Cbcb:Pop-Lab:Papers: Difference between revisions
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#Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples] | #Tringe SG, Rubin EM. [http://www.nature.com/nrg/journal/v6/n11/full/nrg1709.html Metagenomics: DNA sequencing of environmental samples] | ||
# Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms] | # Handelsman J. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590779 Metagenomics: Application of Genomics to Uncultured Microorganisms] | ||
# Riesenfeld CS, Schloss PD, Handelsman J. [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091216?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Metagenomics: genomic analysis of microbial communities.] | |||
== Pioneering papers == | == Pioneering papers == | ||
Revision as of 17:52, 19 February 2009
Metagenomics Reviews
- V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. A Bioinformatician's guide to Metagenomics.
- Clarridge J.E. 16S sequencing and clinical microbiology review
- C. Riesenfield, P. Schloss, and J. Handelsman. 2004 Metagenomics review.
- J. Eisen. Light metagenomics review for GOS expedition.
- Tringe SG, Hugenholtz P. A renaissance for the pioneering 16S rRNA gene
- Warnecke F, Hugenholtz P. Building on basic metagenomics with complementary technologies
- Raes J, Foerstner KU, Bork P. Get the most out of your metagenome: computational analysis of environmental sequence data.
- McHardy AC, Rigoutsos I. What's in the mix: phylogenetic classification of metagenome sequence samples.
- Kevin Chen, Lior Pachter Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
- Foerstner KU, von Mering C, Bork P. Comparative analysis of environmental sequences: potential and challenges
- Ward N. New directions and interactions in metagenomics research
- Tringe SG, Rubin EM. Metagenomics: DNA sequencing of environmental samples
- Handelsman J. Metagenomics: Application of Genomics to Uncultured Microorganisms
- Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities.
Pioneering papers
- G Muyzer, E C de Waal and A G Uitterlinden PCR amplifying 16S rRNA genes and DGGE
- 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