| Week (date) | Topics | Notes | |
| Week 1 (Jan 9th) |
Lecture 1: Brief overview of the course, and microbial genomics and metagenomics Ref: Jurkowski et al. Metagenomics: A Call for Bringing a New Science into the Classroom (While It's Still New). CBE Life Sci Educ 6(4): 260-265 2007 (paper link) |
lecture slides |
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| Week 2 (Jan 16th) |
Lecture 2: Introduction of microbial diversity & DNA sequencing technology Ref: handouts |
lecture slides |
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| Week 3 (Jan 23th) |
Lecture 3: Bioinformatics analysis of microbial genomics sequences (shotgun sequence assembly; functional annotation; comparative analysis; pathway reconstruction and comparison, microbial genomics resources, etc) Ref: Field et al. How do we compare hundreds of bacterial genomes. Curr Opin Microbiol. 9(5):499-504, 2006 (paper link) |
lecture slides |
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| Week 4 (Jan 30th) |
Lecture 4: From genomics to metagenomics Overview of metagenomics: metagenomics basics and a few metagenomics projects Ref 1: Jonathan Eisen. Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes PLoS Biology 5(3):e82, 2007 (paper link) Ref 2: Tringe et al. Comparative Metagenomics of Microbial Communities. Science, 308(5721):554-557 (paper link) Ref 3: Warnecke and Hugenholtz. Building on basic metagenomics with complementary technologies. Genome Biology 2007, 8:231. (paper link) Ref 4: Metagenomics book Chapter 3, 4 & 5 |
lecture slides (handout) |
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| Week 5 (Feb 6th) |
Lecture 5: Metagenomics data analysis and applications Ref: Raes et al. Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin in Microbiol, 10:490-498, 2007 (paper link) |
lecture slides (handout) | |
| Week 6 (Feb 13th) |
Paper presentation 1 (comparative genomics) Paper 1: Hogg et al. Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biology, 2007, 8:R103. (paper link) (related paper: Tettelin et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome". PNAS, 102: 13950-13955, 2005. (paper link)) ** presenter: Kwangmin Paper 2: Oh set al. Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks. BMC Bioinformatics, 7:284, 2006. (paper link) ** presenter: Haleh |
Slides (Kwangmin) Slides (Haleh) |
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| Week 7 (Feb 20th) |
Paper presentation 2 (metagenomics bioinformatics warming up) Paper 3: Mavromatis et al. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods 2007, 4:495. (paper link) **presenter: Chao Paper 4: Wommack et al. Metagenomics: Read length matters. (paper link) **presenter: Ashwini Paper 5: Jojic et al. Population Sequencing Using Short Reads: HIV as a Case Study. PSB 13:126-136 (2008). (paper link) **presenter: Yong |
Slides (Chao) Slides (Ashwini) Slides (Yong) |
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| Week 8 (Feb 27th) |
Paper presentation 3 (community species diversity analysis) Paper 6: Chatterji et al. CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads (RECOMB 2008) (paper link) **presenter: Mina Paper 7: von Mering et al. Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments. Science 315(5815):1126-1130, 2007. (paper link) (a related paper: Ciccarelli et al. Toward Automatic Reconstruction of a Highly Resolved Tree of Life. Science, 311(5765):1283-1287, 2006) **presenter: Mira |
Slides (Mina) Slides (Mira) |
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| Week 9 (Mar 5th) |
Paper presentation 4 (community species diversity analysis II) Paper 8: Huson et al. MEGAN analysis of metagenomics data. Genome Research, 17:377-386, 2007. (paper link) **presenter: Ankita Paper 9: McHardy et al. Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods, 4:63-72, 2007. (paper link) **presenter: Yu-Wei Note: Project proposal due by Mar 7th (Friday) (Guidance on the course project) |
Slides (Ankita) Slides (Yu-Wei) |
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| 10 | Spring break | ||
| Week 11 (Mar 19) |
Project proposal presentations & discussions (I) Mina & Mira Yu-Wei & Ankita |
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| Week 12 (Mar 26) |
Project proposal presentations & discussions (II) Vivek & Kashi Haleh & Kwangmin Yong & Fuxiao Manasa & Richard Rita Chao & Ashwini |
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| Week 13 (Apr 2) |
Paper presentation 5 (function prediction/analysis) Paper 10: Harrington et al. Quantitative assessment of protein function prediction from metagenomics shotgun sequences. PNAS, 104(35):13913-13918, 2007. (paper link) **presenter: Fuxiao Paper 11: Schloss and Handelsman. A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics 2008, 9:34. (paper link) **presenter: Rita |
Slides (Fuxiao) Slides (Rita) |
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| Week 14 (Apr 9) |
Paper presentation 6 (function prediction/analysis II) Paper 12: Mou et al. Bacterial carbon processing by generalist species in the coastal ocean. Nature 451, 708-711, 2008. (paper link) **presenter: Richard Paper 13: Robidart et al. Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environmental Microbiology, 727-737, 2008. (paper link) **presenter: Manasa |
Slides (Manasa) Slides (Richard)? |
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| Week 15 (Apr 16) | Paper presentation 7 (metagenomics applications and beyond) Paper 14: Frias-Lopaz et al. Microbial community gene expression in ocean surface waters. PNAS, 105(10):3805-106, 2008 (paper link) **presenter: Vivek Paper 15: Dinsdale et al. Microbial ecology of four coral atolls in the northern line islands. PLos ONE, 3(2):e1584. (paper link) **presenter: Kashi |
Slides (Vivek) Slides (Kashi) |
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| Week 16 (Apr 23) | Project final presentations Mina & Mira Yu-Wei & Ankita Vivek & Kashi Haleh & Kwangmin Yong & Fuxiao Manasa & Richard Rita Chao & Ashwini |
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| Week 17 | Final project report due on Apr 28 (Monday) (don't know what you need to turn in? check out here) |