Three decades of nanopore sequencing
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Sufficient pore utilization for high sequencing throughput can only be realized for long fragments (>1 kb).
“sufficient pore utilization for high sequencing throughput can only be realized for long fragments (>1 kb).”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [88]
The high error rate of nanopore sequencing is approximately 10% per nucleotide in the single read.
“The high error rate of nanopore sequencing (∼10% per nt in the single read),70,88”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [88]
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Cites
Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
Viterbi, A. J. (1967) · IEEE Transactions on Information Theory · doi:10.1109/tit.1967.1054010 · Cited by 6,877 · see citing works
Characterization of individual polynucleotide molecules using a membrane channel
Kasianowicz, J. J., Brandin, E., Branton, D., & Deamer, D. W. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.24.13770 · Cited by 3,350 · see citing works
Self-citationStructure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore
Song, L., Hobaugh, M. R., Shustak, C., Cheley, S., Bayley, H., & Gouaux, J. E. (1996) · Science · doi:10.1126/science.274.5294.1859 · Cited by 2,378 · see citing works
Real-time, portable genome sequencing for Ebola surveillance
Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L. A., Boré, J. A., Koundouno, F. R., Dudas, G., Mikhail, A. F. W., et al. (2016) · Nature · doi:10.1038/nature16996 · Cited by 1,450 · see citing works
A complete bacterial genome assembled de novo using only nanopore sequencing data
Loman, N. J., Quick, J., & Simpson, J. T. (2015) · Nature Methods · doi:10.1038/nmeth.3444 · Cited by 1,272 · see citing works
Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase
Manrao, E. A., Derrington, I. M., Laszlo, A. H., Langford, K. W., Hopper, M. K., Gillgren, N., Pavlenok, M., Niederweis, M., & Gundlach, J. H. (2012) · Nature Biotechnology · doi:10.1038/nbt.2171 · Cited by 966 · see citing works
Akeson, M. A., Branton, D., Kasianowicz, J. J., Brandin, E., & Deamer, D. W. (1999) · Biophysical Journal · doi:10.1016/s0006-3495(99)77153-5 · Cited by 959 · see citing works
Self-citationRapid nanopore discrimination between single polynucleotide molecules
Meller, A., Nivón, L. G., Brandin, E., Golovchenko, J. A., & Branton, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.3.1079 · Cited by 936 · see citing works
Self-citationVoltage-Driven DNA Translocations through a Nanopore
MELLER, A., Nivón, L. G., & Branton, D. (2001) · Physical Review Letters · doi:10.1103/physrevlett.86.3435 · Cited by 894 · see citing works
Self-citationImproved data analysis for the MinION nanopore sequencer
Jain, M., Fiddes, I. T., Miga, K. H., Olsen, H. E., Paten, B., & Akeson, M. A. (2015) · Nature Methods · doi:10.1038/nmeth.3290 · Cited by 639 · see citing works
Self-citationAutomated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision
Cherf, G. M., Lieberman, K. R., Rashid, H., Lam, C. E., Karplus, K. J., & Akeson, M. A. (2012) · Nature Biotechnology · doi:10.1038/nbt.2147 · Cited by 615 · see citing works
Self-citationNanopore DNA sequencing with MspA
Derrington, I. M., Butler, T. Z., Collins, M. D., Manrao, E. A., Pavlenok, M., Niederweis, M., & Gundlach, J. H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1001831107 · Cited by 586 · see citing works
Single-molecule DNA detection with an engineered MspA protein nanopore
Butler, T. Z., Pavlenok, M., Derrington, I. M., Niederweis, M., & Gundlach, J. H. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807514106 · Cited by 512 · see citing works
Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore
Stoddart, D., Heron, A. J., Mikhailova, E., Maglia, G., & Bayley, H. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0901054106 · Cited by 478 · see citing works
Ashton, P., Nair, S., Dallman, T. J., Rubino, S., Rabsch, W., Mwaigwisya, S., Wain, J. R., & O’Grady, J. (2014) · Nature Biotechnology · doi:10.1038/nbt.3103 · Cited by 462 · see citing works
Decoding long nanopore sequencing reads of natural DNA
Laszlo, A. H., Derrington, I. M., Ross, B. C., Brinkerhoff, H. D., Adey, A., Nova, I. C., Craig, J. M., Langford, K. W., Samson, J. M., Daza, R. M., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2950 · Cited by 444 · see citing works
The Structure of a Mycobacterial Outer-Membrane Channel
Faller, M., Niederweis, M., & Schulz, G. E. (2004) · Science · doi:10.1126/science.1094114 · Cited by 422 · see citing works
Menestrina, G. (1986) · The Journal of Membrane Biology · doi:10.1007/bf01869935 · Cited by 357 · see citing works
Orientation discrimination of single-stranded DNA inside the α-hemolysin membrane channel
Mathé, J., Aksimentiev, A., Nelson, D. R., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0502947102 · Cited by 333 · see citing works
Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG
Goyal, P., Krasteva, P. V., Gerven, N. V., Gubellini, F., den Broeck, I. V., Troupiotis-Tsaïlaki, A., Jonckheere, W., Pehau‐Arnaudet, G., Pinkner, J. S., Chapman, M. R., et al. (2014) · Nature · doi:10.1038/nature13768 · Cited by 326 · see citing works
Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA
Laszlo, A. H., Derrington, I. M., Brinkerhoff, H., Langford, K. W., Nova, I. C., Samson, J. M., Bartlett, J. J., Pavlenok, M., & Gundlach, J. H. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1310240110 · Cited by 321 · see citing works
MinION Analysis and Reference Consortium: Phase 1 data release and analysis
Ip, C. L. C., Loose, M., Tyson, J. R., de Cesare, M., Brown, B. L., Jain, M., Leggett, R. M., Eccles, D., Zalunin, V. V., Urban, J. M., et al. (2015) · F1000Research · doi:10.12688/f1000research.7201.1 · Cited by 317 · see citing works
Single-molecule analysis of DNA-protein complexes using nanopores
Hornblower, B., Coombs, A., Whitaker, R. D., et al. (2007) · Nature Methods · doi:10.1038/nmeth1021 · Cited by 309 · see citing works
Molecule-hugging graphene nanopores
Garaj, S., Liu, S., Golovchenko, J. A., & Branton, D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1220012110 · Cited by 268 · see citing works
Self-citationAccurate whole-genome sequencing and haplotyping from 10 to 20 human cells
Peters, B. A., Kermani, B. G., Sparks, A. B., Alferov, O., Hong, P., Alexeev, A., Jiang, Y., Dahl, F., Tang, Y. T., Haas, J., et al. (2012) · Nature · doi:10.1038/nature11236 · Cited by 251 · see citing works
Dynamics and Free Energy of Polymers Partitioning into a Nanoscale Pore
Bezrukov, S. M., Vodyanoy, I., Brutyan, R. A., & Kasianowicz, J. J. (1996) · Macromolecules · doi:10.1021/ma960841j · Cited by 247 · see citing works
Processive Replication of Single DNA Molecules in a Nanopore Catalyzed by phi29 DNA Polymerase
Lieberman, K. R., Cherf, G. M., Doody, M. J., et al. (2010) · Journal of the American Chemical Society · doi:10.1021/ja1087612 · Cited by 233 · see citing works
Recapturing and trapping single molecules with a solid-state nanopore
Gershow, M. H., & Golovchenko, J. A. (2007) · Nature Nanotechnology · doi:10.1038/nnano.2007.381 · Cited by 224 · see citing works
Quick, J., Quinlan, A. R., & Loman, N. J. (2014) · GigaScience · doi:10.1186/2047-217x-3-22 · Cited by 224 · see citing works
A Single-Molecule Nanopore Device Detects DNA Polymerase Activity with Single-Nucleotide Resolution
Cockroft, S. L., Chu, J., Amorín, M., et al. (2008) · Journal of the American Chemical Society · doi:10.1021/ja077082c · Cited by 224 · see citing works
Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool
Hoenen, T., Groseth, A., Rosenke, K., Fischer, R. J., Hoenen, A., Judson, S. D., Martellaro, C., Falzarano, D., Marzi, A., Squires, R. B., et al. (2015) · Emerging infectious diseases · doi:10.3201/eid2202.151796 · Cited by 218 · see citing works
Recognizing a Single Base in an Individual DNA Strand: A Step Toward DNA Sequencing in Nanopores
Ashkenasy, N., Sánchez‐Quesada, J., Bayley, H., et al. (2005) · Angewandte Chemie International Edition · doi:10.1002/anie.200462114 · Cited by 216 · see citing works
Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore
Benner, S., Chen, R. J. A., Wilson, N. A., et al. (2007) · Nature Nanotechnology · doi:10.1038/nnano.2007.344 · Cited by 202 · see citing works
Bezrukov, S. M., & Kasianowicz, J. J. (1993) · Physical Review Letters · doi:10.1103/physrevlett.70.2352 · Cited by 195 · see citing works
Schreiber, J. M., Wescoe, Z. L., Abu-Shumays, R. L., Vivian, J., Baatar, B., Karplus, K. J., & Akeson, M. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1310615110 · Cited by 181 · see citing works
Self-citationGenome assembly using Nanopore-guided long and error-free DNA reads
Madoui, M., Engelen, S., Cruaud, C., Belser, C., Bertrand, L., Alberti, A., Lemainque, A., Wincker, P., & Aury, J. (2015) · BMC Genomics · doi:10.1186/s12864-015-1519-z · Cited by 181 · see citing works
Replication of individual DNA molecules under electronic control using a protein nanopore
