David Schwartz

Research Description:
Nanotechnology is fueling our exponentially growing knowledge of genome structure, populations, and ourselves. This new biology is melding computation with experimental systems that are increasingly miniature, comprehensive, information-dense, and capable of dealing with complexity. Within this environment we create fully-integrated systems for discovery and use them for uniquely revealing genome structure / function relationships, and the full spectrum of mutations in cancer genomes.

Representative Publications:
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Teague, B., Waterman, M.S., Goldstein, S., Potamousis, K., Zhou, S., Reslewic, S., Sarkar, D., Valouev, A., Churas, C., Kidd, J., Kohn, S., Runnhein, R., Lamers, C., Forrest, D., Newton, M.A., Eichler, E.E., Kent-First, M., Surti, U., Livny, M., and Schwartz, D.C. 2010. High-resolution human genome structure by single molecule analysis. Proc. Natl. Acad. Sci. USA, Jun 15; 107 (24):10848-53. Open access: http://www.pnas.org/content/107/24/10848.full

Schwartz, D.C. and Waterman, M.S. 2010. New generations: sequencing machines and their computational challenges, J. of Comp. Sci. and Tech. 25(1): 3-9.

Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M., Churas, C., Pasternak, S., Forrest, D.K., Wise, R., Ware, D., Wing, R., Waterman, M.S., Livny, M., and Schwartz, D.C. 2010. A single molecule scaffold for the maize genome. PLoS Genetics 5: e1000711. Open access: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000711

Sambriski, E.J., Schwartz, D.C., and de Pablo, J.J. Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis. 2009. Proc Natl Acad Sci U S A 106(43):18125-30. Open access: http://www.pnas.org/content/106/43/18125.full?sid=b59afaa0-2922-4ec4-adc4-670c4c7c40ce

Yu, H., Jo, K., Kounovsky, K.L., de Pablo, J.J., and Schwartz, D.C. Molecular propulsion: Chemical sensing and chemotaxis of DNA driven by RNA polymerase. J. Amer. Chem. Soc., 131:5722-5723, 2009. (Featured in KurzweilAI.net, PhysOrg, InSciences)

Fuller, C.W., Middendorf, L.R., Benner, S.A., Church, G.M., Harris, T., Huang, X., Jovanovich, S.B., Nelson, J.R., Schloss, J.A., Schwartz, D.C., and Vezenov, D.V. 2009. The challenges of sequencing by synthesis. Nature Biotechnology 27: 1013-23.

Jo, K., Dhingra, D.M., Odijk, T., de Pablo, J.J., Graham, M.D., Runnheim, R., Forrest, D., and Schwartz, D.C. A single-molecule barcoding system using nanoslits for DNA analysis. 2007. Proc. Nat’l. Acad. Sci. USA 104: 2673-2678. (Featured in Nature Nanotechnology, Research Highlights, February 23, 2007 and in Proc. Nat’l. Acad. Sci. USA, In This Issue)

Ramanathan, A., Huff, E.J., Lamers, C.C., Potamoousis, K.D., Forrest, D.K., and Schwartz, D.C. An integrative approach for the Optical Sequencing of single DNA molecules. 2004. Anal. Biochem. 330:227-241.