Bacterial c-di-GMP has a key role in establishing host–microbe symbiosis

Exploring Effects of C. elegans Protective Natural Microbiota on Host Physiology

(2022) Kohar Annie B. Kissoyan et al.   Frontiers in Cellular and Infection Microbiology

Search and sequence analysis tools services from EMBL-EBI in 2022

(2022) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

The Wsp system of Pseudomonas aeruginosa links surface sensing and cell envelope stress

(2022) Lindsey O’Neal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single mutation makes Escherichia coli an insect mutualist

(2022) Ryuichi Koga et al.   Nature Microbiology

Evolution of Microbiota–Host Associations: The Microbe’s Perspective

(2021) Nancy Obeng et al.   TRENDS IN MICROBIOLOGY

Evolutionary divergence of the Wsp signal transduction system in β- and γ-proteobacteria

(2021) Collin Kessler et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Host-emitted amino acid cues regulate bacterial chemokinesis to enhance colonization

(2021) Catherine D. Robinson et al.   Cell Host & Microbe

Modeling host-associating microbes under selection

(2021) Florence Bansept et al.   ISME Journal

Community assembly of the native C . elegans microbiome is influenced by time, substrate and individual bacterial taxa

(2020) Julia Johnke et al.   ENVIRONMENTAL MICROBIOLOGY

Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics

(2020) Kendra J. Adams et al.   JOURNAL OF PROTEOME RESEARCH

Linking bacterial growth, survival, and multicellularity – small signaling molecules as triggers and drivers

(2020) Regine Hengge   CURRENT OPINION IN MICROBIOLOGY

CeMbio - The Caenorhabditis elegans Microbiome Resource

(2020) Philipp Dirksen et al.   G3-Genes Genomes Genetics

Surface Sensing and Adaptation in Bacteria

(2020) Benoît-Joseph Laventie et al.   Annual Review of Microbiology

The genomic basis of Red Queen dynamics during rapid reciprocal host–pathogen coevolution

(2019) Andrei Papkou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural C. elegans Microbiota Protects against Infection via Production of a Cyclic Lipopeptide of the Viscosin Group

(2019) Kohar A.B. Kissoyan et al.   CURRENT BIOLOGY

Functional Specialization in Vibrio cholerae Diguanylate Cyclases: Distinct Modes of Motility Suppression and c-di-GMP Production

(2019) David Zamorano-Sánchez et al.   mBio

Multiple Roles of c-di-GMP Signaling in Bacterial Pathogenesis

(2019) Martina Valentini et al.   Annual Review of Microbiology

Sublethal antibiotics collapse gut bacterial populations by enhancing aggregation and expulsion

(2019) Brandon H. Schlomann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-based evolutionary history of Pseudomonas spp

(2018) Cedar Hesse et al.   ENVIRONMENTAL MICROBIOLOGY

Modernized Tools for Streamlined Genetic Manipulation and Comparative Study of Wild and Diverse Proteobacterial Lineages

(2018) Travis J. Wiles et al.   mBio

Cyclic di-GMP: second messenger extraordinaire

(2017) Urs Jenal et al.   NATURE REVIEWS MICROBIOLOGY

Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria

(2017) M Sabrina Pankey et al.   eLife

The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model

(2016) Philipp Dirksen et al.   BMC BIOLOGY

missMDA: A Package for Handling Missing Values in Multivariate Data Analysis

(2016) Julie Josse et al.   Journal of Statistical Software

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange

(2015) Laura R Hmelo et al.   Nature Protocols

Enhanced annotations and features for comparing thousands ofPseudomonasgenomes in the Pseudomonas genome database

(2015) Geoffrey L. Winsor et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Functional Characterization of Core Components of the Bacillus subtilis Cyclic-Di-GMP Signaling Pathway

(2013) X. Gao et al.   JOURNAL OF BACTERIOLOGY

Cellulose as an Architectural Element in Spatially Structured Escherichia coli Biofilms

(2013) D. O. Serra et al.   JOURNAL OF BACTERIOLOGY

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

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

(2011) H. Li   BIOINFORMATICS

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

(2011) F. Sievers et al.   Molecular Systems Biology

Microtiter Dish Biofilm Formation Assay

(2011) George A. O'Toole   Jove-Journal of Visualized Experiments

Receiver domain structure and function in response regulator proteins

(2010) Robert B Bourret   CURRENT OPINION IN MICROBIOLOGY

Evolutionary microbial genomics: insights into bacterial host adaptation

(2010) Christina Toft et al.   NATURE REVIEWS GENETICS

DOG 1.0: illustrator of protein domain structures

(2009) Jian Ren et al.   CELL RESEARCH

Pseudomonas aeruginosa Rugose Small-Colony Variants Have Adaptations That Likely Promote Persistence in the Cystic Fibrosis Lung

(2009) M. Starkey et al.   JOURNAL OF BACTERIOLOGY

Determinants for the Activation and Autoinhibition of the Diguanylate Cyclase Response Regulator WspR

(2009) Nabanita De et al.   JOURNAL OF MOLECULAR BIOLOGY

Simultaneous Inference in General Parametric Models

(2008) Torsten Hothorn et al.   BIOMETRICAL JOURNAL