Publications by authors named "Mark Akeson"

40Publications

Unfolding and Translocation of Proteins Through an Alpha-Hemolysin Nanopore by ClpXP.

Methods Mol Biol 2021 ;2186:145-155

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.

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January 2021

Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing.

Genes (Basel) 2020 01 9;11(1). Epub 2020 Jan 9.

Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX 77058, USA.

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January 2020

Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing.

PLoS One 2019 16;14(5):e0216709. Epub 2019 May 16.

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America.

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January 2020

Linear assembly of a human centromere on the Y chromosome.

Nat Biotechnol 2018 04 19;36(4):321-323. Epub 2018 Mar 19.

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA.

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April 2018

Mapping DNA methylation with high-throughput nanopore sequencing.

Nat Methods 2017 Apr 20;14(4):411-413. Epub 2017 Feb 20.

Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.

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April 2017

Erratum to: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.

Genome Biol 2016 12 13;17(1):256. Epub 2016 Dec 13.

UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA.

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December 2016

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.

Genome Biol 2016 11 25;17(1):239. Epub 2016 Nov 25.

UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA.

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November 2016

Three decades of nanopore sequencing.

Nat Biotechnol 2016 05;34(5):518-24

Department of Molecular &Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.

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May 2016

Author response to John Kasianowicz and Sergey Bezrukov.

Nat Biotechnol 2016 05;34(5):482

Department of Molecular &Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.

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May 2016

Capture, Unfolding, and Detection of Individual tRNA Molecules Using a Nanopore Device.

Front Bioeng Biotechnol 2015 24;3:91. Epub 2015 Jun 24.

Department of Biomolecular Engineering, University of California Santa Cruz , Santa Cruz, CA , USA.

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July 2015

Improved data analysis for the MinION nanopore sequencer.

Nat Methods 2015 Apr 16;12(4):351-6. Epub 2015 Feb 16.

1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.

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April 2015

Discrimination among protein variants using an unfoldase-coupled nanopore.

ACS Nano 2014 Dec 8;8(12):12365-75. Epub 2014 Dec 8.

Nanopore Group, Department of Biomolecular Engineering, University of California , Santa Cruz, California 95064, United States.

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December 2014

Nanopores discriminate among five C5-cytosine variants in DNA.

J Am Chem Soc 2014 Nov 14;136(47):16582-7. Epub 2014 Nov 14.

Department of Biomolecular Engineering, Baskin School of Engineering, MS SOE2, University of California , Santa Cruz, California 95064, United States.

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November 2014

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands.

Proc Natl Acad Sci U S A 2013 Nov 28;110(47):18910-5. Epub 2013 Oct 28.

Nanopore Group, Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064.

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November 2013

Kinetic mechanism of translocation and dNTP binding in individual DNA polymerase complexes.

J Am Chem Soc 2013 Jun 7;135(24):9149-55. Epub 2013 Jun 7.

Department of Biomolecular Engineering, University of California, Santa Cruz, Baskin School of Engineering, 1156 High Street, MS: SOE2, Santa Cruz, California 95064, USA.

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June 2013

Unfoldase-mediated protein translocation through an α-hemolysin nanopore.

Nat Biotechnol 2013 Mar 3;31(3):247-50. Epub 2013 Feb 3.

Nanopore Group, Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, USA.

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March 2013

Dynamics of the translocation step measured in individual DNA polymerase complexes.

J Am Chem Soc 2012 Nov 1;134(45):18816-23. Epub 2012 Nov 1.

Biomolecular Engineering, University of California, Santa Cruz, 95064, United States.

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November 2012

Direct observation of translocation in individual DNA polymerase complexes.

J Biol Chem 2012 Apr 29;287(16):13407-21. Epub 2012 Feb 29.

Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA.

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April 2012

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision.

Nat Biotechnol 2012 Feb 14;30(4):344-8. Epub 2012 Feb 14.

Nanopore Group, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA.

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February 2012

Distinct complexes of DNA polymerase I (Klenow fragment) for base and sugar discrimination during nucleotide substrate selection.

J Biol Chem 2011 Apr 28;286(16):14480-92. Epub 2011 Feb 28.

Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA.

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April 2011

Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase.

J Am Chem Soc 2010 Dec 1;132(50):17961-72. Epub 2010 Dec 1.

Department of Biomolecular Engineering, Baskin School of Engineering, MS SOE2, University of California, Santa Cruz, California 95064, United States.

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December 2010

Replication of individual DNA molecules under electronic control using a protein nanopore.

Nat Nanotechnol 2010 Nov 26;5(11):798-806. Epub 2010 Sep 26.

Department of Biomolecular Engineering, Baskin School of Engineering, MS SOE2, University of California, Santa Cruz, California 95064, USA.

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November 2010

Mapping the position of DNA polymerase-bound DNA templates in a nanopore at 5 A resolution.

ACS Nano 2009 Jun;3(6):1457-66

Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA.

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June 2009

Electronic control of DNA polymerase binding and unbinding to single DNA molecules.

ACS Nano 2009 Apr;3(4):995-1003

Department of Computer Engineering, University of California, Santa Cruz, California, USA.

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April 2009

Specific nucleotide binding and rebinding to individual DNA polymerase complexes captured on a nanopore.

J Am Chem Soc 2009 Mar;131(10):3772-8

Department of Chemistry and Biochemistry, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA.

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March 2009

Feedback control of a DNA molecule tethered in a nanopore to repeatedly probe DNA-binding enzymes.

Annu Int Conf IEEE Eng Med Biol Soc 2008 ;2008:5745-8

Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, CA, USA.

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May 2009

Single-molecule analysis of DNA-protein complexes using nanopores.

Nat Methods 2007 Apr 4;4(4):315-7. Epub 2007 Mar 4.

Department of Chemistry & Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.

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April 2007

Cheminformatics methods for novel nanopore analysis of HIV DNA termini.

BMC Bioinformatics 2006 Sep 6;7 Suppl 2:S22. Epub 2006 Sep 6.

Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA.

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September 2006

Nanopore cheminformatics.

DNA Cell Biol 2004 Oct;23(10):675-83

Department of Computer Science, University of New Orleans, New Orleans, Louisiana, USA.

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October 2004

Discrimination among individual Watson-Crick base pairs at the termini of single DNA hairpin molecules.

Nucleic Acids Res 2003 Feb;31(4):1311-8

Center for Biomolecular Science and Engineering, Department of Chemistry and Biochemistry, and. Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA.

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February 2003

Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules.

Biophys J 2003 Feb;84(2 Pt 1):967-76

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA.

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February 2003

Biosensors for DNA sequence detection.

Curr Opin Chem Biol 2002 Dec;6(6):816-22

National Space Grant Foundation, Bone/Signaling Laboratory, NASA Ames Research Center, Mail-Stop 236-7, Moffett Field, CA 94035, USA.

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December 2002

Evaluation of nanopores as candidates for electronic analyte detection.

Electrophoresis 2002 Aug;23(16):2592-601

Department of Physics and Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, BC, Canada V6T-1Z1.

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August 2002