CISC 889  -   Bioinformatics  -   Spring 2002

T/Th 12:30am--1:45pm, [Smith Hall 102a]

 
Instructor: Keith Decker 
Office: Room 204, The Green House (77 E. Delaware) 
Hours: Tu/Th 2:00-3:00pm
Phone: 831-1959 
Email: decker@cis.udel.edu 
COURSE WEB PAGE: http://www.cis.udel.edu/~decker/courses/889d-bio/index.html

Course Description

This course will allow us to explore the basic computational issues and methods used in molecular biology. Topics may include: dynamic programming algorithms for alignment, structural superposition algorithms, computing with distance information, 3D motif definition and computation, hidden Markov models, phylogenetic trees, statistical feature detection, genetic algorithms, design of data resources, automated analysis of biological literature, database integration, and collaborative environments for supporting biology. We will assume no previous biology background. We also encourage participation by students in the life sciences with minimal computing experience.

Textbook

Bioinformatics: Sequence and Genome Analysis by David W. Mount [Cold Spring Harbor Laboratory Press]. There is a softcover edition. [Book Web site]

I am also borrowing heavily from Dr. Russ Altman's course. Dr. Altman is a leader in bioinformatics education.

Format

Graduate Seminar. We will teach each other. I've invited Dr. Carl Schmidt to give a three-lecture introduction to Molecular Biology for Computer Scientists to start out the semester. After which, each student and myself will take turns teaching a class on a topic from the textbook

Grading:

 
DATE TOPIC READING PERSON
2/5 Overview Decker
2/7
Intro Mol Bio
Basic biology primer (short intro to sequence in biology) [Altman]

Introduction to Biology for Computer Scientists [Hunter]

Carl's Slides from today: (powerpoint)

Schmidt
2/12 Intro Mol Bio Introduction to DNA structure (web tutorial) [Hallick]

Protein Architecture [U Kansas Medical Center Biochemistry]

Schmidt
2/14 Intro Mol Bio Introduction to Genetics [DOE Human Genome Project]

Glossary of Genetic Terms [DOE Human Genome Project]

Schmidt
2/19 Bioinformatics
Intro/history/resources
Chapter 1
Chapter 2
Decker
2/21 Pairwise Alignment Chapter 3 [53-75]
dotmatrix slides
Decker
2/26 Pairwise Alignment [76-134]
slides
sample spreadsheet
Jackoway
2/28 DB sequence similarity Chapter 7 [282-314] slides Tan
3/5 DB sequence similarity Chapter 7 [315-334] slides Decker
3/7 Multiple sequence alignment Chapter 4 [140-173] slides Williamson
3/12 MSA / Hidden Markov Models Chapter 4 [173-200] slides Torii
3/14 Phylogenic prediction Chapter 6 [238-261] slides Khan
3/19 Phylogenic prediction Chapter 6 [262-279] materials Arnold
3/21 Gene prediction Chapter 8 [338-356] slides FINAL PROJECT PLAN DUE Shindo
3/26 Gene prediction Chapter 8 [356-373] slides Koc
3/28 RNA structure Chapter 5 slides Pickard
4/2 SPRING BREAK
4/4 SPRING BREAK
4/9 protein classification Review of protein structure, terminology, representation
Chapter 9 [382-389]; Altman May 3rd lecture. slides
Chen
4/11 protein classification Protein classification
Chapter 9 [389-427]; Altman May 10th lecture. slides
Situ
4/16 protein structure Chapter 9 [427–460]; Altman May 15th lecture
(note that the end slides were moved to the May 17th lecture...) slides
Lin
4/18 protein structure Chapter 9 [460-473]; Altman May 17th lecture slides Ma
4/23 genome analysis Chapter 10 [480–500] Dechev
4/25 genome analysis Chapter 10 [500–519]; see also Altman April 26 slides Miao
4/30 microarray analysis Chapter 10 [519-525] +
short review Raychaudhuri et al.: Basic microarray analysis : grouping and feature reduction (all students should read this)

some other paper (SAGE) SLIDES

Davis
5/2 microarray analysis short review 2 Altman & Raychaudhuri: Whole-genome expression analysis: challenges beyond clustering

Quackenbush J. Computational analysis of microarray data. Nat Rev Genet.
2001 Jun;2(6):418-27. Review

Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays.
Nature. 2000 Jun 15;405(6788):827-36. Review.

slides

Kim
5/7 gene networks Altman 4/19; slides Makkena
5/9 gene networks bayes nets: Segal et al., Rich Probabilistic Models for Gene Expression

BioCyc:

Decker
5/14 knowledge bases, ontology GO: The Gene Ontology Consortium,
Gene Ontology: tool for the unification of biology. Nature Genetics 25: 25-29.
Creating the gene ontology resource: design and implementation. Genome Research 11: 1425-1433

TrEMBL Annotation (bioinformatics V15#3 pp228-233)

BioMAS

Watson
5/22 FINAL PROJECTS DEMO+REPORT DUE


Apr 30, 2002
decker@cis.udel.edu