Kasper Munch



http://ib.berkeley.edu/labs/slatkin/munch

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Research Overview

The assignment of DNA from organic material to species or taxonomic groups is integral to a number of scientific disciplines. It has been suggested that a metagenomics approach can be used to characterize environments according to their genetic fingerprint. Even without taking genomic approaches, however, DNA sequencing of selected markers from environmental samples may provide ecological information or identify relevant species such as human pathogens. A related field where unknown specimens are identified based on Cytochrome Oxidase I (COI) has become know as DNA Barcoding. I am presently engaged in the development statistical assignment of such unknown DNA. Other ongoing research includes population genetics where I am currently developing statistical tools to analyze population structure based ancient DNA. Previous areas of research include gene prediction, genome expression analysis and alternative splice site prediction.

Selected Publications

Johnson, S.S., M.B. Hebsgaard, T. Christensen, M. Mastepanov, M.T. Zuber, R. Nielsen, K. Munch, T. Brand, M.T.P. Gilbert, M. Bunce, R. Rønn, D. Gilichinsky, D. Froese, and E. Willerslev. 2007. Ancient Bacteria Show Evidence of DNA Repair. PNAS 104(36):14401-14405.

Haile, J., R. Holdaway, K. Oliver, M. Bunce, M.T. Gilbert, R. Nielsen, K. Munch, S.Y. Ho, B. Shapiro, and E. Willerslev. 2007. Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible and is DNA Leaching a Problem? Mol Biol Evol 24(4):982-989.

Munch, K. and A. Krogh. Automatic Generation of Gene Finders for Eukaryotic Species. 2006. BMC Bioinformatics 7(1):263.

Munch, K., P.P. Gardner, P. Arctander, and A. Krogh. 2006. A hidden Markov model approach for determining expression from genomic tiling micro arrays. BMC Bioinformatics 7(1):239.