1 |
Jan-21 |
Introduction; DNA sequencing |
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2 |
Jan-26 |
Global sequence alignment;
Needleman-Wunsch |
3 |
Jan-28 |
Local sequence alignment;
Smith-Waterman |
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4 |
Feb-2 |
Heuristic search; FASTA; BLAST |
5 |
Feb-4 |
String matching; suffix arrays |
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6 |
Feb-9 |
Short read alignment; BWA; Bowtie |
7 |
Feb-11 |
Probabilistic models for biological
sequences |
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8 |
Feb-16 |
HMM parsing; Viterbi |
9 |
Feb-18 |
HMM training; Baum-Welch |
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10 |
Feb-23 |
HMM applications |
11 |
Feb-25 |
Profile HMMs; PSIBLAST |
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12 |
Mar-2 |
Phylogenetic trees: UPGMA; NJ |
13 |
Mar-4 |
Unsupervised learning |
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Mar-9 |
NO CLASS |
14 |
Mar-11 |
Clustering; non-negative matrix
factorization |
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15 |
Mar-16 |
Algorithms in single-cell data
analysis |
16 |
Mar-18 |
Supervised learning; classification and
regression |
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17 |
Mar-23 |
SVM; string kernels |
18 |
Mar-25 |
Naive Bayes; logistic regression |
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19 |
Mar-30 |
Deep neural networks |
20 |
Apr-1 |
Motif finding: EM and Gibbs sampling |
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21 |
Apr-6 |
Motif finding: Bayesian networks |
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Apr-8 to Apr-22 |
Student presentations |