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Mark Akeson - Publications

Affiliations: 
University of California, Berkeley, CA, United States 
Area:
Nanopores
Website:
https://www.soe.ucsc.edu/people/makeson
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44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Nivala J, Mulroney L, Luan Q, Abu-Shumays R, Akeson M. Unfolding and Translocation of Proteins Through an Alpha-Hemolysin Nanopore by ClpXP. Methods in Molecular Biology (Clifton, N.J.). 2186: 145-155. PMID 32918735 DOI: 10.1007/978-1-0716-0806-7_11  0.707
2020 Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, ... ... Akeson M, et al. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology. PMID 32686750 DOI: 10.1038/S41587-020-0503-6  0.307
2020 Burton AS, Stahl SE, John KK, Jain M, Juul S, Turner DJ, Harrington ED, Stoddart D, Paten B, Akeson M, Castro-Wallace SL. Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing. Genes. 11. PMID 31936690 DOI: 10.3390/Genes11010076  0.37
2019 Workman RE, Tang AD, Tang PS, Jain M, Tyson JR, Razaghi R, Zuzarte PC, Gilpatrick T, Payne A, Quick J, Sadowski N, Holmes N, de Jesus JG, Jones KL, Soulette CM, ... ... Akeson M, et al. Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome. Nature Methods. PMID 31819268 DOI: 10.1038/S41592-019-0697-Z  0.305
2019 Workman RE, Tang AD, Tang PS, Jain M, Tyson JR, Razaghi R, Zuzarte PC, Gilpatrick T, Payne A, Quick J, Sadowski N, Holmes N, de Jesus JG, Jones KL, Soulette CM, ... ... Akeson M, et al. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nature Methods. PMID 31740818 DOI: 10.1038/S41592-019-0617-2  0.381
2019 Smith AM, Jain M, Mulroney L, Garalde DR, Akeson M. Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing. Plos One. 14: e0216709. PMID 31095620 DOI: 10.1371/Journal.Pone.0216709  0.365
2018 Jain M, Olsen HE, Turner DJ, Stoddart D, Bulazel KV, Paten B, Haussler D, Willard HF, Akeson M, Miga KH. Linear assembly of a human centromere on the Y chromosome. Nature Biotechnology. PMID 29553574 DOI: 10.1038/Nbt.4109  0.312
2017 Byrne A, Beaudin AE, Olsen HE, Jain M, Cole C, Palmer T, DuBois RM, Forsberg EC, Akeson M, Vollmers C. Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. Nature Communications. 8: 16027. PMID 28722025 DOI: 10.1038/Ncomms16027  0.319
2017 Rand AC, Jain M, Eizenga JM, Musselman-Brown A, Olsen HE, Akeson M, Paten B. Mapping DNA methylation with high-throughput nanopore sequencing. Nature Methods. PMID 28218897 DOI: 10.1038/Nmeth.4189  0.383
2016 Jain M, Olsen HE, Paten B, Akeson M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biology. 17: 239. PMID 27887629 DOI: 10.1186/S13059-016-1103-0  0.383
2016 Deamer D, Akeson M, Branton D. Three decades of nanopore sequencing. Nature Biotechnology. 34: 518-24. PMID 27153285 DOI: 10.1038/Nbt.3423  0.634
2016 Deamer D, Akeson M, Branton D. Author response to John Kasianowicz and Sergey Bezrukov. Nature Biotechnology. 34: 482. PMID 27153276 DOI: 10.1038/Nbt.3561  0.435
2015 Smith AM, Abu-Shumays R, Akeson M, Bernick DL. Capture, Unfolding, and Detection of Individual tRNA Molecules Using a Nanopore Device. Frontiers in Bioengineering and Biotechnology. 3: 91. PMID 26157798 DOI: 10.3389/Fbioe.2015.00091  0.432
2015 Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M. Improved data analysis for the MinION nanopore sequencer. Nature Methods. 12: 351-6. PMID 25686389 DOI: 10.1038/Nmeth.3290  0.369
