MB&B 452a / 752a12, Fall 2003



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

Fall 2002, Fall 2001, 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:6:30PM-7:30PM Mondays @ BASS405

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

Genomics Section
 Sep 03 DS Genomics: Overview. The Diversity of Life (Life at 110°C, at pH 1, or in 5M KCl)
08 DS Genomics: Overview of Proteins and Nucleic Acids
08 JLR/MRS Discussion Sections Week of Sept 08
10 DS Genome Sequencing, Sequence Annotation and Bioinformatics tools for Genomics
15 DS Functional Genomics I (array technologies and uses)
15 JLR/MRS Discussion Sections Week of Sept 15
17 DS Functional Genomics II (proteomics)
22 DS Structural Genomics
22 JLR/MRS Discussion Sections Week of Sep 22
24 MS Functional Genomics III
29 MS Functional Genomics IV
29 JLR/MRS Discussion Sections Week of Sep 29
Oct 01 MS Functional Genomics V
06 JLR/MRS Yom Kippur (Genomics Assignment)
6? JLR/MRS Discussion Sections Week of Oct 6
08 KC Web Resources for Genomics I (Kei-Hoi Cheung)
13 JLR Microarrays: How to do it! (John Rinn)
13 JLR/MRS Discussion Sections Week of Oct 13
15 DS Whole Genome Comparisons

Midterm Exam (covering lectures through October 15)

20 JLR/MRS Discussion Sections Week of Oct 20 No discussion -- midterm today!
22 MG Bioinfomatics: Overview
27 MG Analysis of Sequences I
27 JLR/MRS Discussion Sections Week of Oct 27
29 MG Analysis of Sequences II (Substitution Matrix)
Nov 03 MG Analysis of Sequences III (HMM)
5, 6 JLR/MRS Discussion Sections Week of Nov 3
  • 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. 1970 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
05 MG Analysis of Sequences IV (P-value and EVD)
10 MG Database
10 JLR/MRS Discussion Sections Week of Nov 10
12 MG Structure
17 DS Genomics: New Frontiers for Nutrition and Foods (Beat Mollet, Nestle)
17 JLR/MRS Discussion Sections Week of Nov 17
19 MG Surveys I
Dec 01 MG Datamining
01 JLR/MRS Discussion Sections Week of Dec 1
03 MG Simulation

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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