Metabolic network analysis reveals microbial community interactions in anammox granules

Hydroxylamine-dependent anaerobic ammonium oxidation (anammox) by “Candidatus Brocadia sinica”

(2016) Mamoru Oshiki et al.   ENVIRONMENTAL MICROBIOLOGY

Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates

(2016) Elin E Lilja et al.   ISME Journal

Source identification of nitrous oxide emission pathways from a single-stage nitritation-anammox granular reactor

(2016) Muhammad Ali et al.   WATER RESEARCH

Microbial interactions lead to rapid micro-scale successions on model marine particles

(2016) Manoshi S. Datta et al.   Nature Communications

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

(2016) Daan R. Speth et al.   Nature Communications

Assessment of Heterotrophic Growth Supported by Soluble Microbial Products in Anammox Biofilm using Multidimensional Modeling

(2016) Yiwen Liu et al.   Scientific Reports

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements: Fig. 1.

(2015) Kishori M. Konwar et al.   BIOINFORMATICS

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

(2015) Peter D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Rare taxa have potential to make metabolic contributions in enhanced biological phosphorus removal ecosystems

(2015) Christopher E. Lawson et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The effect of inorganic carbon on microbial interactions in a biofilm nitritation–anammox process

(2015) Yiwei Ma et al.   WATER RESEARCH

Role of extracellular polymeric substance in determining the high aggregation ability of anammox sludge

(2015) Xiaolin Hou et al.   WATER RESEARCH

NADPH-generating systems in bacteria and archaea

(2015) Sebastiaan K. Spaans et al.   Frontiers in Microbiology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Microbial community analysis of a full-scale DEMON bioreactor

(2014) Alejandro Gonzalez-Martinez et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

Vitamin B 12 as a Modulator of Gut Microbial Ecology

(2014) Patrick H. Degnan et al.   Cell Metabolism

Physiological characterization of anaerobic ammonium oxidizing bacterium ‘Candidatus Jettenia caeni’

(2014) Muhammad Ali et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial Community Composition and Ultrastructure of Granules from a Full-Scale Anammox Reactor

(2014) Graciela Gonzalez-Gil et al.   MICROBIAL ECOLOGY

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial formate hydrogenlyase complex

(2014) J. S. McDowall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information

(2013) Kishori M Konwar et al.   BMC BIOINFORMATICS

Identification of the type II cytochrome c maturation pathway in anammox bacteria by comparative genomics

(2013) Christina Ferousi et al.   BMC MICROBIOLOGY

Structural Basis of Biological NO Generation by Octaheme Oxidoreductases

(2013) Wouter J. Maalcke et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Genomic Analysis of Melioribacter roseus, Facultatively Anaerobic Organotrophic Bacterium Representing a Novel Deep Lineage within Bacteriodetes/Chlorobi Group

(2013) Vitaly V. Kadnikov et al.   PLoS One

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation

(2012) Wolfgang Buckel et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Anaerobic ammonia oxidation (ANAMMOX) for side-stream treatment of anaerobic digester filtrate process performance and microbiology

(2012) Shireen M. Kotay et al.   BIOTECHNOLOGY AND BIOENGINEERING

Evaluation on the microbial interactions of anaerobic ammonium oxidizers and heterotrophs in Anammox biofilm

(2012) Bing-Jie Ni et al.   WATER RESEARCH

Ecophysiological role and function of uncultured Chloroflexi in an anammox reactor

(2012) Tomonori Kindaichi et al.   WATER SCIENCE AND TECHNOLOGY

The Pathway Tools Pathway Prediction Algorithm

(2012) Peter D. Karp et al.   Standards in Genomic Sciences

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Molecular mechanism of anaerobic ammonium oxidation

(2011) Boran Kartal et al.   NATURE

The Tricarboxylic Acid Cycle in Cyanobacteria

(2011) S. Zhang et al.   SCIENCE

Microbial and Physicochemical Characteristics of Compact Anaerobic Ammonium-Oxidizing Granules in an Upflow Anaerobic Sludge Blanket Reactor

(2010) B. J. Ni et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Subtilases: The superfamily of subtilisin-like serine proteases

(2010) Roland J. Siezen et al.   PROTEIN SCIENCE

Sewage Treatment with Anammox

(2010) B. Kartal et al.   SCIENCE

Upgrading of sewage treatment plant by sustainable and cost-effective separate treatment of industrial wastewater

(2010) W. R. Abma et al.   WATER SCIENCE AND TECHNOLOGY

Aggregate Size and Architecture Determine Microbial Activity Balance for One-Stage Partial Nitritation and Anammox

(2009) S. E. Vlaeminck et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Candidatus ‘Brocadia fulgida’: an autofluorescent anaerobic ammonium oxidizing bacterium

(2009) Boran Kartal et al.   FEMS MICROBIOLOGY ECOLOGY

The bacterial diversity in an anaerobic ammonium-oxidizing (anammox) reactor community

(2009) Xiao-Ran Li et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Another multiheme protein, hydroxylamine oxidoreductase, abundantly produced in an anammox bacterium besides the hydrazine-oxidizing enzyme

(2008) Munetaka Shimamura et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS