Jonas Korlach

Jonas Korlach

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Jonas Korlach

Publications by authors named "Jonas Korlach"

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Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nat Commun 2019 04 16;10(1):1784. Epub 2019 Apr 16.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.

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http://www.nature.com/articles/s41467-018-08148-z
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http://dx.doi.org/10.1038/s41467-018-08148-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467913PMC
April 2019

Porous Zero-Mode Waveguides for Picogram-Level DNA Capture.

Nano Lett 2019 02 3;19(2):921-929. Epub 2018 Dec 3.

Pacific Biosciences , Menlo Park , California 94025 , United States.

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http://dx.doi.org/10.1021/acs.nanolett.8b04170DOI Listing
February 2019

Improved reference genome of Aedes aegypti informs arbovirus vector control.

Nature 2018 11 14;563(7732):501-507. Epub 2018 Nov 14.

Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.

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http://www.nature.com/articles/s41586-018-0692-z
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http://dx.doi.org/10.1038/s41586-018-0692-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421076PMC
November 2018

Genome and Methylome Variation in Helicobacter pylori With a cag Pathogenicity Island During Early Stages of Human Infection.

Gastroenterology 2018 02 21;154(3):612-623.e7. Epub 2017 Oct 21.

Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Hannover, Germany; Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, München, Germany; National Reference Center for Helicobacter pylori, München, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00165085173627
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http://dx.doi.org/10.1053/j.gastro.2017.10.014DOI Listing
February 2018

Length-independent DNA packing into nanopore zero-mode waveguides for low-input DNA sequencing.

Nat Nanotechnol 2017 12 11;12(12):1169-1175. Epub 2017 Sep 11.

Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nnano.2017.176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718969PMC
December 2017

Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing.

Stand Genomic Sci 2017 23;12:27. Epub 2017 Mar 23.

Population Health and Reproduction Department, School of Veterinary Medicine, University of California-Davis, Davis, CA USA.

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http://dx.doi.org/10.1186/s40793-017-0239-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5363030PMC
March 2017

AgIn: measuring the landscape of CpG methylation of individual repetitive elements.

Bioinformatics 2016 10 17;32(19):2911-9. Epub 2016 Jun 17.

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btw360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5039925PMC
October 2016

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.

MBio 2016 Feb 9;7(1):e01948-15. Epub 2016 Feb 9.

Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA

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http://dx.doi.org/10.1128/mBio.01948-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752602PMC
February 2016

Genome annotation provides insight into carbon monoxide and hydrogen metabolism in Rubrivivax gelatinosus.

PLoS One 2014 5;9(12):e114551. Epub 2014 Dec 5.

Department of Chemical and Petroleum Engineering, University of Wyoming, Laramie, Wyoming, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114551PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257681PMC
December 2015

Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars.

PLoS One 2015 10;10(4):e0123639. Epub 2015 Apr 10.

Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123639PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393132PMC
December 2015

Enzymatic Degradation of Phenazines Can Generate Energy and Protect Sensitive Organisms from Toxicity.

MBio 2015 Oct 27;6(6):e01520-15. Epub 2015 Oct 27.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA Howard Hughes Medical Institute, Pasadena, California, USA

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http://dx.doi.org/10.1128/mBio.01520-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626857PMC
October 2015

Genetic Stabilization of the Drug-Resistant PMEN1 Pneumococcus Lineage by Its Distinctive DpnIII Restriction-Modification System.

MBio 2015 Jun 16;6(3):e00173. Epub 2015 Jun 16.

Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania, USA Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA

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http://dx.doi.org/10.1128/mBio.00173-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4471560PMC
June 2015

Resolving the complexity of the human genome using single-molecule sequencing.

Nature 2015 Jan 10;517(7536):608-11. Epub 2014 Nov 10.

1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.

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https://www.nature.com/articles/nature13907.pdf
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317254/
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http://www.nature.com/articles/nature13907
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http://dx.doi.org/10.1038/nature13907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317254PMC
January 2015

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea.

Proc Natl Acad Sci U S A 2014 Dec 18;111(48):E5149-58. Epub 2014 Nov 18.

Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093

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http://www.pnas.org/lookup/doi/10.1073/pnas.1419513111
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http://dx.doi.org/10.1073/pnas.1419513111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260599PMC
December 2014

Returning to more finished genomes.

Authors:
Jonas Korlach

Genom Data 2014 Dec 1;2:46-8. Epub 2014 Mar 1.

Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, United States.

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https://linkinghub.elsevier.com/retrieve/pii/S22135960140000
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http://dx.doi.org/10.1016/j.gdata.2014.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535613PMC
December 2014

Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing.

Antimicrob Agents Chemother 2014 Oct 28;58(10):5947-53. Epub 2014 Jul 28.

Institute for Genome Sciences, University of Maryland, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1128/AAC.03180-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187971PMC
October 2014

Reversible positioning of single molecules inside zero-mode waveguides.

Nano Lett 2014 Oct 15;14(10):6023-9. Epub 2014 Sep 15.

Department of Physics and ‡Department of Chemistry/Chemical Biology, Northeastern University , 110 Forsyth Street, Boston, Massachusetts 02115, United States.

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http://dx.doi.org/10.1021/nl503134xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189617PMC
October 2014

First Fully Closed Genome Sequence of Salmonella enterica subsp. enterica Serovar Cubana Associated with a Food-Borne Outbreak.

Genome Announc 2014 Oct 30;2(5). Epub 2014 Oct 30.

Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA.

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http://genomea.asm.org/cgi/doi/10.1128/genomeA.01112-14
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http://dx.doi.org/10.1128/genomeA.01112-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214993PMC
October 2014

Improved performance of the PacBio SMRT technology for 16S rDNA sequencing.

J Microbiol Methods 2014 Sep 27;104:59-60. Epub 2014 Jun 27.

Stroud Water Research Center, Avondale, PA 19311, United States. Electronic address:

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http://dx.doi.org/10.1016/j.mimet.2014.06.012DOI Listing
September 2014

Complete Genome Sequences of Two Escherichia coli O145:H28 Outbreak Strains of Food Origin.

Genome Announc 2014 May 22;2(3). Epub 2014 May 22.

Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA

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http://dx.doi.org/10.1128/genomeA.00482-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032123PMC
May 2014

Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.

Genome Announc 2014 Apr 3;2(2). Epub 2014 Apr 3.

Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA; Department of Nutrition & Food Science and Joint Institute for Food Safety & Applied Nutrition, University of Maryland, College Park, Maryland, USA; Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA; Pacific Biosciences, Menlo Park, California, USA; New England BioLabs, Inc., Ipswich, Massachusetts, USA.

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http://genomea.asm.org/cgi/doi/10.1128/genomeA.00294-14
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http://dx.doi.org/10.1128/genomeA.00294-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974949PMC
April 2014

The complex methylome of the human gastric pathogen Helicobacter pylori.

Nucleic Acids Res 2014 Feb 2;42(4):2415-32. Epub 2013 Dec 2.

Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany, German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Straße 1, 30625 Hannover, Germany, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany and Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.

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http://dx.doi.org/10.1093/nar/gkt1201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3936762PMC
February 2014

Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7.

BMC Genomics 2014 Jan 10;15:17. Epub 2014 Jan 10.

Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, US Department of Agriculture, Albany, CA 94710, USA.

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http://dx.doi.org/10.1186/1471-2164-15-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893438PMC
January 2014

Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.

Genome Announc 2013 12 19;1(6). Epub 2013 Dec 19.

Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA.

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http://dx.doi.org/10.1128/genomeA.01068-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3868858PMC
December 2013

Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

PLoS Comput Biol 2013 14;9(3):e1002935. Epub 2013 Mar 14.

Tsinghua National Laboratory for Information Science and Technology, and Department of Automation, Tsinghua University, Beijing, China.

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http://dx.doi.org/10.1371/journal.pcbi.1002935DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597545PMC
November 2013

Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1.

J Bacteriol 2013 Nov 30;195(21):4966-74. Epub 2013 Aug 30.

DOE Joint Genome Institute, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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http://dx.doi.org/10.1128/JB.00935-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807482PMC
November 2013

Fully assembled genome sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.

