Access the full text.
Sign up today, get DeepDyve free for 14 days.
M. Haroon, Shihu Hu, Yinguen Shi, Michael Imelfort, J. Keller, P. Hugenholtz, Zhiguo Yuan, G. Tyson (2013)
Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineageNature, 500
A. Meyerdierks, M. Kube, Ivaylo Kostadinov, H. Teeling, F. Glöckner, R. Reinhardt, R. Amann (2010)
Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group.Environmental microbiology, 12 2
Christian Rinke, P. Schwientek, A. Sczyrba, Natalia Ivanova, I. Anderson, Jan-Fang Cheng, A. Darling, S. Malfatti, B. Swan, E. Gies, J. Dodsworth, B. Hedlund, G. Tsiamis, S. Sievert, Wen-Tso Liu, J. Eisen, S. Hallam, N. Kyrpides, R. Stepanauskas, E. Rubin, P. Hugenholtz, T. Woyke (2013)
Insights into the phylogeny and coding potential of microbial dark matterNature, 499
Michael Imelfort, G. Tyson, Donovan Parks, B. Woodcroft, P. Dennis, P. Hugenholtz
Distributed under Creative Commons Cc-by 4.0 Groopm: an Automated Tool for the Recovery of Population Genomes from Related Metagenomes
Daniel McDonald, M. Price, Julia Goodrich, Eric Nawrocki, T. DeSantis, Alexander Probst, G. Andersen, R. Knight, P. Hugenholtz (2011)
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaeaThe ISME Journal, 6
B. Swan, B. Tupper, A. Sczyrba, F. Lauro, M. Martínez-García, José González, Haiwei Luo, Jody Wright, Z. Landry, Niels Hanson, Brian Thompson, N. Poulton, P. Schwientek, S. Acinas, S. Giovannoni, M. Moran, S. Hallam, R. Cavicchioli, T. Woyke, R. Stepanauskas (2013)
Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface oceanProceedings of the National Academy of Sciences, 110
J. McCutcheon, N. Moran (2011)
Extreme genome reduction in symbiotic bacteriaNature Reviews Microbiology, 10
Itai Sharon, Michael Morowitz, B. Thomas, E. Costello, D. Relman, J. Banfield (2013)
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonizationGenome Research, 23
Dongying Wu, P. Hugenholtz, K. Mavromatis, R. Pukall, Eileen Dalin, Natalia Ivanova, V. Kunin, Lynne Goodwin, Martin Wu, B. Tindall, S. Hooper, Amrita Pati, A. Lykidis, S. Spring, I. Anderson, P. D’haeseleer, A. Zemla, M. Singer, A. Lapidus, Matt Nolan, A. Copeland, Cliff Han, Feng Chen, Jan-Fang Cheng, S. Lucas, C. Kerfeld, E. Lang, S. Gronow, P. Chain, D. Bruce, E. Rubin, N. Kyrpides, H. Klenk, J. Eisen (2009)
A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaNature, 462
F. Yamao, A. Muto, Y. Kawauchi, M. Iwami, S. Iwagami, Y. Azumi, S. Osawa (1985)
UGA is read as tryptophan in Mycoplasma capricolum.Proceedings of the National Academy of Sciences of the United States of America, 82 8
Sajia Akhter, R. Aziz, R. Edwards (2012)
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategiesNucleic Acids Research, 40
Dawn Field, George Garrity, Tanya Gray, Norman Morrison, Jeremy Selengut, P. Sterk, Tatiana Tatusova, Nicholas Thomson, Michael Allen, Michael Ashburner, Sandra Baldauf, Stuart Ballard, Jeffrey Boore, Guy Cochrane, James Cole, Claude dePamphilis, Robert, Edwards, Nadeem Faruque, Robert Feldman, F. Glöckner, Dan Haft, David, Hancock, Henning Hermjakob, Christiane Hertz-Fowler, Phil Hugenholtz, I. Joint, Matthew, Kane, Jessie Kennedy, George Kowalchuk, R. Kottmann, Eugene Kolker, Nikos, Kyrpides, Jim Leebens-Mack, Suzanna Lewis, Allyson Liste, Phillip Lord, Natalia Maltsev, V. Markowitz, Jennifer Martiny, Barbara Methé, Richard Moxon, Karen Nelson, Julian, Parkhill, Susanna-Assunta Sansone, Andrew Spiers, Robert Stevens, Paul Swift, Chris Taylor, Yoshio Tateno, Adrian Tett, Sarah Turner, D. Ussery, Bob Vaughan, Naomi Ward, Trish, Whetzel, Gareth Wilson, A. Wipat (2008)
The minimum information about a genome sequence (MIGS) specificationNature Biotechnology, 26
G. Tyson, Jarrod Chapman, P. Hugenholtz, E. Allen, Rachna Ram, P. Richardson, Victor Solovyev, E. Rubin, D. Rokhsar, J. Banfield (2004)
Community structure and metabolism through reconstruction of microbial genomes from the environmentNature, 428
James Campbell, P. O'Donoghue, A. Campbell, P. Schwientek, A. Sczyrba, T. Woyke, D. Söll, M. Podar (2013)
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiotaProceedings of the National Academy of Sciences, 110
