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David Schwartz

Research Profile

Procedures

Chemicals & Drugs

Genes & Molecular Sequences

Bacterial Genomes

Activities & Behaviors

Image Processing, Computer-Assisted

Concepts & Ideas

Anatomy

Bacterial Chromosomes

Living Beings

Occupations

Optics and Photonics

Co-author Network

Publications

TOP 3
Brian Teague; Michael S Waterman; Steven Goldstein; Konstantinos Potamousis; Shiguo Zhou; Susan Reslewic; Deepayan Sarkar; Anton Valouev; Chris Churas; Jeffrey M Kidd; Scott Kohn; Rod Runnheim; Casey Lamers; Dan Forrest; Michael A Newton; Evan E Eichler; Marijo Kent-First; Urvashi Surti; Miron Livny; David C Schwartz
High-resolution human genome structure by single-molecule analysis.
Penghua Zhang; Priscilla Hiu-Mei Too; James C Samuelson; Siu-Hong Chan; Tamas Vincze; Stephanie Doucette; Stefan Bäckström; Konstantinos D Potamousis; Timothy M Schramm; Dan Forrest; David C Schwartz; Shuang-Yong Xu
Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.
Shiguo Zhou; Fusheng Wei; John Nguyen; Mike Bechner; Konstantinos Potamousis; Steve Goldstein; Louise Pape; Michael R Mehan; Chris Churas; Shiran Pasternak; Dan K Forrest; Roger Wise; Doreen Ware; Rod A Wing; Michael S Waterman; Miron Livny; David C Schwartz
A single molecule scaffold for the maize genome.

