Cbcb:Pop-Lab:Papers

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. Kevin Chen, Lior Pachter Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
9. Foerstner KU, von Mering C, Bork P. Comparative analysis of environmental sequences: potential and challenges
10. Ward N. New directions and interactions in metagenomics research
11. Tringe SG, Rubin EM. Metagenomics: DNA sequencing of environmental samples
12. Handelsman J. Metagenomics: Application of Genomics to Uncultured Microorganisms
13. 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  • OTU picker (unpublished)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
6. CARMA Pfam and Phylogeny
7. What's in the mix: phylogenetic classification of metagenome sequence samples REVIEW