David Schwartz
Professor of Chemistry and Genetics
Ph.D., Columbia University, 1985
Postdoctoral Research: n/a
Lab Website: http://www.lmcg.wisc.edu/
Address: 5434 Genetics/Biotech
Telephone: 265-0546
E-mail: dcschwartz@wisc.edu
Research Interests:
Genomics (human, personal, cancer, plant, microbial,…), systems, synthetic biology, and chromatin
Research Fields:
Genomics
Human and Mammalian
Cancer Genetics
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:
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.
Professor of Chemistry and Genetics
Ph.D., Columbia University, 1985
Postdoctoral Research: n/a
Address: 5434 Genetics/Biotech
Telephone: 265-0546
E-mail: dcschwartz@wisc.edu
Research Interests:
Genomics (human, personal, cancer, plant, microbial,…), systems, synthetic biology, and chromatin
Research Fields:
Genomics
Human and Mammalian
Cancer Genetics
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.
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.
