Selected Publications

(Click on citations with a (+) to view the abstract)
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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., Altmüller, 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., Stüber, 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
  7. 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.
  8. 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.
  9. 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., Jöcker, 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.
  10. 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., Göker, 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.
  11. Roe, BA, Debelle, F., Oldroyd, G et al., Medicago truncatula genome sequence, submitted to GenBank, 2011.
  12. 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.
  13. 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..
  14. 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
  15. Zhang, P., Too, P.H., Samuelson J.C., Chan SH, Vincze, T., Doucette, S., Bäckström 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.
  16. 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.
  17. 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.
  18. 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
  19. 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.
  20. Schnable, P.S. et al. (~100 authors). The B73 maize genome: complexity, diversity and dynamics. Science 326: 1112-1115, 2009.
  21. 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 ofthe Maize B73 genome. PLoS Genetics 5: e1000715, 2009. Open access http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000715
  22. 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: contributionof supernumerary chromosomes to gene expansion. PLoS Genetics 5(8): e1000618.; Epub Aug 28, 2009.Open access: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000618
  23. Wei, F., Stein, J.C., 2, Liang, C., Zhang, J., Fulton, R.S., Baucom, R.S., De Paoli, E., Zhou, S., 6, Yang, L., Han, Y., Pasternak, S., Narechania,A., Zhang, L., Yeh, C.-T., Ying, K., Nagel, D.H., Collura, K., Kudrna, D., Currie, J., Lin, J., Kim, H.R., Angelove, A., Scara, G., Wissotski, M.,Golser, W., Courtney, L., Kruchowski, S., Graves, T., Rock, S., Adams, S., Fulton, L., Fronick, C., Courtney, W., Kramer, M., Spiegel, L.,Nascimento, L., Kalyanaraman, A., Chaparro, C., Deragon, J.-M., SanMiguel, P., 11, Ning Jiang, N., Wessler, S.R., Green, P.J., Yeisoo Yu, Y.,Schwartz, D.C., Meyers, B.C., Bennetzen, J., Martienssen, R., McCombie, W.R., Srinivas Aluru, S., Clifton, S.W., Schnable, P.S., Ware, D., Wilson,R.K., Wing, R.A., Detailed analysis of a contiguous 22-Mb region of the maize genome, PLoS Genetics 5: e1000728, 2009. Open access: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000728
  24. Sambriski, E.J., Schwartz, D.C., and de Pablo, J.J. A mesoscale model of DNA and its renaturation. Biophysical Journal, 95: 1675-90, 2009.
  25. 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, 544: pp. 29-42, 2009.
  26. Jo, K., Chen, Y., de Pablo, J.J., and Schwartz, D.C. Elongation and migration of single DNA molecules in microchannels using oscillatory shearflows. Lab on a Chip, 9(16): 2348-55, 2009.
  27. Haas, B., Kamoun, S., Zody, M.C., Jiang R.H.Y., Handsaker, R.E., Cano, L.M., Grabherr, M., Kodira, C.D., Raffaele, S., Torto-Alalibo, T., Bozkurt,T.O., O'Neill, K., Ah-Fong, A.M.V., Alvarado, L., Anderson, V.L., Armstrong, M.R., Avrova, A., Baxter, L., Beynon, J., Boevink, P.C., Bos, J.I.B.,Broad Institute Genome Sequencing Platform, Bulone, V., Cai, G., Cakir. C., Carrington, J.C., Chawner, M., Costanzo, S., Fahlgren, N., Fugelstad,J., Gilroy, E.M., Gnerre. S., Green, P.J., Grenville-Briggs, L.J., Griffith, J., Gupta, S., Horn, K., Horner, N.R., Hu, C.H., Huitema, E., Jeong,D.H., Jones, A., Jones, J.D.G., Jones, R., Karlsson, E., Lamour, K., Liu, Z., Ma, L., MacLean, D., Marcus, C., McDonald, H., McWalters, J., Meijer,H.J.G., Morgan, W., Morris, P.F., Munro, C.A., Ospina-Giraldo, M., Pinzón, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy. S.,Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D.C., Schumann, U.D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J.,Studholme, D.J., Sykes, S., van de Vondervoort, P.J.I., Vipaporn, P., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B.C.,van West, P., Ristaino, J., Govers, F., Birch, P.R.J., Whisson, S., Judelson, H.S., and Nusbaum, C. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461 (7262):393-8, 2009. Epub Sep 9, 2009. (Featured in Nature’s Editor’s Summary and cover).
  28. 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, 27: 1013-1023, 2009.
  29. 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 5(8): e1000618, 2009; Epub Aug 28, 2009. Open access: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000618
  30. (+) 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 7(5):e1000112, 2009. Epub May 26, 2009. (Featured in Nature 459: 619, 2009, Research Highlights – “Genetics: Filling mouse holes”) Open access: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000112
    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 RNApolymerase. J. Amer. Chem. Soc., 131: 5722-5723, 2009. (Featured in KurzweilAI.net, PhysOrg, InSciences)
  31. Mazurie, A.J., Alves, J.M., Ozaki, L.S., Zhou, S., Schwartz, D.C., and Buck, G.A. Comparative genomics of Cryptosporidium. Molecular Microbiology, submitted, 2009.
  32. 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, 2008.
  33. 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 Open access: http://www.biomedcentral.com/1471-2199/9/68
  34. Yu, H. and Schwartz, D.C. Imaging and analysis of transcription on large, surface-mounted single template DNA molecules. Anal. Biochem.380: 111-121, 2008. PMCID: PMC2561992
  35. 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. Nature 453: 56-64, 2008.PMCID: PMC2424287
  36. Izmitli, A., Schwartz, D.C., Graham, M.D., and de Pablo, J.J. The effect of hydrodynamic interactions on the dynamics of DNA translocation throughpores. J. Chem. Phys. 128: 085102 1-7, 2008.
