Introduction (8/30/2010)
The New Science of Metagenomics:
Revealing the Secrets of Our Microbial Planet.
Committee on
Metagenomics: Challenges and Functional Applications, National
Research Council
ISBN: 978-0-309-10676-4, 170 pages, 6 x 9,
paperback (2007)
Note: NO CLASS Wed 9/1/2010 and Mon 9/6/2010
Wed 9/8/2010 - A typical metagenomic study
Gill, S. R., M. Pop, et al. (2006). "Metagenomic analysis of the human distal gut microbiome." Science 312(5778): 1355-1359.
Qin, J., R. Li, et al. (2010). "A human gut microbial gene catalogue established by metagenomic sequencing." Nature 464(7285): 59-65.
Metagenomic assembly
Mon 9/13/2010 - Metagenomic assembly basics
Mavromatis, K., N. Ivanova, et al. (2007). "Use of simulated data sets to evaluate the fidelity of metagenomic processing methods." Nat Methods 4(6): 495-500.
Tyson, G. W., J. Chapman, et al. (2004). "Community structure and metabolism through reconstruction of microbial genomes from the environment." Nature 428(6978): 37-43.
Wed 9/15/2010 - What is genomic variation (and why we care)
Deitsch, K. W., S. A. Lukehart, et al. (2009). "Common strategies for antigenic variation by bacterial, fungal and protozoan pathogens." Nat Rev Microbiol 7(7): 493-503.
Lauring, A. S. and R. Andino (2010). "Quasispecies theory and the behavior of RNA viruses." PLoS Pathog 6(7): e1001005.
Mon 9/20/2010 - Detecting genomic variation
Eppley, J. M., G. W. Tyson, et al. (2007). "Strainer: software for analysis of population variation in community genomic datasets." BMC Bioinformatics 8: 398.
Denisov, G., B. Walenz, et al. (2008). "Consensus generation and variant detection by Celera Assembler." Bioinformatics 24(8): 1035-1040.
Wed 9/22/2010 - Quasi-species detection
Eriksson, N., L. Pachter, et al. (2008). "Viral population estimation using pyrosequencing." PLoS Comput Biol 4(4): e1000074.
Laserson, J., V. Jojic, D. Koller. (2010). "Genovo: De novo assembly for metagenomes.". RECOMB 2010.
Metagenomic gene finding (9/27, 9/29)
Taxonomic classification (10/4, 10/6, 10/11, 10/13)
16S rRNA analysis - clustering (10/18, 10/20)
Statistical comparisons of communities (10/25, 10/27, 11/1, 11/3)
Dynamic modeling (11/8, 11/10)
Metabolic reconstruction (11/15, 11/17)