Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation

Metabolic versatility in methanogens

(2014) Kyle C Costa et al.   CURRENT OPINION IN BIOTECHNOLOGY

Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

(2014) Celia Méndez-García et al.   ISME Journal

Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps

(2014) Sara Kleindienst et al.   ISME Journal

Metaproteomics: Evaluation of protein extraction from activated sludge

(2014) Susan Hove Hansen et al.   PROTEOMICS

Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria

(2014) Dragana Bozinovski et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Effective bioremediation strategy for rapid in situ cleanup of anoxic marine sediments in mesocosm oil spill simulation

(2014) Maria Genovese et al.   Frontiers in Microbiology

Selection of human tissue-specific elementary flux modes using gene expression data

(2013) Alberto Rezola et al.   BIOINFORMATICS

A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype

(2013) Jon Pey et al.   BMC Systems Biology

Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill

(2013) Adam R Rivers et al.   ISME Journal

Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP

(2013) Tony Gutierrez et al.   ISME Journal

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies

(2013) Pratik Jagtap et al.   PROTEOMICS

Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica

(2013) Michael Kube et al.   Nature Communications

Metagenomic analysis and metabolite profiling of deep–sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill

(2013) Nikole E. Kimes et al.   Frontiers in Microbiology

GOHTAM: a website for 'Genomic Origin of Horizontal Transfers, Alignment and Metagenomics'

(2012) S. Menigaud et al.   BIOINFORMATICS

Characterization of the anaerobic microbial community in oil-polluted subtidal sediments: aromatic biodegradation potential after thePrestigeoil spill

(2012) Alejandro Acosta-González et al.   ENVIRONMENTAL MICROBIOLOGY

Sizing up metatranscriptomics

(2012) Mary Ann Moran et al.   ISME Journal

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium

(2012) Martin Taubert et al.   ISME Journal

Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples

(2012) Bart Mesuere et al.   JOURNAL OF PROTEOME RESEARCH

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Dispersed Oil Disrupts Microbial Pathways in Pelagic Food Webs

(2012) Alice C. Ortmann et al.   PLoS One

Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill

(2012) Melanie J. Beazley et al.   PLoS One

Characterisation of Oil-Degrading Bacteria Isolated from Bilge Water

(2012) S. Cappello et al.   WATER AIR AND SOIL POLLUTION

Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium

(2012) Brandon E. L. Morris et al.   Environmental Microbiology Reports

Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill

(2011) Joel E. Kostka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Anaerobic Biodegradation of Longer-Chainn-Alkanes Coupled to Methane Production in Oil Sands Tailings

(2011) Tariq Siddique et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

(2011) Zhenmei Lu et al.   ISME Journal

Growth ofPseudomonas putidaat low temperature: global transcriptomic and proteomic analyses

(2011) Pilar Fonseca et al.   Environmental Microbiology Reports

Systems approaches to microbial communities and their functioning

(2010) Wilfred FM Röling et al.   CURRENT OPINION IN BIOTECHNOLOGY

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

(2010) Yuting Liang et al.   ISME Journal

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

(2010) Terry C. Hazen et al.   SCIENCE

Genome sequence ofDesulfobacterium autotrophicumHRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide

(2009) Axel W. Strittmatter et al.   ENVIRONMENTAL MICROBIOLOGY

False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule

(2009) Nitin Gupta et al.   JOURNAL OF PROTEOME RESEARCH

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

(2008) Nicola Zamboni et al.   BMC BIOINFORMATICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY