Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

(2018) Stilianos Louca et al.   Microbiome

The European Nucleotide Archive in 2018

(2018) Peter W Harrison et al.   NUCLEIC ACIDS RESEARCH

Competitive lottery-based assembly of selected clades in the human gut microbiome

(2018) Adrian J. Verster et al.   Microbiome

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

(2016) Benjamin R. K. Roller et al.   Nature Microbiology

A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments

(2015) Piotr Bentkowski et al.   Genome Biology and Evolution

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

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

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula

(2015) Jeff S. Bowman et al.   PLoS One

UProC: tools for ultra-fast protein domain classification

(2014) Peter Meinicke   BIOINFORMATICS

Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria

(2014) Albert Barberán et al.   ECOLOGY LETTERS

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

The emergence and promise of functional biogeography

(2014) C. Violle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

(2014) Sascha Krause et al.   Frontiers in Microbiology

Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities

(2014) Noah Fierer et al.   Frontiers in Microbiology

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

(2014) Florent E Angly et al.   Microbiome

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Metabolically versatile large-genome prokaryotes

(2012) Benoit Guieysse et al.   CURRENT OPINION IN BIOTECHNOLOGY

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Marine Microbes See a Sea of Gradients

(2012) R. Stocker   SCIENCE

The return of the variance: intraspecific variability in community ecology

(2012) Cyrille Violle et al.   TRENDS IN ECOLOGY & EVOLUTION

Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph

(2012) Mario López-Pérez et al.   Scientific Reports

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

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

(2011) Daniel McDonald et al.   ISME Journal

Exploration of community traits as ecological markers in microbial metagenomes

(2011) ALBERT BARBERÁN et al.   MOLECULAR ECOLOGY

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

(2011) J. Raes et al.   Molecular Systems Biology

Microbial Metagenomics: Beyond the Genome

(2010) Jack A. Gilbert et al.   Annual Review of Marine Science

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Average genome size: a potential source of bias in comparative metagenomics

(2010) Bánk Beszteri et al.   ISME Journal

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre

(2009) K. T. Konstantinidis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Distinct Gene Number-Genome Size Relationships for Eukaryotes and Non-Eukaryotes: Gene Content Estimation for Dinoflagellate Genomes

(2009) Yubo Hou et al.   PLoS One

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

(2009) Florent E. Angly et al.   PLoS Computational Biology

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One