| Topic |
Date |
Handouts |
| Basic molecular biology, sequence alignment, multiple
alignment |
09/01/04 |
h1,
h2,
h3 |
| Sequence alignment heuristics, local search, protein
structure prediction |
09/08/04 |
h1, h2, h3, h4, h5=algorithms handout, h6=local search handout |
| Protein structure prediction I |
09/15/04 |
h1=local search handout#2, h2, h3, h4 |
| Protein structure prediction II |
09/22/04 |
h1=protein structure handout#1, h2=protein structure
handout#2, h3=algorithms handout, h4 |
| Quiz #1, Gene expression clustering I |
09/29/04 |
h1
h2
h3
h4
h5=iterated local search clustering handout |
| Gene expression clustering II |
10/06/04 |
h1 h2 h3 |
| DNA fragment assembly, Hidden Markov Models |
10/13/04 |
h1 h2 |
| EM algorithm, Bayesian networks, Phylogenetics---model based
estimation, |
10/20/04 |
h1 h2, h3=EM handout, |
| Quiz #2, Bayesian network inference,
Phylogenetics---distance based reconstruction |
10/27/04 |
disance-based methods handout#1, h2 |
| Phylogenetics---distance based reconstruction |
11/03/04 |
|
| Phylogenetics---Neighbor Joining and Maximum
Parsimony, review |
11/10/04 |
|
| Quiz #3, student presentation |
11/17/04 |
(1)
Prediction of protein subcellular locations by support
vector machines using compositions of amino acids and acimo acid pairs (Use NJIT on-campus machine to download article via NJIT library) |
| Student presentations |
11/24/04 |
(1)
Protein structure prediction using Rosetta (2) A comprehensive comparison of multiple sequence alignment programs |
| Student presentations |
12/01/04 |
(1)
Base-By-Base: Single nucleotide-level analysis of whole viral genome
alignments (2) Gene prediction with a hidden Markov model and a new intron submodel |
| Student presentations |
12/08/04 |
(1)(a)
Protein-Ligand Docking as an Energy Optimization Problem (1)(b) A Detailed Comparison of Current Docking and Scoring Methods on Systems of Pharmaceutical Relevance (2)Genetic algorithms for protein folding simulations |