Selected Publications

(Click on citations with a (+) to view the abstract)
  1. 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. The challenges of sequencing by synthesis. Nature Biotechnology, accepted, 2009.
  2. Sambriski, E.J., Schwartz, D.C., and de Pablo, J.J. Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis.Proc. Natl. Acad. Sci. USA, Epub before print, Oct. 8, 2009.
  3. 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, in press, 2009.
  4. Wei, F., Zhang, J., Zhou, S., He, R., Schaeffer, M., Collura, K., Kudrna, D., Faga, B.P., Wissotski, M., Golser, W., Rock, S.M., Graves, T.A., Fulton, R.S., Coe, E., Schnable, P.S., Schwartz, D.C., Ware, D. Clifton, S.W., Wilson, R.K., and Wing, R.W. The physical and genetics framework of the Maize B73 genome. PLoS Genetics, accepted, 2009.
  5. Coleman, J.J., Rounsley, S.D., Rodriguez-Carres, M., Kuo, A., Wasmann, C.C., Grimwood, J., Schmutz, J. , Taga, M., White, G.J., Zhou, S., Schwartz, D.C., Freitag, M., Ma, L., Danchin, E.G.J., Henrissat, B., Coutinho, P.M., Nelson, D.R., Straney, D., Napoli, C.A., Gribskov, M., Rep, M., Kroken, S., Molnár, I., Rensing, C., Kennell, J.C., Zamora, J., Farman, M.L., Selker, E.U.,Salamov, A., Shapiro, H., Pangilinan, J., Lindquist, E., Lamers, C., Grigoriev, I., Geiser, D.M., Covert, S.F., Temporini, E., and VanEtten, H.D. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genetics, accepted, 2009.
  6. Zhang, P., Too, P.H., Samuelson J.C., Chan, S., Vincze, T., Doucette, S., Bäckström, S., Potamousis, K.D., Schramm, T.M., Forrest, D., Schwartz, D.C., and Xu, S. Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA. Protein Expression and Purification, Epub before print, Sept. 9, 2009.
  7. Haas, B., et al. The genome sequence of the Irish potato famine pathogen Phytophthora infestans. Nature, in press, 2009.
  8. Jo, K., Chen, Y., de Pablo, J.J., and Schwartz, D.C. Elongation and migration of single DNA molecules in microchannels using oscillatory shear flows. Lab on a Chip, 9: 2348-2355, 2009.
  9. Sidorova, J.M., Li, N., Schwartz, D.C., Folch, A., and Monnat, R.J. Microfluidic-assisted analysis of replicating DNA molecules. Nature Protocols, 4: 849-861, 2009.
  10. 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.
  11. Church, D.M., Goodstadt, L., Hillier, L.W., Zody, M.C., Goldstein, S. She, X., Bult, C.J., Agarwala, R., Cherry, J.L., DiCuccio, M., Hlavina, W., Kapustin, Y., Meric, P., Maglott, D., Birtle, Z., Marques, A.C., Graves, T., Zhou, S., Teague, B., Potamousis, K., Churas, C., Place, M., Herschleb, J., Runnheim, R., Forrest, D., Amos-Landgraf, J., Schwartz, D.C., Cheng, Z., Lindblad-Toh, K., Eichler, E.E., Ponting, C.P., and The Mouse Genome Sequencing Consortium. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biology, epub, 2009.
  12. Wu, C.W., Schramm, T.M., Zhou, S., Schwartz, D.C., and Talaat, A.M. Optical Mapping of the Mycobacterium avium subspecies paratuberculosis genome. BMC Genomics, 10: 25, 2009.
  13. Jo, K., Schramm, T.M., and Schwartz, D.C. A single-molecule barcoding system using nanoslits for DNA analysis--Nanocoding. Methods in Molecular Biology (Ed., J.W. Lee and R.S. Foote) Humana Press, pp. 29-42, 2009.
