Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution

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

(2020) Alexander Crits-Christoph et al.   ISME Journal

Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica

(2019) Jingqiu Liao et al.   BMC EVOLUTIONARY BIOLOGY

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations

(2019) Philip Arevalo et al.   CELL

Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence

(2019) Jaime Iranzo et al.   Nature Communications

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

Chemoenzymatic Assembly of Isotopically Labeled Folates

(2017) Antonio Angelastro et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Why prokaryotes have pangenomes

(2017) James O. McInerney et al.   Nature Microbiology

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

(2016) Leighton Pritchard et al.   Analytical Methods

Latitude delineates patterns of biogeography in terrestrial Streptomyces

(2016) Mallory J. Choudoir et al.   ENVIRONMENTAL MICROBIOLOGY

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome: Table 1

(2015) Shea N Gardner et al.   BIOINFORMATICS

Gene-Wide Identification of Episodic Selection

(2015) Ben Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reservoirs of Listeria Species in Three Environmental Ecosystems

(2014) Kristina Linke et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter

(2014) Guillaume Méric et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Molybdenum cofactors, enzymes and pathways

(2009) Günter Schwarz et al.   NATURE

Sequencing the species pan-genome

(2009) Stephen Bentley   NATURE REVIEWS MICROBIOLOGY

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY