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 |
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.
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.
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 [427460]; 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 [480500] | Dechev |
4/25 | genome analysis | Chapter 10 [500519]; 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. |
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 | 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) |
Watson |
5/22 | FINAL PROJECTS DEMO+REPORT DUE |