MICaB Graduate Program
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Arkady Khodursky, Ph.D.
Department of Biochemistry, Molecular Biology and Biophysics
University of California - Berkeley, 1997, Ph.D.
612-625-3799 - office and lab
Functional genomics and bioinformatics
My laboratory studies transcriptional activity of genomes of model microbes: Escherichia coli, Synechocystis and Saccaromyces cerevisiae. We design, produce and use whole genome DNA microarrays to understand the relationships between genotypes and phenotypes, between the structure of a chromosome and its transcriptional activity, between environmental perturbations and transcriptional responses.
We are determining temporal sequences of transcriptional events in response to elementary stimuli and we expect that such analysis will provide insights into the basis of regulation, pathway connectivity and the flow of information inside the cell.
Analysis of transcriptional profiles as a function of the position of genes on the chromosome revealed remarkable complexity in the organization of the bacterial chromosome. Our studies aim at understanding global and local chromosomal structural properties and how these properties contribute to the chromosome function in the processes of transcription, replication and recombination and determine the positional basis of genetic plasticity.
Selected Recent Publications:
- Kyeong S. Jeong, Yang Xie, Hiroshi Hiasa and Arkady B. Khodursky. 2006. Analysis of pleiotropic transcriptional profiles: a case study of DNA gyrase inhibition. PLoS Genetics. Sep 29;2(9).
- Yang Xie, Wei Pan, Kyeong S. Jeong, and Arkady B Khodursky. 2006. Incorporating prior information via shrinkage: a combined analysis of genome-wide location data and gene expression data.” Stat Med. Sep 7; [Epub ahead of print].
- G.N. Vemuri, E. Altman, D. Sangurdekar, A.B. Khodursky, M.A. Eiteman. 2006. Regulation of overflow metabolism in Escherichia coli. Appl Environ Microbiol. May;72(5):3653-61.
- Dipen Sangurdekar, Friedrich Srienc and Arkady Khodursky. 2006. Classification based framework for quantitative description of large-scale microarray data. Genome Biology, Apr 20;7(4):R32.
- Guanghua Xiao, Betsy M. Martinez-Vaz, Wei Pan, and Arkady B. Khodursky. 2006. Operon information improves gene expression estimation for cDNA microarrays. BMC Genomics, Apr 21;7(1):87.
- Yang Xie, Wei Pan, and Arkady B. Khodursky. 2005. A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data. Bioinformatics. Dec 1;21(23):4280-8.
- Betsy M. Martinez-Vaz, Yang Xie, Wei Pan, and Arkady B. Khodursky. 2005. Genome-wide localization of mobile elements: experimental, statistical and biological considerations. BMC Genomics, Jun 1;6(1):81.