All Faculty and Research Staff Publications

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2010
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, Dufresne M, Freitag M, Grabherr M, Henrissat B, et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 2010 ;464:367-373.
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 & 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.
Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, et al. The challenges of sequencing by synthesis. Nature Biotechnology. 2009 ;27:1013-1023.
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.
Jo K, Schramm TM, Schwartz DC. A single-molecule barcoding system using nanoslits for DNA analysis: nanocoding. Methods Mol. Biol. . 2009 ;544:29-42.
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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