Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach

Geo- and biogeochemical processes in a heliothermal hypersaline lake

(2016) John M. Zachara et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.

(2016) Alejandro Palomo et al.   ISME Journal

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

The number of limiting resources in the environment controls the temporal diversity patterns in the algal benthos

(2016) Chad A. Larson et al.   MICROBIAL ECOLOGY

The ecology and biogeochemistry of stream biofilms

(2016) Tom J. Battin et al.   NATURE REVIEWS MICROBIOLOGY

2016 update of the PRIDE database and its related tools

(2016) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments

(2016) Petter Thureborn et al.   PeerJ

Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia

(2015) William C. Nelson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Light availability affects stream biofilm bacterial community composition and function, but not diversity

(2015) Karoline Wagner et al.   ENVIRONMENTAL MICROBIOLOGY

A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling

(2015) Linda E. Graham et al.   JOURNAL OF PHYCOLOGY

Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities

(2015) Kemal Sanli et al.   Frontiers in Microbiology

Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011

(2015) Brandon M. Satinsky et al.   Microbiome

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Automated Design of Probes for rRNA-Targeted FluorescenceIn SituHybridization Reveals the Advantages of Using Dual Probes for Accurate Identification

(2014) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Light-Driven Na+ Pump from Gillisia limnaea: A High-Affinity Na+ Binding Site Is Formed Transiently in the Photocycle

(2014) Sergei P. Balashov et al.   BIOCHEMISTRY

Integrated metagenomic and metaproteomic analyses of marine biofilm communities

(2014) Dagmar H. Leary et al.   BIOFOULING

Dynamics in microbial communities: unraveling mechanisms to identify principles

(2014) Allan Konopka et al.   ISME Journal

Characterization of individual mouse cerebrospinal fluid proteomes

(2014) Jeffrey S. Smith et al.   PROTEOMICS

Spatially tracking 13 C-labelled substrate (bicarbonate) accumulation in microbial communities using laser ablation isotope ratio mass spectrometry

(2014) James J. Moran et al.   Environmental Microbiology Reports

Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

(2014) Jessica K. Cole et al.   Frontiers in Microbiology

Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change

(2013) Loïc Nazaries et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic Makeup of the Marine Flavobacterium Nonlabens (Donghaeana) dokdonensis and Identification of a Novel Class of Rhodopsins

(2013) Soon-Kyeong Kwon et al.   Genome Biology and Evolution

Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria

(2013) Ronald C. Taylor et al.   Integrative Biology

Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring

(2013) Christian G Klatt et al.   ISME Journal

Metaproteomics of our microbiome — Developing insight in function and activity in man and model systems

(2013) Carolin A. Kolmeder et al.   Journal of Proteomics

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics

(2013) Becky M. Hess et al.   PLoS One

Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes

(2013) Emily B. Graham et al.   SOIL BIOLOGY & BIOCHEMISTRY

The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling

(2013) Stephen R. Lindemann et al.   Frontiers in Microbiology

Exploring mixed microbial community functioning: recent advances in metaproteomics

(2012) Alma Siggins et al.   FEMS MICROBIOLOGY ECOLOGY

A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis

(2012) Tobias J Erb et al.   Nature Chemical Biology

The photosynthetic apparatus and photoinduced electron transfer in the aerobic phototrophic bacteria Roseicyclus mahoneyensis and Porphyrobacter meromictius

(2012) Christopher Rathgeber et al.   PHOTOSYNTHESIS RESEARCH

Transcriptome and Proteome Dynamics of a Light-Dark Synchronized Bacterial Cell Cycle

(2012) Jacob R. Waldbauer et al.   PLoS One

Bioenergetics of photoheterotrophic bacteria in the oceans

(2012) David L. Kirchman et al.   Environmental Microbiology Reports

Everglades Periphyton: A Biogeochemical Perspective

(2011) Scot E. Hagerthey et al.   CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY

Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies

(2011) P. B. Pope et al.   SCIENCE

Spatial and temporal changes in phosphorus partitioning within a freshwater cyanobacterial mat community

(2010) Jakub Borovec et al.   BIOGEOCHEMISTRY

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering

(2009) Ze-Qiang Ma et al.   JOURNAL OF PROTEOME RESEARCH

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry

(2009) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets

(2009) Vladislav A. Petyuk et al.   MOLECULAR & CELLULAR PROTEOMICS

Carbohydrate Metabolism and Carbon Fixation in Roseobacter denitrificans OCh114

(2009) Kuo-Hsiang Tang et al.   PLoS One

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

(2008) A. M. Mayampurath et al.   BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

Biophysical controls on organic carbon fluxes in fluvial networks

(2008) Tom J. Battin et al.   Nature Geoscience

Proteorhodopsins: an array of physiological roles?

(2008) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques

(2008) Rudolf Amann et al.   NATURE REVIEWS MICROBIOLOGY