Laboratory mice born to wild mice have natural microbiota and model human immune responses

Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair

(2018) Jonathan L. Linehan et al.   CELL

CX3CR1+mononuclear phagocytes control immunity to intestinal fungi

(2018) Irina Leonardi et al.   SCIENCE

Rapid environmental effects on gut nematode susceptibility in rewilded mice

(2018) Jacqueline M. Leung et al.   PLOS BIOLOGY

The influence of caging, bedding, and diet on the composition of the microbiota in different regions of the mouse gut

(2018) Aaron C. Ericsson et al.   Scientific Reports

White Adipose Tissue Is a Reservoir for Memory T Cells and Promotes Protective Memory Responses to Infection

(2017) Seong-Ji Han et al.   IMMUNITY

Next generation antibody drugs: pursuit of the 'high-hanging fruit'

(2017) Paul J. Carter et al.   NATURE REVIEWS DRUG DISCOVERY

VirusSeeker, a computational pipeline for virus discovery and virome composition analysis

(2017) Guoyan Zhao et al.   VIROLOGY

The comparative immunology of wild and laboratory mice, Mus musculus domesticus

(2017) Stephen Abolins et al.   Nature Communications

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination

(2016) Scott A. Handley et al.   Cell Host & Microbe

Sequential Infection with Common Pathogens Promotes Human-like Immune Gene Expression and Altered Vaccine Response

(2016) Tiffany A. Reese et al.   Cell Host & Microbe

Wild immunology assessed by multidimensional mass cytometry

(2016) Alberto Sada Japp et al.   CYTOMETRY PART A

Not all mice are the same: Standardization of animal research data presentation

(2016) M. Bishr Omary et al.   HEPATOLOGY

Accounting for reciprocal host–microbiome interactions in experimental science

(2016) Thaddeus S. Stappenbeck et al.   NATURE

Normalizing the environment recapitulates adult human immune traits in laboratory mice

(2016) Lalit K. Beura et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Transkingdom control of viral infection and immunity in the mammalian intestine

(2016) J. K. Pfeiffer et al.   SCIENCE

Of mice and microbes

(2016) K. Servick   SCIENCE

The Bacterial Microbiome and Virome Milestones of Infant Development

(2016) Efrem S. Lim et al.   TRENDS IN MICROBIOLOGY

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Mycobiome: Approaches to analysis of intestinal fungi

(2015) Jie Tang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut

(2014) Henning Seedorf et al.   CELL

The Virome in Mammalian Physiology and Disease

(2014) Herbert W. Virgin   CELL

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Kingdom-Agnostic Metagenomics and the Importance of Complete Characterization of Enteric Microbial Communities

(2014) Jason M. Norman et al.   GASTROENTEROLOGY

ImmPort: disseminating data to the public for the future of immunology

(2014) Sanchita Bhattacharya et al.   IMMUNOLOGIC RESEARCH

Standardised animal models of host microbial mutualism

(2014) A J Macpherson et al.   Mucosal Immunology

Clinical development success rates for investigational drugs

(2014) Michael Hay et al.   NATURE BIOTECHNOLOGY

Geographic variation in the eukaryotic virome of human diarrhea

(2014) Lori R. Holtz et al.   VIROLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Normalization of mass cytometry data with bead standards

(2013) Rachel Finck et al.   CYTOMETRY PART A

The Collaborative Cross: A Recombinant Inbred Mouse Population for the Systems Genetic Era

(2013) D. W. Threadgill et al.   ILAR JOURNAL

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Conservation and divergence in the transcriptional programs of the human and mouse immune systems

(2013) T. Shay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic responses in mouse models poorly mimic human inflammatory diseases

(2013) Junhee Seok et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota

(2012) Hachung Chung et al.   CELL

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Animal models of sepsis: Why does preclinical efficacy fail to translate to the clinical setting?

(2008) Alex Dyson et al.   CRITICAL CARE MEDICINE

Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery

(2008) Stacy R. Finkbeiner et al.   PLoS Pathogens