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Metagenomics for studying unculturable microorganisms: cutting the Gordian knot
Patrick D Schloss, Jo Handelsman
Genome Biol. 2005; 6(8): 229. Published online 2005 August 1. doi: 10.1186/gb-2005-6-8-229
PMCID:
PMC1273625
Abstract Full Text PDF–62K
 Is Cited by the Following 17 Articles in this Archive:
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
David R. Kelley, Bo Liu, Arthur L. Delcher, Mihai Pop, Steven L. Salzberg
Nucleic Acids Res. 2012 January; 40(1): e9. Published online 2011 November 17. doi: 10.1093/nar/gkr1067
PMCID:
PMC3245904
Abstract Full Text PDF–933K Supplementary Material
Those Who Can See Invisible Can Do Impossible!
Gaya Prasad
Indian J Microbiol. 2011 January; 51(1): 113–115. Published online 2011 March 18. doi: 10.1007/s12088-011-0169-3
PMCID:
PMC3209864
Full Text PDF–120K
PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data
Thomas J. Sharpton, Samantha J. Riesenfeld, Steven W. Kembel, Joshua Ladau, James P. O'Dwyer, Jessica L. Green, Jonathan A. Eisen, Katherine S. Pollard
PLoS Comput Biol. 2011 January; 7(1): e1001061. Published online 2011 January 20. doi: 10.1371/journal.pcbi.1001061
PMCID:
PMC3024254
Abstract Full Text PDF–777K Supplementary Material
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets
Robert Schmieder, Yan Wei Lim, Forest Rohwer, Robert Edwards
BMC Bioinformatics. 2010; 11: 341. Published online 2010 June 23. doi: 10.1186/1471-2105-11-341
PMCID:
PMC2910026
Abstract Full Text PDF–1.8M Supplementary Material
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
Wolfgang Gerlach, Sebastian Jünemann, Felix Tille, Alexander Goesmann, Jens Stoye
BMC Bioinformatics. 2009; 10: 430. Published online 2009 December 18. doi: 10.1186/1471-2105-10-430
PMCID:
PMC2801688
Abstract Full Text PDF–753K Supplementary Material
Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
James Robert White, Niranjan Nagarajan, Mihai Pop
PLoS Comput Biol. 2009 April; 5(4): e1000352. Published online 2009 April 10. doi: 10.1371/journal.pcbi.1000352
PMCID:
PMC2661018
Abstract Full Text PDF–701K Supplementary Material
Local RNA structure alignment with incomplete sequence
Diana L. Kolbe, Sean R. Eddy
Bioinformatics. 2009 May 15; 25(10): 1236–1243. Published online 2009 March 20. doi: 10.1093/bioinformatics/btp154
PMCID:
PMC2677745
Abstract Full Text PDF–366K Supplementary Material
Topological Signatures of Species Interactions in Metabolic Networks
Elhanan Borenstein, Marcus W. Feldman
J Comput Biol. 2009 February; 16(2): 191–200. doi: 10.1089/cmb.2008.06TT
PMCID:
PMC3035845
Abstract Full Text PDF–388K
The Expanding World of Methylotrophic Metabolism
Ludmila Chistoserdova, Marina G. Kalyuzhnaya, Mary E. Lidstrom
Annu Rev Microbiol. Author manuscript; available in PMC 2010 February 24.
Published in final edited form as: Annu Rev Microbiol. 2009; 63: 477–499. doi: 10.1146/annurev.micro.091208.073600
PMCID:
PMC2827926
Abstract Full Text PDF–1001K
A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
Patrick D Schloss, Jo Handelsman
BMC Bioinformatics. 2008; 9: 34. Published online 2008 January 23. doi: 10.1186/1471-2105-9-34
PMCID:
PMC2238731
Abstract Full Text PDF–707K
Picoeukaryotic sequences in the Sargasso Sea metagenome
Gwenael Piganeau, Yves Desdevises, Evelyne Derelle, Herve Moreau
Genome Biol. 2008; 9(1): R5. Published online 2008 January 7. doi: 10.1186/gb-2008-9-1-r5
PMCID:
PMC2395239
Abstract Full Text PDF–269K Supplementary Material
The Pfam protein families database
Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-Rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman
Nucleic Acids Res. 2008 January; 36(Database issue): D281–D288. Published online 2008 January. doi: 10.1093/nar/gkm960
PMCID:
PMC2238907
Abstract Full Text PDF–8.6M
Signal Mimics Derived from a Metagenomic Analysis of the Gypsy Moth Gut Microbiota
Changhui Guan, Jianhua Ju, Bradley R. Borlee, Lynn L. Williamson, Ben Shen, Kenneth F. Raffa, Jo Handelsman
Appl Environ Microbiol. 2007 June; 73(11): 3669–3676. Published online 2007 April 13. doi: 10.1128/AEM.02617-06
PMCID:
PMC1932686
Abstract Full Text PDF–479K Supplementary Material
Deciphering RNA structural diversity and systematic phylogeny from microbial metagenomes
Yanglong Zhu, Dileep K. Pulukkunat, Yong Li
Nucleic Acids Res. 2007 April; 35(7): 2283–2294. Published online 2007 March 27. doi: 10.1093/nar/gkm057
PMCID:
PMC1874661
Abstract Full Text PDF–2.0M Supplementary Material
Prediction of effective genome size in metagenomic samples
Jeroen Raes, Jan O Korbel, Martin J Lercher, Christian von Mering, Peer Bork
Genome Biol. 2007; 8(1): R10. Published online 2007 January 15. doi: 10.1186/gb-2007-8-1-r10
PMCID:
PMC1839125
Abstract Full Text PDF–622K Supplementary Material
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing
Robert Pinard, Alex de Winter, Gary J Sarkis, Mark B Gerstein, Karrie R Tartaro, Ramona N Plant, Michael Egholm, Jonathan M Rothberg, John H Leamon
BMC Genomics. 2006; 7: 216. Published online 2006 August 23. doi: 10.1186/1471-2164-7-216
PMCID:
PMC1560136
Abstract Full Text PDF–7.5M Supplementary Material
ASAP: a resource for annotating, curating, comparing, and disseminating genomic data
Jeremy D. Glasner, Michael Rusch, Paul Liss, Guy Plunkett, III, Eric L. Cabot, Aaron Darling, Bradley D. Anderson, Paul Infield-Harm, Michael C. Gilson, Nicole T. Perna
Nucleic Acids Res. 2006 January 1; 34(Database issue): D41–D45. Published online 2005 December 28. doi: 10.1093/nar/gkj164
PMCID:
PMC1347526
Abstract Full Text PDF–232K
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