Lecture notes archive
Algorithms in Molecular Biology
(Computational Genomics)
Instructor: Ron Shamir
Course Outline
This course discusses algorithms for some important computational problems in Molecular Biology. In particular, we shall study problems that are pertinent to the Human Genome Project and to the so-called "post-Genome era". We shall study exact algorithms for those problems which can be solved efficiently, as well as complexity, approximation algorithms and heuristics for the more difficult problems. We shall concentrate on discrete realistic models for the biological problems. Many biological examples will be presented.
This course discusses algorithms for some important computational problems in Molecular Biology. In particular, we shall study problems that are pertinent to the Human Genome Project and to the so-called "post-Genome era". We shall study exact algorithms for those problems which can be solved efficiently, as well as complexity, approximation algorithms and heuristics for the more difficult problems. We shall concentrate on discrete realistic models for the biological problems. Many biological examples will be presented.
Course Lecture Notes:
| Lecture | Date | Topic | Notes |
| 1 | 2002 | Introductory Concepts | |
| 2 | 2004 | Suffix Trees | |
| 3 | 2002 | Pairwise alignment | |
| 4 | 2002 | Sequence Alignment Heuristics | |
| 5 | 2002 | Multiple Sequence Alignment | |
| 5 | 2002 | Hidden Markov Models | |
| 6 | 2007 | RNA Secondary Structure | |
| 7 | 2002 | Bioinformatics Tools | |
| 8 | 2002 | Gene Finding | |
| 9 | 2002 | Phylogeny | |
| 10 | 2002 | Physical Mapping | |
| 11 | 2002 | Genome Rearrangements | |
| 12 | 2002 | DNA Chips and Gene Networks | |
| 13 | 2002 | Protein Structure | |
| 14 | 2002 | Linkage Analysis | |
| 15 | 2004 | Bayesian Networks | |
| 16 | 2010 | Stochastic Context Free Grammars | |
| 17 | 2011 | Algorithms for deep sequencing (Next Generation Sequencing) |
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