Comparative Functional Genomics
Biology 431 Spring 2008
Februray 14th 2008
Laurel Brehm and Rachel Bond
Meta Genomics of Microbial Communities
This review looks to be intersting enough to justify its length. Truly a comparative and functional approach through genomic analysis.
Riesenfeld, C. S., Scholss, P.D., Handelsman, J., (2004) METAGENOMICS: Genomic Analysis of Microbial Communities. Annual Review of Genetics 38:525-552.
And a specific research paper by the same authors addresses the "Plate Problem". Despite our inability to easily culture 99% of the microbes, these authors present a means to understand functional components of the genomes from these unidentified microbes.
Riesenfeld, C. S., Goodman, R.M., Handelsman, J., (2004) Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environmental Microbiology 6:981-989.
(drinks by Max, "whoswho" by Garon and Iggy)
Cleanup from last week
In case anyone is keen to learn more details about the different sequencing techniques that are emerging I reccommend the following 3 papers
Shendure, J. Mitra, R.D., Varma, C., Church, G.M. (2004) Advanced Sequencing Technologies: Methods and Goals. Nature Reviews Genetics 5:335-344.
Wold, B. Myers, R.M. (2008) Sequence Census Methods for Fuctional Genomics. Nature Methods 5:19-21.
Ju, J., Kim, D.H., Bi, L., Meng, Q., Bai, X., Xi, Z., Li, X., Marma, M.S., Shi, S., Wu, J., Edwards, J.R., Romu, A., Turro, N.J., (2006) Four-color DNA Sequencing by Synthesis Using Cleavable Fluorescent Nucleotide Reversible Terminators. PNAS 103:19635-19640.
Tom Keller also left a web version of his lecture outline which has some useful links.