4.8 Article

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

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 Biochemistry & Molecular Biology

Investigating Evolutionary Rate Variation in Bacteria

Beth Gibson et al.

JOURNAL OF MOLECULAR EVOLUTION (2019)

Review Biochemistry & Molecular Biology

The Ecology and Evolution of Pangenomes

Michael A. Brockhurst et al.

CURRENT BIOLOGY (2019)

Article Ecology

Variation in range size and dispersal capabilities of microbial taxa

Mallory J. Choudoir et al.

ECOLOGY (2018)

Article Biochemistry & Molecular Biology

Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics

Eduardo P. C. Rocha

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Multidisciplinary Sciences

A global atlas of the dominant bacteria found in soil

Manuel Delgado-Baquerizo et al.

SCIENCE (2018)

Article Infectious Diseases

Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi

Elizabeth M. Batty et al.

PLOS NEGLECTED TROPICAL DISEASES (2018)

Article Microbiology

Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.

Mikhail A. Moldovan et al.

FRONTIERS IN MICROBIOLOGY (2018)

Article Evolutionary Biology

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

Louis-Marie Bobay et al.

BMC EVOLUTIONARY BIOLOGY (2018)

Article Genetics & Heredity

Metabolic adaptations underlying genome flexibility in prokaryotes

Akshit Goyal

PLOS GENETICS (2018)

Article Biochemistry & Molecular Biology

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

Daniel R. Mende et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Evolutionary Biology

Biological Species Are Universal across Life's Domains

Louis-Marie Bobay et al.

GENOME BIOLOGY AND EVOLUTION (2017)

Article Ecology

Prokaryote genome fluidity is dependent on effective population size

Nadia Andrea Andreani et al.

ISME JOURNAL (2017)

Article Multidisciplinary Sciences

Genomic characterization of Nontuberculous Mycobacteria

Tarcisio Fedrizzi et al.

SCIENTIFIC REPORTS (2017)

Letter Microbiology

The population genetics of pangenomes

B. Jesse Shapiro

NATURE MICROBIOLOGY (2017)

Letter Microbiology

Reply to 'The population genetics of pangenomes'

James O. McInerney et al.

NATURE MICROBIOLOGY (2017)

Article Microbiology

Environmental drivers of a microbial genomic transition zone in the ocean's interior

Daniel R. Mende et al.

NATURE MICROBIOLOGY (2017)

Article Microbiology

Why prokaryotes have pangenomes

James O. McInerney et al.

NATURE MICROBIOLOGY (2017)

Article Biochemical Research Methods

MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis

Joao F. Matias Rodrigues et al.

BIOINFORMATICS (2017)

Article Biotechnology & Applied Microbiology

Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa

Marta Cobo-Simon et al.

BMC GENOMICS (2017)

Article Biochemistry & Molecular Biology

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Jaime Huerta-Cepas et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Article Ecology

phylosignal: an R package to measure, test, and explore the phylogenetic signal

Francois Keck et al.

ECOLOGY AND EVOLUTION (2016)

Article Biochemical Research Methods

Roary: rapid large-scale prokaryote pan genome analysis

Andrew J. Page et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

micropan: an R-package for microbial pan-genomics

Lars Snipen et al.

BMC BIOINFORMATICS (2015)

Review Microbiology

Ten years of pan-genome analyses

George Vernikos et al.

CURRENT OPINION IN MICROBIOLOGY (2015)

Article Statistics & Probability

A Toolbox for Nonlinear Regression inR: The Packagenlstools

Florent Baty et al.

Journal of Statistical Software (2015)

Article Biochemistry & Molecular Biology

The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes

Mario Alberto Martinez-Nunez et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2015)

Review Microbiology

Prochlorococcus: the structure and function of collective diversity

Steven J. Biller et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Review Ecology

Implications of streamlining theory for microbial ecology

Stephen J. Giovannoni et al.

