Postdoctoral Fellow

Steven Goldstein Genome Center of Wisconsin UW Biotechnology Center Faculty Advisors: David Schwartz and Michael Newton Email: steveg@lmcg.wisc.edu 265-4430

Optical Mapping is a system capable of producing ordered restriction maps of single molecules. Taken in the aggregate, an ensemble of single molecule maps can be combined to yield an accurate, high-resolution map. Several projects underway in the Schwartz lab are adapting this technique to study genomic variations and alterations on a global basis. As a CIBM postdoctoral fellow, I plan to participate in this effort by developing algorithms to compare pairs of optical maps and by developing methods for analyzing the data resulting from those comparisons.

Gentig, the Schwartz lab’s optical map assembly algorithm, uses a technique known as geometric hashing in one of its steps. Gentig’s hashing scheme leads to an effective heuristic for microbial genomes, but attempts to scale it up and apply it to mammalian genomes have run into obstacles. Most genomic-scale sequence assembly algorithms make extensive use of an analogous scheme, one based on hashing of the k-mers. My hypothesis is that some ideas used in the hashing implementation of sequence assembly algorithms can be applied to optical mapping assembly to overcome the obstacles.

CV

CV (.pdf format, Download Reader)

Publications

Goldstein S, Briska A, Zhou S, Schwartz D. Sequences, Maps, Genomes, and Graphs. RECOMB Satellite Conference on DNA Sequencing Technologies and Computation, Stanford, CA, May, 2003.

Goldstein S. Improving Assemblers with Graph Based Optimizations and Heuristics. Abstract, Second Annual RECOMB Satellite Meeting on DNA Sequencing and Characterization, 2002.

Goldstein S. Computing with branching processes for cancer chemotherapy and carcinogenesis models. Biostatistics Technical Report No. 50, Wisconsin Clinical Cancer Center, 1989.

Goldstein S and M. Gehring. WCCC tumor growth and chemotherapy model, computer program implemented on the Wisconsin Clinical Cancer VAX system, 1987.

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