Bioinformatics Seminar I (3 CR)

Topics: Bioinformatics for Microbial Genomics and Metagenomics

I690, Spring 2010
Instructor: Yuzhen Ye, School of Informatics and Computing, Indiana University, Bloomington
Contact: yye@indiana.edu
Class meets: Tuesdays 1:00-3:45PM, room I2 122 (Informatics **East**)


  • Topics & schedule

     

    Week (date)TopicsNotes
    Week 1
    (Tue, Jan 12th)
    Brief overview of the course, and microbial genomics and metagenomics
    Ref 1: 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)
    Ref 2: Hunter. The secret garden (paper link)
    lecture slides (handout)
    Week 2
    (Tue, Jan 19th)
    What is a bacterial species (guest lecture by Thomas G. Doak from IU Biology)
    Review article: Wooley and Ye. Metagenomics: Facts and Artifacts, and Computational Challenges
    lecture slides (handout)
    Week 3
    (Tue, Jan 26th)
    Introduction to microbial genomics
    Microbial diversity
    Bioinformatics basics for microbial genome analysis
    lecture slides (handout1)
    lecture slides (handout1)
    Week 4
    (Tue, Feb 2nd)
    Introduction to metagenomics
    lecture slides (handout)
    Week 5
    (Tue, Feb 9th)
    Paper presentation 1: Bacterial genome dynamics

    Paper 1: Lapierre et al. Estimating the size of the bacterial pan-genome. Trends in Genetics, 25:107-110, 2008. (paper link)
    And a related short paper: Sequencing the species pan-genome (paper link)
    **presenter: Heewook

    Paper 2: Xu et al. Evolution of Symbiotic Bacteria in the Distal Human Intestine. PLoS Biol. 2007 July; 5(7): e156. (paper link)
    **presenter: Anoop
    slides (Heewook) slides (Anoop)
    Week 6
    (Tue, Feb 16th)
    Paper presentation 2: Estimation of microbial diversity from pyrosequences

    Paper 3: Quince et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods 6, 639-641, 2009. (paper link)
    **presenter: Samuel

    Paper 4: Schloss et al. Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness. Applied and Environmental Microbiology, 71:1501-1506, 2005. (paper link)
    **presenter: Mingjie

    Paper 5: Sun et al. ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Research, doi:10.1093/nar/gkp285, 2009. (paper link)
    **presenter: Xiaoqian
    slides (Samuel)
    slides (Mingjie)
    slides (Xiaoqian)
    Week 7
    (Tue, Feb 23rd)
    Paper presentation 3: Similarity-based and phylogeny-based phylotyping

    Paper 6: Huson et al. MEGAN analysis of metagenomics data. Genome Research, 17:377-386, 2007. (paper link) (MEGAN 2.0 paper, and MEGAN 3.0 paper)
    **presenter: Heejoon

    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: Xinjun

    Paper 8: Brady et al. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nature Methods 6, 673-676, 2009 (paper link)
    **presenter: Vikas
    slides (Heejoon)
    slides (Vikas)
    slides (Xinjun)
    Week 8
    (Tue, Mar 2nd)
    Paper presentation 4: Binning of metagenomic sequences

    Paper 9: Chatterji et al. CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads (RECOMB 2008) (paper link)
    **presenter: Mohsen

    Paper 10: Zhou et al. Barcodes for genomes and applications. BMC Bioinformatics 2008, 9:546 (paper link)
    **presenter: Simo
    slides (Mohsen)
    slides (Simo)
    Week 9
    (Tue, Mar 9th)
    Paper presentation 5: Function annotation I

    Paper 11: Hoff et al. Gene prediction in metagenomic fragments: A large scale machine learning approach. BMC Bioinformatics, 2008, 9: 217. (paper link)
    **presenter: Jose

    Paper 12: Li. Analysis and comparison of very large metagenomes with fast clustering and functional annotation. BMC Bioinformatics, 10:359, 2009. (paper link)
    **presenter: Chuan-Yih
    slides (Jose)
    slides (Chuan-Yih)
    Week 10
    (Tue, Mar 16th)
    Spring recess
    Week 11
    (Tue, Mar 23rd)
    Paper presentation 6: Function annotation II

    Paper 13: Sharon et al. A Statistical Framework for the Functional Analysis of Metagenomes. RECOMB 2009. (paper link)
    **presenter: Xin

    Paper 14: Pasic et al. Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber. BMC Genomics, 10:570, 2009. (paper link)
    **presenter: Neethu
    slides (Xin)
    slides (Neethu)
    Week 12
    (Tue, Mar 30th)
    Paper presentation 7: Statistical tools for metagenomics

    Paper 15: White et al. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS CB, 5(4):e1000352, 2009. (paper link)
    **presenter: Sashikiran

    Paper 16: Angly et al. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 2005, 6:41. (paper link)
    **presenter: Yongan
    slides (Sashikiran)
    slides (Yongan)
    Week 13
    (Tue, Apr 6th)
    Paper presentation 8: Comparative metagenomics

    Paper 17: Lozupone and Knight. UniFrac: a New Phylogenetic Method for Comparing Microbial Communities. Applied and Environmental Microbiology, 71:8228-8235, 2005. (paper link)
    **presenter: Chad

    Paper 18: Parks and Beiko. Identifying biologically relevant differences between metagenomic communities. Bioinformatics. 2010 Feb 3. [Epub ahead of print]
    **presenter: Rajeswari
    slides (Chad)
    slides (Rajeswari)
    Week 14
    (Tue, Apr 13th)
    Paper presentation 9: Microbe-environment(host) interaction

    Paper 19: Ley et al. Worlds within worlds: evolution of the vertebrate gut microbiota. Nature Reviews Microbiology 6, 776-788, 2008. (paper link)
    **presenter: Yahong

    Paper 20: Gionaulis et al. Quantifying environmental adaptation of metabolic pathways in metagenomics. PNAS, 106:1374-1379, 2009. (paper link)
    **presenter: Quan
    slides (Yahong)
    slides (Quan)
    Week 15
    (Tue, Apr 20th)
    Paper presentation 10: Targeted metagenomics (and viral metagenomics)

    Paper 21: Sommer et al. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 325(5944):1128 - 1131, 2009. (paper link)
    **presenter: Sushmitha

    Paper 22: Monier et al. Taxonomic distribution of large DNA viruses in the sea. Genome Biol. 2008; 9(7): R106. (paper link)
    **presenter: Liting
    slides (Sushmitha)
    slides (Liting)
    Week 16
    (Tue, Apr 27th)
    Paper presentation 11: Metatranscriptomics & metaproteomics

    Paper 23: Verberkmoes et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2009 Feb;3(2):179-89. (paper link)
    **presenter: Lei

    Paper 24: Shi et al. Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature, 2009, 459(7244): 266-269. (paper link)
    **presenter: Rahul
    slides (Lei)
    Week 17
    (Tue, May 4th)
    Project presentation

    Bioinformatics program at IUB