Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise

The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions

(2017) Michael D Lee et al.   ISME Journal

Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean

(2017) Kyle R Frischkorn et al.   ISME Journal

Search for 5′-leader regulatory RNA structures based on gene annotation aided by the RiboGap database

(2017) Mohammad Reza Naghdi et al.   METHODS

The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system

(2017) Tobias Sahr et al.   PLoS Genetics

Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships

(2017) Justin R. Seymour et al.   Nature Microbiology

Flexible genomic islands as drivers of genome evolution

(2016) Francisco Rodriguez-Valera et al.   CURRENT OPINION IN MICROBIOLOGY

Microbial diversity within the T richodesmium holobiont

(2016) Mónica Rouco et al.   ENVIRONMENTAL MICROBIOLOGY

Spatial variation of bacterial community composition at the expiry of spring phytoplankton bloom in Sendai Bay, Japan

(2016) Tomoko Sakami et al.   GENE

Pangenome Evolution in the Marine BacteriumAlteromonas

(2016) Mario López-Pérez et al.   Genome Biology and Evolution

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus

(2016) Steven J Biller et al.   ISME Journal

Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals

(2016) Dikla Aharonovich et al.   ISME Journal

Genome wide transcription start sites analysis of Xanthomonas campestris pv. campestris B100 with insights into the gum gene cluster directing the biosynthesis of the exopolysaccharide xanthan

(2016) Rabeaa S. Alkhateeb et al.   JOURNAL OF BIOTECHNOLOGY

Trimethylated homoserine functions as the major compatible solute in the globally significant oceanic cyanobacteriumTrichodesmium

(2016) Nadin Pade et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria

(2016) Steven Smriga et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms

(2016) Rachel E. Diner et al.   Frontiers in Microbiology

Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans

(2015) Matthias Wietz et al.   ENVIRONMENTAL MICROBIOLOGY

Different utilization of alginate and other algal polysaccharides by marineAlteromonas macleodiiecotypes

(2015) Anna M. Neumann et al.   ENVIRONMENTAL MICROBIOLOGY

Differential RNA-seq ofVibrio choleraeidentifies the VqmR small RNA as a regulator of biofilm formation

(2015) Kai Papenfort et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria

(2015) Matthias Kopf et al.   Scientific Reports

Genomes of Alteromonas australica, a world apart

(2014) Mario López-Pérez et al.   BMC GENOMICS

RNA sequencing provides evidence for functional variability between naturally co-existing Alteromonas macleodii lineages

(2014) Nikole E Kimes et al.   BMC GENOMICS

Stress responses go three dimensional - the spatial order of physiological differentiation in bacterial macrocolony biofilms

(2014) Diego O. Serra et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity

(2014) Karsten Voigt et al.   ISME Journal

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

(2014) Ana-Belen Martin-Cuadrado et al.   ISME Journal

Identification of proteolytic bacteria from the Arctic Chukchi Sea expedition cruise and characterization of cold-active proteases

(2014) Ha Ju Park et al.   JOURNAL OF MICROBIOLOGY

Depth dependent metatranscriptomes of the marine pico-/nanoplanktonic communities in the Gulf of Aqaba/Eilat during seasonal deep mixing

(2014) Ulrike Pfreundt et al.   Marine Genomics

A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa

(2014) P. R. Kulkarni et al.   NUCLEIC ACIDS RESEARCH

Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean

(2014) B. E. Pedler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Diversity of “Deep Ecotype” Alteromonas macleodii Isolates: Evidence for Pan-Mediterranean Clonal Frames

(2013) Mario López-Pérez et al.   Genome Biology and Evolution

The Ribonucleoprotein Csr Network

(2013) Ethel Seyll et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling

(2013) Brett J Baker et al.   ISME Journal

Repression of Flagellar Genes in Exponential Phase by CsgD and CpxR, Two Crucial Modulators of Escherichia coli Biofilm Formation

(2013) O. Dudin et al.   JOURNAL OF BACTERIOLOGY

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

A Hybrid NRPS-PKS Gene Cluster Related to the Bleomycin Family of Antitumor Antibiotics in Alteromonas macleodii Strains

(2013) Carolina Megumi Mizuno et al.   PLoS One

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

(2013) Gaurav Dugar et al.   PLoS Genetics

Characterization of bacterial epibionts on the cyanobacterium Trichodesmium

(2012) LR Hmelo et al.   AQUATIC MICROBIAL ECOLOGY

Post-transcriptional regulation on a global scale: form and function of Csr/Rsm systems

(2012) Tony Romeo et al.   ENVIRONMENTAL MICROBIOLOGY

The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences

(2012) S. Luehr et al.   NUCLEIC ACIDS RESEARCH

The Csr/Rsm system of Yersinia and related pathogens

(2012) Ann Kathrin Heroven et al.   RNA Biology

Marine Microbes See a Sea of Gradients

(2012) R. Stocker   SCIENCE

Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph

(2012) Mario López-Pérez et al.   Scientific Reports

Differing Growth Responses of Major Phylogenetic Groups of Marine Bacteria to Natural Phytoplankton Blooms in the Western North Pacific Ocean

(2011) Yuya Tada et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment

(2011) Yanmei Shi et al.   ENVIRONMENTAL MICROBIOLOGY

Response of Prochlorococcus ecotypes to co-culture with diverse marine bacteria

(2011) Daniel Sher et al.   ISME Journal

Regulated proteolysis in Gram-negative bacteria — how and when?

(2011) Eyal Gur et al.   NATURE REVIEWS MICROBIOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

The RpoS-Mediated General Stress Response inEscherichia coli

(2010) Aurelia Battesti et al.   Annual Review of Microbiology

Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli

(2010) Tao Dong et al.   MOLECULAR MICROBIOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

(2010) J. McCarren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterioplankton diversity and community composition in the Southern Lagoon of Venice

(2010) Francesca Simonato et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects

(2009) Francis Repoila et al.   BIOLOGY OF THE CELL

The RNA Binding Protein CsrA Is a Pleiotropic Regulator of the Locus of Enterocyte Effacement Pathogenicity Island of Enteropathogenic Escherichia coli

(2009) S. Bhatt et al.   INFECTION AND IMMUNITY

Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean

(2009) Ian Hewson et al.   ISME Journal

Two small ncRNAs jointly govern virulence and transmission inLegionella pneumophila

(2009) Tobias Sahr et al.   MOLECULAR MICROBIOLOGY

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

Facilitation of Robust Growth of Prochlorococcus Colonies and Dilute Liquid Cultures by "Helper" Heterotrophic Bacteria

(2008) J. J. Morris et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter

(2008) Elena Ivars-Martinez et al.   ISME Journal

A Csr-type regulatory system, including small non-coding RNAs, regulates the global virulence regulator RovA of Yersinia pseudotuberculosis through RovM

(2008) Ann Kathrin Heroven et al.   MOLECULAR MICROBIOLOGY

Significance ofrpoSduring maturation ofEscherichia colibiofilms

(2007) Akinobu Ito et al.   BIOTECHNOLOGY AND BIOENGINEERING