Ph.D. program: graduate study in Scientific Computation with an emphasis in Computational Genomics. My advisor is Dr. Chad Myers in the Computer Science department at the University of Minnesota. Course-work completed, I’m negotiating thesis topics with my advisor and collaborators. My primary area of interest is the application of functional genomics in the clinical setting. This dovetails with previous work in genome scale processing and annotation systems in various model organisms.

Laboratory

University of Minnesota: Computational Biology and Functional Genomics Lab

Our research focuses on machine learning approaches for integrating diverse genomic data to make inferences about biological networks. The main purpose of our work is to further our understanding of gene function and how genes or proteins interact to carry out cellular processes.

Teaching

Adjunct Faculty at the University of St. Thomas, St. Paul, MN

SEIS 701-01 Bioinformatics: This course introduces students to Bioinformatics through the presentation of current algorithms, databases, and tools used in computational molecular biology and the critique of current literature in the field. The following topics will be discussed: introduction to molecular biology, genomics, genetics and privacy issues, genome maps, sequencing alignment, assembly, and analysis, gene finding techniques, annotated databases such as NCBI:Genbank and Swiss-Prot, Perl-based tools for data manipulation, and genome-scale bioinformatics software tools. (Fall 2010)

Publications

Pavy N, Johnson J, Crow JA, Paule C, Kunau TM, MacKay J, Retzel EF, ForestTreeDB: a database dedicated to the mining of tree transcriptomes. Nucleic Acids Res. 2007 Jan;35(Database issue):D888-94. Epub 2006 Nov 27. [NAR|pubmed|pdf]

Cannon SB, Crow JA, Heuer ML, Wang X, Cannon EK, Dwan C, Lamblin AF, Vasdewani J, Mudge J, Cook A, Gish J, Cheung F, Kenton S, Kunau TM, Brown D, May GD, Kim D, Cook DR, Roe BA, Town CD, Young ND, Retzel EF. Databases and information integration for the Medicago truncatula genome and transcriptome. Plant Physiol. 2005 May;138(1):38-46. [pubmed]

Lamblin AF, Crow JA, Johnson JE, Silverstein KAT, Kunau TM, Kilian A, Benz D, Stromvik M, Endre G, VandenBosch KA, Cook DR, Young ND, Retzel EF. MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome. Nucleic Acids Res. 2003 Jan 1;31(1):196-201. [pubmed]

Silverstein KAT, Shoop EE, Johnson JE, Kilian A, Freeman JL, Kunau TM, Awad IA, Mayer MA, Retzel EF. The MetaFam server: a comprehensive protein family resource. Nucleic Acids Res. 2001 Jan 1;29(1):49-51. [pubmed]

Yang P, Kunau TM, Bennett BH, Davis E, Wren B. Reconfigurable Parallel Sorting and Load Balancing on a Beowulf Cluster: HeteroSort. Proceedings of the 15th IEEE/IPDPS 2000 Workshops on Parallel and Distributed Processing (May 01-05, 2000). J. D. Rolim, Ed. Lecture Notes In Computer Science, vol. 1800. Springer-Verlag, London, 862-869. (2000) [ieee-pdf|pdf]