Genome Announc 2013 03 21;1(2):e0008113. Epub 2013 Mar 21.

Office of Regulatory Science, Center for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, Maryland, USA.

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http://dx.doi.org/10.1128/genomeA.00081-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622996PMC
March 2013

The impact of aminoglycosides on the dynamics of translation elongation.

Cell Rep 2013 Feb 14;3(2):497-508. Epub 2013 Feb 14.

Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.

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http://dx.doi.org/10.1016/j.celrep.2013.01.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766726PMC
February 2013

The methylomes of six bacteria.

Nucleic Acids Res 2012 Dec 2;40(22):11450-62. Epub 2012 Oct 2.

New England Biolabs, 240 County Road, Ipswich, MA 01938, USA.

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http://dx.doi.org/10.1093/nar/gks891DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526280PMC
December 2012

Live-cell imaging of single receptor composition using zero-mode waveguide nanostructures.

Nano Lett 2012 Jul 8;12(7):3690-4. Epub 2012 Jun 8.

Division of Biology 156-29, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States.

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http://dx.doi.org/10.1021/nl301480hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3397148PMC
July 2012

Heterogeneous pathways and timing of factor departure during translation initiation.

Nature 2012 Jul;487(7407):390-3

Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA.

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http://dx.doi.org/10.1038/nature11172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465488PMC
July 2012

Going beyond five bases in DNA sequencing.

Curr Opin Struct Biol 2012 Jun 9;22(3):251-61. Epub 2012 May 9.

Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, United States.

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https://linkinghub.elsevier.com/retrieve/pii/S0959440X120006
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http://dx.doi.org/10.1016/j.sbi.2012.04.002DOI Listing
June 2012

Direct detection and sequencing of damaged DNA bases.

Genome Integr 2011 Dec 20;2:10. Epub 2011 Dec 20.

Pacific Biosciences, 1380 Willow Rd, Menlo Park, California, USA.

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http://dx.doi.org/10.1186/2041-9414-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264494PMC
December 2011

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine.

Nat Methods 2011 Nov 20;9(1):75-7. Epub 2011 Nov 20.

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1038/nmeth.1779DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646335PMC
November 2011

Real-time tRNA transit on single translating ribosomes at codon resolution.

Nature 2010 Apr;464(7291):1012-7

Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA.

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http://dx.doi.org/10.1038/nature08925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466108PMC
April 2010

Conformational changes of calmodulin upon Ca2+ binding studied with a microfluidic mixer.

Proc Natl Acad Sci U S A 2008 Jan 4;105(2):542-7. Epub 2008 Jan 4.

School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1073/pnas.0710810105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2206572PMC
January 2008

Achieving uniform mixing in a microfluidic device: hydrodynamic focusing prior to mixing.

Anal Chem 2006 Jul;78(13):4465-73

School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1021/ac060572nDOI Listing
July 2006

Detection of motional heterogeneities in lipid bilayer membranes by dual probe fluorescence correlation spectroscopy.

Biochim Biophys Acta 2005 Mar 19;1668(2):158-63. Epub 2005 Jan 19.

School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S000527360400311
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http://dx.doi.org/10.1016/j.bbamem.2004.11.016DOI Listing
March 2005

Spontaneous nucleotide exchange in low molecular weight GTPases by fluorescently labeled gamma-phosphate-linked GTP analogs.

Proc Natl Acad Sci U S A 2004 Mar 18;101(9):2800-5. Epub 2004 Feb 18.

Field of Biochemistry, Molecular and Cell Biology, School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0308579100
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http://dx.doi.org/10.1073/pnas.0308579100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC365700PMC
March 2004

Focal volume confinement by submicrometer-sized fluidic channels.

Anal Chem 2004 Mar;76(6):1618-26

School of Applied & Engineering Physics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1021/ac035088oDOI Listing
March 2004

DNA fragment sizing by single molecule detection in submicrometer-sized closed fluidic channels.

Anal Chem 2002 Mar;74(6):1415-22

School of Applied & Engineering Physics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1021/ac011076wDOI Listing
March 2002