May 2007. 39th Symposium on the Interface: Computing Science and Statistics
Detecting Peaks in Gas and Liquid Chromatography Mass Spectrometric Metabolomics Data
M. Lawrence, H. Hofmann, S. Choi, D. Cook, O. Nikolova, E. Wurtele
March 2007. ACM Special Interest Group on Computer Science Education
Using interdisciplinary bioinformatics undergraduate research to recruit and retain computer science students
Jon Beck, Brent Buckner, Olga Nikolova, Diane Janick-Buckner
Technical Symposium on Computer Science Education
Proceedings of the 38th SIGCSE technical symposium on Computer science education
June 2007. Genetics.
Involving Undergraduates in the Annotation and Analysis of Global Gene Expression Studies: Creation of a Maize Shoot Apical Meristem Expression Database
B. Buckner, J. Beck, K. Browning, A. Fritz, L. Grantham, E. Hoxha, Z. Kamvar, A. Lough, O. Nikolova, P. S. Schnable, M. J. Scanlon and D. Janick-Buckner
- BCB 570. Computational Functional Genomics & Systems Biology.
- BCB 568. Advanced Genome Informatics.
- CprE 526. Introduction to Parallel Algorithms and Programming.
- BCB 569. Structural Genome Informatics.
- Statistics 430X. Empirical Methods for Computer Science.
- BCB/ComS/CprE/Gen 548. Fundamentals of Genome Informatics
- GEN 411. Molecular Genetics.
- Biol 313. Principles of Genetics.
- BCB 690. Student Seminar in BCB
- BCB 691. Faculty Seminar in Bioinformatics and Computational Biology.
Publication in preparation.
LC/MS stands for Liquid Chromatography/Mass Spectrometry, which is an efficient analytical chemistry technique for identifying different chemical components in mixtures. Our goal is to build a pipeline for LC/MS data processing, including the pre-processing component, which we have found to be problematic in the somewhat new field of metabolomics. Software packages exist to solve the problem in proteomics but we have shown that metabolomics requires a new statistical approach for adequate peak detection, retention time correction, peak quantification, etc. Besides learning about metabolomics, this project introduced me to some new (to me) statistical approaches and the basics of R.
May 2007. Detecting Peaks in Gas and Liquid Chromatography Mass Spectrometric Metabolomics Data
M. Lawrence, H. Hofmann, S. Choi, D. Cook, O. Nikolova, E. Wurtele
I tested and evaluated The GenomeThreader (GTH) gene prediction software using zebrafish genomic data as testing ground. I was able to identify some problematic parameter sets and other miscellaneous bugs in the program. Mainly, I was investigating the feasibility to use human/mouse homologs for zebrafish gene structure prediction.
While at Truman, I worked on The Maize Shoot Apical Meristem Project and designed and implemented GENEVA. [More]