Project Title:
GENEVA Gene Expression and Visualization Application

Project Description (short):
A bioinformatics project to develop and maintain algorithms, software, database systems, and web-based front end to annotate expressed sequence tags and gene information from microarray studies of maize shoot apical meristem tissue. (A longer project description is [here].)

Skills needed:
High-quality software development and coding skills essential. Experience with Perl and cgi scripting, and with database design are desirable. Basic knowledge of biology and genetics very helpful.

Start Date:
January 2006

End Date:
on-going

Mentors:
Prof. Jon Beck (Computer Science), jbeck@truman.edu
Prof. Brent Buckner (Biology), bbuckner@truman.edu
Prof. Diane Janick-Buckner (Biology), djb@truman.edu

Accomplishments:

• O. Nikolova, "GENEVA: Gene Expression Visualization Application - Gene Expression of Shoot Apical Meristem in Maize", CIMMYT (The International Maize and Wheat Improvement Center), Mexico City, Mexico, July 2005.
• O. Nikolova, "GENEVA: Gene Expression Visualization Application", Mathematics and Computer Science Division colloquium, Truman State University, October, 2005.
• O. Nikolova and J. Beck, "GENEVA: Gene Expression and Visualization Application", Sixteenth Annual Argonne Symposium for Undergraduates in Science, Engineering and Mathematics, Argonne, IL, November 2005.
• O. Nikolova, A. Lough, L. Grantham, D. Janick-Buckner, B. Buckner, L. Borsuk, K. Ohtsu, P. Schnable, M. Scanlon, J. Beck. "Gene Expression and Visualization Application (GENEVA): Development and Use in Shoot Apical Meristem Gene Expression Analysis". Poster at 48th annual Maize Genetics Meeting, Monterey, CA, 9-12 March, 2006.
• O. Nikolova, "Gene Expression Visualization Application (GENEVA): Development and Use in Shoot Apical Meristem Gene Expression Analysis". Poster at 19th annual Student Research Conference, Truman State University, 20 April, 2006.
• Beck, J., B. Buckner, O. Nikolova, and D. Janick-Buckner. "Using Interdisciplinary Bioinformatics Undergraduate Research to Recruit and Retain Computer Science Students." SIGCSE Bulletin vol. 39 no. 1 (March 2007).
• Brent Buckner, Jon Beck, Kate F. Browning, Ashleigh E. Fritz, Eneda Hoxha, Lisa D. Grantham, Zhian N. Kamvar, Ashley N. Lough, Olga Nikolova, Patrick S. Schnable, Michael J. Scanlon, and Diane Janick-Buckner. "Involving Undergraduates in the Annotation and Analysis of Global Gene Expression Studies: Creation of a Maize Shoot Apical Meristem Expression Database." Genetics 176(2), June 2007.
• X. Zhang, S. Medi, L. Borsuk, D. Nettleton, B. Buckner, D. Janick-Buckner, J. Beck, M. Timmermans, P. Schnable, and M. Scanlon. "Meristem laser microdissection reveals domain-specific gene expression during maize leaf development." PLoS Genetics 3(6): e101, 2007.
• K. Ohtsu, M. Smith, S. Emrich, L. Borsuk, R. Zhou, T. Chen, X. Zhang, M. Timmermans, J. Beck, B. Buckner, D. Janick-Buckner, D. Nettleton, M. Scanlon, and P. Schnable, "Expression of retrotransposons in the shoot apical meristem of maize (Zea mays L.)", accepted to Plant Journal.
• Ohtsu K, Smith M, Emrich SJ, Borsuk LA, Zhou R, Chen T, Zhang X, Timmermans MPC, Beck J, Buckner B, Janick-Buckner D, Nettleton DS, Scanlon MJ and Schnable PS. "Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.)." Plant Journal 52: 391-404.
• Lisa Grantham and Olga Nikolova, "Global gene expression patterns in the maize shoot apical meristem; creation of a maize shoot apical meristem database", Applied Biotechnology Research Group, CIMMYT, Texcoco, Mexico, August 2005
• Joshua Kangas, "Automated Functional Annotation of Maize Genes Using Artificial Neural Networks for Literature Analysis",€ Society for Mathematical Biology Conference, San Jose, CA, 2007; Truman Student Research Conference, 2008.
• Joshua Kangas, "Automated Functional Annotation of Maize Genes Using Artificial Neural Networks for Literature Analysis",€ Society for Mathematical Biology Conference, San Jose, CA, 2007; Truman Student Research Conference, 2008 and Midwest Section of ASPB Meetings, Ames, IA, 2008. Best undergraduate poster presentation.