  37. 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. Open access: http://www.biomedcentral.com/1471-2164/8/278
  38. Herschleb, J., Ananiev, G., and Schwartz, D.C. Pulsed-field gel electrophoresis. Nature Protocols 2: 677-684, 2007.
  39. Li, H., Valouev, A., Schwartz, D.C., Waterman, M.S., and Li, L.M. A quantile method for sizing Optical Maps. J. Computational Biology 14:255-266, 2007.
  40. 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.
  41. 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.
  42. 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. Proc. Nat’l. Acad. Sci. USA 104: 2673-2678, 2007. PMCID: PMC1815240
  43. Wu, T. and Schwartz, D.C. Transchip: Single-molecule detection of transcriptional elongation complexes. Anal. Biochem. 361: 31-46, 2007.PMCID: PMC1945215
  44. 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.
  45. Zody, M.C., et al. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature 440: 1045-1049, 2006.
  46. Valouev, A., Zhang, Y., Schwartz, D.C., and Waterman, M.S. Refinement of Optical Map assemblies. Bioinformatics 22: 1217-1224, 2006.
  47. Valouev, A., Li, L., Liu, Y., Schwartz, D.C., Yang, Y., Zhang, Y., and Waterman, M.S. Alignment of Optical Maps. J. Computational Biology13: 442-462, 2006.
  48. 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
  49. 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.
  50. Ivens, A.C., et al. The genome of the kinetoplastid parasite, Leishmania major. Science 309: 436-442, 2005. PMCID: PMC1470643
  51. Reslewic, S., Herschleb, J., and Schwartz, D.C. Looking at whole genomes one molecule at a time. Amer. Biotechnology Laboratory 23: 26-29,2005.
  52. Ramanathan, A., Pape, L., and Schwartz, D.C. High density polymerase-mediated incorporation of fluorochrome-labeled nucleotides. Anal. Biochem. 337: 1-11, 2005.
  53. 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.
  54. 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
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  57. Zhou, S. and Schwartz, D.C. The Optical Mapping of microbial genomes. ASM News 70: 323-330, 2004.
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  59. 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.
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  61. 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.
  62. Zhou, S., Kvikstad, E., Kile, A., Severin, J., Forrest, D., Runnheim, R., Churas, C., Hickman, J.W., Mackenzie, C., Choudhary, M., Donohue, T.,Kaplan, S., and Schwartz,, D.C. Whole-genome shotgun Optical Mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgunsequence assembly. Genome Research 13: 2142-2151, 2003. PMCID: PMC403714 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.
  63. 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.
  64. 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.
  65. Lim, A., Dimalanta, E.T., Potamousis, K.D., Yen, G., Apodoca, J., Tao, C., Lin, J., Qi, R., Skiadas, J., Ramanathan, A., Perna, N.T., Plunkett, 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 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., andSchwartz, D.C. A shotgun Optical Map of the entire Plasmodium falciparum genome. Nature Genetics 23: 309-313, 1999.
  66. 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.
  67. 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.
  68. 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
  69. Aston, C., Mishra, B., and Schwartz, D.C. Optical Mapping and its potential for large-scale sequencing projects. Trends in Biotechnology 17:297-302, 1999. Aston, C., Hiort, C., and Schwartz, D.C. Optical Mapping: An approach for fine mapping. Methods in Enzymology 303: 55-73,1999.
  70. Jing, J., Reed, J., Huang, J., Hu, X., Clarke, V., Edington, J., Housman, D., Anantharaman, T.S., Huff, E.J., Mishra, B., Porter, B., Shenker, A.,Wolfson, E., Hiort, C., Kantor, R., Aston, C., and Schwartz, D.C. Automated high resolution Optical Mapping using arrayed, fluid-fixed, DNA molecules. Proc. Natl. Acad. Sci. USA 95: 8046-8051, 1998.
  71. Cai, W., Jing, J., Irvin, B., Ohler, L., Rose, E., Shizuya, H., Kim, U.J., Simon, M., Anantharaman, T. and Schwartz, D.C. High-resolutionrestriction maps of bacterial artificial chromosomes constructed by Optical Mapping. Proc. Natl. Acad. Sci. USA 95: 3390-3395, 1998.
  72. Ananthraman, T.S., Mishra, B., and Schwartz, D.C. Genomics via Optical Mapping II: Ordered restriction maps. J. Computational Biology 4:91-118, 1997.
  73. Schwartz, D.C. and Samad, A. Optical Mapping approaches to molecular genomics. Curr. Opinion in Biotechnology 8: 70-74, 1997.
  74. 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.
  75. Samad, A.H., Huff, E., Cai, W., and Schwartz, D.C. Optical Mapping: A novel, single-molecule approach to genomic analysis. Genome Research5: 1-4, 1995.
  76. Cai, W., Aburatani, H., Stanton, V.P., Housman, D.E., Wang, Y.K., and Schwartz, D.C. Ordered restriction endonuclease maps of yeast artificialchromosomes created by Optical Mapping on surfaces. Proc. Natl. Acad. Sci. USA 92: 5164-5168, 1995.
  77. 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.
  78. 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.
  79. Schwartz, D.C., Li, X., Hernandez, L.I., Ramnarain, S.P., Huff, E.J., and Wang, Y.K. Ordered restriction maps of Saccharomyces cerevisiaechromosomes constructed by Optical Mapping. Science 262: 110-114, 1993.
  80. Schwartz, D.C. and Koval, M. Conformational dynamics of individual DNA molecules during gel electrophoresis. Nature 338: 520-522, 1989.
  81. Schwartz, D.C. and Cantor, C.R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37: 67-75,1984.
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