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Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, et al. Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence. G3-Genes Genomes Genetics. 2013;3:41-63. |
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Bannantine JP, Wu CW, Hsu CY, Zhou SG, Schwartz DC, Bayles DO, et al. Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association. Bmc Genomics. 2012;13. |
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Chen SL, Xu J, Liu C, Zhu YJ, Nelson DR, Zhou SG, et al. Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nature Communications. 2012;3. |
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Lin HC, Goldstein S, Mendelowitz L, Zhou SG, Wetzel J, Schwartz DC, et al. AGORA: Assembly Guided by Optical Restriction Alignment. Bmc Bioinformatics. 2012;13. |
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Sarkar D, Goldstein S, Schwartz DC, Newton MA, Rr Db JOTASAVP. Statistical Significance of Optical Map Alignments. Journal of Computational Biology. 2012;19:478-492. |
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Schwartz DC, Zhou S, Goldstein S, Potomousis K, Place M, Teague B, et al. Dealing with the Threads of Life: A Singular View of the GenomeGlyoxal in Aqueous Ammonium Sulfate Solutions: Products, Kinetics and Hydration Effects. In Vitro Cellular & Developmental Biology-Animal. 2011;47:507-507. |
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Kim Y, Kim KS, Kounovsky KL, Chang R, Jung GY, De Pablo JJ, et al. Nanochannel confinement: DNA stretch approaching full contour length. Lab on a Chip. 2011;11:1721-1729. |
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Antonacci F, Kidd JM, Marques-Bonet T, Teague B, Ventura M, Girirajan S, et al. A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nature Genetics. 2010;42:745-U29. |
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Schwartz DC, Waterman MS. New Generations: Sequencing Machines and Their Computational Challenges. Journal of Computer Science and Technology. 2010;25:3-9. |
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Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, et al. High-resolution human genome structure by single-molecule analysis. Proceedings of the National Academy of Sciences of the United States of America. 2010;107:10848-10853. |
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Zhang P, Too PH-M, Samuelson JC, Chan S-H, Vincze T, Doucette S, et al. Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA. Protein Expression and Purification. 2010;69:226-234. |
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Haas BJ, Kamoun S, Zody MC, Jiang RHY, Handsaker RE, Cano LM, et al. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 2009;461:393-398. |
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Jo K, Chen YL, de Pablo JJ, Schwartz DC. Elongation and migration of single DNA molecules in microchannels using oscillatory shear flows. Lab on a Chip. 2009;9:2348-2355. |
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Sambriski EJ, Schwartz DC, de Pablo JJ. A Mesoscale Model of DNA and Its Renaturation. Biophysical Journal. 2009;96:1675-1690. |
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Sambriski EJ, Schwartz DC, de Pablo JJ. Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis. Proceedings of the National Academy of Sciences of the United States of America. 2009;106:18125-18130. |
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Sambriski EJ, Schwartz DC, de Pablo JJ. Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis (vol 106, pg 18125, 2009). Proceedings of the National Academy of Sciences of the United States of America. 2009;106:21007-21007. |
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Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science. 2009;326:1112-1115. |
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Sidorova JM, Li NZ, Schwartz DC, Folch A, Monnat RJ. Microfluidic-assisted analysis of replicating DNA molecules. Nature Protocols. 2009;4:849-861. |
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Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, et al. Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome. Plos Genetics. 2009;5. |
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Wei F, Zhang J, Zhou S, He R, Schaeffer M, Collura K, et al. The Physical and Genetic Framework of the Maize B73 Genome. Plos Genetics. 2009;5. |
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Wu CW, Schramm TM, Zhou SG, Schwartz DC, Talaat AM. Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome. Bmc Genomics. 2009;10. |
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Yu H, Jo K, Kounovsky KL, de Pablo JJ, Schwartz DC. Molecular Propulsion: Chemical Sensing and Chemotaxis of DNA Driven by RNA Polymerase. Journal of the American Chemical Society. 2009;131:5722-+. |
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Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, et al. A Single Molecule Scaffold for the Maize Genome. Plos Genetics. 2009;5. |
