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Nucleic Acids Res
v.40(1); 2012 Jan
PMC3245904
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Nucleic Acids Res. 2012 Jan; 40(1): e9.
Published online 2011 Nov 17. doi: 10.1093/nar/gkr1067
Find articles by Steven L. Salzberg
1 Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, Department of Computer Science, 3115 Biomolecular Sciences Building 296, University of Maryland, College Park, MD 20742, 2 Department of Stem Cell and Regenerative Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, 3 Broad Institute, 7 Cambridge Center, Cambridge, MA 02142 and 4 McKusick-Nathans Institute of Genetic Medicine Johns Hopkins University School of Medicine Baltimore, MD, USA
*To whom correspondence should be addressed. Tel: +1 301 405 3234; Email: ude.dmu.scaimu@yellekad
Received 2011 Jul 29; Revised 2011 Sep 19; Accepted 2011 Oct 28.
Copyright © The Author(s) 2011. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0 ), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
GUID: 9400F55D-0352-4CEB-8112-5CED0DDCA967
GUID: 625628FC-A2B7-40C6-A23E-50083CF9B18B
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10. Tringe SG, Von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, et al. Comparative metagenomics of microbial communities. Science. 2005; 308 :554. [ PubMed ] [ Google Scholar ]
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Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press
1. Curtis TP, Sloan WT, Scannell JW. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA. 2002; 99 :10494. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
3. Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA. 1998; 95 :6578. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
4. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett MC, Knight R, Gordon JI. The human microbiome project. Nature. 2007; 449 :804–810. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
5. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995; 269 :496. [ PubMed ] [ Google Scholar ] [ Ref list ]
6. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 2004; 68 :669. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
7. Schloss PD, Handelsman J. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol. 2005; 6 :229. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
8. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004; 428 :37–43. [ PubMed ] [ Google Scholar ] [ Ref list ]
9. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, et al. The Sorcerer II Global Ocean Sampling Expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 2007; 5 :e77. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
10. Tringe SG, Von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, et al. Comparative metagenomics of microbial communities. Science. 2005; 308 :554. [ PubMed ] [ Google Scholar ] [ Ref list ]
11. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science. 2009; 326 :1694. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
12. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, et al. The Sorcerer II Global Ocean Sampling Expedition: expanding the universe of protein families. PLoS Biol. 2007; 5 :e16. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
13. Brulc JM, Antonopoulos DA, Berg Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, et al. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc. Natl. Acad. Sci. USA. 2009; 106 :1948. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
14. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, et al. Functional metagenomic profiling of nine biomes. Nature. 2008; 452 :629–632. [ PubMed ] [ Google Scholar ] [ Ref list ]
15. Kristiansson E, Hugenholtz P, Dalevi D. ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics. 2009; 25 :2737. [ PubMed ] [ Google Scholar ] [ Ref list ]
16. Sharon I, Bercovici S, Pinter RY, Shlomi T. Pathway-based functional analysis of metagenomes. J. Comput. Biol. 2011; 18 :495–505. [ PubMed ] [ Google Scholar ] [ Ref list ]
17. Borodovsky M, Mclninch JD, Koonin EV, Rudd KE, Médigue C, Danchin A. Detection of new genes in a bacterial genome using Markov models for three gene classes. Nucleic Acids Res. 1995; 23 :3554–3562. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
18. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999; 27 :4636–4641. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
19. Fickett JW, Tung C. Assessment of protein coding measures. Nucleic Acids Res. 1992; 20 :6441–6450. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
20. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007; 23 :673–679. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
21. Chen K, Pachter L. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput. Biol. 2005; 1 :106–12. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
22. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, et al. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat. Methods. 2007; 4 :495–500. [ PubMed ] [ Google Scholar ] [ Ref list ]
23. Hoff KJ. The effect of sequencing errors on metagenomic gene prediction. BMC Genomics. 2009; 10 :520. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
24. Hoff KJ, Lingner T, Meinicke P, Tech M. Orphelia: predicting genes in metagenomic sequencing reads. Nucleic Acids Res. 2009; 37 (Suppl. 2):W101–W105. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
28. Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010; 38 :e132. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
29. Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat. Methods. 2009; 6 :673–676. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
32. Patil KR, Haider P, Pope PB, Turnbaugh PJ, Morrison M, Scheffer T, McHardy AC. Taxonomic metagenome sequence assignment with structured output models. Nat. Methods. 2011; 8 :191–192. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
33. Chatterji S, Yamazaki I, Bai Z, Eisen J. Research in Computational Molecular Biology. Springer: 2008. CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads; pp. 17–28. [ Google Scholar ] [ Ref list ]
35. Kislyuk A, Bhatnagar S, Dushoff J, Weitz JS. Unsupervised statistical clustering of environmental shotgun sequences. BMC Bioinformatics. 2009; 10 :316. [ PMC free article ] [ PubMed ] [ Google Scholar ] [ Ref list ]
36. Hu G, Guo J, Liu Y, Zhu H. MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction. Bioinformatics. 2009; 25 :1843–1845. [ PubMed ] [ Google Scholar ] [ Ref list ]
34. Kelley DR, Salzberg SL. Clustering metageno
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