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.




 
1.  Aug. 30 
Introduction to computational biology and genomics
PS0 (due Sept. 6). 
Review biology and algorithms background  
2.  Sep. 1 
Global pairwise sequence alignment

courtesy Dr. M. Singh, Princeton University 


3.  Sep. 6 
Semiglobal pairwise sequence alignment
PS0 due 



4.  Sep. 8 
Local pairwise alignment PW alignment examples PS1 due Sept. 20. 
courtesy Dr. M. Singh, Princeton University 

5.  Sep. 13  Global Multiple Sequence Alignment 



6.  Sep. 15 
Intro to Markov
chains,
notation 


7.  Sep. 20 
Local multiple alignment
lecture notes
PS1 due 711/856 only: Literature assignment 1, Due Sept 27. Hawkins et al., 2010. 

8.  Sep. 22 
Position Specific Scoring Matrices (PSSMs),
lecture notes A PSSM for the WEIRD motif A PSSM with pseudocounts 

9.  Sep. 27 
Local MSA, discovery. Literature assignment 1 due. 



10.  Sep. 29 
Intro to Hidden Markov Models
lecture notes PS2a (due Oct. 6). 

11.  Oct. 4 
Hidden Markov Models lecture notes Viterbi algorithm exercise Viterbi algorithm example 

Hidden Markov Models in Computational
Biology: Applications to Protein
Modeling, Krogh et al., JMB 235, pp 15011531,(1994). Available through  electronic reserves. 

12.  Oct. 6 
Science2011
(map)
NO CLASS. PS2a due PS2b (due Oct. 13). 711/856 only: Literature assignment 2, Due Oct. 14 Edgar, 2009 


13.  Oct. 11 
Hidden Markov Models Viterbi and Forward algorithms lecture notes Today's examples 

14.  Oct. 13 
Hidden Markov Models PS2b due Lit assignment 2 due Friday the 14th. 

15.  Oct. 18 
Hidden Markov Models 

16.  Oct. 20 
Midterm
Exam This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. 

17.  Oct. 25 
Profile HMMs,
lecture notes 


18.  Oct. 27 
Substitution Matrices PAM matrices Lecture notes PAM250, PAM30 


19.  Nov. 1 
Substitution Matrices BLOSUM matrices 


20.  Nov. 3 
BLAST,
Lecture
notes 711/856 only: Literature assignment 3, Due Nov. 15 


21.  Nov. 8 
Blast, gapped and ungapped. Lecture notes BLAST home page Two recommended tutorials for students unfamiliar with BLAST 



22.  Nov. 10 
Blast statistics, information content. Lecture notes PS3a (due Nov 22). 

23.  Nov. 15 
Introduction to trees. Lecture notes Lit Assignment 3 due. 
Navigating
tree space
pp. 3744


24.  Nov. 17 
Trees: Maximum parsimony Lecture notes 
Dr. M. Singh, Princeton University 
Sankoff's algorithm for inferring ancestral sequences; in Inferring Phylogenies, J. Felsenstein, Sinauer, pp 1316.  
25.  Nov. 22 
No class
PS3a due in MI464 before 5pm or electronically: compbio@cs.cmu.edu. PS3b (due Dec. 3). 

Nov. 24  No class (Thanksgiving Holiday)  
26.  Nov. 29 
Trees: Distancebased methods. Jukes Cantor model. Lecture outline 
Distancebased methods
courtesy Dr. M. Singh, Princeton University 

27.  Dec. 1 
Trees: Additive and ultrametric distances:
Lecture notes PS4 (due Dec 9th). 711/856 only: Lit. assignment 4, Due Dec 9th 
Felsenstein^{*}, Ch. 11 UPGMA and NJ, pp. 161169  
28.  Dec. 6 
Trees: UPGMA and NJ:
Lecture notes UPGMA, NJ 

29.  Dec. 8 
Trees: Maximum likelihood
Lecture notes 

Tues. Dec. 20 
Final
Exam:
1pm  4pm, Location: PH 125C 
This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Study questions 