Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences

(2014) Laura M. Cox et al.   CELL

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Acyl-Homoserine Lactone Quorum Sensing: From Evolution to Application

(2013) Martin Schuster et al.   Annual Review of Microbiology

Microbe-Dependent and Nonspecific Effects of Procedures To Eliminate the Resident Microbiota from Drosophila melanogaster

(2013) Emma V. Ridley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Intestinal microbiota, diet and health

(2013) Susan E. Power et al.   BRITISH JOURNAL OF NUTRITION

Specific Gut Commensal Flora Locally Alters T Cell Tuning to Endogenous Ligands

(2013) Pascal Chappert et al.   IMMUNITY

Bridging immunity and lipid metabolism by gut microbiota

(2013) Renee L. Greer et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Physiological Framework for the Regulation of Quorum Sensing-Dependent Public Goods in Pseudomonas aeruginosa

(2013) B. Mellbye et al.   JOURNAL OF BACTERIOLOGY

An archaeal origin of eukaryotes supports only two primary domains of life

(2013) Tom A. Williams et al.   NATURE

Commensal Bacteria Control Cancer Response to Therapy by Modulating the Tumor Microenvironment

(2013) N. Iida et al.   SCIENCE

Bactericidal Antibiotics Induce Mitochondrial Dysfunction and Oxidative Damage in Mammalian Cells

(2013) S. Kalghatgi et al.   Science Translational Medicine

Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer

(2013) Karina L. Mine et al.   Nature Communications

Adverse Effects of Antimicrobials via Predictable or Idiosyncratic Inhibition of Host Mitochondrial Components

(2012) Alison E. Barnhill et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis

(2012) Jason E McDermott et al.   BMC Systems Biology

Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma

(2012) Shannon L Russell et al.   EMBO REPORTS

B Cell-Intrinsic MyD88 Signaling Prevents the Lethal Dissemination of Commensal Bacteria during Colonic Damage

(2012) Donna Kirkland et al.   IMMUNITY

Probiotics for the Prevention and Treatment of Antibiotic-Associated Diarrhea

(2012) Sydne J. Newberry   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa

(2012) P. Nadal Jimenez et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Guarding the perimeter: protection of the mucosa by tissue-resident memory T cells

(2012) L S Cauley et al.   Mucosal Immunology

Antibiotics in early life alter the murine colonic microbiome and adiposity

(2012) Ilseung Cho et al.   NATURE

Commensal bacteria–derived signals regulate basophil hematopoiesis and allergic inflammation

(2012) David A Hill et al.   NATURE MEDICINE

Lethal inflammasome activation by a multidrug-resistant pathobiont upon antibiotic disruption of the microbiota

(2012) Janelle S Ayres et al.   NATURE MEDICINE

The intestinal environment of surgical injury transforms Pseudomonas aeruginosa into a discrete hypervirulent morphotype capable of causing lethal peritonitis

(2012) Trissa Babrowski et al.   SURGERY

Antibiotics, microbiota, and immune defense

(2012) Carles Ubeda et al.   TRENDS IN IMMUNOLOGY

Reverse-engineering human regulatory networks

(2012) Celine Lefebvre et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview

(2011) Jeff Skinner et al.   BMC BIOINFORMATICS

Principles and Strategies for Developing Network Models in Cancer

(2011) Dana Pe'er et al.   CELL

Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut

(2011) Natalia Shulzhenko et al.   NATURE MEDICINE

Depletion of Murine Intestinal Microbiota: Effects on Gut Mucosa and Epithelial Gene Expression

(2011) Dag Henrik Reikvam et al.   PLoS One

Intestinal Microbiota Promote Enteric Virus Replication and Systemic Pathogenesis

(2011) S. K. Kuss et al.   SCIENCE

Integrated Microbial Survey Analysis of Prokaryotic Communities for the PhyloChip Microarray

(2010) M. C. Schatz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Interactional and functional centrality in transcriptional co-expression networks

(2010) Edi Prifti et al.   BIOINFORMATICS

Antibiotic use and inflammatory bowel diseases in childhood

(2010) A. Hviid et al.   GUT

Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans

(2010) Carles Ubeda et al.   JOURNAL OF CLINICAL INVESTIGATION

Reversible Microbial Colonization of Germ-Free Mice Reveals the Dynamics of IgA Immune Responses

(2010) S. Hapfelmeier et al.   SCIENCE

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Contribution of the RsaL global regulator toPseudomonas aeruginosavirulence and biofilm formation

(2009) Giordano Rampioni et al.   FEMS MICROBIOLOGY LETTERS

Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation

(2009) D. A. Antonopoulos et al.   INFECTION AND IMMUNITY

Role of Gut Commensal Microflora in the Development of Experimental Autoimmune Encephalomyelitis

(2009) J. Ochoa-Reparaz et al.   JOURNAL OF IMMUNOLOGY

Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis

(2009) D A Hill et al.   Mucosal Immunology

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Commensal DNA Limits Regulatory T Cell Conversion and Is a Natural Adjuvant of Intestinal Immune Responses

(2008) Jason A. Hall et al.   IMMUNITY

Transcription Regulation of the rRNA Gene by a Multifunctional Nucleolar Protein, B23/Nucleophosmin, through Its Histone Chaperone Activity

(2008) K. Murano et al.   MOLECULAR AND CELLULAR BIOLOGY

Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficits

(2008) Katharina Brandl et al.   NATURE

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY