Nanopore Papers by Year


Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing. AM Smith, M Jain, L Mulroney, DR Garalde, M Akeson. 2019, PloS one 14 (5), e0216709.

Bioinformatic Analysis of Nanopore Data. M Jain. Nanopore Sequencing: An Introduction, 147, 2019.


Methods of Producing Size-Selected Nucleic Acid Libraries and Compositions and Kits for Practicing Same. HE Olsen, M Jain, MA Akeson. US Patent App. 2018; 15/970,690.

Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing. N Ring, JS Abrahams, M Jain, H Olsen, A Preston, S Bagby. Microbial genomics. 2018, 4 (11).

Methods for determining base locations in a polynucleotide. M Jain, HE Olsen, MA Akeson. US Patent App. 2018; 15/564,386.

Linear assembly of a human centromere on the Y chromosome. M Jain, HE Olsen, DJ Turner, D Stoddart, KV Bulazel, B Paten, D Haussler, et al. Nature biotechnology. 2018, 36 (4), 321.

Nanopore sequencing and assembly of a human genome with ultra-long reads. M Jain, S Koren, KH Miga, J Quick, AC Rand, TA Sasani, JR Tyson, et al. Nature biotechnology. 2018, 36 (4), 338.

MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome. JR Tyson, NJ O'Neil, M Jain, HE Olsen, P Hieter, TP Snutch. Genome research. 2018, 28 (2), 266-274.

Nanopore native RNA sequencing of a human poly (A) transcriptome. RE Workman, A Tang, PS Tang, M Jain, JR Tyson, PC Zuzarte, et al. BioRxiv, 2018. 459529.


Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. A Byrne, AE Beaudin, HE Olsen, M Jain, C Cole, T Palmer, RM DuBois, et al. Nature communications. 2017, 8, 16027.

Mapping DNA methylation with high-throughput nanopore sequencing. AC Rand, M Jain, JM Eizenga, A Musselman-Brown, HE Olsen, M Akeson, et al. Nature methods. 2017, 14 (4), 411.

MinION analysis and reference consortium: phase 2 data release and analysis of R9. 0 chemistry. M Jain, JR Tyson, M Loose, CLC Ip, DA Eccles, J O'Grady, S Malla, et al. F1000Research. 2017, 6.

High-Coverage Long Read DNA Sequencing with the Oxford Nanopore MinION. M Jain. UC Santa Cruz, 2017.

Erratum to: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. M Jain, HE Olsen, B Paten, M Akeson. Genome biology 2016, 17 (1), 256.


The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. M Jain, HE Olsen, B Paten, M Akeson Genome biology. 2016, 17 (1), 239.


Improved data analysis for the MinION nanopore sequencer. M Jain, IT Fiddes, KH Miga, HE Olsen, B Paten, M Akeson. Nature methods, 2015, 12 (4), 351.

Use of MinION data to assemble the 67% GC genome sequence of Bordetella pertussis. S Bagby, M Jain, H Olsen, A Preston, M Akeson. Genome Science, 2015.

MinION Analysis and Reference Consortium: Phase 1 data release and analysis CLC Ip. M Loose, JR Tyson, M de Cesare, BL Brown, M Jain, RM Leggett, et al. F1000Research. 2015, 4.


Centromere reference models for human chromosomes X and Y satellite arrays. KH Miga, Y Newton, M Jain, N Altemose, HF Willard, WJ Kent. Genome research. 2014, 24 (4), 697-707.

Dynamics of Translocation and Substrate Binding in Individual Complexes Formed with Active Site Mutants of Φ29 DNA Polymerase. Dahl JM, Wang H, Lazaro JM, Salas M, Lieberman KR. J Biol Chem. 2014 Jan 24. [Epub ahead of print]


Kinetic mechanism of translocation and dNTP binding in individual DNA polymerase complexes. Lieberman KR, Dahl JM, Mai AH, Cox A, Akeson M, Wang H. J Am Chem Soc. 2013 Jun 19;135(24):9149-55. doi: 10.1021/ja403640b. Epub 2013 Jun 7.

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands. Schreiber J, Wescoe ZL, Abu-Shumays R, Vivian JT, Baatar B, Karplus K, Akeson M. Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):18910-5. doi: 10.1073/pnas.1310615110. Epub 2013 Oct 28.

Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nivala J, Marks DB, Akeson M. Nat Biotechnol. 2013 Mar;31(3):247-50. doi: 10.1038/nbt.2503. Epub 2013 Feb 3.


Automated forward and reverse ratcheting of DNA in a nanopore at 5Å precision.  Cherf GM, Lieberman KR, Rashid H, Lam CE, Karplus K, Akeson A. Nature BioTechnology Epub 2012 Feb 14.

Direct observation of translocation in individual DNA polymerase complexes. Dahl JM, Mai AH, Cherf GM, Jetha NN, Garalde DR, Marziali A, Akeson M, Wang H, Lieberman KR. J Biol Chem 2012, 287, 13407-13421 

Dynamics of the translocation step measured in individual DNA polymerase complexes. Lieberman KR, Dahl JM, Mai AH, Akeson M, Wang H. J Am Chem Soc. 2012 Nov 14;134(45):18816-23. doi: 10.1021/ja3090302. Epub 2012 Nov 1.

Dynamics of the Translocation Step Measured in Individual DNA Polymerase Complexes. Lieberman KR, Dahl JM, Mai AH, Akeson M, Wang H. J Am Chem Soc. 2012 Oct 26. published online

Single-cell manipulation using Nanopipettes. MM Maalouf, M Jain, P Actis, N Pourmand. Nanotech 2012 2, 384 - 387.


