Expanding our view of genomic diversity inCandidatus Accumulibacter clades

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

Characterization of the Denitrification-Associated Phosphorus Uptake Properties of “Candidatus Accumulibacter phosphatis” Clades in Sludge Subjected to Enhanced Biological Phosphorus Removal

(2013) Jeong Myeong Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal

(2013) Jason J Flowers et al.   ISME Journal

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

(2013) Dongying Wu et al.   PLoS One

Pan-Genome and Comparative Genome Analyses of Propionibacterium acnes Reveal Its Genomic Diversity in the Healthy and Diseased Human Skin Microbiome

(2013) S. Tomida et al.   mBio

‘CandidatusHalomonas phosphatis’, a novel polyphosphate-accumulating organism in full-scale enhanced biological phosphorus removal plants

(2012) Hien Thi Thu Nguyen et al.   ENVIRONMENTAL MICROBIOLOGY

A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal

(2012) Rikke Kristiansen et al.   ISME Journal

Metabolic shift of polyphosphate-accumulating organisms with different levels of polyphosphate storage

(2012) B. Acevedo et al.   WATER RESEARCH

Dynamics of Microbial Community Structure of and Enhanced Biological Phosphorus Removal by Aerobic Granules Cultivated on Propionate or Acetate

(2011) Graciela Gonzalez-Gil et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

Granule Formation Mechanisms within an Aerobic Wastewater System for Phosphorus Removal

(2010) J. J. Barr et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Legionella pneumophila pangenome reveals strain-specific virulence factors

(2010) Giuseppe D'Auria et al.   BMC GENOMICS

Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes

(2010) Eva Biegel et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Metatranscriptomic array analysis of ‘Candidatus Accumulibacter phosphatis’-enriched enhanced biological phosphorus removal sludge

(2010) Shaomei He et al.   ENVIRONMENTAL MICROBIOLOGY

Genome Sequence of the Deep-Rooted Yersinia pestis Strain Angola Reveals New Insights into the Evolution and Pangenome of the Plague Bacterium

(2010) M. Eppinger et al.   JOURNAL OF BACTERIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Monitoring associations between clade-level variation, overall community structure and ecosystem function in enhanced biological phosphorus removal (EBPR) systems using terminal-restriction fragment length polymorphism (T-RFLP)

(2010) F.R. Slater et al.   WATER RESEARCH

Assessing the abundance and activity of denitrifying polyphosphate accumulating organisms through molecular and chemical techniques

(2010) Adrian Oehmen et al.   WATER SCIENCE AND TECHNOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Radiolabelled proteomics to determine differential functioning ofAccumulibacterduring the anaerobic and aerobic phases of a bioreactor operating for enhanced biological phosphorus removal

(2009) Margaret Wexler et al.   ENVIRONMENTAL MICROBIOLOGY

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Denitrification capabilities of two biological phosphorus removal sludges dominated by different ‘CandidatusAccumulibacter’ clades

(2009) Jason J. Flowers et al.   Environmental Microbiology Reports

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal

(2008) S. Brook Peterson et al.   ENVIRONMENTAL MICROBIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment

(2008) Paul Wilmes et al.   PLoS One

Involvement of the TCA cycle in the anaerobic metabolism of polyphosphate accumulating organisms (PAOs)

(2008) Yan Zhou et al.   WATER RESEARCH