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Lequieu J, Schwartz DC, de Pablo JJ. In silico evidence for sequence-dependent nudeosome sliding. Proceedings of the National Academy of Sciences of the United States of America. 2017;114:E9197-E9205.
Lee S, Oh Y, Lee J, Choe S, Lim S, Lee HS, et al.. DNA binding fluorescent proteins for the direct visualization of large DNA molecules. Nucleic Acids Research. 2016;44:e6.
Li Y, Zhou SG, Schwartz DC, Ma J. Allele-Specific Quantification of Structural Variations in Cancer Genomes. Cell Systems. 2016;3:21-34.
Zhu YJ, Xu J, Sun C, Zhou SG, Xu HB, Nelson DR, et al.. Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense. Scientific Reports. 2015;5.
Gupta A, Place M, Goldstein S, Sarkar D, Zhou SG, Potamousis K, et al.. Single-molecule analysis reveals widespread structural variation in multiple myeloma. Proceedings of the National Academy of Sciences of the United States of America. 2015;112:7689-7694.
Zhou SG, Goldstein S, Place M, Bechner M, Patino D, Potamousis K, et al.. A clone-free, single molecule map of the domestic cow (Bos taurus) genome. Bmc Genomics. 2015;16.
Yuan B, Liu PF, Gupta A, Beck CR, Tejomurtula A, Campbell IM, et al.. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates. Plos Genetics. 2015;11.
Tang HB, Krishnakumar V, Bidwell S, Rosen B, Chan AN, Zhou SG, et al.. An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics. 2014;15.
van Heesch S, Kloosterman WP, Lansu N, Ruzius FP, Levandowsky E, Lee CC, et al.. Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing. Bmc Genomics. 2013;14.
Ray M, Goldstein S, Zhou S, Potamousis K, Sarkar D, Newton MA, et al.. Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis. Bmc Genomics. 2013;14.
Mazurie AJ, Alves JM, Ozaki LS, Zhou SG, Schwartz DC, Buck GA. Comparative Genomics of Cryptosporidium. International Journal of Genomics. 2013;.
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.
Kounovsky-Shafer KL, Hernandez-Ortiz JP, Jo K, Odijk T, de Pablo JJ, Schwartz DC. Presentation of Large DNA Molecules for Analysis as Nanoconfined Dumbbells. Macromolecules. 2013;46:8356-8368.
Sarkar D, Goldstein S, Schwartz DC, Newton MA. Statistical Significance of Optical Map Alignments. Journal of Computational Biology. 2012;19:478-492.
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.
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.
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.
O'Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, et al.. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nature Genetics. 2012;44:1060-1065.
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Young ND, Debellé F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, et al.. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 2011;480:520-524.
A. Munk C, Copeland A, Lucas S, Lapidus A, Del Rio TG, Barry K, et al.. Complete genome sequence of Rhodospirillum rubrum type strain (S1T). Stand. Genomic Sci. 2011;4:293-302.
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 & Purification. 2010;69:226-234.
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.
Schwartz DC, Waterman MS. New Generations: Sequencing Machines and Their Computational Challenges. Journal of Computer Science and Technology. 2010;25:3-9.
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.
Sambriski EJ, Schwartz DC, de Pablo JJ. Association free energy of DNA oligonucleotides from expanded ensembles. AIP Conference Proceedings. 2010;1319:148-159.
Ma L-J, H. van der Does C, Borkovich KA, Coleman JJ, Daboussi M-J, Di Pietro A, et al.. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 2010;464:367-373.
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.
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-+.
Wu CW, Schramm TM, Zhou SG, Schwartz DC, Talaat AM. Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome. Bmc Genomics. 2009;10.
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.
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.
Sidorova JM, Li NZ, Schwartz DC, Folch A, Monnat RJ. Microfluidic-assisted analysis of replicating DNA molecules. Nature Protocols. 2009;4:849-861.
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.
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.
Sambriski EJ, Schwartz DC, de Pablo JJ. A Mesoscale Model of DNA and Its Renaturation. Biophysical Journal. 2009;96:1675-1690.
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.
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.
Jo K, Schramm TM, Schwartz DC. A single-molecule barcoding system using nanoslits for DNA analysis: nanocoding. Methods Mol. Biol. . 2009;544:29-42.
Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, et al.. The challenges of sequencing by synthesis. Nature Biotechnology. 2009;27:1013-1023.
Yu H, Schwartz DC. Imaging and analysis of transcription on large, surface-mounted single template DNA molecules. Analytical Biochemistry. 2008;380:111-121.
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.
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.
Zhou S, Pape L, Schwartz DC. Optical sequencing: acquisition from mapped single-molecule templates. Next-Gener. Genome Sequencing. 2008;:133-151.
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.
Wu T, Schwartz DC. Transchip: Single-molecule detection of transcriptional elongation complexes. Analytical Biochemistry. 2007;361:31-46.
Knotts TA, Rathore N, Schwartz DC, De Pablo JJ. A coarse grain model for DNA. Journal of Chemical Physics. 2007;126.
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.
Herschleb J, Ananiev G, Schwartz DC. Pulsed-field gel electrophoresis. Nature Protocols. 2007;2:677-684.
Schwartz DC, Felberbaum R, Hochstrasser M. The Ulp2 SUMO protease is required for cell division following termination of the DNA damage checkpoint. Molecular and Cellular Biology. 2007;27:6948-6961.
Li H, Valouev A, Schwartz DC, Waterman MS, Li LM. A quantile method for sizing optical maps. Journal of Computational Biology. 2007;14:255-266.
Zody MC, Garber M, Adams DJ, Sharpe T, Harrow J, Lupski JR, et al.. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature. 2006;440:1045-1049.
Valouev A, Zhang Y, Schwartz DC, Waterman MS. Refinement of optical map assemblies. Bioinformatics. 2006;22:1217-1224.
Valouev A, Schwartz DC, Zhou S, Waterman MS. An algorithm for assembly of ordered restriction maps from single DNA molecules. Proceedings of the National Academy of Sciences of the United States of America. 2006;103:15770-15775.
Valouev A, Li L, Liu Y-C, Schwartz DC, Yang Y, Zhang Y, et al.. Alignment of optical maps. Journal of Computational Biology. 2006;13:442-462.
Reslewic S, Zhou SG, Place M, Zhang YP, Briska A, Goldstein S, et al.. Whole-genome shotgun optical mapping of Rhodospirillum rubrum. Applied & Environmental Microbiology. 2005;71:5511-5522.
Ramanathan A, Pape L, Schwartz DC. High-density polymerase-mediated incorporation of fluorochrome-labeled nucleotides. Analytical Biochemistry. 2005;337:1-11.
Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, Berriman M, et al.. The genome of the kinetoplastid parasite, Leishmania major. Science. 2005;309:436-442.
Chen YL, Graham MD, de Pablo JJ, Jo K, Schwartz DC. DNA Molecules in Microfluidic Oscillatory Flow. Macromolecules. 2005;38:6680-6687.
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.
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.
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 Parasitology. 2004;138:97-106.
Ramanathan A, Huff EJ, Lamers CC, Potamousis KD, Forrest DK, Schwartz DC. An integrative approach for the optical sequencing of single DNA molecules. Analytical Biochemistry. 2004;330:227-241.
Dimalanta ET, Lim A, Runnheim R, Lamers C, Churas C, Forrest DK, et al.. A microfluidic system for large DNA molecule arrays. Analytical Chemistry. 2004;76:5293-5301.
E. Armbrust V, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, et al.. The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science. 2004;306:79-86.
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.
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.
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 Research. 2003;13:2142-2151.
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 Immunity. 2003;71:2775-2786.
Steiger M, Carr-Schmid A, Schwartz DC, Kiledjian M, Parker R. Analysis of recombinant yeast decapping enzyme. RNA. 2003;9:231-238.
Schwartz DC, Hochstrasser M. A superfamily of protein tags: ubiquitin, SUMO and related modifiers. Trends in Biochemical Sciences. 2003;28:321-328.
Deng W, Liou S-R, Plunkett, III G, Mayhew GF, Rose DJ, Burland V, et al.. Comparative genomics of Salmonella enterica serovar typhi strains Ty2 and CT18. Journal of Bacteriology. 2003;185:2330-2337.
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.
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 Microbiology. 2002;68:6321-6331.
Welch RA, Burland V, Plunkett, III G, Redford P, Roesch P, Rasko D, et al.. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 2002;99:17020-17024.
Perna NT, Plunkett G, Burland V, Mau B, Glasner JD, Rose DJ, et al.. Genome sequence of enterohaemorrhagic Escherichia coli O157 : H7. Nature. 2001;409:529-533.
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. 2001;11:1584-1593.
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.
Schwartz DC, Parker R. Interaction of mRNA translation and mRNA degradation in Saccharomyces cerevisiae. Cold Spring Harbor Monogr. Ser. 2000;39:807-825.
Schwartz DC, Parker R. mRNA decapping in yeast requires dissociation of the cap binding protein, eukaryotic translation initiation factor 4E. Molecular and Cellular Biology. 2000;20:7933-7942.
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.
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.
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.
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.
Schwartz DC, Parker R. Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae. Molecular and Cellular Biology. 1999;19:5247-5256.
Kantor RM, Guo X-H, Huff EJ, Schwartz DC. Dynamics of DNA Molecules in Gel Studied by Fluorescence Microscopy. Biochemical & Biophysical Research Communications. 1999;258:102-108.
Jing J, Lai Z, Aston C, Lin J, Carucci DJ, Gardner MJ, et al.. Optical mapping of Plasmodium falciparum chromosome 2. Genome Research. 1999;9:175-181.
Hu X, Aston C, Schwartz DC. Optical mapping of DNA polymerase I action and products. Biochemical & Biophysical Research Communications. 1999;254:466-473.
Aston C, Mishra B, Schwartz DC. Optical mapping and its potential for large-scale sequencing projects. Trends in Biotechnology. 1999;17:297-302.
