Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex

Stenotrophomonas tumulicola sp. nov., a major contaminant of the stone chamber interior in the Takamatsuzuka Tumulus

(2016) Yutaka Handa et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Occurrence of Stenotrophomonas maltophilia in agricultural soils and antibiotic resistance properties

(2016) Amélie Deredjian et al.   RESEARCH IN MICROBIOLOGY

What Is Speciation?

(2016) B. Jesse Shapiro et al.   PLoS Genetics

Genome Sequence of Type Strains of Genus Stenotrophomonas

(2016) Prashant P. Patil et al.   Frontiers in Microbiology

Comparative Genomics of Environmental and ClinicalStenotrophomonas maltophiliaStrains with Different Antibiotic Resistance Profiles

(2015) Benjamin Youenou et al.   Genome Biology and Evolution

Clumpak : a program for identifying clustering modes and packaging population structure inferences across K

(2015) Naama M. Kopelman et al.   Molecular Ecology Resources

Multilocus sequence analysis (MLSA) in prokaryotic taxonomy

(2015) Stefanie P. Glaeser et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

Update on infections caused by Stenotrophomonas maltophilia with particular attention to resistance mechanisms and therapeutic options

(2015) Ya-Ting Chang et al.   Frontiers in Microbiology

Antibiotic resistance in the opportunistic pathogen Stenotrophomonas maltophilia

(2015) María B. Sánchez   Frontiers in Microbiology

Friends or foes: can we make a distinction between beneficial and harmful strains of the Stenotrophomonas maltophilia complex?

(2015) Gabriele Berg et al.   Frontiers in Microbiology

Interplay between intrinsic and acquired resistance to quinolones inStenotrophomonas maltophilia

(2014) Guillermo García-León et al.   ENVIRONMENTAL MICROBIOLOGY

Explaining microbial genomic diversity in light of evolutionary ecology

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

Marginal Likelihood Estimate Comparisons to Obtain Optimal Species Delimitations in Silene sect. Cryptoneurae (Caryophyllaceae)

(2014) Zeynep Aydin et al.   PLoS One

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not

(2014) Jessica Hedge et al.   mBio

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

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

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

New strategies againstStenotrophomonas maltophilia: a serious worldwide intrinsically drug-resistant opportunistic pathogen

(2013) Joanna S Brooke   Expert Review of Anti-Infective Therapy

Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle

(2013) N. A. Rosenberg   MOLECULAR BIOLOGY AND EVOLUTION

Sympatric Speciation: When Is It Possible in Bacteria?

(2013) Jonathan Friedman et al.   PLoS One

Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data

(2013) Noah M. Reid et al.   SYSTEMATIC BIOLOGY

Species Delimitation Using Bayes Factors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae)

(2013) Jared A. Grummer et al.   SYSTEMATIC BIOLOGY

Stenotrophomonas maltophilia: an Emerging Global Opportunistic Pathogen

(2012) J. S. Brooke   CLINICAL MICROBIOLOGY REVIEWS

Water-sediment niche differentiation in ancient marine lineages of Exiguobacterium endemic to the Cuatro Cienegas Basin

(2012) Eria A. Rebollar et al.   ENVIRONMENTAL MICROBIOLOGY

Genome Sequence of Stenotrophomonas maltophilia RR-10, Isolated as an Endophyte from Rice Root

(2012) B. Zhu et al.   JOURNAL OF BACTERIOLOGY

Whole-Genome Sequence of Stenotrophomonas maltophilia D457, a Clinical Isolate and a Model Strain

(2012) F. Lira et al.   JOURNAL OF BACTERIOLOGY

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Coalescent-based species delimitation in an integrative taxonomy

(2012) Matthew K. Fujita et al.   TRENDS IN ECOLOGY & EVOLUTION

Patterns of Gene Flow Define Species of Thermophilic Archaea

(2012) Hinsby Cadillo-Quiroz et al.   PLOS BIOLOGY

Prokaryotic taxonomy in the sequencing era - the polyphasic approach revisited

(2011) Peter Kämpfer et al.   ENVIRONMENTAL MICROBIOLOGY

Stenotrophomonas interspecies differentiation and identification by gyrB sequence analysis

(2011) Liselott A. Svensson-Stadler et al.   FEMS MICROBIOLOGY LETTERS

Identification of Stenotrophomonas maltophilia strains isolated from environmental and clinical samples: a rapid and efficient procedure

(2011) C. Pinot et al.   JOURNAL OF APPLIED MICROBIOLOGY

Genotyping of Environmental and Clinical Stenotrophomonas maltophilia Isolates and their Pathogenic Potential

(2011) Martina Adamek et al.   PLoS One

Delineation of Stenotrophomonas spp. by multi-locus sequence analysis and MALDI-TOF mass spectrometry

(2011) Zinaida Vasileuskaya-Schulz et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

Screening for endophytic nitrogen-fixing bacteria in Brazilian sugar cane varieties used in organic farming and description of Stenotrophomonas pavanii sp. nov.

(2010) P. L. Ramos et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Evolutionary divergence and biogeography of sympatric niche-differentiated bacterial populations

(2010) Brian B Oakley et al.   ISME Journal

Stenotrophomonas panacihumi sp. nov., isolated from soil of a ginseng field

(2010) Hoonbok Yi et al.   JOURNAL OF MICROBIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

A species concept for bacteria based on adaptive divergence

(2010) Michiel Vos   TRENDS IN MICROBIOLOGY

A Stenotrophomonas maltophilia Multilocus Sequence Typing Scheme for Inferring Population Structure

(2009) S. Kaiser et al.   JOURNAL OF BACTERIOLOGY

Stenotrophomonas maltophilia: an emerging opportunist human pathogen

(2009) W John Looney et al.   LANCET INFECTIOUS DISEASES

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

The versatility and adaptation of bacteria from the genus Stenotrophomonas

(2009) Robert P. Ryan et al.   NATURE REVIEWS MICROBIOLOGY

primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies

(2009) B. Contreras-Moreira et al.   NUCLEIC ACIDS RESEARCH

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Multilocus Sequence Analysis for Assessment of the Biogeography and Evolutionary Genetics of Four Bradyrhizobium Species That Nodulate Soybeans on the Asiatic Continent

(2008) P. Vinuesa et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Synonymous and Nonsynonymous Polymorphisms versus Divergences in Bacterial Genomes

(2008) A. L. Hughes et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics

(2008) A. Koeppel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY

The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants

(2008) Lisa C Crossman et al.   GENOME BIOLOGY