  14. Zhou, S., Pape, L., Schwartz, D.C. Optical Sequencing: Acquisition from Mapped Single-Molecule Templates. Next-Generation Genome Sequencing: Towards Personalized Medicine (Ed., Michal Janitz) Wiley VCH, pp. 133 - 151, 2008.
  15. Ananiev, G.E., Goldstein, S., Runnheim, R., Forrest, D.K., Zhou, S., Potamousis, K., Churas, C.P., Begrendahl, V., Thomson, J.A., and Schwartz, D.C. Optical Mapping discerns genome wide DNA methylation profiles. BMC Molecular Biology 9: 68, 2008. PMCID: PMC2516518
  16. Yu, Hua and Schwartz, David C. Imaging and analysis of transcription on large, surface-mounted single template DNA molecules. Anal. Biochem. 380: 111-121, 2008. PMCID: PMC2561992
  17. Kidd, J.M., Cooper, G.M., Donahue, W.F., Hayden, H.S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., Haugen E., Zerr, T., Yamada, N.A., Tsang, P., Newman, T.L., Tüzün, E., Cheng, Z., Ebling, H.M., Tusneem, N., David, R., Gillett, W., Phelps, K.A., Weaver, M., Saranga, D., Brand, A., Tao, W., Gustafson, E., McKernan, K., Chen, L., Malig, M., Smith, J.D., Korn, J.M., McCarroll, S.A., Altshuler, D.A., Peiffer, D.A., Dorschner, M., Stamatoyannopoulos, J., Schwartz, D., Nickerson, D.A., Mullikin, J.C., Wilson, R.K., Bruhn, L., Olson, M.V., Kaul, R., Smith, D.R., and Eichler, E.E. Mapping and sequencing of structural variation from eight human genomes. Nature453: 56-64, 2008. PMCID: PMC2424287
  18. 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. J. Chem. Phys. 128: 085102 1-7, 2008.
  19. 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. PMCID: PMC2048515
  20. Herschleb, J., Ananiev, G., and Schwartz, D.C. Pulsed-field gel electrophoresis. Nature Protocols 2: 677-684, 2007.
  21. 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.
  22. 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.
  23. Wu, T. and Schwartz, D.C. Transchip: Single-molecule detection of transcriptional elongation complexes. Anal. Biochem. 361: 31-46, 2007. PMCID: PMC1945215
  24. Valouev, A., Schwartz, D., Zhou, S., and Waterman, M.S. An algorithm for assembly of ordered restriction maps from single DNA molecules. Proc. Natl. Acad. Sci. USA 103: 15770-15775, 2006.
  25. Valouev, A., Zhang, Y., Schwartz, D.C., and Waterman, M.S. Refinement of Optical Map assemblies. Bioinformatics 22: 1217-1224, 2006.
  26. Valouev, A., Li, L., Liu, Y., Schwartz, D.C., Yang, Y., Zhang, Y., and Waterman, M.S. Alignment of Optical Maps. J. Computational Biology 13: 442-462, 2006.
  27. Reslewic, S., Zhou, S., Place, M., Zhang, Y., Briska, A., Goldstein, S., Churas, C., Runnheim, R., Forrest, D., Lim, A., Lapidus, A., Han, C.S., Roberts, G.P., and Schwartz, D.C. Whole-genome shotgun Optical Mapping of Rhodospirillum rubrum. Appl. and Environ. Microbiol. 71: 5511-5522, 2005. PMCID: PMC1214604
  28. Chen, Y.L., Graham, M.D., de Pablo, J.J., Jo, K., and Schwartz, D.C. DNA molecules in microfluidic oscillatory flow. Macromolecules 38: 6680-6687, 2005.
  29. Ivens, A.C., et al. The genome of the kinetoplastid parasite, Leishmania major. Science 309: 436-442, 2005. PMCID: PMC1470643
  30. Reslewic, S., Herschleb, J., and Schwartz, D.C. Looking at whole genomes one molecule at a time. Amer. Biotechnology Laboratory 23: 26-29, 2005.
