个人简介

B.A. 1976, Hampshire College Ph.D. 1985, Columbia University Also: Kellett Professor of Chemistry and Genetics .

研究领域

Analytical/Chemical Biology

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.

近期论文

查看导师最新文章 （温馨提示：请注意重名现象，建议点开原文通过作者单位确认）

Heesch, S., Kloosterman, W., Lansu, N., Ruzius, R.P., Levandowsky, E., Lee, C., Simonis, M., Zhou, S., Goldstein, Schwartz, D.C., Harkins, T.,Guryev, V., and Cuppen, E., Uncovering mammalian genome structure by extra long mate-pair next-generation sequencing, submitted to Nature Methods, 2012. Manning, V.A., Pandelova, I., Dhillon, B., Wilhelm, L.J., Goodwin, S.B., Berlin , A.B., Figueroa, M., Freitag, M., Hane, J.K., Henrissat, B.Holman, W.H., Kodira, C.D., Martin, J., Oliver, R.P., Robbertse, B. Schackwitz, W., Schwartz, D.C., Spatafora, J.W., Turgeon, B.G., Yandava, C.,Young, S., Zhou, S., Zeng, Q., Grigoriev, I.V., Ma, L.-J., and Ciuffetti, L.M., Comparative Genomics of a Pathogenic Fungus Reveals Transduplication and the Impact of Repeat elements on Pathogenicity and Population Divergence, submitted to PLoS Genetics, 2012. Chen, S., Xu, J., Liu, C., Zhu, Y., Nelson D.R., Zhou, S., Li, C., Wang, L., Guo, X., Sun, Y., Luo, H., Li, Y., Song, Y., Henrissat, B., Levasseur,A., Qian, J., Li, J., Luo, X., Shi, L., Liu, H., Xiang, L., Xu , X.,Niu, Y., Li, Q., V. Han, M., Yan, H., Zhang, J., Chen, H., Lv, A., Wang, Z.,Liu, M., Schwartz, D.C., and Sun, C. Genome sequence of the model medicinal mushroom Ganoderma lucidum, Nature Communications,Jun 26; 3:913. doi: 10.1038/ncomms1923, 2012. Lin, H.C., Goldstein, S., Mendelowitz, L., Zhou, S., Wetzel, J Schwartz, D.C., and Pop, M., AGORA: Assembly Guided by Optical Restriction Alignment, BMC Genomics, Aug 2;13(1):189. [Epub ahead of print] 2012. Kounovsky-Shafer, K.L., Hernández-Ortiz, J.P., Jo, K., Odijk, T., de Pablo, J.J., and David C. Schwartz, D.C. Presentation of large DNA moleculesfor analysis as nanoconfined dumbbells, submitted to Proc. Natl. Acad. Sci. USA, 2012. O’Connell, R.J., Thon, M.R., Hacquard, S.., van Themaat, E.V.L. Stefan G Amyotte, S.G., Jochen Kleemann, J., Torres, M.F., Damm, U., Buiate, E.A.,Epstein, L., Alkan, N., Altmu?ller, J., Alvarado-Balderrama, L.A., Bauser, C.L., Christian Becker, C., Birren, B.W., Chen, Z., Choi, J., Crouch,J.A., Duvick, J.P., Farman, M.L., Gan, P., Heiman, D., Henrissat, B., Howard, R.J., Kabbage, M., Koch, C., Kubo, Y., Law, A.D., Lebrun, M.-H., Lee,Y.-H., Miyara, I., Moore, N., Neumann, U., Panaccione, D.G., Panstruga, R., Place, M., Proctor, R.H., Prusky, D., Rech, G., Reinhardt, R., Rollins,J.A., Rounsley, S., Schardl, C.L., , Schwartz, D.C., Shenoy, N., Shirasu, K., Sikhakolli, U.R., Stu?ber, K., Sukno, S.A., Sweigard, J.A., Takano,Y., Takahara, H., Trail, F., van der Does, H.C., Voll, L.M., Will, I., Young, S., Zeng, Q., Zhang, J., Zhou, S., Dickman, M.B., Schulze-Lefert, P.,Ma, L.J.-, Vaillancourt, L.J., Life-style transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses, Nature Genetics Aug 12. doi: 10.1038/ng.2372 [Epub ahead of print], 2012 Bannantine, J.P., Wu, C.-W., Hsu, C., Zhou, S., Schwartz, D.C., Bayles, D.O., Paustian, M.L., Alt, D.P., Sreevatsan, S., Kapur, V., and Talaat,A.M. Genome Sequencing of Ovine Isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association, BMC Genomics, Mar 12;13(1):89, 2012. Sarkar, D., Goldstein, S., Schwartz, D. C. and Newton, M. A. Statistical significance of optical map alignments. J. Comp. Biol., 19(5):478-92, 2012. Epub 2012 Apr 16, 2012. Young, N.D., Debellé, F., Oldroyd, G., Geurts, R., Cannon, S.B., Udvardi, M.K., Benedito, V.A., Mayer, K.F.X., Gouzy, J., Heiko Schoof, H., Van dePeer, Y., Proost, S., Cook, D.R., Meyers, B.C., Spannagl, M., Cheung, F., De Mita, S., Krishnakumar, V., Heidrun Gundlach, H., Zhou, S., Mudge, J.,Bharti, A.K., Murray, J.D., Naoumkina, M.A., Rosen, B., Silverstein, K.A.T., Tang, H., Rombauts, S., Zhao, P.X., Zhou, P., Barbe, V., Bardou, P.,Bechner, M., Bellec, A., Berger, A., Bergès, H., Bidwell, S., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Doyle, J., Dudez,A.-M., Farmer, A.D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Goldstein, S., González, A.J., Green, P.J., Hallab, A., Hartog, M., Hua, A.,Humphray, S., Jeong, D.