[REU] NSF-sponsored Research Experience for Undergraduates in Computational Genomics

William H. Hsu bhsu at cis.ksu.edu
Fri Mar 28 20:53:23 EST 2003

K-State Bioinformatics REU Summer Program

The College of Agriculture and the Department of Computing and
Information Sciences at Kansas State University is offering a Research
Experience for Undergraduates Summer Program that immerses students in
bioinformatics research with the Laboratory for Knowledge Discovery in
Databases. This program will engage undergraduate students in the
latest research methodologies and techniques from both the web lab and
computing lab to address multi-disciplinary applications in
computational genomics. The goal of this project is to provide a
diverse set of undergraduate students with the research skill set to
uniquely position themselves in the expanding field of genome

Who May Apply 

Undergraduate student participants supported with NSF funds must be
citizens or
permanent residents of the United States or its possessions. An
undergraduate student is a student who is enrolled in a degree program
(part-time or full-time) leading to a bachelor's degree.

Students with basic biology background (general biology and organic
chemistry; molecular cell biology preferred) and introductory
programming experience (C/C++ or Java preferred).

Kansas State University (KSU) especially encourages applications from
students attending liberal arts colleges, small universities, and
non-research oriented institutions serving populations
underrepresented in the scientific and engineering professions. We
also encourage applications from women and minorities.
Student Intern Activities 

The students will have a unique opportunity to work with established
teams headed by Dr. Jan Leach and Dr. William Hsu at K-State and Dr.
Richard Bruskiewich, a K-State affiliate researcher at the
International Rice Research Institute (IRRI) in the Phillippines, in
the use of technologies and methodologies for functional genomics,
especially in using the biological and computational tools for gene
discovery and to understand gene function. They will become part of
the working team and will contribute to research projects on
identification of deletion mutants in a gene of interest from the rice
mutant collection maintained by K-State, IRRI, and their

Wet lab research: The formalization of CG experiments demands an
understanding of the protocols for detection of specific deletion
mutants. This will involve the design and implementation of PCR
experiments, use of software for data collection and processing, data
modeling and information retrieval (for comparative purposes), and
finally statistical algorithms for learning from data and
classification of new data. In our application domain of CG, we will
show students how to use (1) software (e.g., UTRdb, UTRsite, EBI
ClustalW, Whitehead Institute's Primer Picker, and IRRI's IRIS) in
support of molecular biology experiments such as development of PCR
primers for screening the DNA pools, and (2) computational analyses
such as gene clustering and expression network discovery. Basic
programming background can be fulfilled by a first course in computer

Use and development of intelligent systems software for functional
genomics: In May, 2002, the K-State KDD Lab released software packages
called Machine Learning in Java (MLJ) and Bayesian Network Tools in
Java (BNJ), containing a number of previously published algorithms, as
well as several developed by the KDD Lab, that are useful in building
computational models of gene regulatory dynamics. We intend to expose
students in this program to basic bioinformatics software development.
This includes use of the BNJ package as a standalone application as
well as understanding and modifying the documented source code.

Appointment Dates and Compensation  

The application deadline is Friday 04 April 2003. 
The notification date is Monday 14 April 2003.
The appointment runs from Friday 16 May 2003 - Thursday 31 July 2003.
However, we can be flexible to work within summer intersessions at
other universities.

Interns will receive a $3600.00 stipend to cover living expenses
during the summer. Off-site students will also receive travel support
to and from Manhattan, KS.

For further information, contact:

Dr. William H. Hsu
234 Nichols Hall
Manhattan, KS 66506-2302
Phone: (785) 532-6350 x29
Fax: (785) 532-7353

 William H. Hsu, Ph.D.
 Assistant Professor of CIS, Kansas State University
 Director, Lab for Knowledge Discovery in Databases
 bhsu-AT-cis.ksu.edu, bhsu-AT-ncsa.uiuc.edu
 http://www.kddresearch.org              ICQ: 28651394

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