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Lectures
1. Course outline
Course Outline.pdf
2. Introduction to
biology
Lecture1_1.MolecularBasisLife.pdf
Quiz 1.pdf
Lecture1_2.IntroGenomicPeriod.pdf
Quiz 2.pdf
3. Biomolecules as
strings
Lecture2_KnuthMorrisPratt.pdf
Quiz 3.pdf
Lecture3_IntroductionToSuffixTree.pdf
Quiz 4.pdf
Lecture4_ApplicationsSuffixTree.pdf
Quiz 5.pdf
Lecture5 Dynamicprogramming.pdf
CheapestPath.xls Quiz
6.pdf Quiz 7.pdf
Lecture6_More
Edit Distance.pdf Quiz 8.pdf
Lecture
7_String similarity and alignments.pdf
Lecture
8_Alignment heuristics.pdf Quiz 9.pdf
Lecture
9_Biological applications of stringalgorithms.pdf
4. Gene finding
Lecture10_Markov
Models.pdf Quiz 10.pdf Quiz
11.pdf Quiz 12.pdf
Lecture11_Gene
finding.pdf
5. Phylogenies
Lecture12_Algorithms
for multiple sequence alignment.pdf Quiz 13.pdf
Lecture13_Parsimony
and perfect phylogeny.pdf Quiz 14.pdf
Lecture15_Distance-based
phylogenies.pdf Quiz 15.pdf
Lecture16_Character-based
phylogeny.pdf
LastLecture.pdf
Assignments
Assignment 1.pdf
Assignment 2.pdf
Assignment 3.pdf
Midterms
Midterm 1
Midterm 2
Selected student projects
Khushwinder Sekhon. Faster
Algorithms for Finding Tandem repeats. Report.
Zahra
Sasanian. Genetic
algorithms. Slides. Report.
Jared
Gaertner. Diagnosing
cancer using gene signatures. Report.
Tyler
Cadigan, Ann Chou.
How encephalitis came to North America (Hierarchical clustering). Slides. Report.
Tom
Spreen, Andre Van Slyke.
Exact set matching with Aho-Corasick automaton. Slides. Report.
Steven
Lonergan. Fixed
parameter tractable algorithms for perfect phylogeny. Report.
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