-H., Jing, Y., J?cker, A., Kenton, S.M., Kim, D.-J., Klee, K., Lai, H., Lang, C., Lin, S., Macmil, S.L., Magdelenat, G.,Matthews, L., McCorrison, J., Monaghan, E.L., Mun, J.-H., Najar, F.Z., Nicholson, C., Noirot, C., O’Bleness, M., Paule, C.R., Poulain, J., Prion,F., Qin, B., Qu, C., Retzel, D.F., Riddle, C., Sallet, E., Samain, S., Samson, N., Sanders, I., Saurat, O., Scarpelli, C., Schiex, T., Segurens,B., Severin, A.J., Sherrier, D.J., Shi, R., Sims, S., Singer, S.R., Sinharoy, S., Sterck, L., Viollet, A., Wang, B.-B., Wang, K., Wang, X.,Warfsmann, J., Weissenbach, J., White, D.D., White, J.D., Wiley, G.B., Wincker, P., Xing, Y., Yang, L., Yao, Z., Ying, F., Zhai, J., Zhou, L.,Zuber, A., Dénarié, J., Dixon, R.A., May, G.D., Schwartz, D.C., Rogers, J., Quétier, F., Town, C.D., and Roe, B.A. The Medicago genome provides insight into the evolution of rhizobial symbioses, Nature, 480, 520–524, 2011. Munk, A.C., Copeland, A., Lucas, S., Lapidus, A., Del Rio, T.G., Barry, K., Detter, J.C., Hammon, N., Israni, S., Pitluck, S., Brettin, T., Bruce,D., Han, C., Tapia, R., Gilna, P., Schmutz, J., Larimer, F., Land, M., Kyrpides, N.C., Mavromatis, K., Richardson, P., Rohde, M., G?ker, M., Klenk,H.P., Zhang, Y., Roberts, G.P., Reslewic, S., and Schwartz D.C. Complete genome sequence of Rhodospirillum rubrum type strain (S1). Stand Genomic Sci. 2011 Jul 1;4(3):293-302. Epub 2011 Jun 30. Roe, BA, Debelle, F., Oldroyd, G et al., Medicago truncatula genome sequence, submitted to GenBank, 2011. Kim, Y., K.S. Kim, K.L. Kounovsky, R. Chang, G.Y. Jung, J.J. de Pablo, K. Jo, and D.C. Schwartz, Nanochannel confinement: DNA stretch approaching full contour length. Lab on a chip, 2011. Antonacci, F., Kidd, J. M., Marques-Bonet, T., Teague, B., Ventura, M., Girirajan, S., Alkan, C., Vives, L., Malig, M., Rosenfeld, J. A., Shaffer,L. G., Graves, T. A., Wilson, R. K., Schwartz, D. C. and Eichler, E. E. Dynamic evolution and complex human genome polymorphism at 16p12.1 underlies microdeletion disease risk. Nature Genetics, 42(9):745-50, 2010. Epub 2010 Aug 22.. 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. High-resolution human genome structure by single molecule analysis. Proc. Natl. Acad. Sci. USA, Jun 15; 107 (24):10848-53, 2010. Epub May 31, 2010. Open access: http://www.pnas.org/content/107/24/10848.full Zhang, P., Too, P.H., Samuelson J.C., Chan SH, Vincze, T., Doucette, S., B?ckstr?m S, Potamousis, K.D., Schramm, T.M., Forrest, D., Schwartz, D.C.,and Xu, S.Y. Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA. Protein Expr Purif. 69(2): 226-234, 2010. Epub Sep 9, 2009. Ma, L. J., van der Does, H. C., Borkovich, K. A., Coleman, J. J., Daboussi, M. J., Di Pietro, A., Dufresne, M., Freitag, M., Grabherr, M.,Henrissat, B., Houterman, P. M., Kang, S., Shim, W. B., Woloshuk, C., Xie, X., Xu, J. R., Antoniw, J., Baker, S. E., Bluhm, B. H., Breakspear, A.,Brown, D. W., Butchko, R. A., Chapman, S., Coulson, R., Coutinho, P. M., Danchin, E. G., Diener, A., Gale, L. R., Gardiner, D. M., Goff, S.,Hammond-Kosack, K. E., Hilburn, K., Hua-Van, A., Jonkers, W., Kazan, K., Kodira, C. D., Koehrsen, M., Kumar, L., Lee, Y. H., Li, L., Manners, J.M., Miranda-Saavedra, D., Mukherjee, M., Park, G., Park, J., Park, S. Y., Proctor, R. H., Regev, A., Ruiz-Roldan, M. C., Sain, D., Sakthikumar, S.,Sykes, S., Schwartz, D. C., Turgeon, B. G., Wapinski, I., Yoder, O., Young, S., Zeng, Q., Zhou, S., Galagan, J., Cuomo, C. A., Kistler, H. C. and Rep, M. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464 (7287): 367-73, 2010. Epub March18, 2010. Schwartz, D.C. and Waterman, M.S. New generations: sequencing machines and their computational challenges, J. of Comp. Sci. and Tech.25(1): 3-9, 2010. 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. A single molecule scaffold for the maize genome. PLoS Genetics 5:e1000711, 2009. Open access: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000711 Sidorova, J.M., Li, N., Schwartz, D.C., Folch, A., and Monnat, R.J. Microfluidic-assisted analysis of replicating DNA molecules. Nature Protocols, 4(6): 849-861, 2009. Epub May 14, 2009. Schnable, P.S. et al. (~100 authors). The B73 maize genome: complexity, diversity and dynamics. Science 326: 1112-1115, 2009.