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Ananiev GE, Goldstein S, Runnheim R, Forrest DK, Zhou S, Potamousis K, et al. Optical mapping discerns genome wide DNA methylation profiles. Bmc Molecular Biology. 2008;9. |
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lzmitli A, Schwartz DC, Graham MD, De Pablo JJ. The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores. Journal of Chemical Physics. 2008;128. |
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Yu H, Schwartz DC. Imaging and analysis of transcription on large, surface-mounted single template DNA molecules. Analytical Biochemistry. 2008;380:111-121. |
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Herschleb J, Ananiev G, Schwartz DC. Pulsed-field gel electrophoresis. Nature Protocols. 2007;2:677-684. |
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Jo K, Dhingra DM, Odijk T, De Pablo JJ, Graham MD, Runnheim R, et al. A single-molecule barcoding system using nanoslits for DNA analysis. Proceedings of the National Academy of Sciences of the United States of America. 2007;104:2673-2678. |
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Knotts TA, Rathore N, Schwartz DC, De Pablo JJ. A coarse grain model for DNA. Journal of Chemical Physics. 2007;126. |
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Wu T, Schwartz DC. Transchip: Single-molecule detection of transcriptional elongation complexes. Analytical Biochemistry. 2007;361:31-46. |
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Zhou S, Bechner MC, Place M, Churas CP, Pape L, Leong SA, et al. Validation of rice genome sequence by optical mapping. Bmc Genomics. 2007;8. |
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Lim A, Dimalanta ET, Potamousis KD, Yen G, Apodoca J, Tao CH, et al. Shotgun optical maps of the whole Escherichia coli O157 : H7 genome. Genome Research. 2006;13:442-462. |
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Reslewic S, Zhou SG, Place M, Zhang YP, Briska A, Goldstein S, et al. Whole-genome shotgun optical mapping of Rhodospirillum rubrum. Applied & Environmental MicrobiologyApplied & Environmental Microbiology. 2005;71:5511-5522. |
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Ramanathan A, Pape L, Schwartz DC. High-density polymerase-mediated incorporation of fluorochrome-labeled nucleotides. Analytical BiochemistryAnalytical Biochemistry. 2005;337:1-11. |
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Chen Y-L, Graham MD, de Pablo JJ, Jo K, Schwartz DC. DNA Molecules in Microfluidic Oscillatory Flow. Macromolecules. 2005;38(15):6680-6687. |
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Zhou SG, Kile A, Kvikstad E, Bechner M, Severin J, Forrest D, et al. Shotgun optical mapping of the entire Leishmania major Friedlin genome. Molecular & Biochemical ParasitologyMolecular & Biochemical Parasitology. 2004;138:97-106. |
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Zhou S, Kile A, Bechner M, Place M, Kvikstad E, Deng W, et al. Single-molecule approach to bacterial genomic comparisons via optical mapping. Journal of Bacteriology. 2004;186:7773-7782. |
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Ramanathan A, Huff EJ, Lamers CC, Potamousis KD, Forrest DK, Schwartz DC. An integrative approach for the optical sequencing of single DNA molecules. Analytical BiochemistryAnalytical Biochemistry. 2004;330:227-241. |
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Jendrejack RM, Schwartz DC, de Pablo JJ, Graham MD. Shear-induced migration in flowing polymer solutions: Simulation of long-chain DNA in microchannels (vol 120, pg 2513, 2004). Journal of Chemical Physics. 2004;120:6315. |
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Jendrejack RM, Schwartz DC, de Pablo JJ, Graham MD. Shear-induced migration in flowing polymer solutions: Simulation of long-chain deoxyribose nucleic acid in microchannels. Journal of Chemical Physics. 2004;120:2513-2529. |
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Dimalanta ET, Lim A, Runnheim R, Lamers C, Churas C, Forrest DK, et al. A microfluidic system for large DNA molecule arrays. Analytical ChemistryAnalytical Chemistry. 2004;76:5293-5301. |
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Zhou SG, Kvikstad E, Kile A, Severin J, Forrest D, Runnheim R, et al. Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly. Genome ResearchGenome Research. 2003;13:2142-2151. |
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Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, et al. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T (vol 71, pg 2775, 2003). Infection & ImmunityInfection & Immunity. 2003;71:4223. |
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Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, et al. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infection and ImmunityInfection & Immunity. 2003;71:2775-2786. |
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Jendrejack RM, Schwartz DC, Graham MD, de Pablo JJ. Effect of confinement on DNA dynamics in microfluidic devices. Journal of Chemical Physics. 2003;119:1165-1173. |
