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2004 BSI news article

Summer Experience
DTC Bioinformatics Summer Institute offers undergraduates research opportunities

As part of the 2004 Bioinformatics Summer Institute (BSI) at the DTC, 14 students from throughout the country experienced research in a cutting-edge arena with faculty experts as guides.

From June 6 to Aug. 13, students attended workshops and worked in faculty labs on research projects. They learned firsthand about the growing fields of bioinformatics and computational biology.

As one of a few such programs nationwide, the DTC received funding from the National Institutes of Health (NIH) and the National Science Foundation (NSF) to run the institute from 2003 through 2006.

“The NIH and NSF recognize the impact that computational biology and bioinformatics are having on biomedical research,” says Yiannis Kaznessis, BSI director, assistant professor of chemical engineering and materials science, and DTC faculty member.

“Through this program, they want to introduce undergraduates to the field and encourage them to consider it as a possibility for graduate study and a potential career path.”

The participation of 18 faculty members from areas as diverse as chemical engineering, mathematics, laboratory medicine and pathology, biochemistry, plant biology, and computer science and engineering make it possible to offers students an impressive array of research projects. Students also received a thorough overview of bioinformatics.

“The main goal of the BSI is to provide the highest possible quality education and research experiences in bioinformatics and computational, biology,” says Kaznessis. “We want them to understand bioinformatics concepts, so they can apply information technology solutions to understanding biological systems.”

BSI also is tracking students to determine the impact of the experience on their career path. Already the signs of success are strong: Students from the first year have indicated that they are considering bioinformatics, biological engineering, and related fields for graduate studies.

The 2004 class featured talented participants with majors in information technology, chemical engineering, biology, chemistry, computer science, mathematics, biomedical computation, and electrical engineering. The list below highlights those students, their projects, and their faculty advisors.

Ariel Abell
Georgia Southern University
Project: Visualization Techniques Developed for Researching Genome Structure and Evolution
Faculty Advisor: Nevin Young

Benjamin Anderson
University of Minnesota
Project: Investigation into the Membrane Association of Residues 1-22 of Cytolytic NK-lysin using Molecular Dynamic Simulations
Faculty Advisor: Yiannis Kaznessis

Andrea Carlson
Augsburg College
Project: A Survey of Splice Variation in Medicago truncatula
Faculty Advisor: Kevin Silverstein

Benjamin Chacko
Taylor University
Project: Implementation of Exact Base Spacing Calculation in DNA Base Calling
Faculty Advisor: Christian Domnisoru, University of St. Thomas

John Chilton
University of Minnesota
Project: GAMSA — A Graphical Application for Microarray Statistical Analysis
Faculty Advisor: Arkady Khodursky

Katayoun Jafari
University of Texas, Austin
Project: Alternative Splicing Variants in Medicago
Faculty Advisor: Kevin Silverstein

Angelo Kontgas
Salt Lake Community College
Project: Mayo Clinic University of Minnesota Collaborative Projects — Antibody Engineering for Prostate Specific Antigen
Faculty Advisors: Yiannis Kaznessis and George Vasmatzis

Akash Kumar
University of Minnesota
Project: Stochastic Modeling of a Tetracycline-Induced Gene Network for Implementation in Gene Therapy Applications
Faculty Advisor: Yiannis Kaznessis

Katherine Lauer
Saint Mary’s College
Project: Motif Analysis of M.truncatula ESTs of Unknown Function
Faculty Advisors: Kevin Silverstein and Kathryn VandenBosch

Christopher Lin
Stanford University
Project: Initial Study of Distant Residue Contact Constraints in Monte Carlo Simulation of Protein Folding
Faculty Advisor: Yiannis Kaznessis

Vanessa Louis
Clark Atlanta University
Project: Identifying Secreted Proteins
Faculty Advisor: Lynda Ellis

Erika Remillard-Hagen
Francis Marion University
Project: Mayo Clinic University of Minnesota Collaborative Projects — Antibody Engineering for Prostate Specific Antigen
Faculty Advisors: Yiannis Kaznessis and George Vasmatzis

Evan Ribnick
University of Minnesota
Project: Retrotransposon Activity in Maize
Faculty Advisor: Ron Phillips

Lingnan Tong
University of Texas at Austin
Project: Protein-DNA Conservation Distance Relation
Faculty Advisor: Boojala Reddy