CSE 591 Computational Molecular Biology
Spring 2003
MW 1:40 -- 2:55 PM; PSA 113
- Tentative Content:
* Introduction to molecular Biology
( DNA, RNA, Chromososme,
Genes, Proteins, ammino acids,
cell dynamics, signal transduction,
Genome Organization)
* Introduction to active areas
of research in CMB.
( Human GenomeProject, Transcription
maps, Linkage analysis,
Functional Genomics, Comparative
Genomics, Cell informatics,
Rational drug design)
* Introduction to algorithms.
* Genome Sequencing
(restriction enzymes, digression, restriction
maps, clone library,
restriction
maps, molecular cloning, sequence assembly, matching rules,
islands and contigs, shotgun mapping, overlap rule,
Genomic contig algorithm,
DNA ligase, hybridization,
DNA amplification, Polymerase chain reaction)
* Models and Algorithms
( Genome sequencing algorithms: sequence reconstruction,
problem,
shortest superstring problem, pairwise sequence,
alignment, Edit distance,
Scoring models,
multiple sequence
alignment:optimal global alignment,
local alignment: local
suffix alignment problem,
BLAST, FAST, Hidden Markov modelss, Motif
finding)
* Analysis of Gene expression
data
(Clustering
genes: microarrays, complementary hybridization, spoted arrays,
Oligonucleotide arrays, cluster analysis,
hierarchical clustering, gene similarity metric,
Classifying Genes and gene expressions:
classifying cancer, ranking genes,
weighted voting, cancer class discovery,
support vector, machines,
Inferring regulatory networks)
* Phylogeny
* Bioinformatics Tools and Databases: data and knowledge integration
-- Finding paralogues
by clustering (BLASTCLUST, CD-HIT)
-- Finding
homologues and Orthologues (BLAST)
-- Finding
remote homologues (PSI-BLAST)
-- Finding
functional annotation (PFAM, INTERPRO)
-- Finding
structural annotation (Blast PDB)
-- Finding low complex regions (SEG, CAST)
-- Finding transmembrane regions (TMHMM)
-- Finding disordered regions (COILS, PONDR)
-- Finding secondary structure (JPRED, TOPpred)
-- NCBI, EBI, PDB, PFAM
- Textbook and CD-ROM:
Bioinformatics: Sequence and Genome Analysis -- David Mount
Roche Genetics Education program CD from www.rochegenetics.com
3. Referenec
Books:
Biological Sequence analysis: probabilistic models of proteins and nucleic
acids --
Durbin, Eddy, Krogh and Mitchison
Computational molecular biology: an algorithmic approach -- Pevzner
Computational methods in molecular biology -- edited by Salzberg, Searls
and Kasif.
Discovering
Genomics, Proteomics and Bioinformatics --
A. Malcolm
Campbell and Laurie J. Heyer.
A Practical
Approach to Microarray Data Analysis. -- edited by Daniel P. Berrar,
Werner Dubitzky, and Martin Granzow, Kluwer.
4. Grading (tentative
and subject to change):
40 % Two Class tests (Mid March and
Last day of Class) (No finals)
40 % Project
20 % Homework, Presentation, Notetaking