  31. Ramanathan, A., Pape, L., and Schwartz, D.C. High density polymerase-mediated incorporation of fluorochrome-labeled nucleotides. Anal. Biochem. 337: 1-11, 2005.
  32. 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.
  33. 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. PMCID: PMC524920
  34. 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., Kröger, 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.
  35. 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.
  36. Zhou, S. and Schwartz, D.C. The Optical Mapping of microbial genomes. ASM News 70: 323-330, 2004.
  37. Ramanathan, A., Huff, E.J., Lamers, C.C., Potamousis, K.D., Forrest, D.K., and Schwartz, D.C. An integrative approach for the Optical Sequencing of single DNA molecules. Anal. Biochem. 330: 227-241, 2004.
  38. 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.
  39. El-Sayed, N.M.A., Ghedin, E., Song, J., MacLeod, A., Bringaud, F., Larkin, C., Wanless, D., Peterson, J., Hou, L., Taylor, S., Tweedie, A., Biteau, N., Khalak, H.G., Lin, X., Mason, T., Hannick, L., Caler, E., Blandin, G., Bartholomeu, D., Simpson, A.J., Kaul, S., Zhao, H., Pai, G., Van Aken, S., Utterback, T., Haas, B., Koo, H.L., Umayam, L., Suh, B., Gerrard, C., Leech, V., Qi, R., Zhou, S., Schwartz, D., Feldblyum, T., Salzberg, S., Tait, A., Turner, C.M.R., Ullu, E., White, O., Melville, S., Adams, M.D., Fraser, C.M., and Donelson, J.E. The sequence and analysis of Trypanosoma brucei chromosome II. Nucl. Acids Research 31: 4856-4863, 2003.
  40. Kaplan, S., and Schwartz,, D.C. Whole-genome shotgun Optical Mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly. Genome Research 13: 2142-2151, 2003. PMCID: PMC403714
  41. Jendrejack, R.M., Dimalanta, E.T., Schwartz, D.C., Graham, M.D., and de Pablo, J.J. DNA dynamics in a microchannel. Phys. Rev. Lett. 91: 038102(1)-038102(4), 2003.
  42. Jendrejack, R.M., Schwartz, D.C., Graham, M.D., and de Pablo, J.J. Effect of confinement on DNA dynamics in microfluidic devices. J. Chem. Phys. 119: 1165-1173, 2003.
  43. Zhou, S., Deng, W., Anantharaman, T.S., Lim, A., Dimalanta, E.T., Wang, J., Wu, T., Chunhong, T., Creighton, R., Kile, A., Kvikstad, E., Bechner, M., Yen, G., Garic-Stankovic, A., Severin, J., Forrest, D., Runnheim, R., Churas, C., Lamers, C., Perna, N.T., Burland, V., Blattner, F.R., Mishra, B., and Schwartz, D.C. A whole-genome shotgun Optical Map of Yersinia pestis strain KIM. Appl. Environ. Microbiol. 68: 6321-6331, 2002.
  44. G. III, Burland, V., Mau, B., Hackett, J., Blattner, F.R., Anantharaman, T.S., Mishra, B., and Schwartz, D.C. Shotgun Optical Maps of the whole Escherichia coli O157:H7 genome. Genome Research 11: 1584-1593, 2001. PMCID: PMC311123
  45. Lai, Z., Jing, J., Aston, C., Clarke, V., Apodaca, J., Dimalanta, E.T., Carucci, D.J. Gardner, M.J., Mishra, B., Anantharaman, T.S., Paxia, S., Hoffman, S.L., Venter, J.C., Huff, E.J., and Schwartz, D.C. A shotgun Optical Map of the entire Plasmodium falciparum genome. Nature Genetics 23: 309-313, 1999.
  46. Skiadas, J., Aston, C., Samad, A., Anantharaman, T.S., Mishra, B., and Schwartz, D.C. Optical PCR: Genomic analysis by long-range PCR and Optical Mapping. Mamm. Genome 10: 1005-1009, 1999.
  47. Lin, J., Qi, R., Aston, C., Jing, J., Anantharaman, T.S., Mishra, B., White, O., Daly, M.J., Minton, K.W., Venter, J.C., and Schwartz, D.C. Whole genome shotgun Optical Mapping of Deinococcus radiodurans. Science 285: 1558-1562, 1999.
  48. Jing, J., Lai, Z., Aston, C., Lin, J., Carucci, D.J., Gardner, M.J., Mishra, B., Anantharaman, T.S., Tettelin, H., Cummings, L.M., Hoffman, S.L., Venter, J.C., and Schwartz, D.C. Optical Mapping of Plasmodium falciparum chromosome 2. Genome Research 9: 175-181, 1999. PMCID: PMC310721
  49. Aston, C., Hiort, C., and Schwartz, D.C. Optical Mapping: An approach for fine mapping. Methods in Enzymology 303: 55-73, 1999.
  50. DNA molecules. Proc. Natl. Acad. Sci. USA 95: 8046-8051, 1998.
  51. Cai, W., Jing, J., Irvin, B., Ohler, L., Rose, E., Shizuya, H., Kim, U.J., Simon, M., Anantharaman, T. and Schwartz, D.C. High-resolution restriction maps of bacterial artificial chromosomes constructed by Optical Mapping. Proc. Natl. Acad. Sci. USA 95: 3390-3395, 1998.
  52. Ananthraman, T.S., Mishra, B., and Schwartz, D.C. Genomics via Optical Mapping II: Ordered restriction maps. J. Computational Biology 4: 91-118, 1997.
  53. Schwartz, D.C. and Samad, A. Optical Mapping approaches to molecular genomics. Curr. Opinion in Biotechnology 8: 70-74, 1997.
  54. Samad, A.H., Cai, W.W., Hu, X., Irvin, B., Jing, J., Reed, J., Meng, X., Huang, J., Huff, E., Porter, B., Shenkar, A., Anantharaman, T., Mishra, B., Clarke, V., Dimalanta, E., Edington, J., Hiort, C., Rabbah, R., Skiada, J., and Schwartz, D.C. Mapping the genome one molecule at a time-Optical Mapping. Nature 378: 516-517, 1995.
  55. Samad, A.H., Huff, E., Cai, W., and Schwartz, D.C. Optical Mapping: A novel, single-molecule approach to genomic analysis. Genome Research 5: 1-4, 1995.
  56. Cai, W., Aburatani, H., Stanton, V.P., Housman, D.E., Wang, Y.K., and Schwartz, D.C. Ordered restriction endonuclease maps of yeast artificial chromosomes created by Optical Mapping on surfaces. Proc. Natl. Acad. Sci. USA 92: 5164-5168, 1995.
  57. Meng, X., Benson, K., Chada, K., Huff, E.J., and Schwartz, D.C. Optical Mapping of lambda bacteriophage clones using restriction endonucleases. Nature Genetics 9: 432-438, 1995.
  58. Wang, Y.K., Huff, E.D., and Schwartz, D.C. Optical Mapping of site-directed cleavages on single DNA molecules by the RecA-assisted restriction endonuclease technique. Proc. Natl. Acad. Sci. USA 92: 165-169, 1995.
  59. Schwartz, D.C., Li, X., Hernandez, L.I., Ramnarain, S.P., Huff, E.J., and Wang, Y.K. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by Optical Mapping. Science 262: 110-114, 1993.
©2007 The Regents of the University of Wisconsin. Permission is granted for nonprofit educational uses of this website and its contents. All other uses require written permission from Prof. D. C. Schwartz.
©2007 The Regents of the University of Wisconsin. All Rights Reserved.