Bioinformatics Seminar II (3 CR)

Topics: Bioinformatics for Microbial Genomics and Metagenomics

I690, Spring 2008
Instructor: Yuzhen Ye, School of Informatics, Indiana University, Bloomington
Contact: yye@indiana.edu
Class meets: Weds 1:00-3:30PM, room I105 (informatics building)


  • Topics & schedule

     

    Week (date)TopicsNotes
    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
    Week 2
    (Jan 16th)
    Lecture 2: Introduction of microbial diversity & DNA sequencing technology
    Ref: handouts
    lecture slides
    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
    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)
    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)
    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)
    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)
    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)
    10 Spring break
    Week 11
    (Mar 19)
    Project proposal presentations & discussions (I)

    Mina & Mira
    Yu-Wei & Ankita
    Week 12
    (Mar 26)
    Project proposal presentations & discussions (II)

    Vivek & Kashi
    Haleh & Kwangmin
    Yong & Fuxiao

    Manasa & Richard
    Rita
    Chao & Ashwini
    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)
    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)?
    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)
    Week 16 (Apr 23) Project final presentations

    Mina & Mira
    Yu-Wei & Ankita
    Vivek & Kashi
    Haleh & Kwangmin

    Yong & Fuxiao
    Manasa & Richard
    Rita
    Chao & Ashwini
    Week 17Final project report due on Apr 28 (Monday)
    (don't know what you need to turn in? check out here)

    Bioinformatics program at IUB