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Friday, 4th of December 2009 at 02:52:21 PM

INFO-I 690

Category:

I690: Bioinformatics seminar:Introduction to Glycoinformatics

Class Webpage

Fall semester 2009
Lecture: MW 1-2:15pm, I107
Contact: Haixu Tang

Description: This course is designed to discuss advanced topics in glycoinformatics, an emerging area which studies the computational problems in in glycobiology and glycomics. We will first introduce the basic concepts in glycobiology and high throughput experimental approaches used in glycomics, then will focus on the research topics around four has four main subareas:

  • Databases for glycobiology and glycomics, focusing on the acquisition, collection and sharing of the data related to glycobiology and glycomics;
  • Systems biology of glycosylation, studying the organization and function of the glycosylation machinery using multiple data resources from genomics, proteomics and glycomics;
  • Structural glycoinformatics, focusing on the research of the structural (mainly 3D conformational) basis of oligosaccharides functions;
  • Algorithm and software development for the high throughput technologies used in glycomics, such as carbohydrate microarray and mass spectrometry.

    • We will distribute lecture notes along with the progress of the class. The evaluation of the class will be mainly based on five home assignments, each consisting of 2-3 papers, and a final project.

    Reference:Essentials of Glycobiology Grading: HW/Paper presentation/discussion (50%), final project (50%).

    Homework

    Project List

    Preliminary agenda

    Week Date Topics
    1 8/31 & 9/2 Introduction to glycobiology: concepts of glycobiology; glycan conformations slides
    2 9/7 Protein glycosylation: N-linked and O-linked; slides
    3 9/14 Comparative and evolutionary genomics of glycan synthesis slides
    4 9/21 Glycan-binding proteins; slides
    5 9/28 Glycans and diseases; Paper presentation 1 slides
    6 10/5 Databases for glycobiology; slides
    7 10/12 Database presentation; Paper presentation 2
    8 10/19 Glycomics; slides
    9 10/26 Glycomics;
    10 11/2 Final project discussion;
    11 11/9 Final project discussion; Structural modeling of glycans; slides
    12 11/17 Structual bioinformatics for glycobiology; Paper presentation 4
    13 11/24 Structural bioinformatics for glycobiology; Thanksgiving holidays
    14 12/1 Systems glycobiology; slides
    15 12/8 Final project presentations / discussions
    16 12/15 Final project report due

    Papers

    • Hashimoto K, Tokimatsu T, Kawano S, Yoshizawa AC, Okuda S, Goto S, Kanehisa  Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans.  Carbohydr Res. 2009 May 12;344(7):881-7. [paper, Presentation, Summary]
    • Tangvoranuntakul P, Gagneux P, Diaz S, et al. Human uptake and incorporation of an immunogenic nonhuman dietary sialic acid. Proc Natl Acad Sci USA 2003;100:12045–12050.[paper, Presentation, Summary]
    • Herget S, Ranzinger R, Maass K, Lieth CW. GlycoCT-a unifying sequence format for carbohydrates. Carbohydr Res. 2008 Aug 11;343(12):2162-71.[Paper, Presentation, Summary]
    • Cui J, Smith T, Robbins PW, Samuelson J, Darwinian selection for sites of Asn-linked glycosylation in phylogenetically disparate eukaryotes and viruses. Proc Natl Acad Sci U S A. 2009.[paper, Presentation, Summary]
    • Marathe DD, Chandrasekaran EV, Lau JT, Matta KL, Neelamegham S. Systems-level studies of glycosyltransferase gene expression and enzyme activity that are associated with the selectin binding function of human leukocytes. FASEB J. 2008 Dec;22(12):4154-67.[Paper, Presentation, Summary]
    • Wollscheid B, Bausch-Fluck D, Henderson C, O’Brien R, Bibel M, Schiess R, Aebersold R, Watts JD. Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol. 2009 Apr;27(4):378-86.[Paper, Presentation, Summary]
    • Liang PH, Wang SK, Wong CH. Quantitative analysis of carbohydrate-protein interactions using glycan microarrays: determination of surface and solution dissociation constants. J Am Chem Soc. 2007 Sep 12;129(36):11177-84.[Paper, Presentation, Summary]
    • Bosques CJ, Tschampel SM, Woods RJ, Imperiali B. Effects of glycosylation on peptide conformation: a synergistic experimental and computational study. J Am Chem Soc. 2004 Jul 14;126(27):8421-5.[Paper,Presentation, Summary]
    • Wang, D. , Liu, S. , Trummer, B. J. , Deng, C. & Wang, A. Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells. Nature Biotechnol. 20, 275–281 (2002).[Paper, Presentation, Summary]
    • Wang CC, Huang YL, Ren CT, Lin CW, Hung JT, Yu JC, Yu AL, Wu CY, Wong CH. Glycan microarray of Globo H and related structures for quantitative analysis of breast cancer. Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11661-6. [Paper, Presentation, Summary]

    Database

    • CaZY: Carbohydrate-active enzyme

    Project

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