D. Siddavattam, T. Karegoudar, Santosh Mudde, Narender Kumar, Ramani Baddam, Tiruvayipati Avasthi, N. Ahmed (2011)
Genome of a Novel Isolate of Paracoccus denitrificans Capable of Degrading N,N-DimethylformamideJournal of Bacteriology, 193
K. Patil, P. Haider, P. Pope, P. Turnbaugh, M. Morrison, T. Scheffer, A. Mchardy (2011)
Taxonomic metagenome sequence assignment with structured output modelsNature Methods, 8
R. Soo, Connor Skennerton, Y. Sekiguchi, Michael Imelfort, Samuel Paech, P. Dennis, J. Steen, Donovan Parks, G. Tyson, P. Hugenholtz (2014)
An Expanded Genomic Representation of the Phylum CyanobacteriaGenome Biology and Evolution, 6
S. Salzberg, A. Phillippy, A. Zimin, D. Puiu, Tanja Magoc, S. Koren, Todd Treangen, Michael Schatz, A. Delcher, Michael Roberts, G. Marçais, Mihai Pop, J. Yorke (2012)
GAGE: A critical evaluation of genome assemblies and assembly algorithms.Genome research, 22 3
D. Haft, J. Selengut, O. White (2003)
The TIGRFAMs database of protein familiesNucleic acids research, 31 1
Results are summarized using box-and-whisker plots showing the 1 st
(2013)
Genome Research: doi:10.1101/gr.186072.114
R. Finn, A. Bateman, J. Clements, Penny Coggill, Ruth Eberhardt, S. Eddy, A. Heger, Kirstie Hetherington, L. Holm, Jaina Mistry, E. Sonnhammer, J. Tate, M. Punta (2013)
Pfam: the protein families databaseNucleic Acids Research, 42
N. Yutin, Michael Galperin (2013)
A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia.Environmental microbiology, 15 10
Donovan Parks, Norman MacDonald, R. Beiko (2011)
Classifying short genomic fragments from novel lineages using composition and homologyBMC Bioinformatics, 12
Ziheng Yang (1994)
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methodsJournal of Molecular Evolution, 39
V. Markowitz, I. Chen, Krishna Palaniappan, Ken Chu, E. Szeto, Manoj Pillay, Anna Ratner, Jinghua Huang, T. Woyke, Marcel Huntemann, Iain Anderson, Konstantinos Billis, N. Varghese, K. Mavrommatis, Amrita Pati, Natalia Ivanova, N. Kyrpides (2013)
IMG 4 version of the integrated microbial genomes comparative analysis systemNucleic Acids Research, 42
S. Whelan, N. Goldman (2001)
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.Molecular biology and evolution, 18 5
K. Wrighton, B. Thomas, Itai Sharon, C. Miller, C. Castelle, N. Verberkmoes, M. Wilkins, R. Hettich, M. Lipton, K. Williams, P. Long, J. Banfield (2012)
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial PhylaScience, 337
P. Turnbaugh, R. Ley, M. Hamady, Claire Fraser-Liggett, R. Knight, J. Gordon (2007)
The Human Microbiome ProjectNature, 449
(2005)
Access the most recent version at doi: 10.1110/ps.051767306 References
Arthur Brady, S. Salzberg (2009)
Phymm and PhymmBL: Metagenomic Phylogenetic Classification with Interpolated Markov ModelsNature methods, 6
J. McCutcheon, B. McDonald, N. Moran (2009)
Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial SymbiontPLoS Genetics, 5
P. Chain, D. Grafham, Robert Fulton, Michael Fitzgerald, J. Hostetler, D. Muzny, Johar Ali, B. Birren, D. Bruce, C. Buhay, J. Cole, Yan Ding, Shannon Dugan, D. Field, G. Garrity, R. Gibbs, T. Graves, Cliff Han, S. Harrison, S. Highlander, P. Hugenholtz, H. Khouri, C. Kodira, E. Kolker, N. Kyrpides, D. Lang, A. Lapidus, S. Malfatti, V. Markowitz, T. Metha, K. Nelson, J. Parkhill, S. Pitluck, X. Qin, T. Read, J. Schmutz, S. Sozhamannan, P. Sterk, R. Strausberg, G. Sutton, N. Thomson, J. Tiedje, G. Weinstock, A. Wollam, J. Detter (2009)
Genome Project Standards in a New Era of SequencingScience, 326
Jeet Sukumaran, M. Holder (2010)
DendroPy: a Python library for phylogenetic computingBioinformatics, 26 12
(2012)
ISME J 6: 610-618
N. Segata, Daniela Börnigen, X. Morgan, C. Huttenhower (2013)
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbesNature communications, 4
C. Dupont, D. Rusch, Shibu Yooseph, M. Lombardo, R. Richter, Ruben Valas, M. Novotny, Joyclyn Yee-Greenbaum, J. Selengut, D. Haft, A. Halpern, R. Lasken, K. Nealson, R. Friedman, J. Venter (2011)
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineageThe ISME Journal, 6
