All Department Publications

Found 68 results
Author Title Type [ Year(Asc)]
Filters: Author is Schwartz, D. C.  [Clear All Filters]
2013
Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, 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.
2012
Lin HC, Goldstein S, Mendelowitz L, Zhou SG, Wetzel J, Schwartz DC, Pop M. AGORA: Assembly Guided by Optical Restriction Alignment. Bmc Bioinformatics. 2012;13.
Chen SL, Xu J, Liu C, Zhu YJ, Nelson DR, Zhou SG, Li CF, Wang LZ, Guo X, Sun YZ, 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, Paustian ML, Alt DP, Sreevatsan S, Kapur V, et al. Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association. Bmc Genomics. 2012;13.
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.
2011
Schwartz DC, Zhou S, Goldstein S, Potomousis K, Place M, Teague B, Kounovsky-Shafer K, Yu G, Bayer AR, Galloway MM, 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.
Kim Y, Kim KS, Kounovsky KL, Chang R, Jung GY, De Pablo JJ, Jo K, Schwartz DC. Nanochannel confinement: DNA stretch approaching full contour length. Lab on a Chip. 2011;11:1721-1729.
2010
Zhang P, Too PH-M, Samuelson JC, Chan S-H, Vincze T, Doucette S, Backstrom S, Potamousis KD, Schramm TM, Forrest D, 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.
Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, Sarkar D, Valouev A, Churas C, Kidd JM, 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.
Antonacci F, Kidd JM, Marques-Bonet T, Teague B, Ventura M, Girirajan S, Alkan C, Campbell CD, Vives L, Malig M, et al. A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nature Genetics. 2010;42:745-U29.
Schwartz DC, Waterman MS. New Generations: Sequencing Machines and Their Computational Challenges. Journal of Computer Science and Technology. 2010;25:3-9.
2009
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science. 2009;326:1112-1115.
Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, et al. Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome. Plos Genetics. 2009;5.
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, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, et al. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 2009;461:393-398.
Sambriski EJ, Schwartz DC, de Pablo JJ. A Mesoscale Model of DNA and Its Renaturation. Biophysical Journal. 2009;96:1675-1690.
Sidorova JM, Li NZ, Schwartz DC, Folch A, Monnat RJ. Microfluidic-assisted analysis of replicating DNA molecules. Nature Protocols. 2009;4:849-861.
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, Kudrna D, Faga BP, Wissotski M, Golser W, et al. The Physical and Genetic Framework of the Maize B73 Genome. Plos Genetics. 2009;5.
Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S, et al. A Single Molecule Scaffold for the Maize Genome. Plos Genetics. 2009;5.
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. 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.
2008
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.
Yu H, Schwartz DC. Imaging and analysis of transcription on large, surface-mounted single template DNA molecules. Analytical Biochemistry. 2008;380:111-121.
Ananiev GE, Goldstein S, Runnheim R, Forrest DK, Zhou S, Potamousis K, Churas CP, Bergendahl V, Thomson JA, Schwartz DC. Optical mapping discerns genome wide DNA methylation profiles. Bmc Molecular Biology. 2008;9.
2007
Knotts TA, Rathore N, Schwartz DC, De Pablo JJ. A coarse grain model for DNA. Journal of Chemical Physics. 2007;126.
Herschleb J, Ananiev G, Schwartz DC. Pulsed-field gel electrophoresis. Nature Protocols. 2007;2:677-684.
Jo K, Dhingra DM, Odijk T, De Pablo JJ, Graham MD, Runnheim R, Forrest D, Schwartz DC. 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.
Wu T, Schwartz DC. Transchip: Single-molecule detection of transcriptional elongation complexes. Analytical Biochemistry. 2007;361:31-46.
Zhou S, Bechner MC, Place M, Churas CP, Pape L, Leong SA, Runnheim R, Forrest DK, Goldstein S, Livny M, et al. Validation of rice genome sequence by optical mapping. Bmc Genomics. 2007;8.
2006
Lim A, Dimalanta ET, Potamousis KD, Yen G, Apodoca J, Tao CH, Lin JY, Qi R, Skiadas J, Ramanathan A, et al. Shotgun optical maps of the whole Escherichia coli O157 : H7 genome. Genome Research. 2006;13:442-462.
2005
Chen Y-L, Graham MD, de Pablo JJ, Jo K, Schwartz DC. DNA Molecules in Microfluidic Oscillatory Flow. Macromolecules. 2005;38(15):6680-6687.
Ramanathan A, Pape L, Schwartz DC. High-density polymerase-mediated incorporation of fluorochrome-labeled nucleotides. Analytical BiochemistryAnalytical Biochemistry. 2005;337:1-11.
Reslewic S, Zhou SG, Place M, Zhang YP, Briska A, Goldstein S, Churas C, Runnheim R, Forrest D, Lim A, et al. Whole-genome shotgun optical mapping of Rhodospirillum rubrum. Applied & Environmental MicrobiologyApplied & Environmental Microbiology. 2005;71:5511-5522.
2004
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.
Dimalanta ET, Lim A, Runnheim R, Lamers C, Churas C, Forrest DK, de Pablo JJ, Graham MD, Coppersmith SN, Goldstein S, et al. A microfluidic system for large DNA molecule arrays. Analytical ChemistryAnalytical Chemistry. 2004;76:5293-5301.
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.
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, Runnheim R, Churas C, Anantharaman TS, Myler P, et al. Shotgun optical mapping of the entire Leishmania major Friedlin genome. Molecular & Biochemical ParasitologyMolecular & Biochemical Parasitology. 2004;138:97-106.
Zhou S, Kile A, Bechner M, Place M, Kvikstad E, Deng W, Wei J, Severin J, Runnheim R, Churas C, et al. Single-molecule approach to bacterial genomic comparisons via optical mapping. Journal of Bacteriology. 2004;186:7773-7782.
2003
Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, Mayhew GF, Plunkett G, Rose DJ, Darling A, 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.
Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, Mayhew GF, Plunkett G, Rose DJ, Darling A, et al. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infection and ImmunityInfection & Immunity. 2003;71:2775-2786.
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.
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.
Zhou SG, Kvikstad E, Kile A, Severin J, Forrest D, Runnheim R, Churas C, Hickman JW, Mackenzie C, Choudhary M, 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.
2002
Deng W, Burland V, Plunkett G, Boutin A, Mayhew GF, Liss P, Perna NT, Rose DJ, Mau B, Zhou SG, 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, Wu T, Chunhong T, Creighton R, Kile A, et al. A whole-genome shotgun optical map of Yersinia pestis strain KIM. Applied & Environmental MicrobiologyApplied & Environmental Microbiology. 2002;68:6321-6331.
2001
Perna NT, Plunkett G, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, et al. Genome sequence of enterohaemorrhagic Escherichia coli O157 : H7. NatureNature. 2001;409:529-533.
Lim A, Dimalanta ET, Potamousis KD, Yen G, Apodoca J, Tao CH, Lin JY, Qi R, Skiadas J, Ramanathan A, et al. Shotgun optical maps of the whole Escherichia coli O157 : H7 genome. Genome ResearchGenome Research. 2001;11:1584-1593.

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