2014 Nivala J, Mulroney L, Li G, Schreiber J, Akeson M. Discrimination among protein variants using an unfoldase-coupled nanopore. Acs Nano. 8: 12365-75. PMID 25402970 DOI: 10.1021/Nn5049987  0.71
2014 Wescoe ZL, Schreiber J, Akeson M. Nanopores discriminate among five C5-cytosine variants in DNA. Journal of the American Chemical Society. 136: 16582-7. PMID 25347819 DOI: 10.1021/Ja508527B  0.471
2014 Nivala J, Akeson M. Distinguishing Protein Domains and Folded States with Unfoldase-Mediated Nanopore Analysis Biophysical Journal. 106: 214a. DOI: 10.1016/J.Bpj.2013.11.1256  0.705
2013 Schreiber J, Wescoe ZL, Abu-Shumays R, Vivian JT, Baatar B, Karplus K, Akeson M. Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands. Proceedings of the National Academy of Sciences of the United States of America. 110: 18910-5. PMID 24167260 DOI: 10.1073/Pnas.1310615110  0.441
2013 Lieberman KR, Dahl JM, Mai AH, Cox A, Akeson M, Wang H. Kinetic mechanism of translocation and dNTP binding in individual DNA polymerase complexes. Journal of the American Chemical Society. 135: 9149-55. PMID 23705688 DOI: 10.1021/Ja403640B  0.412
2013 Nivala J, Marks DB, Akeson M. Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nature Biotechnology. 31: 247-50. PMID 23376966 DOI: 10.1038/Nbt.2503  0.737
2012 Lieberman KR, Dahl JM, Mai AH, Akeson M, Wang H. Dynamics of the translocation step measured in individual DNA polymerase complexes. Journal of the American Chemical Society. 134: 18816-23. PMID 23101437 DOI: 10.1021/Ja3090302  0.436
2012 Dahl JM, Mai AH, Cherf GM, Jetha NN, Garalde DR, Marziali A, Akeson M, Wang H, Lieberman KR. Direct observation of translocation in individual DNA polymerase complexes. The Journal of Biological Chemistry. 287: 13407-21. PMID 22378784 DOI: 10.1074/Jbc.M111.338418  0.403
2012 Cherf GM, Lieberman KR, Rashid H, Lam CE, Karplus K, Akeson M. Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nature Biotechnology. 30: 344-8. PMID 22334048 DOI: 10.1038/Nbt.2147  0.518
2011 Garalde DR, Simon CA, Dahl JM, Wang H, Akeson M, Lieberman KR. Distinct complexes of DNA polymerase I (Klenow fragment) for base and sugar discrimination during nucleotide substrate selection. The Journal of Biological Chemistry. 286: 14480-92. PMID 21362617 DOI: 10.1074/Jbc.M111.218750  0.436
2010 Lieberman KR, Cherf GM, Doody MJ, Olasagasti F, Kolodji Y, Akeson M. Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase Journal of the American Chemical Society. 132: 17961-17972. PMID 21121604 DOI: 10.1021/Ja1087612  0.472
2010 Olasagasti F, Lieberman KR, Benner S, Cherf GM, Dahl JM, Deamer DW, Akeson M. Replication of individual DNA molecules under electronic control using a protein nanopore. Nature Nanotechnology. 5: 798-806. PMID 20871614 DOI: 10.1038/Nnano.2010.177  0.628
2009 Gyarfas B, Olasagasti F, Benner S, Garalde D, Lieberman KR, Akeson M. Mapping the position of DNA polymerase-bound DNA templates in a nanopore at 5 Å resolution Acs Nano. 3: 1457-1466. PMID 19489560 DOI: 10.1021/Nn900303G  0.442
2009 Wilson NA, Abu-Shumays R, Gyarfas B, Wang H, Lieberman KR, Akeson M, Dunbar WB. Electronic control of DNA polymerase binding and unbinding to single DNA molecules. Acs Nano. 3: 995-1003. PMID 19338283 DOI: 10.1021/Nn9000897  0.488