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Jendrejack RM, Dimalanta ET, Schwartz DC, Graham MD, de Pablo JJ. DNA dynamics in a microchannel - art. no. 038102. Physical Review Letters. 2003;9103:8102. |
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Zhou SG, Deng W, Anantharaman TS, Lim A, Dimalanta ET, Wang J, et al. A whole-genome shotgun optical map of Yersinia pestis strain KIM. Applied & Environmental MicrobiologyApplied & Environmental Microbiology. 2002;68:6321-6331. |
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Deng W, Burland V, Plunkett G, Boutin A, Mayhew GF, Liss P, et al. Genome sequence of Yersinia pestis KIM. Journal of Bacteriology. 2002;184:4601-4611. |
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Perna NT, Plunkett G, Burland V, Mau B, Glasner JD, Rose DJ, et al. Genome sequence of enterohaemorrhagic Escherichia coli O157 : H7. NatureNature. 2001;409:529-533. |
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Lim A, Dimalanta ET, Potamousis KD, Yen G, Apodoca J, Tao CH, et al. Shotgun optical maps of the whole Escherichia coli O157 : H7 genome. Genome ResearchGenome Research. 2001;11:1584-1593. |
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Giacalone J, Delobette S, Gibaja V, Ni L, Skiadas Y, Qi R, et al. Optical mapping of BAC clones from the human Y chromosome DAZ locus. Genome Research. 2000;10:1421-1429. |
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Lai ZW, Jing JP, Aston C, Clarke V, Apodaca J, Dimalanta ET, et al. A shotgun optical map of the entire Plasmodium falciparum genome. Nature Genetics. 1999;23:309-313. |
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Lin JY, Qi R, Aston C, Jing JP, Anantharaman TS, Mishra B, et al. Whole-genome shotgun optical mapping of Deinococcus radiodurans. Science. 1999;285:1558-1562. |
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Skiadas J, Aston C, Samad A, Anantharaman TS, Mishra B, Schwartz DC. Optical PCR: Genomic analysis by long-range PCR and optical mapping. Mammalian Genome. 1999;10:1005-1009. |
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Aston C, Mishra B, Schwartz DC. Optical mapping and its potential for large-scale sequencing projects. Trends Biotechnol. 1999;17(7):297-302. |
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Skiadas J, Aston C, Samad A, Anantharaman TS, Mishra B, Schwartz DC. Optical PCR: genomic analysis by long-range PCR and optical mapping. Mamm Genome. 1999;10(10):1005-9. |
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Cai W, Jing J, Irvin B, Ohler L, Rose E, Shizuya H, et al. High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping. Proc Natl Acad Sci U S A. 1998;95(7):3390-5. |
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Jing J, Reed J, Huang J, Hu X, Clarke V, Edington J, et al. Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules. Proc Natl Acad Sci U S A. 1998;95(14):8046-51. |
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Schwartz DC, Samad A. Optical mapping approaches to molecular genomics. Curr Opin Biotechnol. 1997;8(1):70-4. |
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Anantharaman TS, Mishra B, Schwartz DC. Genomics via optical mapping. II: Ordered restriction maps. J Comput Biol. 1997;4(2):91-118. |
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Cai W, Aburatani H, Stanton VP, Housman DE, Wang YK, Schwartz DC. Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces. Proc Natl Acad Sci U S A. 1995;92(11):5164-8. |
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Meng X, Benson K, Chada K, Huff EJ, Schwartz DC. Optical mapping of lambda bacteriophage clones using restriction endonucleases. Nat Genet. 1995;9(4):432-8. |
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Samad A, Huff EF, Cai W, Schwartz DC. Optical mapping: a novel, single-molecule approach to genomic analysis. Genome Res. 1995;5(1):1-4. |
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Schwartz DC, Li X, Hernandez LI, Ramnarain SP, Huff EJ, Wang YK. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science. 1993;262(5130):110-4. |
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Schwartz DC, Cantor CR. SEPARATION OF YEAST CHROMOSOME-SIZED DNAS BY PULSED FIELD GRADIENT GEL-ELECTROPHORESIS. Cell. 1984;37:67-75. |
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Vanderploeg LHT, Schwartz DC, Cantor CR, Borst P. ANTIGENIC VARIATION IN TRYPANOSOMA BRUCEI ANALYZED BY ELECTROPHORETIC SEPARATION OF CHROMOSOME-SIZED DNA-MOLECULES. Cell. 1984;37:77-84. |
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Schwartz DC, Cantor CR. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell. 1984;37(1):67-75. |
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Schwartz DC, Saffran W, Welsh J, Haas R, Goldenberg M, Cantor CR. NEW TECHNIQUES FOR PURIFYING LARGE DNAS AND STUDYING THEIR PROPERTIES AND PACKAGING. Cold Spring Harbor Symposia on Quantitative Biology. 1982;47:189-195. |
