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CS 439 Computational Biology Course Web Site, Fall 1996
Professor: Steven Salzberg,
salzberg@cs.jhu.edu
Time: Tuesdays and Thursdays, 4:30-5:45 p.m.
Location: Shaffer Hall Room 304
This course is co-listed in the Medical School, Department of
Biomedical Information Sciences, as ME 600.802.
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Textbook: Introduction to Computational Biology: Maps, Sequences,
and Genomes by
Michael Waterman.
Publisher: Chapman & Hall.
Publication date: June 1995. 430 pages. ISBN 0-412-99391-0.
Homework assignments
Syllabus
Week 0, Sept. 5. First day of class. Introduction to the
course and text. Overview of computational biology.
Week 1, Sept. 10 and 12. Introduction, biological background.
Topic: Molecular biology for non-biologists. Restriction mapping
and interval graphs.
Reading:
Week 2, Sept. 17 and 19.
Mapping probes and clones. Sequence-tagged site mapping and why it is
computationally ``hard.'' Simulated annealing applied to contig
assembly. Mapping by fingerprinting.
Reading:
- Waterman, Chapter 2 and pages 101-118 of Chapter 6 (section
6.1.4 is optional).
- F. Alizadeh, R. Karp, D. Weisser, and G. Zweig (1995). Physical
mapping of chromosomes using
unique probes, J. Computational Biology 2:2, 159-184.
- Waterman, Sections 4.4.1 and 6.4. (The Alizadeh et al. article
is a more thorough treatment of the material in 6.4.)
- (Optional) S. Kirkpatrick, C. Gelatt, and M. Vecchi. Optimization by
Simulated Annealing. Science 220:4598, May 13, 1983, 671-680.
Week 3, Sept. 24 and 27. No class on Thursday, Sept 26. Instead,
there is a special seminar on Friday.
SPECIAL SEMINAR on Friday, Sept. 27, the first in our
Computational Biology Seminar Series. David
Searls of SmithKline Beecham Pharmaceuticals and the
University of Pennsylvania will speak on "The Linguistics of DNA."
The lecture is at 4:30pm in Shaffer Hall room 3.
Week 4, Oct. 1 and 3.
Sequence alignment, part 1: global distance alignment, global
similarity alignment, and local alignment.
Reading:
- Waterman, Chapter 9, Sections 9.3 through 9.8.
- Temple Smith and Mike Waterman (1981). Identification of
Common Molecular Subsequences. J. Mol. Biol. 147, 195-197.
Week 5, Oct. 8 and 10.
Large-scale shotgun assembly (guest lecture by Prof. Art Delcher).
Sequence alignment, part 2: heuristic alignment methods including BLAST.
Reading:
- S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman (1990).
Basic Local Alignment Search Tool. J. Mol. Biology, 215, 403-410.
Some documentation for
BLAST
is available on-line.
- Waterman, Chapter 8.
- (Optional) A survey of sequence
comparison algorithms (350K) is available from Gene Myers' home page;
I've put a copy here for faster downloading.
Week 6, Oct. 15 and 17.
Thursday: guest lecture by Dr. Granger Sutton
of The Institute for Genomic Research on
whole-genome sequence assembly.
Tuesday: Sequencing by hybridization.
Reading:
- Granger Sutton, Owen White, Mark Adams, and Anthony Kerlavage.
TIGR Assembler: A New Tool for Assembling Large Shotgun Sequencing
Projects. Genomics 1:1 (1995), 9-19. An on-line version
of this paper is available here,
courtesy of Granger Sutton.
- Waterman, Section 7.2 of Chapter 7.
- (Optional) Ramana Idury and Michael Waterman (1995).
A New Algorithm for DNA
Sequence Assembly (320K) J. of Computational Biology,
Vol. 2, 291-306.
Week 7, Oct. 23 and 24. This week we have two special
seminars. There will be no class on Tuesday, Oct. 22. Instead, we
have a special seminar on Wednesday, Oct. 23. We also have a special
seminar on Thursday, Oct. 24.
SPECIAL SEMINAR on Wednesday, Oct. 23, the second in our
Computational Biology Seminar Series. Temple Smith of
Boston University will speak on "A Review of the Threading Approach
to Inverse Protein Structure Prediction." The lecture is at 4:30pm
in Shaffer Hall room 303.
SPECIAL SEMINAR on Thursday, Oct. 24, the third in our
Computational Biology Seminar Series. Alejandro Schaffer of
the National Center for Biotechnology Information at the National
Institutes of Health will speak on "Parallel Genetic Linkage
Analysis." The lecture is at 4:30pm in Shaffer Hall Room 3.
