Evolutionary Trajectory of the Replication Mode of Bacterial Replicons

A predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria

(2020) Bai-Lu Tang et al.   Nature Communications

The Relative Importance of Modeling Site Pattern Heterogeneity Versus Partition-Wise Heterotachy in Phylogenomic Inference

(2019) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Replication termination without a replication fork trap

(2019) Elisa Galli et al.   Scientific Reports

Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae

(2018) Franziska S. Kemter et al.   PLoS Genetics

Periodic Variation of Mutation Rates in Bacterial Genomes Associated with Replication Timing

(2018) Marcus M. Dillon et al.   mBio

Accelerated Laboratory Evolution Reveals the Influence of Replication on the GC Skew in Escherichia coli

(2018) Nobuaki Kono et al.   Genome Biology and Evolution

Segregation but Not Replication of the Pseudomonas aeruginosa Chromosome Terminates at Dif

(2018) Bijit K. Bhowmik et al.   mBio

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Early photosynthetic eukaryotes inhabited low-salinity habitats

(2017) Patricia Sánchez-Baracaldo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Pseudoalteromonas piratica strain OCN003 is a coral pathogen that causes a switch from chronic to acute Montipora white syndrome in Montipora capitata

(2017) Silvia Beurmann et al.   PLoS One

The properties of spontaneous mutations in the opportunistic pathogen Pseudomonas aeruginosa

(2016) Jeremy R. Dettman et al.   BMC GENOMICS

Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations inVibrio choleraeandVibrio fischeri

(2016) Marcus M. Dillon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification and analysis of integrons and cassette arrays in bacterial genomes

(2016) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Orderly Replication and Segregation of the Four Replicons of Burkholderia cenocepacia J2315

(2016) Wen-Li Du et al.   PLoS Genetics

Characterization of a New Cold-Adapted and Salt-Activated Polysaccharide Lyase Family 7 Alginate Lyase from Pseudoalteromonas sp. SM0524

(2016) Xiu-Lan Chen et al.   Frontiers in Microbiology

A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae

(2016) M.-E. Val et al.   Science Advances

Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation–Accumulation Experiments

(2015) Way Sung et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Neoproterozoic Transition in the Marine Nitrogen Cycle

(2014) Patricia Sánchez-Baracaldo et al.   CURRENT BIOLOGY

Mutation Rate, Spectrum, Topology, and Context-Dependency in the DNA Mismatch Repair-Deficient Pseudomonas fluorescens ATCC948

(2014) Hongan Long et al.   Genome Biology and Evolution

Development of a genetic system for the deep-sea psychrophilic bacterium Pseudoalteromonas sp. SM9913

(2014) Zi-Chao Yu et al.   Microbial Cell Factories

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromosome I Controls Chromosome II Replication in Vibrio cholerae

(2014) Jong Hwan Baek et al.   PLoS Genetics

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Atmospheric oxygenation three billion years ago

(2013) Sean A. Crowe et al.   NATURE

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Evolution of Divergent Life History Strategies in Marine Alphaproteobacteria

(2013) H. Luo et al.   mBio

On the Mutational Topology of the Bacterial Genome

(2013) Patricia L. Foster et al.   G3-Genes Genomes Genetics

Chromosome Replication and Segregation in Bacteria

(2012) Rodrigo Reyes-Lamothe et al.   Annual Review of Genetics

Chromosome dynamics in multichromosome bacteria

(2012) Jyoti K. Jha et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Elastolytic Mechanism of a Novel M23 Metalloprotease Pseudoalterin from Deep-seaPseudoalteromonassp. CF6-2

(2012) Hui-Lin Zhao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

Integrative mobile elements exploiting Xer recombination

(2012) Bhabatosh Das et al.   TRENDS IN MICROBIOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes

(2011) Nobuaki Kono et al.   BMC GENOMICS

Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing

(2011) Ole Skovgaard et al.   GENOME RESEARCH

Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

(2011) M. d. Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transition from a plasmid to a chromosomal mode of replication entails additional regulators

(2011) T. Venkova-Canova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

(2011) Alessandro M Varani et al.   GENOME BIOLOGY

Latitudinal patterns in the abundance of major marine bacterioplankton groups

(2010) M Wietz et al.   AQUATIC MICROBIAL ECOLOGY

BioRuby: bioinformatics software for the Ruby programming language

(2010) N. Goto et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913

(2010) Qi-Long Qin et al.   ISME Journal

Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid

(2010) Peter W. Harrison et al.   TRENDS IN MICROBIOLOGY

Why Genes Evolve Faster on Secondary Chromosomes in Bacteria

(2010) Vaughn S. Cooper et al.   PLoS Computational Biology

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Termination Structures in the Escherichia coli Chromosome Replication Fork Trap

(2009) Iain G. Duggin et al.   JOURNAL OF MOLECULAR BIOLOGY

The Organization of the Bacterial Genome

(2008) Eduardo P.C. Rocha   Annual Review of Genetics

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

DNAPlotter: circular and linear interactive genome visualization

(2008) T. Carver et al.   BIOINFORMATICS

Hydrolysis of Insoluble Collagen by Deseasin MCP-01 from Deep-seaPseudoalteromonassp. SM9913

(2008) Guo-Yan Zhao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land

(2008) F. U. Battistuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment

(2008) Torsten Thomas et al.   PLoS One

FtsK-Dependent Dimer Resolution on Multiple Chromosomes in the Pathogen Vibrio cholerae

(2008) Marie-Eve Val et al.   PLoS Genetics