MB&B 452a / 752a12, Fall 2001



Previous Year's Course Pages (all links still work)

Fall 2000, Fall 1999, Spring 1999, Spring 1998

Timing and Location

Meeting from 1:00-2:15 PM on Mondays and Wednesday, in Bass 305.

Discussion Section Times: Tuesdays 6 pm & Wednesdays 7:30 pm

The papers for the discussion are only available from a Yale University Domain


Genomics Section

Bioinformatics Section

Teaching Fellows

Brief Description

Genomics describes the determination of the nucleotide sequence as well as many further analyses used to discover functional and structural gene information on all the genes of an organism. Topics include the methods and results of analysis on a genome-wide scale as well as a discussion of the implications of this research. Bioinformatics describes the computational analysis of gene sequences and protein structures on a large scale. Topics include sequence alignment, biological database design, geometric analysis of protein structure, and macromolecular simulation. [Blue Book Entry]

Rough Outline of Topics

Discussion of Topics for Final Project

Genomics Section
 Sep 05 DS Genomics: Overview. The Diversity of Life (Life at 110°C, at pH 1, or in %M KCl)
10 DS Genomics: Overview of Proteins and Nucleic Acids
12 DS Physical and Genetic Maps, Whole Genome Sequences, Annotation
18, 19 JS Discussion Sections Week of Sept 17
17 DS Functional Genomics I (array technologies and uses)
19 MS Functional Genomics II (gene disruptions, fusions, ect.)
25,26 JS & DG Discussion Sections Week of Sept 24
  • DNA polymorphisms amplified by arbitrary primers are useful as genetic markers
    Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV
    Nucleic Acids Res. 1990 Nov 25;18(22):6531-5
  • Happy mapping: a proposal for linkage mapping the human genome
    Dear PH, Cook PR
    Nucleic Acids Res. 1989 Sep 12;17(17):6795-807
  • A high-resolution metric HAPPY map of human chromosome 14
    Dear PH, Bankier AT, Piper MB
    Genomics. 1998 Mar 1;48(2):232-41
24 MS Functional Genomics III
26 MS Proteomics
Oct 2,3 JS Discussion Sections Week of Oct 1
01 DS Structural Genomics
03 DS Whole Genome Comparisons

Bioinformatics Section (also includes updated READING LIST)
Good Review to Read: What is Bioinformatics
08 MG Bioinformatics: Overview
10 DS Agricultural Genomics (Robert Last, Cereon )
9,10 JS Discussion Sections Week of Oct 8
15 MG Sequence Alignment I (Via Dynamic Programming)
17 MG Sequence Alignment II
16, 17 JS & DG Discussion Sections Week of Oct 15
22 MG Sequence Alignment III
23 JS & DG tentative EXAM REVIEW


(Covering only the Genomics Section)
29 MG Sequence Alignment IV
31 MG Databases
30, 31 DG Discussion Sections Week of Oct 29
Nov 05 MG Structures
7 MG Surveys
Covering up to and including Oct 31 -- databases
6, 7 JS & DG Discussion Sections Week of Nov 5
  • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    Needleman, S. B. & Wunsch, C. D.
    J. Mol. Biol. 1971 48: 443-453.
  • Issues in searching molecular sequence databases.
    Altschul, S. F., Boguski, M. S., Gish, W. and Wootton, J. C.
    Nature Genetics. 1994 6(2): 119-29.
  • A Unified Statistical Framework for Sequence Comparison and Structure Comparison.
    M Levitt & M Gerstein
    PNAS 1998 95: 5913-5920
12 Genomics and Society (Claire Fraser)
14 SNPs & Drug Development (Peter Rae, Bayer Corporation)
13, 14 JS & DG Discussion Sections Week of Nov 12
  • Hidden Markov models
    Eddy, S. R.
    Curr. Opin. Struc. Biol. 1996 6, 361-365.
  • Protein Structure Comparison by Alignment of Distance Matrices
    Holm, L. and Sander
    J. Mol. Biol. 1993 233: 123-128
  • Identification and application of the concepts important for accurate and reliable protein secondary structure prediction
    King, R. D. & Sternberg, M. J. E.
    Prot. Sci. 1996 5, 2298-2310
26 MG Datamining
28 MG Simulation
Submission of Paper topic DUE by end of the week
PLEASE email in a brief note stating your project.
27, 28 JS & DG Discussion Sections Week of Nov 27
Dec 03 MG Quiz Covering up to and including Nov 28, Structure and Simulation II
Tentative Web Review
05 MG Summary (Industrial Perspectives) and Discussion of Final Paper
4, 5 JS & DG Discussion Sections Week of Dec 3
13 PAPER DUE BY 9 AM at Joann Delvecchio's Office (Gibbs 309C)

Work Required and Grading


Research Jobs in Bioinformatics

If you're really motivated, take a look at http://bioinfo.mbb.yale.edu/jobs.

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