Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single-Molecule Real-Time sequencing

[1]  H. O. D. op den Camp,et al.  Mimicking microbial interactions under nitrate‐reducing conditions in an anoxic bioreactor: enrichment of novel Nitrospirae bacteria distantly related to Thermodesulfovibrio , 2017, Environmental microbiology.

[2]  M. V. van Loosdrecht,et al.  Discovery and metagenomic analysis of an anammox bacterial enrichment related to Candidatus "Brocadia caroliniensis" in a full-scale glycerol-fed nitritation-denitritation separate centrate treatment process. , 2017, Water research.

[3]  M. Haroon,et al.  Draft Genome Sequence of the Anaerobic Ammonium-Oxidizing Bacterium “Candidatus Brocadia sp. 40” , 2016, Genome Announcements.

[4]  Shang-Hao Huang,et al.  Multi-CAR: a tool of contig scaffolding using multiple references , 2016, BMC Bioinformatics.

[5]  Alexandre Renaux,et al.  MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes , 2016, Nucleic Acids Res..

[6]  J. Chun,et al.  OrthoANI: An improved algorithm and software for calculating average nucleotide identity. , 2016, International journal of systematic and evolutionary microbiology.

[7]  J. Keltjens,et al.  Immunogold Localization of Key Metabolic Enzymes in the Anammoxosome and on the Tubule-Like Structures of Kuenenia stuttgartiensis , 2015, Journal of bacteriology.

[8]  Matthew R. Laird,et al.  IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis , 2015, Nucleic Acids Res..

[9]  S. Okabe,et al.  Draft Genome Sequence of an Anaerobic Ammonium-Oxidizing Bacterium, “Candidatus Brocadia sinica” , 2015, Genome Announcements.

[10]  B. Dutilh,et al.  Draft Genome Sequence of Anammox Bacterium “Candidatus Scalindua brodae,” Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor Enrichments , 2015, Genome Announcements.

[11]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[12]  H. O. D. op den Camp,et al.  Identification of the type II cytochrome c maturation pathway in anammox bacteria by comparative genomics , 2013, BMC Microbiology.

[13]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[14]  H. O. D. op den Camp,et al.  How to make a living from anaerobic ammonium oxidation. , 2013, FEMS microbiology reviews.

[15]  Tyson A. Clark,et al.  Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation , 2013, BMC Biology.

[16]  Stefan Engelen,et al.  MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data , 2012, Nucleic Acids Res..

[17]  R. Gibbs,et al.  Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology , 2012, PloS one.

[18]  Glenn Tesler,et al.  Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory , 2012, BMC Bioinformatics.

[19]  Mark J. P. Chaisson,et al.  Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory , 2012, BMC Bioinformatics.

[20]  H. Stunnenberg,et al.  Comparative Genomics of Two Independently Enriched “Candidatus Kuenenia Stuttgartiensis” Anammox Bacteria , 2012, Front. Microbio..

[21]  Richard J. Roberts,et al.  Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing , 2011, Nucleic acids research.

[22]  Jolein Gloerich,et al.  Molecular mechanism of anaerobic ammonium oxidation , 2011, Nature.

[23]  J. Fuerst,et al.  Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function , 2011, Nature Reviews Microbiology.

[24]  N. Perna,et al.  progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement , 2010, PloS one.

[25]  M. Loosdrecht,et al.  Sewage Treatment with Anammox , 2010, Science.

[26]  Tyson A. Clark,et al.  Direct detection of DNA methylation during single-molecule, real-time sequencing , 2010, Nature Methods.

[27]  M. Aragno,et al.  Molecular detection of anammox bacteria in terrestrial ecosystems: distribution and diversity , 2010, The ISME Journal.

[28]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[29]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[30]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[31]  M. Strous,et al.  Biochemistry and molecular biology of anammox bacteria , 2009, Critical reviews in biochemistry and molecular biology.

[32]  Mathieu Bastian,et al.  Gephi: An Open Source Software for Exploring and Manipulating Networks , 2009, ICWSM.

[33]  Fiona S. L. Brinkman,et al.  Evaluation of genomic island predictors using a comparative genomics approach , 2008, BMC Bioinformatics.

[34]  Marc Strous,et al.  Combined structural and chemical analysis of the anammoxosome: a membrane-bounded intracytoplasmic compartment in anammox bacteria. , 2008, Journal of structural biology.

[35]  Ibtissem Grissa,et al.  CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats , 2007, Nucleic Acids Res..

[36]  J. Tiedje,et al.  Molecular Evidence for the Broad Distribution of Anaerobic Ammonium-Oxidizing Bacteria in Freshwater and Marine Sediments , 2006, Applied and Environmental Microbiology.

[37]  Dmitrij Frishman,et al.  Deciphering the evolution and metabolism of an anammox bacterium from a community genome , 2006, Nature.

[38]  Carsten Damm,et al.  Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models , 2006, BMC Bioinformatics.

[39]  M C M van Loosdrecht,et al.  Global impact and application of the anaerobic ammonium-oxidizing (anammox) bacteria. , 2006, Biochemical Society transactions.

[40]  K. Arrigo Marine microorganisms and global nutrient cycles , 2005, Nature.

[41]  Marc Strous,et al.  Structural identification of ladderane and other membrane lipids of planctomycetes capable of anaerobic ammonium oxidation (anammox) , 2005, The FEBS journal.

[42]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[43]  A. Devol Nitrogen cycle: Solution to a marine mystery , 2003, Nature.

[44]  Steven J. M. Jones,et al.  IslandPath: aiding detection of genomic islands in prokaryotes , 2003, Bioinform..

[45]  B. Thamdrup,et al.  Production of N2 through Anaerobic Ammonium Oxidation Coupled to Nitrate Reduction in Marine Sediments , 2002, Applied and Environmental Microbiology.

[46]  M. Adams,et al.  Characterization of Hydrogenase II from the Hyperthermophilic Archaeon Pyrococcus furiosus and Assessment of Its Role in Sulfur Reduction , 2000, Journal of bacteriology.

[47]  Eugene W. Myers,et al.  A whole-genome assembly of Drosophila. , 2000, Science.

[48]  J. G. Kuenen,et al.  Missing lithotroph identified as new planctomycete , 1999, Nature.

[49]  J. G. Kuenen,et al.  The anaerobic oxidation of ammonium. , 1998, FEMS microbiology reviews.

[50]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[51]  Eugene W. Myers,et al.  Basic local alignment search tool. Journal of Molecular Biology , 1990 .

[52]  H. O. D. op den Camp,et al.  Anammox--growth physiology, cell biology, and metabolism. , 2012, Advances in microbial physiology.

[53]  M. Jetten,et al.  Cultivation, detection, and ecophysiology of anaerobic ammonium-oxidizing bacteria. , 2011, Methods in enzymology.

[54]  S. Turner,et al.  Real-time DNA sequencing from single polymerase molecules. , 2010, Methods in enzymology.

[55]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[56]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[57]  J. G. Kuenen,et al.  The anaerobic oxidation of hydrazine: a novel reaction in microbial nitrogen metabolism. , 1998, FEMS microbiology letters.

[58]  J. G. Kuenen,et al.  Copyright � 1995, American Society for Microbiology Anaerobic Oxidation of Ammonium Is a Biologically Mediated Process , 1994 .