ISME JOURNAL (2014)

Review Microbiology

Bacterial Genome Instability

Elise Darmon et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2014)

Article Biochemistry & Molecular Biology

PATRIC, the bacterial bioinformatics database and analysis resource

Alice R. Wattam et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biotechnology & Applied Microbiology

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

Bruno Contreras-Moreira et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2013)

Article Evolutionary Biology

Gene Frequency Distributions Reject a Neutral Model of Genome Evolution

Alexander E. Lobkovsky et al.

GENOME BIOLOGY AND EVOLUTION (2013)

Article Biochemical Research Methods

Accurate and universal delineation of prokaryotic species

Daniel R. Mende et al.

NATURE METHODS (2013)

Review Genetics & Heredity

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

Martin F. Polz et al.

TRENDS IN GENETICS (2013)

Article Multidisciplinary Sciences

Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria

Rohit Ghai et al.

SCIENTIFIC REPORTS (2013)

Review Biochemical Research Methods

Metabolically versatile large-genome prokaryotes

Benoit Guieysse et al.

CURRENT OPINION IN BIOTECHNOLOGY (2012)

Article Evolutionary Biology

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

Franz Baumdicker et al.

GENOME BIOLOGY AND EVOLUTION (2012)

Review Ecology

Bacterial Genomes: Habitat Specificity and Uncharted Organisms

Francisco Dini-Andreote et al.

MICROBIAL ECOLOGY (2012)

Article Multidisciplinary Sciences

Drift-barrier hypothesis and mutation-rate evolution

Way Sung et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

B. Jesse Shapiro et al.

SCIENCE (2012)

Article Ecology

How to measure and test phylogenetic signal

Tamara Muenkemueller et al.

METHODS IN ECOLOGY AND EVOLUTION (2012)

Article Genetics & Heredity

Selection-Driven Gene Loss in Bacteria

Sanna Koskiniemi et al.

PLOS GENETICS (2012)

Article Biotechnology & Applied Microbiology

Genomic fluidity: an integrative view of gene diversity within microbial populations

Andrey O. Kislyuk et al.

BMC GENOMICS (2011)

Article Biochemistry & Molecular Biology

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

Fabian Sievers et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Biochemistry & Molecular Biology

High-Dimensional Regression and Variable Selection Using CAR Scores

Verena Zuber et al.

STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY (2011)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Article Ecology

Genome streamlining and the elemental costs of growth

Dag O. Hessen et al.

TRENDS IN ECOLOGY & EVOLUTION (2010)

Article Multidisciplinary Sciences

The impact of long-distance horizontal gene transfer on prokaryotic genome size

Otto X. Cordero et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Computer Science, Interdisciplinary Applications

FactoMineR: An R package for multivariate analysis

Sebastien Le et al.

JOURNAL OF STATISTICAL SOFTWARE (2008)

Article Multidisciplinary Sciences

Genome-wide experimental determination of barriers to horizontal gene transfer

Rotem Sorek et al.

SCIENCE (2007)

Article Multidisciplinary Sciences

Quantitative phylogenetic assessment of microbial communities in diverse environments

C. von Mering et al.

SCIENCE (2007)

Article Multidisciplinary Sciences

Toward automatic reconstruction of a highly resolved tree of life

FD Ciccarelli et al.

SCIENCE (2006)

Review Cell Biology

The microbial pan-genome

D Medini et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2005)

Article Multidisciplinary Sciences

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae:: Implications for the microbial pan-genome

H Tettelin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

Evolutionary origins of genomic repertoires in bacteria

E Lerat et al.

PLOS BIOLOGY (2005)

Article Multidisciplinary Sciences

Genomic insights that advance the species definition for prokaryotes

KT Konstantinidis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

Trends between gene content and genome size in prokaryotic species with larger genomes

KT Konstantinidis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Review Biochemistry & Molecular Biology

Transcription regulation and environmental adaptation in bacteria

I Cases et al.

TRENDS IN MICROBIOLOGY (2003)