Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS

A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction

(2021) Yu-Ming Huang et al.   Microbial Physiology

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

(2020) Eli L. Moss et al.   NATURE BIOTECHNOLOGY

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies

(2020) Arkadiy I. Garber et al.   Frontiers in Microbiology

Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents

(2020) Sean M. McAllister et al.   mSystems

GapMind: Automated Annotation of Amino Acid Biosynthesis

(2020) Morgan N. Price et al.   mSystems

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline

(2020) Daniel Straub et al.   Frontiers in Microbiology

Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing

(2019) Sarah Goldstein et al.   BMC GENOMICS

Quantitative proteomics links the intermediate filament nestin to resistance to targeted BRAF inhibition in melanoma cells

(2019) Marisa Schmitt et al.   MOLECULAR & CELLULAR PROTEOMICS

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers

(2019) Baoli Zhu et al.   Frontiers in Microbiology

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

High microbial diversity of the nitric oxide dismutation reaction revealed by PCR amplification and analysis of the nod gene

(2019) Qian-Qian Hu et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Ferrigenium kumadai gen. nov., sp. nov., a microaerophilic iron-oxidizing bacterium isolated from a paddy field soil

(2018) Ashraf Khalifa et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Insights into Carbon Metabolism Provided by Fluorescence In Situ Hybridization-Secondary Ion Mass Spectrometry Imaging of an Autotrophic, Nitrate-Reducing, Fe(II)-Oxidizing Enrichment Culture

(2018) Claudia Tominski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Growth and Population Dynamics of the Anaerobic Fe(II)-Oxidizing and Nitrate-Reducing Enrichment Culture KS

(2018) Claudia Tominski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial anaerobic Fe(II) oxidation - ecology, mechanisms and environmental implications

(2018) C Bryce et al.   ENVIRONMENTAL MICROBIOLOGY

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

The Occurrence of Putative Nitric Oxide Dismutase (Nod) in an Alpine Wetland with a New Dominant Subcluster and the Potential Ability for a Methane Sink

(2018) Yanfen Zhang et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Fe(II)-mediated autotrophic denitrification: A new bioprocess for iron bioprecipitation/biorecovery and simultaneous treatment of nitrate-containing wastewaters

(2017) K. Kiskira et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Comparative Genomic Analysis of Neutrophilic Iron(II) Oxidizer Genomes for Candidate Genes in Extracellular Electron Transfer

(2017) Shaomei He et al.   Frontiers in Microbiology

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS

(2016) Shaomei He et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Peeking under the Iron Curtain: Development of a Microcosm for Imaging the Colonization of Steel Surfaces by Mariprofundus sp. Strain DIS-1, an Oxygen-Tolerant Fe-Oxidizing Bacterium

(2016) Adam C. Mumford et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evidence for the Existence of Autotrophic Nitrate-Reducing Fe(II)-Oxidizing Bacteria in Marine Coastal Sediment

(2016) Katja Laufer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Improvement of biological nitrogen removal with nitrate-dependent Fe(II) oxidation bacterium Aquabacterium parvum B6 in an up-flow bioreactor for wastewater treatment

(2016) Xiaoxin Zhang et al.   BIORESOURCE TECHNOLOGY

Addition of Fe 2+ increase nitrate removal in vertical subsurface flow constructed wetlands

(2016) Xinshan Song et al.   ECOLOGICAL ENGINEERING

Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer

(2016) Talia N M Jewell et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Effect of nitrate concentration, pH, and hydraulic retention time on autotrophic denitrification efficiency with Fe(II) and Mn(II) as electron donors

(2016) J.-f. Su et al.   WATER SCIENCE AND TECHNOLOGY

Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis

(2015) Danilo J. P. Rocha et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Coexistence of Microaerophilic, Nitrate-Reducing, and Phototrophic Fe(II) Oxidizers and Fe(III) Reducers in Coastal Marine Sediment

(2015) Katja Laufer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

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

Phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803 and its dynamics during nitrogen starvation

(2015) Philipp Spät et al.   Frontiers in Microbiology

Enzymatic Characterization and In Vivo Function of Five Terminal Oxidases in Pseudomonas aeruginosa

(2014) H. Arai et al.   JOURNAL OF BACTERIOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Fe(II) Oxidation Is an Innate Capability of Nitrate-Reducing Bacteria That Involves Abiotic and Biotic Reactions

(2013) H. K. Carlson et al.   JOURNAL OF BACTERIOLOGY

Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics

(2013) David Emerson et al.   Frontiers in Microbiology

Biogeochemistry and microbiology of microaerobic Fe(II) oxidation

(2012) David Emerson   BIOCHEMICAL SOCIETY TRANSACTIONS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Toward a Mechanistic Understanding of Anaerobic Nitrate-Dependent Iron Oxidation: Balancing Electron Uptake and Detoxification

(2012) Hans K. Carlson et al.   Frontiers in Microbiology

Isolation of Phyllosilicate–Iron Redox Cycling Microorganisms from an Illite–Smectite Rich Hydromorphic Soil

(2012) Evgenya Shelobolina et al.   Frontiers in Microbiology

Identification and Characterization of MtoA: A Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-Oxidizing Bacterium Sideroxydans lithotrophicus ES-1

(2012) Juan Liu et al.   Frontiers in Microbiology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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

The iron-oxidizing proteobacteria

(2011) S. Hedrich et al.   MICROBIOLOGY-SGM

Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models

(2010) N. Borchert et al.   GENOME RESEARCH

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

(2010) Katharina F. Ettwig et al.   NATURE

Composition and Activity of an Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture

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

Iron Requirement for Mn(II) Oxidation by Leptothrix discophora SS-1

(2008) I. A. El Gheriany et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Physiology of phototrophic iron(II)-oxidizing bacteria: implications for modern and ancient environments

(2008) Florian Hegler et al.   FEMS MICROBIOLOGY ECOLOGY

A New Iron-oxidizing/O2-reducing Supercomplex Spanning Both Inner and Outer Membranes, Isolated from the Extreme AcidophileAcidithiobacillus ferrooxidans

(2008) Cindy Castelle et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle

(2008) Murray Ronald Badger et al.   JOURNAL OF EXPERIMENTAL BOTANY

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