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Lecture Contents CSI5126 Fall 2010

Chapter sections refer to the textbook by Sung (2009).

Tentative schedule (it will be updated as changes occur):
dates and tasks  Lecture Contents: textbook sections
and extra materials
Sep 10 Course overview/admin;
Intro to Molecular Biology
L01: Course handout;
Ch 1; 01Introduction.pdf
Sep 14, 17 Intro to Molecular Biology (cont'd)
Review Dynamic Programming; Sequence Similarity
L02: Ch1, 02MolecularBiologyII.pdf,
02_B_Turcotte L1 p42-175, Body Code (movie)/source
L03: Ch 2, 03-05SequenceSimilarity.pdf
Sep 21,24 Sequence Similarity Ch 2, 03-05SequenceSimilarity.pdf
Sep 28, Oct 1 Suffix Trees and variants Ch 3, 06Turcotte_lect02-2.pdf (p.1-14,21-62)
07-09Turcotte_lect03.pdf (p.1-23)
Oct 5 (A1 due),8(no class) Suffix trees & variants: applications
Ch 3, 07-09Turcotte_lect03.pdf (p.24-46)
Oct 12,15 Suffix trees and variants
Genome Alignment
Ch 3,07-09Turcotte_lect03.pdf (p.47-101), 09SuffixTreesAndVariants.pdf
Ch. 4, 10-11GenomeAlignment.pdf
Oct 19,22 (A2 due) Genome Alignment
Multiple alignment
Ch 4, 10-11GenomeAlignment.pdf
Ch 6, 12-13MultipleAlignment.pdf
Oct 24-30 Study break. -
Nov 2,5 Student Presentations (Nov 2: 11:30-2:30)
Multiple Alignment
Presence is compulsory to all talks.
Ch 6, 12-13MultipleAlignment.pdf
Nov 9,12 Phylogeny Reconstruction Ch 7, 14InferingPhylogeny_Turcotte.pdf
Nov 16,19 Phylogeny Reconstruction
Ch 7, 16-17PhylogenyReconstruction.pdf
Nov 23,26 Genome Rearrangement (lecturer: Ghada Badr) Ch 9, Guest lectures.
Nov 30 (A3 due), Dec 3 RNA secondary structure (lecturer: Marcel Turcotte)
Last lecture (topic to be decided).
Guest lecture.
Presence is compulsory to all guest lecture.
Dec 7 Project Presentations Presence is compulsory
to all talks.