Computational Molecular Biology and Genomics Syllabus and Reading Assignments

Computational Molecular Biology and Genomics Syllabus - Fall 2016

The materials in the "Assigned Reading" column are directly related to the topics covered in class. Readings under "Additional Topics" are strictly optional and will not be covered on the exams.
In some cases, the same material is covered in more than one textbook. You have the choice of selecting the text that presents a treatment of the material most to your liking. It is your responsibility to make sure that you understand the material covered in class and you may read as many or as few of these texts needed to achieve that goal.

CLASS	DATE	TOPICS	ASSIGNED READING	ADDITIONAL TOPICS
1.	Aug. 30	Introduction to computational biology and genomics part 1 , part 2 PS0 due September 6th.	Review biology and algorithms background
2.	Sep. 1	Global pairwise sequence alignment PAIRWISE ALIGNMENT NOTES Alignment example - distance scoring.	Global pairwise alignment - Global sequence alignment notes, courtesy Dr. M. Singh, Princeton University - Setubal and Meidanis 47-55, 89-92, 96-98; (electronic reserve) - Durbin, pp. 17-22, (electronic reserves)
3.	Sep. 6	Global and semiglobal alignment Alignment example - similarity scoring. PS0 DUE	Semi-global alignment: - Setubal and Meidanis, 56-57 (electronic reserve)	Saving space: Setubal and Meidanis, 58-60; (physical reserve) General gap penalty functions: Setubal and Meidanis, 60-64 (physical reserve)
4.	Sep. 8	Semiglobal and local pairwise alignment local alignment examples	Local sequence alignment notes, courtesy Dr. M. Singh, Princeton University Setubal and Meidanis, p. 55 (electronic reserve) Durbin, pp. 23-24 (electronic reserves)
5.	Sep. 13	Local sequence alignment local alignment examples Global multiple sequence alignment GLOBAL MSA NOTES	Global multiple alignment using dynamic programming - Setubal and Meidanis, 69-72 (electronic reserve) - MSA Notes: I courtesy Dr. M. Singh, Princeton University - Durbin, 6.1 -- 6.3 (electronic reserve)	Protein multiple sequence alignment , Do and Katoh, 2008.
6.	Sep. 15	The progressive multiple alignment heuristic PS1 due Friday, Sept 23rd	Global MSA with the progressive alignment heuristic - MSA Notes: II, courtesy Dr. M. Singh, Princeton University - Durbin, 6.4 (electronic reserve)
7.	Sep. 20	Introduction to Markov chains MARKOV CHAIN NOTES	Markov Chain background - Ewens and Grant, 4.4-4.8 - Durbin et al., 48-51 (Section 3.1) (electronic reserves)
8.	Sep. 22	Markov chains, continued. PS1 due tomorrow (9/23) at 4pm Lit assignment 1: Due Sep 29
9.	Sep. 27	Markov models of sequence evolution, Jukes-Cantor model SEQUENCE EVOLUTION MODEL NOTES	Durbin, et al: 8.2, pp. 193 - 197 only (electronic reserves)
10.	Sep. 29	Markov models of DNA sequence evolution, cont'd. Lit1 due at 4pm PS2 due Oct 7th
11.	Oct. 4	Markov models of amino acid replacement PAM MATRIX LECTURE NOTES	Substitution matrices: Setubal and Meidanis, pp. 80-84; (electronic reserve) Mount, pp. 76-89; (electronic reserve) Durbin et al, pp. 14-16 (electronic reserves)
12.	Oct. 6	Markov models of amino acid replacement BLOSUM MATRIX LECTURE NOTES PS2 due tomorrow (Oct 7th) at 4pm	BLOSUM Matrices: Ewens and Grant, 6.5.2. Amino acid substitution matrices from protein blocks, Henikoff S, Henikoff JG., PNAS 89(22):10915-9, 1992 (electronic reserve)
13.	Oct. 11	Amino acid substitution matrices, continued. Comparing PAM and Blosum matrices. PAM30, BLOSUM62, PAM250, BLOSUM45
14.	Oct. 13	In-class exam I This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Study guide
