Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

Prokaryotic taxonomy and nomenclature in the age of big sequence data

(2021) Philip Hugenholtz et al.   ISME Journal

Challenges in benchmarking metagenomic profilers

(2021) Zheng Sun et al.   NATURE METHODS

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

(2021) Kalen Cantrell et al.   mSystems

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes

(2021) George W Armstrong et al.   GENOME RESEARCH

Human Skin, Oral, and Gut Microbiomes Predict Chronological Age

(2020) Shi Huang et al.   mSystems

SHOGUN: a modular, accurate, and scalable framework for microbiome quantification

(2020) Benjamin Hillmann et al.   BIOINFORMATICS

Microbiome analyses of blood and tissues suggest cancer diagnostic approach

(2020) Gregory D. Poore et al.   NATURE

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

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

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

(2020) Francesco Asnicar et al.   Nature Communications

Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs

(2020) Julia M. Gauglitz et al.   mSystems

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

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans

(2020) Connie W.Y. Ha et al.   CELL

Publisher Correction: A genomic catalog of Earth’s microbiomes

(2020) Stephen Nayfach 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

Phylofactorization: a graph partitioning algorithm to identify phylogenetic scales of ecological data

(2019) Alex D. Washburne et al.   ECOLOGICAL MONOGRAPHS

Extensive transmission of microbes along the gastrointestinal tract

(2019) Thomas SB Schmidt et al.   eLife

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Benchmarking Metagenomics Tools for Taxonomic Classification

(2019) Simon H. Ye et al.   CELL

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

(2019) Qiyun Zhu et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

(2018) Cindy J. Castelle et al.   CELL

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

(2018) Stefan Janssen et al.   mSystems

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Striped UniFrac: enabling microbiome analysis at unprecedented scale

(2018) Daniel McDonald et al.   NATURE METHODS

Evaluating the Information Content of Shallow Shotgun Metagenomics

(2018) Benjamin Hillmann et al.   mSystems

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Cohort Profile: The National FINRISK Study

(2017) Katja Borodulin et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R

(2017) Marvin N. Wright et al.   Journal of Statistical Software

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

(2017) Supratim Mukherjee et al.   NATURE BIOTECHNOLOGY

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

(2017) Alex D. Washburne et al.   PeerJ

Atropos: specific, sensitive, and speedy trimming of sequencing reads

(2017) John P. Didion et al.   PeerJ

Uncovering the Horseshoe Effect in Microbial Analyses

(2017) James T. Morton et al.   mSystems

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth

(2013) Connor O. McCoy et al.   PeerJ

Vaginal Microbiome: Rethinking Health and Disease

(2012) Bing Ma et al.   Annual Review of Microbiology

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS