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18.417

Introduction to Computational Molecular Biology

3-0-9 units · Graduate

Introduction to computational molecular biology with a focus on the basic computational algorithms used to solve problems in practice. Covers classical techniques in the field for solving problems such as genome sequencing, assembly, and search; detecting genome rearrangements; constructing evolutionary trees; analyzing mass spectrometry data; connecting gene expression to cellular function; and machine learning for drug discovery. Prior knowledge of biology is not required. Particular emphasis on problem solving, collaborative learning, theoretical analysis, and practical implementation of algorithms. Students taking graduate version complete additional and more complex assignments.

Fall 2004

Topics

  • The Central Dogma: Some Algorithms Introduction
  • Partial Digest Problem
  • Motifs and Median Strings
  • Global Alignment
  • Local Alignment
  • Spliced Alignment
  • More Efficient Alignment
  • Genomics and SBH Graphs
  • Peptide Graphs
  • Exact Pattern Matching
  • Suffix Trees
  • Suffix Arrays and BWTs
  • BLAST
  • Clustering (Guest Lecturer)
  • Trees
  • Review of Phylogenetic Analysis
  • Application: Microarrays (Guest Lecturer)
  • Hidden Markov Models I
  • Hidden Markov Models II
  • Gibbs Sampling
  • Random Projections
  • MCMC and Bayesian Networks
  • The Future: Protein Structure (Guest Lecturer)
  • The Future: Haplotype Mapping (Guest Lecturer)
  • Presentations of Final Projects
  • Presentations of Final Projects (cont.)

Readings

  • Readings are from the textbook: Jones, Neil C., and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms (Computational Molecular Biology), Bradford Books. Cambridge, MA: MIT Press, August 1, 2004. ISBN: 0262101068.
    Listed reading
  • LEC #: 2 · TOPICS: Partial Digest Problem · READINGS: Chapter 4
    Reading assignment
  • LEC #: 3 · TOPICS: Motifs and Median Strings · READINGS: Chapter 4
    Reading assignment
  • LEC #: 4 · TOPICS: Global Alignment · READINGS: Chapter 6
    Reading assignment
  • LEC #: 5 · TOPICS: Local Alignment · READINGS: Chapter 6
    Reading assignment
  • LEC #: 6 · TOPICS: Spliced Alignment · READINGS: Chapter 6
    Reading assignment
  • LEC #: 7 · TOPICS: More Efficient Alignment · READINGS: Chapter 7
    Reading assignment
  • LEC #: 8 · TOPICS: Genomics and SBH Graphs · READINGS: Chapter 8
    Reading assignment
  • LEC #: 9 · TOPICS: Peptide Graphs · READINGS: Chapter 8
    Reading assignment
  • LEC #: 10 · TOPICS: Exact Pattern Matching · READINGS: Chapter 9
    Reading assignment
  • LEC #: 12 · TOPICS: Suffix Arrays and BWTs · READINGS: Chapter 9
    Reading assignment
  • LEC #: 13 · TOPICS: BLAST · READINGS: Chapter 9
    Reading assignment
  • LEC #: 14 · TOPICS: Clustering (Guest Lecturer) · READINGS: Chapter 10
    Reading assignment
  • LEC #: 15 · TOPICS: Trees · READINGS: Chapter 10
    Reading assignment
  • LEC #: 17 · TOPICS: Application: Microarrays (Guest Lecturer) · READINGS: Chapter 10
    Reading assignment
  • LEC #: 18 · TOPICS: Hidden Markov Models I · READINGS: Chapter 11
    Reading assignment
  • LEC #: 19 · TOPICS: Hidden Markov Models II · READINGS: Chapter 11
    Reading assignment
  • LEC #: 20 · TOPICS: Gibbs Sampling · READINGS: Chapter 12
    Reading assignment
  • LEC #: 21 · TOPICS: Random Projections · READINGS: Chapter 12
    Reading assignment
  • Setubal, Carlos, and Joao Meidanis. Introduction to Computational Molecular Biology. 1st ed. Boston, MA: PWS Publishing, January 16, 1997. ISBN: 0534952623.
    Recommended
  • Durbin, Richard, Sean R. Eddy, Anders Krogh, and Graeme Mitchison. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge, UK: Cambridge University Press, Reprint edition, July 1, 1999. ISBN: 0521629713.
    Recommended
  • Gusfield, Dan. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. 1st ed. Cambridge, UK: Cambridge University Press, January 15, 1997. ISBN: 0521585198.
    Recommended
  • Lodish, Harvey, David Baltimore, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, and James Darnell. Molecular Cell Biology. New York, NY: W. H. Freeman & Company, 3rd Package edition, March 1, 1995. ISBN: 0716736861.
    Recommended
  • Branden, Carl-Ivar, and John Tooze. Introduction to Protein Structure. 2nd ed. New York, NY: Garland Publishing, January 15, 1999. ISBN: 0815323050.
    Recommended
  • Clote, Peter, and Rolf Backofen. Computational Molecular Biology: Introduction. 1st ed. New York, NY: John Wiley & Sons, September 22, 2000. ISBN: 0471872520.
    Recommended
  • Jones, Neil C., and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms (Computational Molecular Biology), Bradford Books. Cambridge, MA: MIT Press, August 1, 2004. ISBN: 0262101068.
    Listed reading

Prerequisites & course information

Subject meets with 18.413 Prereq: 6.1210 or permission of instructor Acad Year 2027-2028: G (Spring) Acad Year 2028-2029: Not offered 3-0-9 units

Sources