Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment

(2020) Jordan G Okie et al.   eLife

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

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

Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense

(2020) Kira S Makarova et al.   NUCLEIC ACIDS RESEARCH

Picocyanobacteria Community and Cyanophage Infection Responses to Nutrient Enrichment in a Mesocosms Experiment in Oligotrophic Waters

(2020) Alexandra Coello-Camba et al.   Frontiers in Microbiology

A synthesis of bacterial and archaeal phenotypic trait data

(2020) Joshua S. Madin et al.   Scientific Data

Benchmarking microbial growth rate predictions from metagenomes

(2020) Andrew M. Long et al.   ISME Journal

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

(2019) Edoardo Pasolli et al.   CELL

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

The pan-immune system of bacteria: antiviral defence as a community resource

(2019) Aude Bernheim et al.   NATURE REVIEWS MICROBIOLOGY

Charting the Complexity of the Marine Microbiome through Single-Cell Genomics

(2019) Maria G. Pachiadaki et al.   CELL

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

The Codon Usage of Lowly Expressed Genes Is Subject to Natural Selection

(2018) Adi Yannai et al.   Genome Biology and Evolution

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

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Codon usage of highly expressed genes affects proteome-wide translation efficiency

(2018) Idan Frumkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

sensiPhy : An r -package for sensitivity analysis in phylogenetic comparative methods

(2018) Gustavo B. Paterno et al.   Methods in Ecology and Evolution

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

Factors driving effective population size and pan-genome evolution in bacteria

(2018) Louis-Marie Bobay et al.   BMC EVOLUTIONARY BIOLOGY

Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples

(2018) Yuan Gao et al.   NATURE METHODS

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage

(2018) Akintunde Emiola et al.   Nature Communications

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Impact of Recombination on the Base Composition of Bacteria and Archaea

(2017) Louis-Marie Bobay et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comprehensive classification of the PIN domain-like superfamily

(2017) Dorota Matelska et al.   NUCLEIC ACIDS RESEARCH

The MAR databases: development and implementation of databases specific for marine metagenomics

(2017) Terje Klemetsen et al.   NUCLEIC ACIDS RESEARCH

RefSeq: an update on prokaryotic genome annotation and curation

(2017) Daniel H Haft et al.   NUCLEIC ACIDS RESEARCH

Microbial community assembly and evolution in subseafloor sediment

(2017) Piotr Starnawski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds

(2017) Elizabeth Trembath-Reichert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Strategies to improve reference databases for soil microbiomes

(2016) Jinlyung Choi et al.   ISME Journal

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation

(2016) David M. Kristensen et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

(2016) Benjamin R. K. Roller 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

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Harnessing the landscape of microbial culture media to predict new organism–media pairings

(2015) Matthew A. Oberhardt et al.   Nature Communications

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

SMAL: A Resource of Spontaneous Mutation Accumulation Lines

(2014) W. Wei et al.   MOLECULAR BIOLOGY AND EVOLUTION

Yeast mutation accumulation experiment supports elevated mutation rates at highly transcribed sites

(2014) Xiaoshu Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

A Linear-Time Algorithm for Gaussian and Non-Gaussian Trait Evolution Models

(2014) Lam si Tung Ho et al.   SYSTEMATIC BIOLOGY

CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems

(2014) Kira S. Makarova et al.   Frontiers in Genetics

Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution

(2013) Jaroslav Flegr   Biology Direct

No Gene-Specific Optimization of Mutation Rate in Escherichia coli

(2013) X. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

(2013) B. K. Swan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nature and Extent of the Deep Biosphere

(2013) F. S. Colwell et al.   Reviews in Mineralogy & Geochemistry

Genomic evidence for elevated mutation rates in highly expressed genes

(2012) Chungoo Park et al.   EMBO REPORTS

Strategies for culture of ‘unculturable’ bacteria

(2010) Sonia R. Vartoukian et al.   FEMS MICROBIOLOGY LETTERS

Forces that influence the evolution of codon bias

(2010) P. M. Sharp et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

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

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

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

(2009) T. Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Selection on Codon Bias

(2008) Ruth Hershberg et al.   Annual Review of Genetics

Transcription induces strand-specific mutations at the 5' end of human genes

(2008) P. Polak et al.   GENOME RESEARCH

Whole-genome mutational biases in bacteria

(2008) P. A. Lind et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

(2008) J. R. Coleman et al.   SCIENCE