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Reading and Research in Computational Biology
CSE 590 CB is an informal weekly seminar in Computational
Biology, open to all graduate students in the computer,
biological, and mathematical sciences.
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| Instructors: | Ruzzo, Tompa |
| Credit: | 1-3 Variable |
| Grading: | Credit/No Credit. Talk to us if you're unsure of our expectations, registrar-wise. |
| Date | Topic | Presenters/Participants | Papers/Slides |
|---|---|---|---|
| 9/29 | Organizational Meeting | ||
| 10/06 | Splicing | Dan, Jed, Ken, Monika; Larry | Slides |
| 10/13 | Secondary Structure | Jeremy, Mathieu, Zasha; Martin | |
| 10/20 | Melting & Primers | Amy, Isaac, Keunwoo; Benno | Papers Keunwoo's PCR slides |
| 10/27 | Discussion of Splicing | Don, Justin, and everybody; Larry | Slides |
| 11/3 | Guest Speaker | David Goodlett | |
| 11/10 | Array Applications | Tammy, Ka Yee; Rimli | Papers |
| 11/17 | DNA Arrays for High Resolution HLA Typing | Guest Speaker: Zhen Guo, MBT & FHCRC | Abstract & Papers |
| 11/24 | Deducing Network Dynamics from Node Activity Traces | Guest Speaker: Brendan Mumey, MSU | Abstract |
| 12/1 | Discussion of Array Design | ||
| 12/8 | No Meeting?? | ||
The first two papers are about the primer design problem that, among other places, occurs in the revolutionary lab technique that has transformed molecular biology in the middle of the previous decade, the polymerase chain reaction (PCR). At the end of this decade, a similarly revolutionary technique is maturing rapidly: DNA microarrays, on which we are planning to spend some more time on in subsequent meetings. We will present the basics of both techniques. For both, secondary structure and the estimation of melting temperature are crucially important topics. We are going to discuss two practical methods for primer design and a method for estimating energy parameters/melting temperatures.
The HLA genes are among the most polymorphic genes known in the human genome. Genes in HLA regions encode proteins that are critical in controlling T-cell recognition and determining histocompatibility in bone marrow transplantation procedure. The methodology and applications of DNA array technology in HLA tissue typing will be reviewed. An oligonucleotide array system for high-resolution typing of classical HLA alleles will be described. Applications of PCR arrays in HLA polymorphism study will be evaluated. Important issues in array technology, such as DNA surface density, hybridization kinetics, mismatch discrimination, will be discussed.
In this talk I will describe an approach to detect and represent important aspects of the dynamics of networks. We have two principal areas of application in mind. Interest in the problem of discovering and representing the important aspects of the dynamics of gene regulatory networks has elevated in the last several years due to the ability to collect large quantities of gene expression data using DNA microarrays. A problem from neurobiology that bears a surprising amount of resemblance is that of detecting information coding and flow in a sensory neural system from neural activity trace data. We describe both problems and how our core methodology is adapted to deal with each. An important feature of our approach is that it permits the modeling of feedback loops.
Joint work with Tomas Gedeon, Dept. of Mathematics, Montana State University
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Department of Computer Science & Engineering University of Washington Box 352350 Seattle, WA 98195-2350 (206) 543-1695 voice, (206) 543-2969 FAX cse590cb-webmaster@cs.washington.edu | |