Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

FlexTaxD: flexible modification of taxonomy databases for improved sequence classification

(2021) David Sundell et al.   BIOINFORMATICS

The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping

(2021) Benjamin S. Beresford-Jones et al.   Cell Host & Microbe

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

The Mouse Gut Microbial Biobank expands the coverage of cultured bacteria

(2020) Chang Liu et al.   Nature Communications

An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

(2020) Till R. Lesker et al.   Cell Reports

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

(2020) Silas Kieser et al.   BMC BIOINFORMATICS

A unified catalog of 204,938 reference genomes from the human gut microbiome

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

Diversity within species: interpreting strains in microbiomes

(2020) Thea Van Rossum et al.   NATURE REVIEWS MICROBIOLOGY

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

OUP accepted manuscript

(2018)   BIOINFORMATICS

Common traits between the beige fat-inducing stimuli

(2018) Ozren Stojanović et al.   CURRENT OPINION IN CELL BIOLOGY

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

(2018) Robert D. Stewart et al.   Nature Communications

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Accumulation of succinate controls activation of adipose tissue thermogenesis

(2018) Evanna L. Mills et al.   NATURE

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Subspecies in the global human gut microbiome

(2017) Paul I Costea et al.   Molecular Systems Biology

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Host–Microbiota Mutualism in Metabolic Diseases

(2017) Salvatore Fabbiano et al.   Frontiers in Endocrinology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Altered Microbiota Contributes to Reduced Diet-Induced Obesity upon Cold Exposure

(2016) Marika Ziętak et al.   Cell Metabolism

Microbial signals to the brain control weight

(2016) Mirko Trajkovski et al.   NATURE

An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis

(2016) Jun Chen et al.   Genome Medicine

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

(2016) Ilias Lagkouvardos et al.   Nature Microbiology

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Gut Microbiota Orchestrates Energy Homeostasis during Cold

(2015) Claire Chevalier et al.   CELL

Activation of Human Brown Adipose Tissue by a β3-Adrenergic Receptor Agonist

(2015) Aaron M. Cypess et al.   Cell Metabolism

How informative is the mouse for human gut microbiota research?

(2015) T. L. A. Nguyen et al.   Disease Models & Mechanisms

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Activation of Toll-like Receptor 4 (TLR4) Attenuates Adaptive Thermogenesis via Endoplasmic Reticulum Stress

(2015) Meshail Okla et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A catalog of the mouse gut metagenome

(2015) Liang Xiao et al.   NATURE BIOTECHNOLOGY

Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity

(2014) Amandine Everard et al.   ISME Journal

BioServices: a common Python package to access biological Web Services programmatically

(2013) Thomas Cokelaer et al.   BIOINFORMATICS

Quantitatively Different, yet Qualitatively Alike: A Meta-Analysis of the Mouse Core Gut Microbiome with a View towards the Human Gut Microbiome

(2013) Lukasz Krych et al.   PLoS One

Understanding the brown adipocyte as a contributor to energy homeostasis

(2013) Kanta Chechi et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Symptomatic atherosclerosis is associated with an altered gut metagenome

(2012) Fredrik H. Karlsson et al.   Nature Communications

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

(2011) Steven A. Frese et al.   PLoS Genetics

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One