Current Students:

• Molly Smith, 2008-present (Computer Science)
• Mike Miller, 2008-present (Computer Science)

Past Students:

• Dane Guemple, 2006 (Computer Science)
• Olga Nikolova, 2005-2006 (Computer Science)
• Joshua Kangas 2006-2008 (Computer Science)

About Prof. Beck:
Jon Beck, associate professor of computer science, earned a B.S. in biology from The George Washington University, a M.S. in computer science from Hood College, and a Ph.D. from West Virginia University in computer science, majoring in software engineering and minoring in database systems. Prior to coming to Truman, he served as Director of Academic Computing at Hood College. While at Truman, Dr. Beck served for 4 years as Acting Director of Computer Services and has also worked as a software development consultant at companies in Maryland and Texas. He lives with his wife and two daughters on a small farm outside Kirksville where they raise sheep and poultry. He enjoys bicycling, hiking, canoeing, kayaking, and camping. Beck's research interests include bioinformatics, computational biology, and software engineering.

About Prof. Buckner:
Dr. Buckner is a native of Pennsylvania where he also went to undergraduate school at Lock Haven State University. He earned M.S. and Ph.D. degrees from the University of Vermont in Botany. During his postdoctoral position at Iowa State he began working with maize genetics. Dr. Buckner has been on the faculty of Truman State University for the past 15 years. He enjoys walking, hiking, gardening. His research interests include genetic diversity in maize and related species; gene discovery and mapping of maize genes; global gene expression patterns in maize shoot apical meristems.

About Prof. Janick-Buckner:
Dr. Janick-Buckner is a native of New Jersey and attended undergraduate school at Gettysburg College in Pennsylvania. She earned a Ph.D. degree from the University of Vermont in Cell Biology. During her postdoctoral training she worked at Iowa State University in the Department of Biochemistry studying the influence of retinoids on cells of the immune system. Dr. Janick-Buckner has been on the faculty of Truman State University for the past 15 years. She enjoys walking, hiking, gardening, and reading. Her research interests focus on the cell biology and genetics of maize; gene discovery, isolation and expression studies of maize genes; and global gene expression patterns in maize shoot apical meristems.

Project Description (long):
An interdisciplinary collaboration among Brent Buckner, Diane Janick-Buckner, Jon Beck, and six to eight biology and computer science undergraduate students. Drs. Pat Schnable, Iowa State University, and Mike Scanlon, Cornell, and others are additional external collaborators.

Drs. Scanlon, Schnable, Buckner, Janick-Buckner, et al., are investigators on the NSF-funded Shoot Apical Meristem (SAM) project. This project involves identifying and annotating differentially expressed genes or expressed sequence tags (ESTs) in laser-capture microdissected maize seedling SAM tissue using microarrays. Truman's part of the SAM project is to annotate and analyze the ESTs based on BLAST and literature searches in order to determine their biological significance in the maize SAM.

During the course of the project, several thousand ESTs will be encountered, giving rise to a massive amount of literature to cross-reference as well as to an extremely large amount of information about the expressed sequences themselves.

A part of the GENEVA project is to develop tools to automate some of the tedious manual searching and acquisition tasks associated with the BLAST and literature searches. Perl scripts and web forms developed by the computer science collaborators will greatly speed the process of populating the project database.

The main focus of the GENEVA project is to develop a much more mathematically rigorous process for choosing the order in which ESTs are examined and for establishing and organizing the correlations among the resultant potential gene functions. A quantitative and visual graph theoretic approach will be utilized to organize and find patterns in information acquired through literature searches with the goal of improving the signal to noise ratio in the search results. Various strategies to analyze, visualize, and display the results with a goal of revealing the interactions between the multiple biochemical pathways and molecular mechanisms that underlie meristem development will be developed.

Some existing software tools will be used for data visualization and display, but no existing tools are adequate to the task. Thus, the project will develop new data visualization and correlation tools which will embody the strategies as described above.

The primary indicator of success for this project will be an increase in the speed and accuracy with which the final step of creating a conceptual map that explains and accounts for the relationship between the observed expression patterns from the microarrays and biology of meristem development and function occurs.