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. 24 
Introduction to computational biology and genomics
Introduction to computational biology and genomics
PS0 (due Aug. 31). 
Review biology and algorithms background  
2.  Aug. 26 
Global pairwise sequence alignment

courtesy Dr. M. Singh, Princeton University 

3.  Aug. 31 
Global and semiglobal pairwise sequence alignment
Lecture outline Alignment examples PS0 due. 


4.  Sept. 2 
Local alignment. Lecture outline Alignment examples 
courtesy Dr. M. Singh, Princeton University 

5.  Sept. 7 
Affine gap functions Lecture outline PS1, (due Sept. 16). Alignment template 
Affine gap functions:


6.  Sept. 9  Global Multiple Sequence Alignment
Lecture
notes 


7.  Sept. 14  Global MSA continued Lecture notes 


8.  Sept. 16  Evolutionary trees Lecture notes PS1 due. 
Dr. M. Singh, Princeton University 
Sankoff's algorithm for inferring ancestral sequences; in Inferring Phylogenies, J. Felsenstein, Sinauer, pp 1316. 
9.  Sept. 21  Evolutionary trees  parsimony
methods Lecture
notes 711/856 only: Literature assignment 1  
10.  Sept. 23  Evolutionary trees  distance
methods Lecture
notes 
Distancebased methods
courtesy Dr. M. Singh, Princeton University 

11.  Sept. 28 
Distancebased phylogeny
reconstruction. UPGMA Lecture notes Literature assignment 1 due. PS2 (due Oct. 5th). 

12.  Sept. 30 
Distancebased phylogeny
reconstruction. Neighbor Joining Lecture notes  Felsenstein^{*}, Ch. 11 UPGMA and NJ, pp. 161169 

13.  Oct. 5 
Distancebased phylogeny
reconstruction: optimization criteria,
Lecture notes Intro to Markov chains, notation 

Felsenstein^{*},
Ch. 11
Statistical interpretations of distance matrix methods, pp. 151155 Bryant & Waddell Rapid Evaluation of LeastSquares ... Phylogenetic Trees, MBE, 98. 
14.  Oct. 7 
Models of sequence substitution, Jukes Cantor model. Lecture outline Jukes Cantor R program 
Distancebased methods
courtesy Dr. M. Singh, Princeton University 

15.  Oct. 12  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:

16.  Oct. 14 
Midterm
Exam This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. 

17.  Oct. 19  Class is cancelled.  
18.  Oct. 21  Phylogeny reconstruction summary Lecture notes  
19.  Oct. 26 
Introduction to local MSA
Position Specific Scoring Matrices A PSSM for the WEIRD motif A PSSM with pseudocounts 711/856 only: Literature assignment 2 

20.  Oct. 28 
Local MSA, discovery Lecture notes 


21.  Nov. 2  Introduction to Hidden Markov Models Lecture notes  
22.  Nov. 4 
Hidden Markov Models II The Viterbi algorithm Lecture notes Viterbi algorithm example Forward algorithm example Literature assignment 2 due. 

Hidden Markov Models in Computational
Biology: Applications to Protein Modeling, Krogh et al., JMB 235, pp 15011531,(1994). Available through electronic reserves. 
23.  Nov. 9 
Hidden Markov Models II Forward & Backward algorithms, posterior decoding. Lecture notes PS3 (due Nov. 18th). 

24.  Nov. 11 
Hidden Markov Models III Discovery: Parameter estimation, topology. 
 
25.  Nov. 16 
Hidden Markov Models IV Profile HMMs Lecture notes 


26.  Nov. 18 
Substitution Matrices PAM matrices Lecture notes PAM250, PAM30 PS3 due. 


27.  Nov. 23 
Substitution Matrices BLOSUM matrices Lecture notes PS4 (due Dec. 2). BLOSUM45, BLOSUM62, BLOSUM80, BLAST home page BLAST Tutorial page Recommended for students unfamiliar with BLAST 


Nov. 25 
No class (Thanksgiving Holiday) 

28.  Nov. 30 
BLAST, the heuristic. Statistics of local, ungapped alignments. Lecture notes 


29.  Dec. 2  Gapped BLAST Lecture notes PS4 due in class. 

Dec. 7 
Final
Exam:
1pm  4pm, Location DH1112 
This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Study questions 