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All Publications

2010: Brian Teague; Michael S Waterman; Steven Goldstein; Konstantinos Potamousis; Shiguo Zhou; Susan Reslewic; Deepayan Sarkar; Anton Valouev; Chris Churas; Jeffrey M Kidd; Scott Kohn; Rod Runnheim; Casey Lamers; Dan Forrest; Michael A Newton; Evan E Eichler; Marijo Kent-First; Urvashi Surti; Miron Livny; David C Schwartz
High-resolution human genome structure by single-molecule analysis.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(24):10848-53.
2010: Penghua Zhang; Priscilla Hiu-Mei Too; James C Samuelson; Siu-Hong Chan; Tamas Vincze; Stephanie Doucette; Stefan Bäckström; Konstantinos D Potamousis; Timothy M Schramm; Dan Forrest; David C Schwartz; Shuang-Yong Xu
Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.
Protein expression and purification 2010;69(2):226-34.
2009: Shiguo Zhou; Fusheng Wei; John Nguyen; Mike Bechner; Konstantinos Potamousis; Steve Goldstein; Louise Pape; Michael R Mehan; Chris Churas; Shiran Pasternak; Dan K Forrest; Roger Wise; Doreen Ware; Rod A Wing; Michael S Waterman; Miron Livny; David C Schwartz
A single molecule scaffold for the maize genome.
PLoS genetics 2009;5(11):e1000711.
2009: E J Sambriski; David C Schwartz; Juan J de Pablo
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(43):18125-30.
2009: Hua Yu; Kyubong Jo; Kristy L Kounovsky; Juan J de Pablo; David C Schwartz
Molecular propulsion: chemical sensing and chemotaxis of DNA driven by RNA polymerase.
Journal of the American Chemical Society 2009;131(16):5722-3.
2009: E J Sambriski; David C Schwartz; Juan J de Pablo
A mesoscale model of DNA and its renaturation.
Biophysical journal 2009;96(5):1675-90.
2009: Kyubong Jo; Timothy M Schramm; David C Schwartz
A single-molecule barcoding system using nanoslits for DNA analysis : nanocoding.
Methods in molecular biology (Clifton, N.J.) 2009;544():29-42.
2009: Chia-wei Wu; Timothy M Schramm; Shiguo Zhou; David C Schwartz; Adel M Talaat
Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome.
BMC genomics 2009;10():25.
2008: Hua Yu; David C Schwartz
Imaging and analysis of transcription on large, surface-mounted single template DNA molecules.
Analytical biochemistry 2008;380(1):111-21.
2008: Aslin Izmitli; David C Schwartz; Michael D Graham; Juan J de Pablo
The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores.
The Journal of chemical physics 2008;128(8):085102.
2008: Gene E Ananiev; Steve Goldstein; Rod Runnheim; Dan K Forrest; Shiguo Zhou; Konstantinos Potamousis; Chris P Churas; Veit Bergendahl; James A Thomson; David C Schwartz
Optical mapping discerns genome wide DNA methylation profiles.
BMC molecular biology 2008;9():68.
2007: Kyubong Jo; Dalia M Dhingra; Theo Odijk; Juan J de Pablo; Michael D Graham; Rod Runnheim; Dan Forrest; David C Schwartz
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(8):2673-8.
2007: Tian Wu; David C Schwartz
Transchip: single-molecule detection of transcriptional elongation complexes.
Analytical biochemistry 2007;361(1):31-46.
2007: Shiguo Zhou; Michael Bechner; Michael Place; Chris Churas; Louise Pape; Sally A Leong; Rod Runnheim; Daniel K Forrest; Steve Goldstein; Miron Livny; David C Schwartz
Validation of rice genome sequence by optical mapping.
BMC genomics 2007;8():278.
2007: Jill Herschleb; Gene Ananiev; David C Schwartz
Pulsed-field gel electrophoresis.
Nature protocols 2007;2(3):677-84.
2005: Susan Reslewic; Shiguo Zhou; Michael Place; Yaoping Zhang; Adam Briska; Steve Goldstein; Chris Churas; Rod Runnheim; Dan Forrest; Alex Lim; Alla Lapidus; Cliff S Han; Gary P Roberts; David C Schwartz
Whole-genome shotgun optical mapping of Rhodospirillum rubrum.
Applied and environmental microbiology 2005;71(9):5511-22.
2005: Arvind Ramanathan; Louise Pape; David C Schwartz
High-density polymerase-mediated incorporation of fluorochrome-labeled nucleotides.
Analytical biochemistry 2005;337(1):1-11.
2004: Shiguo Zhou; Andrew Kile; Michael Bechner; Michael Place; Erika Kvikstad; Wen Deng; Jun Wei; Jessica Severin; Rod Runnheim; Chris Churas; Dan Forrest; Eileen T Dimalanta; Casey Lamers; Valerie Burland; Frederick R Blattner; David C Schwartz
Single-molecule approach to bacterial genomic comparisons via optical mapping.
Journal of bacteriology 2004;186(22):7773-82.
2004: Shiguo Zhou; Andrew Kile; Erika Kvikstad; Michael Bechner; Jessica Severin; Dan Forrest; Rod Runnheim; Chris Churas; Thomas S Anantharaman; Peter J Myler; Christy Vogt; Alasdair Ivens; Kenneth Stuart; David C Schwartz
Shotgun optical mapping of the entire Leishmania major Friedlin genome.