Distinct complexes of DNA polymerase I (Klenow fragment) for base and sugar discrimination during nucleotide substrate selection. Garalde DR, Simon CA, Dahl JM, Wang H, Akeson M, Lieberman KR. J Biol Chem. 2011 Apr 22;286(16):14480-92. Epub 2011 Feb 28.


Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase.  Lieberman KR, Cherf GM, Doody MJ, Olasagasti F, Kolodji Y, Akeson M. J Am Chem Soc. 2010 Dec 22;132(50):17961-72. Epub 2010 Dec 1.

Replication of individual DNA molecules under electronic control using a protein nanopore. Olasagasti F, Lieberman KR, Benner S, Cherf GM, Dahl JM, Deamer DW, Akeson M. Nat Nanotechnol. 2010 Nov;5(11):798-806. Epub 2010 Sep 26.


Mapping the position of DNA polymerase-bound DNA templates in a nanopore at 5 A resolution.  Gyarfas B, Olasagasti F, Benner S, Garalde D, Lieberman KR, Akeson M.ACS Nano. 2009 Jun 23;3(6):1457-66.

Electronic control of DNA polymerase binding and unbinding to single DNA molecules. Wilson NA, Abu-Shumays R, Gyarfas B, Wang H, Lieberman KR, Akeson M, Dunbar WB. ACS Nano. 2009 Apr 28;3(4):995-1003.

Specific nucleotide binding and rebinding to individual DNA polymerase complexes captured on a nanopore.  Hurt N, Wang H, Akeson M, Lieberman KR. J Am Chem Soc. 2009 Mar 18;131(10):3772-8.


Feedback control of a DNA molecule tethered in a nanopore to repeatedly probe DNA-binding enzymes.  Wilson NA, U-Shumays RA, Lieberman K, Akeson M, Dunbar WB. Conf Proc IEEE Eng Med Biol Soc. 2008;2008:5745-8.


Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore.  Benner S, Chen RJ, Wilson NA, Abu-Shumays R, Hurt N, Lieberman KR, Deamer DW, Dunbar WB, Akeson M. Nat Nanotechnol. 2007 Nov;2(11):718-24. Epub 2007 Oct 28.

Single-molecule analysis of DNA-protein complexes using nanopores.  Hornblower B, Coombs A, Whitaker RD, Kolomeisky A, Picone SJ, Meller A, Akeson M. Nature Methods. published online 2007 March 4.


Cheminformatics methods for novel nanopore analysis of HIV DNA termini. Winters-Hilt S, Landry M, Akeson M, Tanase M, Amin I, Coombs A, Morales E, Millet J, Baribault C, Sendamangalam S. BMC Bioinformatics. 2006 Sep 6;7 Suppl 2:S22.


Nanopore cheminformatics. Winters-Hilt S, Akeson M. DNA Cell Biol. 2004 Oct;23(10):675-83.


Nanopore sensors for nucleic acid analysis. Nakane JJ, Akeson M, Marziali A. J Phys Condensed Matter. 2003 Aug 20; 15(32):R1365-93.

Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules</a>. Winters-Hilt S, Vercoutere W, DeGuzman VS, Deamer D, Akeson M, Haussler D. Biophys J. 2003 Feb; 84(2 pt 1):967-76.

Discrimination among individual Watson-Crick base pairs at the termini of single DNA hairpin molecules. Vercoutere WA, Winters-Hilt S, DeGuzman VS, Deamer D, Ridino SE, Rodgers JT, Olsen HE, Marziali A, Akeson M. Nucleic Acids Res. 2003 Feb 15; 31(4):1311-8.


Biosensors for DNA sequence detection. Vercoutere W, Akeson M. Curr Opin Chem Biol. 2002 Dec; 6(6):816-22. 

Evaluation of nanopores as candidates for electronic analyte detection. Nakane J, Akeson M, Marziali A. Electrophoresis. 2002 Aug; 23(16):2592-601. 

Use of a nanoscale pore to read short segments within single polynucleotide molecules. Akeson M, Deamer DW, Vercoutere W, Braslau R, Olsen H. In: Structure and Dynamics of Confined Polymers, J Kasianowicz, M Kellermayer, D Deamer (eds). Bikal, Hungary, 2002, pp. 187-200. 

Mechanism of ionic current blockades during polymer transport through pores of nanometer dimensions. Deamer DW, Olsen H, Akeson MA, Kasianowicz J. In: Structure and Dynamics of Confined Polymers, J Kasianowicz, M Kellermayer, D Deamer (eds). Bikal, Hungary, 2002, pp.165-176. 


Rapid discrimination among individual DNA hairpin molecules at single nucleotide resolution using an ion channel. Vercoutere W, Winters-Hilt S, Olsen H, Deamer D, Haussler D, Akeson M. Nat Biotechnol. 2001 Mar; 19(3):248-52.

New DNA sequencing methods. Marziali A, Akeson M. Annu Rev Biomed Eng. 2001; 3:195-223. (Listed among the most cited articles in the Annual Review in Biomedical Engineering Series based on results from 2002-2003.)


Nanopores and nucleic acids: prospects for ultrarapid sequencing. Deamer DW, Akeson M. Trends Biotechnol 2000 Apr; 18(4):147-51. 


Water transport by the bacterial channel alpha-hemolysin. Paula S, Akeson M, Deamer D. Biochim BiophysActa. 1999 Apr 14; 1418(1): 117-26.

Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Akeson M, Branton D, Kasianowicz JJ, Brandin E, Deamer DW. Biophys J. 1999 Dec; 77(6):3227-33.


Characterization of individual polynucleotide molecules using a membrane channel. Kasianowicz JJ, Brandin E, Branton D, Deamer DW. Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13770-3.