Bacterial alkylquinolone signaling contributes to structuring microbial communities in the ocean

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

(2018) Stilianos Louca et al.   Microbiome

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

(2018) Jolinda Pollock et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The chemical cue tetrabromopyrrole induces rapid cellular stress and mortality in phytoplankton

(2018) Kristen E. Whalen et al.   Scientific Reports

IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences

(2018) Adithya Murali et al.   Microbiome

Marine microbial metagenomes sampled across space and time

(2018) Steven J. Biller et al.   Scientific Data

Impact of Phaeobacter inhibens on marine eukaryote-associated microbial communities

(2018) Karen K. Dittmann et al.   Environmental Microbiology Reports

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Identification of new quorum sensing autoinducer binding partners in Pseudomonas aeruginosa using photoaffinity probes

(2017) Y. R. Baker et al.   Chemical Science

Deciphering Physiological Functions of AHL Quorum Quenching Acylases

(2017) Putri D. Utari et al.   Frontiers in Microbiology

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Disruption of N -acyl-homoserine lactone-specific signalling and virulence in clinical pathogens by marine sponge bacteria

(2017) José A. Gutiérrez-Barranquero et al.   Microbial Biotechnology

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Dynamic metabolic exchange governs a marine algal-bacterial interaction

(2016) Einat Segev et al.   eLife

A Bacterial Quorum-Sensing Precursor Induces Mortality in the Marine Coccolithophore, Emiliania huxleyi

(2016) Elizabeth L. Harvey et al.   Frontiers in Microbiology

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

(2016) Jonathan Thorsen et al.   Microbiome

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

The Pseudomonas Quinolone Signal (PQS)

(2015) Thomas Sams et al.   ISRAEL JOURNAL OF CHEMISTRY

Enhancement of Antibiotic Activity against Multidrug-Resistant Bacteria by the Efflux Pump Inhibitor 3,4-Dibromopyrrole-2,5-dione Isolated from a Pseudoalteromonas sp.

(2015) Kristen E. Whalen et al.   JOURNAL OF NATURAL PRODUCTS

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

(2015) Johan Decelle et al.   Molecular Ecology Resources

Predator lipids induce paralytic shellfish toxins in bloom-forming algae

(2015) Erik Selander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Bacterial community transcription patterns during a marine phytoplankton bloom

(2011) Johanna M. Rinta-Kanto et al.   ENVIRONMENTAL MICROBIOLOGY

The Pseudomonas quinolone signal (PQS), and its precursor HHQ, modulate interspecies and interkingdom behaviour

(2011) F. Jerry Reen et al.   FEMS MICROBIOLOGY ECOLOGY

2-Heptyl-4-Quinolone, a Precursor of the Pseudomonas Quinolone Signal Molecule, Modulates Swarming Motility in Pseudomonas aeruginosa

(2011) D.-G. Ha et al.   JOURNAL OF BACTERIOLOGY

Extraction method influences the recovery of phytoplankton pigments from natural assemblages

(2011) Jason R. Graff et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

The Jekyll-and-Hyde chemistry of Phaeobacter gallaeciensis

(2011) Mohammad R. Seyedsayamdost et al.   Nature Chemistry

High Abundance of Ammonia-Oxidizing Archaea in Coastal Waters, Determined Using a Modified DNA Extraction Method

(2010) H. Urakawa et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Induced defences in marine and freshwater phytoplankton: a review

(2010) Ellen Van Donk et al.   HYDROBIOLOGIA

Impact of the diatom oxylipin 15S-HEPE on the reproductive success of the copepod Temora stylifera

(2010) Adrianna Ianora et al.   HYDROBIOLOGIA

Comparison of Bacterioneuston and Bacterioplankton Dynamics during a Phytoplankton Bloom in a Fjord Mesocosm

(2009) M. Cunliffe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Dioxygenase-Mediated Quenching of Quinolone-Dependent Quorum Sensing in Pseudomonas aeruginosa

(2009) Christian Pustelny et al.   CHEMISTRY & BIOLOGY

Quorum sensing and environmental adaptation in Pseudomonas aeruginosa: a tale of regulatory networks and multifunctional signal molecules

(2009) Paul Williams et al.   CURRENT OPINION IN MICROBIOLOGY

Turnover of quorum sensing signal molecules modulates cross-kingdom signalling

(2009) Karen Tait et al.   ENVIRONMENTAL MICROBIOLOGY

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One