Week 8, Oct. 29 and 31.
Algorithms for constructing amino acid substitution matrices.
Introduction to Hidden Markov Models for sequence analysis.
Reading:
- D. Jones, W. Taylor, and J. Thornton (1992). The rapid generation
of mutation
data matrices from protein sequences. Computer Applications in the
Biosciences (CABIOS) 8:3, 275-282.
- Waterman, Chapter 10, especially section 10.5
- Kai-Fu Lee, Automatic Speech Recognition: The Development of the
SPHINX System, Chapter 1 (on HMMs). Copies of this chapter will be
made available in class.
- (optional) Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjolander, and
David Haussler (1993). Hidden Markov Models
in Computational Biology: Applications to Protein Modeling (344K).
The figures are available in a separate file, which you get by
clicking here (1,009K).
This is technical report UCSC-CRL-93-32, UC
Santa Cruz, Dept. of Computer and Information Sciences. A shorter
version appeared in J. Mol. Biology, 1993.
Week 9, Nov. 5 and 7.
Genetic sequence and map databases
and the Human Genome Project. This topic will be presented
in a set of guest lectures by Prof. Stan Letovsky of the Division of
Biomedical Information Sciences.
SPECIAL SEMINAR on Thursday, Nov. 7, the fourth in our
Computational Biology Seminar Series. Christian Overton of the
University of Pennsylvania will speak on "High-Throughput Annotation
of Genomic Sequences." The lecture is at 4:30pm in Shaffer Hall Room 3.
Reading:
- D.A. Benson, M. Boguski, D.J. Lipman, and
J. Ostell (1994). GenBank. Nucleic Acids Research 22(17): 3441-3444.
- (Optional) Kenneth Fasman, A.J. Cuticchia, and David Kingsbury (1994).
The GDB Human Genome Data Base anno 1994. Nucleic Acids Research
22(17): 3462-3469.
- (Optional) Kenneth Fasman, Stanley Letovsky, Robert Cottingham,
and David Kingsbury (1995).
Improvements
to the GDB Human Genome Data Base. (This is a preprint of a 1995
Nucleic Acids Research article about GDB.)
Week 10, Nov. 12 and 14.
The Genome Data Base. (Continuation of Prof. Letovsky's lectures.)
SPECIAL SEMINAR on Thursday, Nov. 14, the fifth in our
Computational Biology Seminar Series.
Eugene Myers of the
University of Arizona will speak on "Approaches to Whole Genome
DNA Sequencing." The lecture is at 4:30pm in Shaffer Hall room 3.
Week 11, Nov. 19 and 21.
On November 19 class will be replaced by a seminar in the Center for
Language and Speech Processing. The seminar is at 4:30pm in Shaffer
Hall room 100, by Prof. Alan Biermann of Duke University. The topic
is "Goal-Oriented Multimedia Dialogue with Variable Initiative."
Nov 21: Final lecture by Prof. Letovsky, on computational models
of morphogenesis.
Reading (for next week):
Week 12, Nov. 26.
Guest lecture by Dr. Owen White
of The Institute for Genomic Research
on comparative genomics.
Reading:
- Sections 14.1 and 14.2 of Waterman.
Week 13, Dec. 3 and 5.
Biological background on the structure of genes: exons, introns, and
inter-genic DNA. Description of the gene finding problem. Computer
systems for gene finding. Time permitting: DNA computing;
molecular evolution.
Reading:
- Leonard Adleman (1994).
Molecular Computation of Solutions to Combinatorial Problems.
Science, 266, November 11, 1994, 1021-1024.
- A Thousand Billion Billion Sums,
reprinted from The Economist, article about Adleman's experiment.
- (optional) Rajgopal Srinivasan and George Rose (1995).
LINUS: A Hierarchic Procedure to
Predict the Fold of a Protein. PROTEINS: Structure, Function,
and Genetics 22, 81-99.
- (Optional)
The Mathematical Basis of Molecular Phylogenetics, Chapter 4 of
the BioComputing Hypertext Coursebook by Andreas Dress.
(This is optional, but you should take a look at least to see what this
on-line textbook contains.)
Assignments and grading
The grade will be based on problem sets, programming assignments, and
either a final exam or final project. There are a total of six assigments which count for a total of 70%
of the grade. The final exam accounts for the remaining 30%. With
approval of the instructor, a final project may take the place of the
final exam.
Useful resources for the course
Last year's (1995) syllabus
Home Page for Computational Biology at Hopkins
Home Page for Computer Science at Hopkins