Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

(2020) Elle M. Barnes et al.   Frontiers in Microbiology

GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms

(2020) Patrick Denis Browne et al.   GigaScience

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

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

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

(2019) Edoardo Pasolli et al.   CELL

Microbiome evolution during host aging

(2019) Francisco Daniel Davila Aleman et al.   PLoS Pathogens

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

(2019) Robert D. Stewart et al.   NATURE BIOTECHNOLOGY

A field guide for the compositional analysis of any-omics data

(2019) Thomas P Quinn et al.   GigaScience

Good Gone Bad: One Toxin Away From Disease for Bacteroides fragilis

(2019) Ezequiel Valguarnera et al.   JOURNAL OF MOLECULAR BIOLOGY

Variable Selection in Compositional Data Analysis Using Pairwise Logratios

(2018) Michael Greenacre   Mathematical Geosciences

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Innate Immunity of Neonates and Infants

(2018) Jack C. Yu et al.   Frontiers in Immunology

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Protecting the Newborn and Young Infant from Infectious Diseases: Lessons from Immune Ontogeny

(2017) Tobias R. Kollmann et al.   IMMUNITY

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

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

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Development of the gut microbiota in infancy and its impact on health in later life

(2017) Masaru Tanaka et al.   ALLERGOLOGY INTERNATIONAL

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model

(2016) Gaorui Bian et al.   ENVIRONMENTAL MICROBIOLOGY

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature 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

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

(2015) Robert M. Bowers et al.   BMC GENOMICS

From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems

(2015) Daniel R. Garza et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

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

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Diet shapes the gut microbiome of pigs during nursing and weaning

(2015) Steven A. Frese et al.   Microbiome

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The abundance and variety of carbohydrate-active enzymes in the human gut microbiota

(2013) Abdessamad El Kaoutari et al.   NATURE REVIEWS MICROBIOLOGY

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

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

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Classification of metagenomic sequences: methods and challenges

(2012) S. S. Mande et al.   BRIEFINGS IN BIOINFORMATICS

What defines extraintestinal pathogenic Escherichia coli?

(2011) Christian-Daniel Köhler et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A single regulatory gene is sufficient to alter bacterial host range

(2009) Mark J. Mandel et al.   NATURE

The immediate environment during postnatal development has long-term impact on gut community structure in pigs

(2008) Claire L Thompson et al.   ISME Journal

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Glycosyltransferases: Structures, Functions, and Mechanisms

(2007) L.L. Lairson et al.   Annual Review of Biochemistry