2009 Hurt N, Wang H, Akeson M, Lieberman KR. Specific nucleotide binding and rebinding to individual DNA polymerase complexes captured on a nanopore. Journal of the American Chemical Society. 131: 3772-8. PMID 19275265 DOI: 10.1021/Ja809663F  0.444
2008 Wilson NA, U-Shumays RA, Lieberman K, Akeson M, Dunbar WB. Feedback control of a DNA molecule tethered in a nanopore to repeatedly probe DNA-binding enzymes. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2008: 5745-8. PMID 19164022 DOI: 10.1109/IEMBS.2008.4650519  0.397
2007 Benner S, Chen RJ, Wilson NA, Abu-Shumays R, Hurt N, Lieberman KR, Deamer DW, Dunbar WB, Akeson M. Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore. Nature Nanotechnology. 2: 718-24. PMID 18654412 DOI: 10.1038/Nnano.2007.344  0.631
2007 Hornblower B, Coombs A, Whitaker RD, Kolomeisky A, Picone SJ, Meller A, Akeson M. Single-molecule analysis of DNA-protein complexes using nanopores. Nature Methods. 4: 315-7. PMID 17339846 DOI: 10.1038/Nmeth1021  0.477
2006 Winters-Hilt S, Landry M, Akeson M, Tanase M, Amin I, Coombs A, Morales E, Millet J, Baribault C, Sendamangalam S. Cheminformatics methods for novel nanopore analysis of HIV DNA termini. Bmc Bioinformatics. 7: S22. PMID 17118144 DOI: 10.1186/1471-2105-7-S2-S22  0.415
2004 Winters-Hilt S, Akeson M. Nanopore cheminformatics. Dna and Cell Biology. 23: 675-83. PMID 15585125 DOI: 10.1089/1044549042476893  0.356
2003 Vercoutere WA, Winters-Hilt S, DeGuzman VS, Deamer D, Ridino SE, Rodgers JT, Olsen HE, Marziali A, Akeson M. Discrimination among individual Watson-Crick base pairs at the termini of single DNA hairpin molecules. Nucleic Acids Research. 31: 1311-8. PMID 12582251 DOI: 10.1093/Nar/Gkg218  0.625
2003 Winters-Hilt S, Vercoutere W, DeGuzman VS, Deamer D, Akeson M, Haussler D. Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules. Biophysical Journal. 84: 967-76. PMID 12547778 DOI: 10.1016/S0006-3495(03)74913-3  0.605
2003 Nakane JJ, Akeson M, Marziali A. Nanopore sensors for nucleic acid analysis Journal of Physics: Condensed Matter. 15. DOI: 10.1088/0953-8984/15/32/203  0.473
2002 Vercoutere W, Akeson M. Biosensors for DNA sequence detection. Current Opinion in Chemical Biology. 6: 816-22. PMID 12470736 DOI: 10.1016/S1367-5931(02)00395-2  0.472
2002 Nakane J, Akeson M, Marziali A. Evaluation of nanopores as candidates for electronic analyte detection. Electrophoresis. 23: 2592-601. PMID 12210162 DOI: 10.1002/1522-2683(200208)23:16<2592::Aid-Elps2592>3.0.Co;2-L  0.376
2002 Marziali A, Akeson M. New DNA sequencing methods. Annual Review of Biomedical Engineering. 3: 195-223. PMID 11447062 DOI: 10.1146/Annurev.Bioeng.3.1.195  0.39
2001 Vercoutere W, Winters-Hilt S, Olsen H, Deamer D, Haussler D, Akeson M. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nature Biotechnology. 19: 248-52. PMID 11231558 DOI: 10.1038/85696  0.637
2000 Deamer DW, Akeson M. Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends in Biotechnology. 18: 147-51. PMID 10740260 DOI: 10.1016/S0167-7799(00)01426-8  0.609
1999 Akeson M, Branton D, Kasianowicz JJ, Brandin E, Deamer DW. Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophysical Journal. 77: 3227-33. PMID 10585944 DOI: 10.1016/S0006-3495(99)77153-5  0.614
1999 Paula S, Akeson M, Deamer D. Water transport by the bacterial channel alpha-hemolysin. Biochimica Et Biophysica Acta. 1418: 117-126. PMID 10209216 DOI: 10.1016/S0005-2736(99)00031-0  0.484
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