Molecular and biochemical parasitology 2004;138(1):97-106.
2004: Eileen T Dimalanta; Alex Lim; Rod Runnheim; Casey Lamers; Chris Churas; Daniel K Forrest; Juan J de Pablo; Michael D Graham; Susan N Coppersmith; Steve Goldstein; David C Schwartz
A microfluidic system for large DNA molecule arrays.
Analytical chemistry 2004;76(18):5293-301.
2004: Arvind Ramanathan; Edward J Huff; Casey C Lamers; Konstantinos D Potamousis; Daniel K Forrest; David C Schwartz
An integrative approach for the optical sequencing of single DNA molecules.
Analytical biochemistry 2004;330(2):227-41.
2004: Richard M Jendrejack; David C Schwartz; Juan J de Pablo; Michael D Graham
Shear-induced migration in flowing polymer solutions: simulation of long-chain DNA in microchannels [corrected].
The Journal of chemical physics 2004;120(5):2513-29.
2003: Shiguo Zhou; Erika Kvikstad; Andrew Kile; Jessica Severin; Dan Forrest; Rod Runnheim; Chris Churas; Jason W Hickman; Chris Mackenzie; Madhusudan Choudhary; Timothy Donohue; samuel kaplan; David C Schwartz
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(9):2142-51.
2003: Richard M Jendrejack; Eileen T Dimalanta; David C Schwartz; Michael D Graham; Juan J de Pablo
DNA dynamics in a microchannel.
Physical review letters 2003;91(3):038102.
2003: J Wei; M B Goldberg; Valerie Burland; Malabi M Venkatesan; W Deng; G Fournier; George F Mayhew; Guy Plunkett; Debra J Rose; Aaron E Darling; Bob Mau; Nicole T Perna; Shelley M Payne; Laura Runyen-Janecky; S Zhou; David C Schwartz; Frederick R Blattner
Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T.
Infection and immunity 2003;71(5):2775-86.
2003: Wen Deng; Shian-Ren Liou; Guy Plunkett; George F Mayhew; Debra J Rose; Valerie Burland; Voula Kodoyianni; David C Schwartz; Frederick R Blattner
Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18.
Journal of bacteriology 2003;185(7):2330-7.
2002: Rodney A Welch; Valerie Burland; Guy Plunkett; Peter Redford; Paula L Roesch; David Rasko; Eric L Buckles; Shian-Ren Liou; Adam T. Boutin; J Hackett; D Stroud; George F Mayhew; Debra J Rose; S Zhou; David C Schwartz; Nicole T Perna; harry mobley; Michael S Donnenberg; Frederick R Blattner
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(26):17020-4.
2002: Shiguo Zhou; Wen Deng; Thomas S Anantharaman; Alex Lim; Eileen T Dimalanta; Jun Wang; Tian Wu; Tao Chunhong; Robert Creighton; Andrew Kile; Erika Kvikstad; Michael Bechner; Galex Yen; Ana Garic-Stankovic; Jessica Severin; Dan Forrest; Rod Runnheim; Chris Churas; Casey Lamers; Nicole T Perna; Valerie Burland; Frederick R Blattner; Bud Mishra; David C Schwartz
A whole-genome shotgun optical map of Yersinia pestis strain KIM.
Applied and environmental microbiology 2002;68(12):6321-31.
2002: Wen Deng; Valerie Burland; Guy Plunkett; Adam T. Boutin; George F Mayhew; Paul Liss; Nicole T Perna; Debra J Rose; Bob Mau; Shiguo Zhou; David C Schwartz; Jacqueline D Fetherston; Luther E Lindler; Robert R Brubaker; Gregory V Plano; Susan C Straley; Kathleen A McDonough; Matthew Nilles; Jyl Matson; Frederick R Blattner; Robert D Perry
Genome sequence of Yersinia pestis KIM.
Journal of bacteriology 2002;184(16):4601-11.
2001: Alex Lim; Eileen T Dimalanta; Konstantinos D Potamousis; Galex Yen; J Apodoca; C Tao; J Lin; R Qi; J Skiadas; Arvind Ramanathan; Nicole T Perna; Guy Plunkett; Valerie Burland; Bob Mau; J Hackett; Frederick R Blattner; Thomas S Anantharaman; Bud Mishra; David C Schwartz
Shotgun optical maps of the whole Escherichia coli O157:H7 genome.
Genome research 2001;11(9):1584-93.
2001: Nicole T Perna; Guy Plunkett; Valerie Burland; Bob Mau; Jeremy D Glasner; Debra J Rose; George F Mayhew; Peter Evans; J Gregor; HA Kirkpatrick; György Pósfai; J Hackett; S Klink; Adam T. Boutin; Y Shao; L Miller; EJ Grotbeck; N W Davis; Alex Lim; Eileen T Dimalanta; Konstantinos D Potamousis; J Apodaca; Thomas S Anantharaman; J Lin; Galex Yen; David C Schwartz; Rodney A Welch; Frederick R Blattner
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.
Nature 2001;409(6819):529-33.
2000: J Giacalone; S Delobette; V Gibaja; L Ni; Y Skiadas; R Qi; J Edington; Z Lai; D Gebauer; H Zhao; Thomas S Anantharaman; Bud Mishra; Laura G Brown; Romil Saxena; David C Page; David C Schwartz
Optical mapping of BAC clones from the human Y chromosome DAZ locus.
Genome research 2000;10(9):1421-9.
1999: Z Lai; J Jing; C Aston; V Clarke; J Apodaca; Eileen T Dimalanta; Daniel J Carucci; Malcolm J Gardner; Bud Mishra; Thomas S Anantharaman; S Paxia; Stephen L Hoffman; J Craig Venter; Edward J Huff; David C Schwartz
A shotgun optical map of the entire Plasmodium falciparum genome.
