4.5 Article

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

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Evolutionary Biology

Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica

Jingqiu Liao et al.

BMC EVOLUTIONARY BIOLOGY (2019)

Article Biochemistry & Molecular Biology

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

Philip Arevalo et al.

Article Chemistry, Multidisciplinary

Chemoenzymatic Assembly of Isotopically Labeled Folates

Antonio Angelastro et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

Letter Biotechnology & Applied Microbiology

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

Martin Steinegger et al.

NATURE BIOTECHNOLOGY (2017)

Article Microbiology

Why prokaryotes have pangenomes

James O. McInerney et al.

NATURE MICROBIOLOGY (2017)

Review Chemistry, Analytical

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

Leighton Pritchard et al.

ANALYTICAL METHODS (2016)

Article Microbiology

Latitude delineates patterns of biogeography in terrestrial Streptomyces

Mallory J. Choudoir et al.

ENVIRONMENTAL MICROBIOLOGY (2016)

Article Biochemical Research Methods

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

Shea N. Gardner et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Gene-Wide Identification of Episodic Selection

Ben Murrell et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Virology

RDP4: Detection and analysis of recombination patterns in virus genomes

Darren P. Martin et al.

VIRUS EVOLUTION (2015)

Article Biotechnology & Applied Microbiology

Reservoirs of Listeria Species in Three Environmental Ecosystems

Kristina Linke et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2014)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Review Microbiology

Explaining microbial genomic diversity in light of evolutionary ecology

Otto X. Cordero et al.

NATURE REVIEWS MICROBIOLOGY (2014)

Article Biotechnology & Applied Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments

Derrick E. Wood et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

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

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Multidisciplinary Sciences

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

B. Jesse Shapiro et al.

SCIENCE (2012)

Article Biochemical Research Methods

The variant call format and VCFtools

Petr Danecek et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Review Multidisciplinary Sciences

Molybdenum cofactors, enzymes and pathways

Guenter Schwarz et al.

NATURE (2009)

News Item Microbiology

Sequencing the species pan-genome

Stephen Bentley

NATURE REVIEWS MICROBIOLOGY (2009)

Review Microbiology

Comparative genomics: the bacterial pan-genome

Herve Tettelin et al.

CURRENT OPINION IN MICROBIOLOGY (2008)

Article Biochemistry & Molecular Biology

PAML 4: Phylogenetic analysis by maximum likelihood

Ziheng Yang

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

Automated phylogenetic detection of recombination using a genetic algorithm

Sergei L. Kosakovsky Pond et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Biochemistry & Molecular Biology

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

Mikita Suyama et al.

NUCLEIC ACIDS RESEARCH (2006)

Review Microbiology

Mechanisms of, and barriers to, horizontal gene transfer between bacteria

CM Thomas et al.

NATURE REVIEWS MICROBIOLOGY (2005)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)

Review Genetics & Heredity

The modern molecular clock

L Bromham et al.

NATURE REVIEWS GENETICS (2003)

Article Biotechnology & Applied Microbiology

Salt stress proteins induced in Listeria monocytogenes

O Duché et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2002)