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.
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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
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courtesy Dr. M. Singh, Princeton University |
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3. | Aug. 31 |
Global and semi-global pairwise sequence alignment
Lecture outline Alignment examples PS0 due. |
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4. | Sept. 2 |
Local alignment. Lecture outline Alignment examples |
courtesy Dr. M. Singh, Princeton University |
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5. | Sept. 7 |
Affine gap functions Lecture outline PS1, (due Sept. 16). Alignment template |
Affine gap functions:
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6. | Sept. 9 | Global Multiple Sequence Alignment
Lecture
notes |
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7. | Sept. 14 | Global MSA continued Lecture notes |
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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 13-16. |
9. | Sept. 21 | Evolutionary trees - parsimony
methods Lecture
notes 711/856 only: Literature assignment 1
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10. | Sept. 23 | Evolutionary trees - distance
methods Lecture
notes |
Distance-based methods
courtesy Dr. M. Singh, Princeton University |
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11. | Sept. 28 |
Distance-based phylogeny
reconstruction. UPGMA Lecture notes Literature assignment 1 due. PS2 (due Oct. 5th). |
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12. | Sept. 30 |
Distance-based phylogeny
reconstruction. Neighbor Joining Lecture notes | Felsenstein*, Ch. 11 UPGMA and NJ, pp. 161-169 |
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13. | Oct. 5 |
Distance-based phylogeny
reconstruction: optimization criteria,
Lecture notes Intro to Markov chains, notation |
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Felsenstein*,
Ch. 11
Statistical interpretations of distance matrix methods, pp. 151-155 Bryant & Waddell Rapid Evaluation of Least-Squares ... Phylogenetic Trees, MBE, 98. |
14. | Oct. 7 |
Models of sequence substitution, Jukes Cantor model. Lecture outline Jukes Cantor R program |
Distance-based methods
courtesy Dr. M. Singh, Princeton University |
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15. | Oct. 12 | Maximum likelihood estimation; |
Phylogeny
Estimation and Hypothesis Testing using Maximum
Likelihood., pp. 1-8 J. P. Huelsenbeck and K. A. Crandall, Ann. Rev. Ecol. Syst. 1997, 28:437-66 |
Complexity results:
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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. |
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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 |
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20. | Oct. 28 |
Local MSA, discovery Lecture notes |
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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. |
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Hidden Markov Models in Computational
Biology: Applications to Protein Modeling, Krogh et al., JMB 235, pp 1501--1531,(1994). Available through electronic reserves. |
23. | Nov. 9 |
Hidden Markov Models II Forward & Backward algorithms, posterior decoding. Lecture notes PS3 (due Nov. 18th). |
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24. | Nov. 11 |
Hidden Markov Models III Discovery: Parameter estimation, topology. |
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25. | Nov. 16 |
Hidden Markov Models IV Profile HMMs Lecture notes |
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26. | Nov. 18 |
Substitution Matrices PAM matrices Lecture notes PAM250, PAM30 PS3 due. |
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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 |
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Nov. 25 |
No class (Thanksgiving Holiday) |
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28. | Nov. 30 |
BLAST, the heuristic. Statistics of local, ungapped alignments. Lecture notes |
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29. | Dec. 2 | Gapped BLAST Lecture notes PS4 due in class. |
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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 |