MB&B 452a / 752a12, Fall 2002



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

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:6:00PM-6:50PM Tue@BASS405 Wed@WLH113

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 04 DS Genomics: Overview. The Diversity of Life (Life at 110°C, at pH 1, or in 5M KCl)
09 MG Bioinfomatics: Overview
10, 11 PY Discussion Sections Week of Sept 09
11 DS Genomics: Overview of Proteins and Nucleic Acids
16 DS Genomics and Society (Claire Fraser, The Institute for Genome Research)
18 DS Genome Sequencing, Sequences Annotation
17, 18 PY Discussion Sections Week of Sept 16
23 DS Functional Genomics I (array technologies and uses)
25 DS Functional Genomics II (proteomics)
24, 25 PY Discussion Sections Week of Sep 23
30 MS Functional Genomics III
Oct 01 DS Structural Genomics
31, 01 PY Discussion Sections Week of Sep 30
07 MS Functional Genomics IV
09 MS Functional Genomics V
9,10 JS Discussion Sections Week of Oct 8
14 DS Genomic Tools in Plant Breeding (Antoni Rafalski, DuPont)
16 MG Analysis of Sequences I(Dynamic Programming)
16, 17 JP Discussion Sections Week of Oct 14


(Covering lectures through October 14)
23 MG Analysis of Sequences II (Substitution Matrix)
29, 30 YU Discussion Sections Week of Oct 28
28 MG Analysis of Sequences III (HMM)
30 MG Analysis of Sequences IV (P-value and EVD)
5, 6 YU Discussion Sections Week of Nov 4
  • 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
Nov 04 MG Analysis of Sequences V (Secondary Structure)
06 MG Analysis of Sequences VI (Secondary Structure)
12, 13 YU Discussion Sections Week of Nov 11
11 MG Structure
Quiz 1: covering up to and including Nov. 04
13 MG Database
19, 20 YU Discussion Sections Week of Nov 18
18 MG Survey
20 MG Datamining
3, 4 YU Discussion Sections Week of Dec 2
Dec 02 MG Simulation
04 MG Simulation II
Quiz 2: covering up to and including Dec 02.

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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