Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy

Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment

(2020) Bennett J. Kapili et al.   ISME Journal

Isolation of an archaeon at the prokaryote–eukaryote interface

(2020) Hiroyuki Imachi et al.   NATURE

An evolving view of methane metabolism in the Archaea

(2019) Paul N. Evans et al.   NATURE REVIEWS MICROBIOLOGY

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Distinct nitrogen cycling and steep chemical gradients in Trichodesmium colonies

(2019) Isabell Klawonn et al.   ISME Journal

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

Gene expression and ultrastructure of meso- and thermophilic methanotrophic consortia

(2018) Viola Krukenberg et al.   ENVIRONMENTAL MICROBIOLOGY

Widespread nitrogen fixation in sediments from diverse deep-sea sites of elevated carbon loading

(2018) Anne E. Dekas et al.   ENVIRONMENTAL MICROBIOLOGY

Subgroup Characteristics of Marine Methane-Oxidizing ANME-2 Archaea and Their Syntrophic Partners as Revealed by Integrated Multimodal Analytical Microscopy

(2018) Shawn E. McGlynn et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Bayesian method for detecting pairwise associations in compositional data

(2017) Emma Schwager et al.   PLoS Computational Biology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the GenusSymbiodinium

(2016) John E. Parkinson et al.   Genome Biology and Evolution

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

(2016) Roland Hatzenpichler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction

(2016) S. Scheller et al.   SCIENCE

Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling

(2016) William H. DePas et al.   mBio

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

(2016) Elizabeth Trembath-Reichert et al.   PeerJ

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments

(2016) Frank Schreiber et al.   Nature Microbiology

Use of Hybridization Chain Reaction-FluorescentIn SituHybridization To Track Gene Expression by Both Partners during Initiation of Symbiosis

(2015) K. Nikolakakis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effects of Diurnal Variation of Gut Microbes and High-Fat Feeding on Host Circadian Clock Function and Metabolism

(2015) Vanessa Leone et al.   Cell Host & Microbe

In situ DNA-hybridization chain reaction (HCR): a facilitated in situ HCR system for the detection of environmental microorganisms

(2015) Tsuyoshi Yamaguchi et al.   ENVIRONMENTAL MICROBIOLOGY

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

Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses

(2015) Anne E Dekas et al.   ISME Journal

Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA

(2015) Olivia U. Mason et al.   MICROBIAL ECOLOGY

Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria

(2015) Gunter Wegener et al.   NATURE

Single cell activity reveals direct electron transfer in methanotrophic consortia

(2015) Shawn E. McGlynn et al.   NATURE

A functional perspective on phenotypic heterogeneity in microorganisms

(2015) Martin Ackermann   NATURE REVIEWS MICROBIOLOGY

Global dispersion and local diversification of the methane seep microbiome

(2015) S. Emil Ruff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages

(2015) David H. Case et al.   mBio

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability

(2014) Harry M. T. Choi et al.   ACS Nano

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

Lineage-Specific Transcriptional Profiles of Symbiodinium spp. Unaltered by Heat Stress in a Coral Host

(2014) Daniel J. Barshis et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Contamination of Commercial 15N2 Gas Stocks with 15N–Labeled Nitrate and Ammonium and Consequences for Nitrogen Fixation Measurements

(2014) Richard Dabundo et al.   PLoS One

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea

(2013) Anne E. Dekas et al.   ENVIRONMENTAL MICROBIOLOGY

Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments

(2013) Jennifer B. Glass et al.   ENVIRONMENTAL MICROBIOLOGY

Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California)

(2013) Adrien Vigneron et al.   ISME Journal

Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane

(2013) A Green-Saxena et al.   ISME Journal

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

(2013) Mohamed F. Haroon et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Look@NanoSIMS - a tool for the analysis of nanoSIMS data in environmental microbiology

(2012) Lubos Polerecky et al.   ENVIRONMENTAL MICROBIOLOGY

Distribution andin situabundance of sulfate-reducing bacteria in diverse marine hydrocarbon seep sediments

(2012) Sara Kleindienst et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Thermophilic anaerobic oxidation of methane by marine microbial consortia

(2011) Thomas Holler et al.   ISME Journal

Reaction–diffusion model of nutrient uptake in a biofilm: Theory and experiment

(2011) Alexander P. Petroff et al.   JOURNAL OF THEORETICAL BIOLOGY

Activity of abundant and rare bacteria in a coastal ocean

(2011) B. J. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Anaerobic Oxidation of Methane: Progress with an Unknown Process

(2009) Katrin Knittel et al.   Annual Review of Microbiology

Patterns of15N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS

(2009) Victoria J. Orphan et al.   ENVIRONMENTAL MICROBIOLOGY

Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia

(2009) A. E. Dekas et al.   SCIENCE

Fluid seepage at the continental margin offshore Costa Rica and southern Nicaragua

(2008) Heiko Sahling et al.   GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS

Bleaching susceptibility and mortality of corals are determined by fine-scale differences in symbiont type

(2008) E. M. Sampayo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics

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