Y. Sekiguchi, Akiko Ohashi, Donovan Parks, Toshihiro Yamauchi, G. Tyson, P. Hugenholtz (2015)
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulkingPeerJ, 3
Gregory Dick, Gregory Dick, Anders Andersson, Anders Andersson, B. Baker, S. Simmons, B. Thomas, A. Yelton, J. Banfield (2009)
Community-wide analysis of microbial genome sequence signaturesGenome Biology, 10
(1860)
This article was published by Genome Research: doi:10.1101/gr
M. Price, Paramvir Dehal, A. Arkin (2009)
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance MatrixMolecular Biology and Evolution, 26
Itai Sharon, J. Banfield (2013)
Genomes from MetagenomicsScience, 342
T. Jørgensen, Zhuofei Xu, M. Hansen, S. Sørensen, L. Hansen (2014)
Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum MetamobilomePLoS ONE, 9
Minghui He, Zhibo Gao, Ying Peng, Yanli Li, Weiwei Zhou, Xiangchun Li, Xu Zhong, Yiming Lei, Hang Wang, Yiran Jiang, Lin Yang, Wei Wei, Xu Yang, Xiuli Jiang, Li Liu, Juan He, Qing Wei, Yingrui Li, Weiqing Wang, Jun Wang (2014)
Stop codon reassignments in the wildScience, 344
M. Langille, W. Hsiao, F. Brinkman (2010)
Detecting genomic islands using bioinformatics approachesNature Reviews Microbiology, 8
P. Shih, Dongying Wu, A. Latifi, S. Axen, D. Fewer, E. Talla, Alexandra Calteau, Fei Cai, N. Marsac, R. Rippka, M. Herdman, K. Sivonen, T. Coursin, Thierry Laurent, Lynne Goodwin, Matt Nolan, K. Davenport, Cliff Han, E. Rubin, J. Eisen, T. Woyke, M. Gugger, C. Kerfeld (2012)
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencingProceedings of the National Academy of Sciences, 110
Alexey Gurevich, V. Saveliev, Nikolay Vyahhi, G. Tesler (2013)
QUAST: quality assessment tool for genome assembliesBioinformatics, 29 8
A. Darling, G. Jospin, E. Lowe, Frederick IV, H. Bik, J. Eisen (2014)
PhyloSift: phylogenetic analysis of genomes and metagenomesPeerJ, 2
E. Mardis, J. McPherson, R. Martienssen, R. Wilson, W. McCombie (2002)
What is finished, and why does it matter.Genome research, 12 5
M. Albertsen, P. Hugenholtz, Adam Skarshewski, K. Nielsen, G. Tyson, P. Nielsen (2013)
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomesNature Biotechnology, 31
H. Arnheiter (2016)
PreprintsPigment Cell & Melanoma Research, 29
Martin Wu, Alexandra Scott (2012)
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2Bioinformatics, 28 7
Dongying Wu, Ladan Doroud, J. Eisen (2013)
TreeOTU: Operational Taxonomic Unit Classification Based on Phylogenetic TreesarXiv: Genomics
(2014)
GroopM: an automated tool for the recovery of population genomes from related metagenomesPeerJ, 2:
K. Konstantinidis, J. Tiedje (2005)
Towards a Genome-Based Taxonomy for ProkaryotesJournal of Bacteriology, 187
M. C, Frederick IV, R. Kodner, V. Armbrust (2010)
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference treeBMC Bioinformatics, 11
D. Mende, S. Sunagawa, G. Zeller, P. Bork (2013)
Accurate and universal delineation of prokaryotic speciesNature Methods, 10
Doug Hyatt, P. LoCascio, L. Hauser, E. Uberbacher (2012)
Gene and translation initiation site prediction in metagenomic sequencesBioinformatics, 28 17
J. Dröge, Ivan Gregor, A. Mchardy (2014)
Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoodsBioinformatics, 31
S. Cole, K. Eiglmeier, J. Parkhill, K. James, N. Thomson, P. Wheeler, N. Honoré, T. Garnier, C. Churcher, D. Harris, K. Mungall, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, S. Duthoy, T. Feltwell, A. Fraser, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, C. Lacroix, J. Maclean, S. Moule, L. Murphy, K. Oliver, M. Quail, M. Rajandream, Kim Rutherford, S. Rutter, K. Seeger, S. Simon, M. Simmonds, J. Skelton, R. Squares, S. Squares, K. Stevens, K. Taylor, S. Whitehead, J. Woodward, B. Barrell (2001)
Massive gene decay in the leprosy bacillusNature, 409
G. Fernald, E. Capriotti, Roxana Daneshjou, Konrad Karczewski, Russ Altman (2011)
Genome AnalysisBioinform., 27
from isolates, single cells, and metagenomes CheckM: assessing the quality of microbial genomes recovered Material Supplemental
Genome Research – Unpaywall
Published: May 14, 2015
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.