Obayashi et al.   NUCLEIC ACIDS RESEARCH

Geometric Interpretation of Gene Coexpression Network Analysis

(2008) Steve Horvath et al.   PLoS Computational Biology