Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

Inferring bacterial recombination rates from large-scale sequencing datasets

(2019) Mingzhi Lin et al.   NATURE METHODS

Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes

(2019) Pedro González-Torres et al.   mBio

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

(2019) Nandita R. Garud et al.   PLOS BIOLOGY

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

(2019) Spencer Diamond et al.   Nature Microbiology

Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces

(2019) Marc G. Chevrette et al.   Frontiers in Microbiology

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

(2018) Karen G. Lloyd et al.   mSystems

Probing the ecological and evolutionary history of a thermophilic cyanobacterial population via statistical properties of its microdiversity

(2018) Michael J. Rosen et al.   PLoS One

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

(2018) Chirag Jain et al.   Nature Communications

Evolution of the Natural Transformation Protein, ComEC, in Bacteria

(2018) Zachary T. Pimentel et al.   Frontiers in Microbiology

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

Atmospheric trace gases support primary production in Antarctic desert surface soil

(2017) Mukan Ji et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents

(2017) Rika E. Anderson et al.   Nature Communications

How clonal are bacteria over time?

(2016) B Jesse Shapiro   CURRENT OPINION IN MICROBIOLOGY

Spatial scale drives patterns in soil bacterial diversity

(2016) Sarah L. O'Brien et al.   ENVIRONMENTAL MICROBIOLOGY

Grassland responses to increased rainfall depend on the timescale of forcing

(2016) Martin J. P. Sullivan et al.   GLOBAL CHANGE BIOLOGY

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall et al.   ISME Journal

A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus

(2016) Sébastien Wielgoss et al.   ISME Journal

Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

(2016) Corinne Cassier-Chauvat et al.   Frontiers in Microbiology

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

(2016) Cristina N. Butterfield et al.   PeerJ

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

(2016) Richard Allen White et al.   mSystems

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

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

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

Epidemic Clones, Oceanic Gene Pools, and Eco-LD in the Free Living Marine Pathogen Vibrio parahaemolyticus

(2015) Yujun Cui et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

(2015) Jenni Hultman et al.   NATURE

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche

(2015) M. J. Rosen et al.   SCIENCE

Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes

(2015) David J. Krause et al.   SYSTEMATIC BIOLOGY

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Estimating and interpreting FST: The impact of rare variants

(2013) G. Bhatia et al.   GENOME RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Contingency in the direction and mechanics of soil organic matter responses to increased rainfall

(2012) Asmeret Asefaw Berhe et al.   PLANT AND SOIL

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

(2011) Gaddy T. Bergmann et al.   SOIL BIOLOGY & BIOCHEMISTRY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Fungal community responses to precipitation

(2010) CHRISTINE V. HAWKES et al.   GLOBAL CHANGE BIOLOGY

Widespread homologous recombination within and between Streptomyces species

(2010) James R Doroghazi et al.   ISME Journal

Global patterns in belowground communities

(2009) Noah Fierer et al.   ECOLOGY LETTERS

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Looking for Darwin's footprints in the microbial world

(2009) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

Mathematical properties of the measure of linkage disequilibrium

(2008) Jenna M. VanLiere et al.   THEORETICAL POPULATION BIOLOGY