15.	Oct. 18	Database searching BLAST HEURISTIC NOTES Midterm scores	Blast 1990 Setubal and Meidanis, 84-87 (electronic reserve) Basic local alignment search tool, Altschul et al., J. Mol. Bio., 1990 (electronic reserve) Strategies for searching sequence databases,Nicholas HB Jr, Ropelewski AJ, Deerfield DW 2nd, Biotechniques 2002 Jun;28(6):1174-8 (electronic reserve) Blast statistics and data base searching: The statistics of sequence similarity scoresS. F. Altschul
16.	Oct. 20	Blast heuristic continued. PS3 due Friday, Oct 28	Gapped BLAST : a new generation of protein database search programs. Altschul et al., Nucl. Acids Res. (1997) 25 (17). Assigned reading: pp. 3389-3394 only.
17.	Oct. 25	BLAST STATISTICS LECTURE NOTES	Blast statistics: Amino acid substitution matrices from an information theoretic perspective, S. F. Altschul, J. Mol. Bio., 219:555-565, 1991 (electronic reserve). A protein alignment scoring system sensitive at all evolutionary distances, S. F. Altschul, J. Mol. Evol., 36:290-300, 1993 (electronic reserve).
18.	Oct. 27	Blast statistics and information content, continued. PS3 due tomorrow. PS4 due Friday, Nov 4 Lit assignment 2: Due Nov 3rd, 4pm.
19.	Nov. 1	Local multiple alignment, PSSM's, the Gibbs sampler PSSM/GIBBS SAMPLER NOTES PSSM example, with and without pseudocounts	Gibbs sampler Ewens and Grant, pp. 211-215. (electronic reserve).	Theoretical framework, convergence proofs Ewens and Grant, 10.5.2, Physical reserves. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment, Lawrence et al., Science. 1993 262(5131):208-14. Explaining the Gibbs sampler, G. Casella & E. I. George, The American Statistician, 46:167-174, 1992
20.	Nov. 3	The Gibbs Sampler
21.	Nov. 8	The Gibbs Sampler
22.	Nov. 10	In-class exam II This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Study guide Exam II scores
23.	Nov. 15	Hidden Markov Models HMM LECTURE NOTES - Part 1 PS5 due Tuesday, Nov 22	What is an HMM? Ewens and Grant, pp. 327-329 (electronic reserve). Durbin, pp. 53-55 (electronic reserve).	Hidden Markov Models in Computational Biology: Applications to Protein Modeling, Krogh et al., JMB 235, pp 1501--1531,(1994). (electronic reserve).
24.	Nov. 17	HMMs cont'd. The Forward and Viterbi algorithms Forward example	Viterbi, Forward, Backward algorithms Durbin, pp. 55 - 61 (electronic reserve). Ewens and Grant, pp. 329-332 (electronic reserve).
25.	Nov. 22	No class. PS5 due at 4pm Lit assignment 3: due Nov 29th
	Nov. 24	Thanksgiving Holiday: No class
26.	Nov. 29	Hidden Markov Models: Decoding Viterbi example PS6 due Monday, Dec 5
27.	Dec. 1	HMMs: Modeling, parameter estimation HMM LECTURE NOTES - Part 2	HMM Topology Durbin, pp. 68-71 (electronic reserve). Parameter estimation, Baum-Welch algorithm Durbin, pp. 61-71 (electronic reserve). Ewens and Grant, pp. 329-332 (electronic reserve).
28.	Dec. 6	Profile HMM's. Optional PS7 due Monday, Dec 5 due Tuesday, 13th at 1pm if you are submitting PS 7 for credit.	Profile HMMs Durbin, pp. 100-110 (electronic reserve).
29.	Dec. 8	Profile HMMs	Multiple alignment using HMMs Ewens and Grant, pp. 335 - 337 (electronic reserve).
Review	Dec 14, 12:00 - 2:00	Porter Hall A19A Question/Answer session. Bring your questions with you.
Final Exam	Dec 15, 5:30pm - 8:30pm	Final exam This exam is closed book. You may bring two pages (or one page, front and back) of your own notes.	Study guide The exam covers the entire semester, but with a strong emphasis on the last third of the course.

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Last modified Jan 30, 2017.
Maintained by Dannie Durand (durand@cs.cmu.edu).