Aston C, Hiort C, Schwartz DC. Optical mapping: an approach for fine mapping. Methods in Enzymology. 1999;303:55-73.
Wang W, Lin J, Schwartz DC. Scanning force microscopy of DNA molecules elongated by convective fluid flow in an evaporating droplet. Biophysical Journal. 1998;75:513-520.
Reed J, Singer E, Kresbach G, Schwartz DC. A quantitative study of optical mapping surfaces by atomic force microscopy and restriction endonuclease digestion assays. Analytical Biochemistry. 1998;259:80-88.
Philipp WJ, Schwartz DC, Telenti A, Cole ST. Mycobacterial genome structure. Electrophoresis. 1998;19:573-576.
Jing J, Reed J, Huang J, Hu X, Clarke V, Edington J, et al.. Automated high resolution optical mapping using arrayed, fluid-fixed molecules. Proceedings of the National Academy of Sciences of the United States of America. 1998;95:8046-8051.
Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Aravind L, Koonin EV, et al.. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science. 1998;282:1126-1132.
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. Proceedings of the National Academy of Sciences of the United States of America. 1998;95:3390-3395.
Schwartz DC, Samad A. Optical mapping approaches to molecular genomics. Current Opinion in Biotechnology. 1997;8:70-74.
Bautsch W, Romling U, Schmidt KD, Samad A, Schwartz DC, Tummler B. Long-range restriction mapping of genomic DNA. Genome Mapp. 1997;:281-313.
Anantharaman TS, Mishra B, Schwartz DC. Genomics via optical mapping II: ordered restriction maps. Journal of Computational Biology. 1997;4:91-118.
Morozov VN, Morozova TY, Hiort C, Schwartz DC. New polyacrylamide gel-based methods of sample preparation for optical microscopy: immobilization of DNA molecules for optical mapping. Journal of Microscopy. 1996;183:205-14.
Morozov VN, Morozova TY, Hiort C, Schwartz DC. New polyacrylamide gel-based methods of sample preparation for optical microscopy: Immobilization of DNA molecules for optical mapping. J. Microsc. (Oxford). 1996;183:205-214.
Meng X, Cai W, Schwartz DC. Inhibition of restriction endonuclease activity by DNA binding fluorchromes. Journal of Biomolecular Structure & Dynamics. 1996;13:945-951.
Wang Y-K, Huff EJ, Schwartz DC. Optical mapping of site-directed cleavages on single DNA molecules by the RecA-assisted restriction endonuclease technique. Proceedings of the National Academy of Sciences of the United States of America. 1995;92:165-9.
Samad A, Huff EJ, Cai W, Schwartz DC. Optical mapping: a novel, single-molecule approach to genomic analysis. Genome Research. 1995;5:1-4.
Meng X, Benson K, Chada K, Huff EJ, Schwartz DC. Optical mapping of lambda bacteriophage clones using restriction endonucleases. Nature Genetics. 1995;9:432-8.
Cai W, Aburatani H, Stanton, Jr. VP, Housman DE, Wang Y-K, Schwartz DC. Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces. Proceedings of the National Academy of Sciences of the United States of America. 1995;92:5164-8.
Dnistrian AM, Schwartz MK, Greenberg EJ, Smith CA, Schwartz DC. Effect of tamoxifen on serum cholesterol and lipoproteins during chemohormonal therapy. Clinica Chimica Acta. 1993;223:43-52.
Wang YKer, Schwartz DC. Chopped inserts: a convenient alternative to agarose/DNA inserts or beads. Nucleic Acids Research. 1993;21:2528.
Schwartz DC, Li X, Hernandez LI, Ramnarain SP, Huff EJ, Wang YKer. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science. 1993;262:110-14.
Guo XHui, Huff EJ, Schwartz DC. Sizing of large DNA molecules by hook formation in a loose matrix. Journal of Biomolecular Structure & Dynamics. 1993;11:1-10.
Guo XHui, Huff EJ, Schwartz DC. Sizing single DNA molecules. Nature. 1992;359:783-4.
Arn PH, Li X, Smith C, Hsu M, Schwartz DC, Jabs EWang. Analysis of DNA restriction fragments greater than 5.7 Mb in size from the centromeric region of human chromosomes. Mammalian Genome. 1991;1:249-54.
Gabriel A, Yen TJ, Schwartz DC, Smith CL, Boeke JD, Sollner-Webb B, et al.. A rapidly rearranging retrotransposon within the miniexon gene locus of Crithidia fasciculata. Molecular and Cellular Biology. 1990;10:615-24.
Schwartz DC, Koval M. Conformational dynamics of individual DNA molecules during gel electrophoresis. Nature. 1989;338:520-2.
Arn PH, Ketabgian AA, Smith C, Schwartz DC, Jabs EWang. The macromolecular organization of human centromeric regions. Progress in Clinical and Biological Research. 1989;318:1-8.
Schwartz DC. Pulsed electrophoresis. ACS Symposium Series. 1987;335:167-81.
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.