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. 25 
Introduction to computational biology and genomics
PS0 (due Sept. 1). 

2.  Aug. 27 
Global pairwise sequence alignment
Lecture outline Alignment examples 
courtesy Dr. M. Singh, Princeton University  
3.  Sept. 1 
Global and semiglobal pairwise sequence alignment
Lecture outline Alignment examples 
 
4.  Sept. 3 
Local alignment.
Lecture outline Alignment examples 
courtesy Dr. M. Singh, Princeton University 

5.  Sept. 8 
Global multiple sequence alignment
711/856 only: Literature assignment 1 Due Sept. 15 


6.  Sept. 10 
Global
multiple sequence alignment continued PS1, (due Sept. 17). 
 
7.  Sept. 15 
Phylogenetic Trees, Parsimony methods
Literature assignment 1 due. 
Dr. M. Singh, Princeton University 
Parsimony, nice examples 
8.  Sept. 17 
PS1 due.
Evolutionary trees: Lecture notes Branch and bound search, rooting a tree. 


9.  Sept. 22 
Distancebased methods JukesCantor model; correcting for multiple substitutions. Lecture outline 
Distancebased methods
courtesy Dr. M. Singh, Princeton University  
10.  Sept. 24 
Class is canceled
PS2, (due October 6th). 711/856 only: Literature assignment 2  
11.  Sept. 29  Distancebased phylogeny reconstruction. Lecture outline  
12.  Oct. 1 
Distancebased methods Minimum evolution, UPGMA and Neighbor Joining Lecture outline Literature assignment 2 due. 
 
13.  Oct. 6 
PS2 due.
Maximum likelihood estimation; 
Phylogeny
Estimation and Hypothesis Testing using Maximum
Likelihood., pp. 18 J. P. Huelsenbeck and K. A. Crandall, Ann. Rev. Ecol. Syst. 1997, 28:43766 
Complexity results:

14.  Oct. 8  Introduction to local MSA  
15.  Oct. 13 
Position Specific Scoring Matrices A PSSM for the WEIRD motif A PSSM with pseudocounts Gibbs Sampler. Lecture notes forthcoming. Office hours will be held Wednesday from 2pm  5pm in MI646. No office hours on Thursday. 


16.  Oct. 15 
Midterm
Exam This exam is closed book. You may bring two pages (or one page, front and back) of your own notes.  
17.  Oct. 20  Gibbs Sampler, Lecture notes  
18.  Oct. 22  Introduction to Hidden Markov Models
Lecture notes
711/856 only: Literature assignment 3  
19.  Oct. 27  Hidden Markov Models II Viterbi, Forward, Backward algorithms Lecture notes Viterbi algorithm example Forward algorithm example 

Hidden Markov Models in Computational
Biology: Applications to Protein Modeling, Krogh et al., JMB 235, pp 15011531,(1994). Available through electronic reserves. 
20.  Oct. 29 
Hidden Markov Models II Forward & Backward algorithms, posterior decoding. Lecture notes 


21.  Nov. 3  Literature assignment 3 due.  
22.  Nov. 5 
Parameter estimation, BaumWelsh algorithm
Lecture notes 


23.  Nov. 10 
HMM topology design, multiple alignment using HMMs.
Lecture notes PS3 (due Nov. 19). 


24.  Nov. 12 
Substitution Matrices PAM matrices Lecture notes 


25.  Nov. 17 
Substitution Matrices BLOSUM matrices; Lecture notes BLOSUM62 
 
26.  Nov. 19 
BLAST, the heuristic. Statistics of local, ungapped alignments. Lecture notes PS3 due. BLAST home page BLAST Tutorial page Recommended for students unfamiliar with BLAST 


27.  Nov. 24 
No class. PS4 (due Dec. 3). PAM250, PAM30 711/856 only: Literature assignment 4 (due Dec. 4).  
Nov. 26 
No class (Thanksgiving Holiday) 

28.  Dec. 1  Blast statistics; Information content of alignments. Lecture notes 
T. D. Schneider C. Adami  
29.  Dec. 3 
Gapped BLAST
PS4 due in class.  Gapped BLAST and PSIBLAST: a new generation of protein database search programs, Altschul et al., Nucleic Acids Research, 1997, pp. 3389  3394 (electronic reserve)  
Dec. 7 
Final
Exam:
1pm  4pm, WEH 5403 This exam is closed book. You may bring two pages (or one page, front and back) of your own notes.  Study questions 