Introduction to Computational Molecular Biology
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.
- LEC #: 2 · TOPICS: Partial Digest Problem · READINGS: Chapter 4
- LEC #: 3 · TOPICS: Motifs and Median Strings · READINGS: Chapter 4
- LEC #: 4 · TOPICS: Global Alignment · READINGS: Chapter 6
- LEC #: 5 · TOPICS: Local Alignment · READINGS: Chapter 6
- LEC #: 6 · TOPICS: Spliced Alignment · READINGS: Chapter 6
- LEC #: 7 · TOPICS: More Efficient Alignment · READINGS: Chapter 7
- LEC #: 8 · TOPICS: Genomics and SBH Graphs · READINGS: Chapter 8
- LEC #: 9 · TOPICS: Peptide Graphs · READINGS: Chapter 8
- LEC #: 10 · TOPICS: Exact Pattern Matching · READINGS: Chapter 9
- LEC #: 12 · TOPICS: Suffix Arrays and BWTs · READINGS: Chapter 9
- LEC #: 13 · TOPICS: BLAST · READINGS: Chapter 9
- LEC #: 14 · TOPICS: Clustering (Guest Lecturer) · READINGS: Chapter 10
- LEC #: 15 · TOPICS: Trees · READINGS: Chapter 10
- LEC #: 17 · TOPICS: Application: Microarrays (Guest Lecturer) · READINGS: Chapter 10
- LEC #: 18 · TOPICS: Hidden Markov Models I · READINGS: Chapter 11
- LEC #: 19 · TOPICS: Hidden Markov Models II · READINGS: Chapter 11
- LEC #: 20 · TOPICS: Gibbs Sampling · READINGS: Chapter 12
- LEC #: 21 · TOPICS: Random Projections · READINGS: Chapter 12
- Setubal, Carlos, and Joao Meidanis. Introduction to Computational Molecular Biology. 1st ed. Boston, MA: PWS Publishing, January 16, 1997. ISBN: 0534952623.
- 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.
- 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.
- 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.
- Branden, Carl-Ivar, and John Tooze. Introduction to Protein Structure. 2nd ed. New York, NY: Garland Publishing, January 15, 1999. ISBN: 0815323050.
- Clote, Peter, and Rolf Backofen. Computational Molecular Biology: Introduction. 1st ed. New York, NY: John Wiley & Sons, September 22, 2000. ISBN: 0471872520.
- 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.
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
- Course catalogue ↗2026–2027
- MIT OpenCourseWare ↗Fall 2004
- MIT OCW calendar ↗
- MIT OCW readings ↗
- MIT OCW syllabus ↗
- Historical MIT OpenCourseWare offering. Named reading entries and schedule topics are automatically extracted from the linked source pages.