Publications by authors named "Mark Akeson"

40Publications

Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station Using Nanopore Sequencing.

Authors:
Sarah Stahl-Rommel Miten Jain Hang N Nguyen Richard R Arnold Serena M Aunon-Chancellor Gretta Marie Sharp Christian L Castro Kristen K John Sissel Juul Daniel J Turner David Stoddart Benedict Paten Mark Akeson Aaron S Burton Sarah L Castro-Wallace

Genes (Basel) 2021 Jan 16;12(1). Epub 2021 Jan 16.

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

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January 2021

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

Authors:
Jeff Nivala Logan Mulroney Qing Luan Robin Abu-Shumays Mark Akeson

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

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.

Authors:
Kishwar Shafin Trevor Pesout Ryan Lorig-Roach Marina Haukness Hugh E Olsen Colleen Bosworth Joel Armstrong Kristof Tigyi Nicholas Maurer Sergey Koren Fritz J Sedlazeck Tobias Marschall Simon Mayes Vania Costa Justin M Zook Kelvin J Liu Duncan Kilburn Melanie Sorensen Katy M Munson Mitchell R Vollger Jean Monlong Erik Garrison Evan E Eichler Sofie Salama David Haussler Richard E Green Mark Akeson Adam Phillippy Karen H Miga Paolo Carnevali Miten Jain Benedict Paten

Nat Biotechnol 2020 09 4;38(9):1044-1053. Epub 2020 May 4.

UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.

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September 2020

CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma.

Authors:
S John Liu Martina Malatesta Brian V Lien Parna Saha Shivani S Thombare Sung Jun Hong Leslie Pedraza Mark Koontz Kyounghee Seo Max A Horlbeck Daniel He Harjus S Birk Miten Jain Hugh E Olsen Mark Akeson Jonathan S Weissman Michelle Monje Nalin Gupta David R Raleigh Erik M Ullian Daniel A Lim

Genome Biol 2020 03 31;21(1):83. Epub 2020 Mar 31.

Department of Neurological Surgery, University of California, San Francisco, CA, 94143, USA.

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March 2020

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

Authors:
Aaron S Burton Sarah E Stahl Kristen K John Miten Jain Sissel Juul Daniel J Turner Eoghan D Harrington David Stoddart Benedict Paten Mark Akeson Sarah L Castro-Wallace

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

Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome.

Authors:
Rachael E Workman Alison D Tang Paul S Tang Miten Jain John R Tyson Roham Razaghi Philip C Zuzarte Timothy Gilpatrick Alexander Payne Joshua Quick Norah Sadowski Nadine Holmes Jaqueline Goes de Jesus Karen L Jones Cameron M Soulette Terrance P Snutch Nicholas Loman Benedict Paten Matthew Loose Jared T Simpson Hugh E Olsen Angela N Brooks Mark Akeson Winston Timp

Nat Methods 2020 Jan;17(1):114

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.

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January 2020

Nanopore native RNA sequencing of a human poly(A) transcriptome.

Authors:
Rachael E Workman Alison D Tang Paul S Tang Miten Jain John R Tyson Roham Razaghi Philip C Zuzarte Timothy Gilpatrick Alexander Payne Joshua Quick Norah Sadowski Nadine Holmes Jaqueline Goes de Jesus Karen L Jones Cameron M Soulette Terrance P Snutch Nicholas Loman Benedict Paten Matthew Loose Jared T Simpson Hugh E Olsen Angela N Brooks Mark Akeson Winston Timp

Nat Methods 2019 12 18;16(12):1297-1305. Epub 2019 Nov 18.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.

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December 2019

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

Authors:
Andrew M Smith Miten Jain Logan Mulroney Daniel R Garalde Mark Akeson

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.

Authors:
Miten Jain Hugh E Olsen Daniel J Turner David Stoddart Kira V Bulazel Benedict Paten David Haussler Huntington F Willard Mark Akeson Karen H Miga

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

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells.

Authors:
Ashley Byrne Anna E Beaudin Hugh E Olsen Miten Jain Charles Cole Theron Palmer Rebecca M DuBois E Camilla Forsberg Mark Akeson Christopher Vollmers

Nat Commun 2017 07 19;8:16027. Epub 2017 Jul 19.

UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, California 95064, USA.

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July 2017

Mapping DNA methylation with high-throughput nanopore sequencing.

Authors:
Arthur C Rand Miten Jain Jordan M Eizenga Audrey Musselman-Brown Hugh E Olsen Mark Akeson Benedict Paten

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.

Authors:
Miten Jain Hugh E Olsen Benedict Paten Mark Akeson

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.

Authors:
Miten Jain Hugh E Olsen Benedict Paten Mark Akeson

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.

Authors:
David Deamer Mark Akeson Daniel Branton

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.

Authors:
David Deamer Mark Akeson Daniel Branton

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.

Authors:
Andrew M Smith Robin Abu-Shumays Mark Akeson David L Bernick

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.

Authors:
Miten Jain Ian T Fiddes Karen H Miga Hugh E Olsen Benedict Paten Mark Akeson

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.

Authors:
Jeff Nivala Logan Mulroney Gabriel Li Jacob Schreiber Mark Akeson

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.

Authors:
Zachary L Wescoe Jacob Schreiber Mark Akeson

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.

Authors:
Jacob Schreiber Zachary L Wescoe Robin Abu-Shumays John T Vivian Baldandorj Baatar Kevin Karplus Mark Akeson

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.

Authors:
Kate R Lieberman Joseph M Dahl Ai H Mai Ashley Cox Mark Akeson Hongyun Wang

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.

Authors:
Jeff Nivala Douglas B Marks Mark Akeson

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.

Authors:
Kate R Lieberman Joseph M Dahl Ai H Mai Mark Akeson Hongyun Wang

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.

Authors:
Joseph M Dahl Ai H Mai Gerald M Cherf Nahid N Jetha Daniel R Garalde Andre Marziali Mark Akeson Hongyun Wang Kate R Lieberman

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.

Authors:
Gerald M Cherf Kate R Lieberman Hytham Rashid Christopher E Lam Kevin Karplus Mark Akeson

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.

Authors:
Daniel R Garalde Christopher A Simon Joseph M Dahl Hongyun Wang Mark Akeson Kate R Lieberman

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.

Authors:
Kate R Lieberman Gerald M Cherf Michael J Doody Felix Olasagasti Yvette Kolodji Mark Akeson

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.

Authors:
Felix Olasagasti Kate R Lieberman Seico Benner Gerald M Cherf Joseph M Dahl David W Deamer Mark Akeson

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.

Authors:
Brett Gyarfas Felix Olasagasti Seico Benner Daniel Garalde Kate R Lieberman Mark Akeson

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.

Authors:
Noah A Wilson Robin Abu-Shumays Brett Gyarfas Hongyun Wang Kate R Lieberman Mark Akeson William B Dunbar

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.

Authors:
Nicholas Hurt Hongyun Wang Mark Akeson Kate R Lieberman

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.

Authors:
Noah A Wilson Robin Ab U-Shumays Kate Lieberman Mark Akeson William B Dunbar

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

Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore.

Authors:
Seico Benner Roger J A Chen Noah A Wilson Robin Abu-Shumays Nicholas Hurt Kate R Lieberman David W Deamer William B Dunbar Mark Akeson

Nat Nanotechnol 2007 Nov 28;2(11):718-24. Epub 2007 Oct 28.

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November 2007

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

Authors:
Breton Hornblower Amy Coombs Richard D Whitaker Anatoly Kolomeisky Stephen J Picone Amit Meller Mark Akeson

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.

Authors:
Stephen Winters-Hilt Matthew Landry Mark Akeson Maria Tanase Iftekhar Amin Amy Coombs Eric Morales John Millet Carl Baribault Srikanth Sendamangalam

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.

Authors:
Stephen Winters-Hilt Mark Akeson

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.

Authors:
Wenonah A Vercoutere Stephen Winters-Hilt Veronica S DeGuzman David Deamer Sam E Ridino Joseph T Rodgers Hugh E Olsen Andre Marziali Mark Akeson

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.

Authors:
Stephen Winters-Hilt Wenonah Vercoutere Veronica S DeGuzman David Deamer Mark Akeson David Haussler

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.

Authors:
Wenonah Vercoutere Mark Akeson

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.

Authors:
Jonathan Nakane Mark Akeson Andre Marziali

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