Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation

Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats

(2018) Xiyang Dong et al.   ISME Journal

Reversibility of citrate synthase allows autotrophic growth of a thermophilic bacterium

(2018) Achim Mall et al.   SCIENCE

Anaerobic degradation of phenanthrene by a sulfate-reducing enrichment culture

(2018) Anne M. Himmelberg et al.   ENVIRONMENTAL MICROBIOLOGY

Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp

(2017) Xiaoli Dong et al.   Frontiers in Microbiology

A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes

(2016) Anestis Gkanogiannis et al.   BMC BIOINFORMATICS

Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons

(2016) Rainer U. Meckenstock et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments

(2016) Sizhong Yang et al.   Scientific Reports

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Two distinct old yellow enzymes are involved in naphthyl ring reduction during anaerobic naphthalene degradation

(2014) Sebastian Estelmann et al.   MOLECULAR MICROBIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

ATP-dependent/-independent enzymatic ring reductions involved in the anaerobic catabolism of naphthalene

(2013) Christian Eberlein et al.   ENVIRONMENTAL MICROBIOLOGY

Identification and characterization of 2-naphthoyl-coenzyme A reductase, the prototype of a novel class of dearomatizing reductases

(2013) Christian Eberlein et al.   MOLECULAR MICROBIOLOGY

Identification of naphthalene carboxylase as a prototype for the anaerobic activation of non-substituted aromatic hydrocarbons

(2012) Housna Mouttaki et al.   ENVIRONMENTAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Identification of new enzymes potentially involved in anaerobic naphthalene degradation by the sulfate-reducing enrichment culture N47

(2011) Franz D. Bergmann et al.   ARCHIVES OF MICROBIOLOGY

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

A Comparative Genomic Analysis of Energy Metabolism in Sulfate Reducing Bacteria and Archaea

(2011) Inês A. Cardoso Pereira et al.   Frontiers in Microbiology

Genomic insights into the metabolic potential of the polycyclic aromatic hydrocarbon degrading sulfate-reducing Deltaproteobacterium N47

(2010) Franz Bergmann et al.   ENVIRONMENTAL MICROBIOLOGY

Genome Sequence of the Dioxin-Mineralizing Bacterium Sphingomonas wittichii RW1

(2010) T. R. Miller et al.   JOURNAL OF BACTERIOLOGY

Genome Sequence of the Deltaproteobacterial Strain NaphS2 and Analysis of Differential Gene Expression during Anaerobic Growth on Naphthalene

(2010) Raymond J. DiDonato et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

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