 Professor of Chemistry and Genetics, Born 1954
B.A. 1976, Hampshire College
Ph.D. 1985, Columbia University
Room: 5434 Gen\Biotech
Phone: 608-265-0546
Email: dcschwartz@wisc.edu
Position: Professor
Kidd, J.M., Cooper, G.M., Schwartz, D., et.al. "Mapping and sequencing of structural variation from eight human genomes." Nature 453: 56-64, 2008. Izmitli, A., Schwartz, D.C., Graham, M.D., and de Pablo, J.J. "The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores." Journal Physical Chemistry 128: 085102 1-7, 2008. Fuller, C.W., Middendorf; Contributing authors: Benner, S.A., Church, G.M.,Huang, X., Jovanovich, S.B., Nelson, J.R., Schloss, J.A., Schwartz, D.C., and Vezenov, D.V. “Sequencing by synthesis.” Under revision, Nature Biotechnology, 2008. Zhou, S., Bechner, M.C., Place, M., Churas, C.P., Pape, L., Leong, S.A., Runnheim, R., Forrest, D.K., Goldstein, S., Livny, M. and Schwartz, D.C. "Validation of rice genome sequence by optical mapping." BMC Genomics 8:278, 2007. Herschleb, J., Ananiev, G., and Schwartz, D.C. "Pulsed-field gel electrophoresis." Nature Protocols 2: 677-684, 2007. Li, H., Valouev, A., Schwartz, D.C., Waterman, M.S. and Li, L.M. "A quantile method for sizing optical maps." Journal of Computational Biology 14: 255-266, 2007 Zhou, S., Herschleb, J., and Schwartz, D.C. "A single molecule system for whole genome analysis." New High Throughput Technologies for DNA Sequencing and Genomics, Volume 2 (Ed., K.R. Mitchelson) Elsevier Scientific Publishers, pp. 265-300, 2007. Knotts, IV, T.A., Rathore, N., Schwartz, D.C., de Pablo, J.J. "A coarse grain model for DNA." J. Chem Phys., 126: 084901 1-12, 2007. 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." Proceedings of the National Academy of Science USA 104:2673-2678, 2007. Wu, T., and Schwartz, D.C. "Transchip: Single-molecule detection of transcriptional elongation complexes." Anal. Biochem 361: 31-46, 2007. Valouev, A., Schwartz, D.C., Zhou, S., and Waterman, M.S. "An algorithm for assembly of ordered rstriction maps from single DNA molecules." Proceedings of the National Academy of Science USA 103:15770-15775, 2006. - Dimalanta, E.T., Lim, A., Runnheim, R., Lamers, C., Churas, C., Forrest, D.K., dePablo, J.J., Graham, M.D., Coppersmith, S.N., and Schwartz, D.C. A microfluidic system for large DNA molecule arrays. Anal. Chem. 76: 5293-5301, 2004.
- Zhou, S., Kile, A., Kvikstad, E., Bechner, M., Severin, J., Forrest, D., Runnheim, R., Churas, C., Anantharaman, T., Myler, P., Vogt, C., Ivens, A., Stuart, K., and Schwartz, D.C. Shotgun Optical Mapping of the entire Leishmania major Friedlin genome. Mol. Biochem. Parasitol. 138: 97-106, 2004.
- Zhou, S., Kile, A., Bechner, M., Place, M., Kvikstad, E., Deng, W., Wei, J., Severin, J., Runnheim, R., Churas, C., Forrest, D., Dimalanta, E., Lamers, C., Burland, V., Blattner, F., and Schwartz, D. Single-molecule approach to bacterial genomic comparisons via Optical Mapping. J. Bacteriol. 186: 7773-7782, 2004.
- Ambrust, E.V., Berges, J.A., Bowler, C., Green, B.R., Martinez, D., Putnam, N.H., Zhou, S., Allen, A.E., Apt, K.E., Bechner, M., Brzezinski, M.A., Chaal, B.K., Chiovitti, A., Davis, A.K., Demarest, M.S., Detter, J.C., Glavina, T., Goodstein, D., Hadi, M.Z., Hellsten, U., Hildebrand, M., Jenkins, B.D., Jurka, J., Kapitonov, V.V., Kr"ger, N., Lau, W.W.Y., Lane, T.W., Larimer, F.W., Lippmeier, J.C., Lucas, S., Medina, M., Montsant, A., Obornik, M., Parker, M.S., Palenik, B., Pazour, G.J., Richardson, P.M., Rynearson, T.A., Saito, M.A., Schwartz, D.C., Thamatrakoln, K., Valentin, K., Vardi, A., Wilkerson, F.P., and Rokhsar, D.S. The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 306: 79-86, 2004.
- Jendrejack, R.M., Schwartz, D.C., de Pablo, J.J., and Graham, M.D. Shear-induced migration in flowing polymer solutions: Simulation of long-chain DNA in microchannels. J. Chem. Phys. 120: 2513-2529, 2004.
| Research Description
Our laboratory creates functional systems for many types of genome analysis engendering large data sets for providing scalable biological insights. For this purpose we investigate the biochemical and physical attributes of individual molecules or complexes because reduction of experimental scale terminates at the level of a single molecule. Single molecules are the ultimate analyte since they represent the pinnacle of miniaturization and, when systematically analyzed as ensembles, offer the greatest advantages for generation of large-scale data sets. Such large and often complex data sets are the currency of modern biological analysis requiring extensive statistical and informatic components for revealing biological stories. In this regard, we have incorporated these components into our single molecule systems allowing us to discover novel human genome polymorphisms and to know the detailed architecture of cancer genomes. The new systems we are developing are pushing us to understand molecular nanoconfinement in ways fostering development of fluidic devices that when combined with novel molecular labeling or detection schemes, will power personal genomics and offer new routes for grappling with the complexity inherent to all biological systems.
Kellett Mid-Career Awardee (2002-2007) American Society for Biochemistry and Molecular Biology - Amgen Prize, 1995 Beckman Young Investigator Award, from the Arnold and Mable Beckman Foundation (1993) Presidential Young Investigator Award, from the National Science Foundation (1990) Lucille P. Markey Scholar Award, 1988 "Biochemical Analysis" Prize for the German Society of Clinical Chemistry, presented at Biotechnica, 1988 and awarded jointly with Dr. Charles Cantor (1988)
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