Cbcb:Pop-Lab:Papers: Difference between revisions

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# [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth976.html Phylopythia] Support Vector Machine (SVM)
# [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth976.html Phylopythia] Support Vector Machine (SVM)
# [http://arxiv.org/abs/0708.3098 CompostBin] Principle Component Analysis (PCA)
# [http://arxiv.org/abs/0708.3098 CompostBin] Principle Component Analysis (PCA)
#
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18218139 AMI] Mutual Information
# [http://www.ncbi.nlm.nih.gov/pubmed/18535082?dopt=Citation HSOM] Hierarchical Sef-Organizing Map
# [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18442374 GSOM] Growing SOM

Revision as of 18:18, 19 February 2009

Metagenomics Reviews

  1. V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. A Bioinformatician's guide to Metagenomics.
  2. Clarridge J.E. 16S sequencing and clinical microbiology review
  3. C. Riesenfield, P. Schloss, and J. Handelsman. 2004 Metagenomics review.
  4. J. Eisen. Light metagenomics review for GOS expedition.
  5. Tringe SG, Hugenholtz P. A renaissance for the pioneering 16S rRNA gene
  6. Warnecke F, Hugenholtz P. Building on basic metagenomics with complementary technologies
  7. Raes J, Foerstner KU, Bork P. Get the most out of your metagenome: computational analysis of environmental sequence data.
  8. McHardy AC, Rigoutsos I. What's in the mix: phylogenetic classification of metagenome sequence samples.
  9. Kevin Chen, Lior Pachter Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
  10. Foerstner KU, von Mering C, Bork P. Comparative analysis of environmental sequences: potential and challenges
  11. Ward N. New directions and interactions in metagenomics research
  12. Tringe SG, Rubin EM. Metagenomics: DNA sequencing of environmental samples
  13. Handelsman J. Metagenomics: Application of Genomics to Uncultured Microorganisms
  14. Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities.

Pioneering papers

  1. G Muyzer, E C de Waal and A G Uitterlinden PCR amplifying 16S rRNA genes and DGGE
  2. D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses

16S sequence analysis

  • Classification.
    • RDP classifier
    • BLAST searches
    • Multilocus classification
    • Sogin-like database search methods
    • Sanger vs. 454
  • Alignment.
    • ClustalW
    • NAST
    • MUSCLE
    • Pairwise
    • Masking approaches (LaneMask)
  • Distance corrections.
    • Jukes-Cantor
    • Kimura-2
    • Felsenstein84
    • Olsen
  • Clustering.
    • DOTUR
    • VI-cut
    • OTU picker (unpublished)
    • Database versions (Sogin papers)
  • Community comparison.
    • Diversity estimators
    • Rarefaction curves
    • DOTUR
    • EstimateS
    • SONs
    • TreeClimber
    • S-libshuff
    • UniFrac
    • MEGAN
    • Xipe - single sample comparisons
    • Metastats

DNA sequence binning

  1. Phylopythia Support Vector Machine (SVM)
  2. CompostBin Principle Component Analysis (PCA)
  3. AMI Mutual Information
  4. HSOM Hierarchical Sef-Organizing Map
  5. GSOM Growing SOM
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