Nature genetics 1999;23(3):309-13.
1999: J Skiadas; C Aston; A Samad; Thomas S Anantharaman; Bud Mishra; David C Schwartz
Optical PCR: genomic analysis by long-range PCR and optical mapping.
Mammalian genome : official journal of the International Mammalian Genome Society 1999;10(10):1005-9.
1999: J Lin; R Qi; C Aston; J Jing; Thomas S Anantharaman; Bud Mishra; Owen R White; Michael J Daly; KW Minton; J Craig Venter; David C Schwartz
Whole-genome shotgun optical mapping of Deinococcus radiodurans.
Science (New York, N.Y.) 1999;285(5433):1558-62.
1999: R M Kantor; X H Guo; Edward J Huff; David C Schwartz
Dynamics of DNA molecules in gel studied by fluorescence microscopy.
Biochemical and biophysical research communications 1999;258(1):102-8.
1999: J Jing; Z Lai; C Aston; J Lin; Daniel J Carucci; Malcolm J Gardner; Bud Mishra; Thomas S Anantharaman; Hervé Tettelin; LM Cummings; Stephen L Hoffman; J Craig Venter; David C Schwartz
Optical mapping of Plasmodium falciparum chromosome 2.
Genome research 1999;9(2):175-81.
1999: X Hu; C Aston; David C Schwartz
Optical mapping of DNA polymerase I action and products.
Biochemical and biophysical research communications 1999;254(2):466-73.
1999: C Aston; C Hiort; David C Schwartz
Optical mapping: an approach for fine mapping.
Methods in enzymology 1999;303():55-73.
1998: Malcolm J Gardner; Hervé Tettelin; Daniel J Carucci; LM Cummings; L Aravind; E V Koonin; S Shallom; T Mason; K Yu; C Fujii; J Pederson; K Shen; J Jing; C Aston; Z Lai; David C Schwartz; Mihaela Pertea; Steven L Salzberg; L Zhou; Granger Sutton; R Clayton; Owen R White; Hamilton O Smith; Claire M Fraser-Liggett; Mark D Adams; J Craig Venter; Stephen L Hoffman
Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum.
Science (New York, N.Y.) 1998;282(5391):1126-32.
1998: J Jing; J Reed; J Huang; X Hu; V Clarke; J Edington; D Housman; Thomas S Anantharaman; Edward J Huff; Bud Mishra; B Porter; A Shenker; E Wolfson; C Hiort; R Kantor; C Aston; David C Schwartz
Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(14):8046-51.
1998: W Wang; J Lin; David C Schwartz
Scanning force microscopy of DNA molecules elongated by convective fluid flow in an evaporating droplet.
Biophysical journal 1998;75(1):513-20.
1998: J Reed; E Singer; G Kresbach; David C Schwartz
A quantitative study of optical mapping surfaces by atomic force microscopy and restriction endonuclease digestion assays.
Analytical biochemistry 1998;259(1):80-8.
1998: W Cai; J Jing; B Irvin; L Ohler; E Rose; H Shizuya; U J Kim; M Simon; Thomas S Anantharaman; Bud Mishra; David C Schwartz
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(7):3390-5.
1997: David C Schwartz; A Samad
Optical mapping approaches to molecular genomics.
Current opinion in biotechnology 1997;8(1):70-4.
1997: Thomas S Anantharaman; Bud Mishra; David C Schwartz
Genomics via optical mapping. II: Ordered restriction maps.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(2):91-118.
1996: Victor Morozov; T Y Morozova; C Hiort; David C Schwartz
New polyacrylamide gel-based methods of sample preparation for optical microscopy: immobilization of DNA molecules for optical mapping.
Journal of microscopy 1996;183(Pt 3):205-14.
1996: X Meng; W Cai; David C Schwartz
Inhibition of restriction endonuclease activity by DNA binding fluorochromes.
Journal of biomolecular structure & dynamics 1996;13(6):945-51.
1995: A Samad; E F Huff; W Cai; David C Schwartz
Optical mapping: a novel, single-molecule approach to genomic analysis.
Genome research 1995;5(1):1-4.
1995: W Cai; H Aburatani; V P Stanton; David E Housman; Y K Wang; David C Schwartz
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(11):5164-8.
1995: X Meng; K Benson; K Chada; Edward J Huff; David C Schwartz
Optical mapping of lambda bacteriophage clones using restriction endonucleases.
Nature genetics 1995;9(4):432-8.
1995: Y K Wang; Edward J Huff; David C Schwartz
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(1):165-9.
1993: David C Schwartz; X Li; L I Hernandez; S P Ramnarain; Edward J Huff; Y K Wang
Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping.
Science (New York, N.Y.) 1993;262(5130):110-4.
1993: X H Guo; Edward J Huff; David C Schwartz
Sizing of large DNA molecules by hook formation in a loose matrix.
Journal of biomolecular structure & dynamics 1993;11(1):1-10.
1993: Y K Wang; David C Schwartz
Chopped inserts: a convenient alternative to agarose/DNA inserts or beads.
Nucleic acids research 1993;21(10):2528.
1992: X H Guo; Edward J Huff; David C Schwartz
Sizing single DNA molecules.
Nature 1992;359(6398):783-4.