Olasagasti, F., Lieberman, K. R., Benner, S., Cherf, G. M., Dahl, J. M., Deamer, D. W., & Akeson, M. A. (2010) · Nature Nanotechnology · doi:10.1038/nnano.2010.177 · Cited by 167 · see citing works
Self-citationCloning of the mspA gene encoding a porin from Mycobacterium smegmatis
Niederweis, M., Ehrt, S., Heinz, C., Klöcker, U., Karosi, S., Swiderek, K. M., Riley, L. W., & Benz, R. (1999) · Molecular Microbiology · doi:10.1046/j.1365-2958.1999.01472.x · Cited by 165 · see citing works
Permeability of the cell wall of Mycobacterium smegmatis
Trias, J., & Benz, R. (1994) · Molecular Microbiology · doi:10.1111/j.1365-2958.1994.tb01289.x · Cited by 163 · see citing works
Nucleotide Discrimination with DNA Immobilized in the MspA Nanopore
Manrao, E. A., Derrington, I. M., Pavlenok, M., Niederweis, M., & Gundlach, J. H. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025723 · Cited by 160 · see citing works
Nanopore sequencing detects structural variants in cancer
Norris, A. L., Workman, R. E., Fan, Y., Eshleman, J. R., & Timp, W. (2016) · Cancer Biology & Therapy · doi:10.1080/15384047.2016.1139236 · Cited by 148 · see citing works
Determining exon connectivity in complex mRNAs by nanopore sequencing
Bolisetty, M. T., Rajadinakaran, G., & Graveley, B. R. (2015) · Genome biology · doi:10.1186/s13059-015-0777-z · Cited by 139 · see citing works
Electrical pulse fabrication of graphene nanopores in electrolyte solution
Kuan, A. T., Lu, B., Xie, P., Szalay, T., & Golovchenko, J. A. (2015) · Applied Physics Letters · doi:10.1063/1.4921620 · Cited by 128 · see citing works
Nucleobase Recognition in ssDNA at the Central Constriction of the α-Hemolysin Pore
Stoddart, D., Heron, A. J., Klingelhoefer, J. W., Mikhailova, E., Maglia, G., & Bayley, H. (2010) · Nano Letters · doi:10.1021/nl101955a · Cited by 122 · see citing works
Multiple Base‐Recognition Sites in a Biological Nanopore: Two Heads are Better than One
Stoddart, D., Maglia, G., Mikhailova, E., et al. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200905483 · Cited by 122 · see citing works
Determination of RNA Orientation during Translocation through a Biological Nanopore
Butler, T. Z., Gundlach, J. H., & Troll, M. A. (2005) · Biophysical Journal · doi:10.1529/biophysj.105.068957 · Cited by 111 · see citing works
Nanopores Discriminate among Five C5-Cytosine Variants in DNA
Wescoe, Z. L., Schreiber, J. M., & Akeson, M. A. (2014) · Journal of the American Chemical Society · doi:10.1021/ja508527b · Cited by 102 · see citing works
Self-citationDe novo sequencing and variant calling with nanopores using PoreSeq
Szalay, T., & Golovchenko, J. A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3360 · Cited by 90 · see citing works
DNA Base-Calling from a Nanopore Using a Viterbi Algorithm
Timp, W., Comer, J. R., & Aksimentiev, A. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.04.009 · Cited by 89 · see citing works
Bhattacharya, S., Derrington, I. M., Pavlenok, M., et al. (2012) · ACS Nano · doi:10.1021/nn3019943 · Cited by 88 · see citing works
A pore-forming protein with a metal-actuated switch
Walker, B. W., Kasianowicz, J. J., Krishnasastry, M. V., et al. (1994) · Protein Engineering Design and Selection · doi:10.1093/protein/7.5.655 · Cited by 87 · see citing works
DNA heterogeneity and phosphorylation unveiled by single-molecule electrophoresis
Wang, H., Dunning, J. E., Huang, A. P.-H., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405568101 · Cited by 64 · see citing works
Chu, J., González‐López, M., Cockroft, S. L., et al. (2010) · Angewandte Chemie International Edition · doi:10.1002/anie.201005460 · Cited by 53 · see citing works
Quick, J. C., Quinlan, A. R., & Loman, N. J. (2015) · GigaScience · doi:10.1186/s13742-015-0043-z · Cited by 30 · see citing works
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Research works printed but not linked: 1
- [16]Church G, Deamer D, Branton D, Baldarelli R & Kasianowicz J Characterization of individual polymer molecules based on monomer-interface interactions. US patent 5,795,782 (1998).
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Detection of ribonucleotides embedded in DNA by Nanopore sequencing
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- Authors
- Deamer, D., Akeson, M., & Branton, D.
- Affiliations
- University of California, Santa Cruz (US)
- Harvard University (US)
- Corresponding author
- Deamer, David
- Venue
- Nature Biotechnology
- Published
- 2016-05
- Volume
- 34
- Issue
- 5
- Pages
- 518-524
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC6733523
- OpenAlex
- W2346680365
- Cited by
- 1,292
- References
- 54
- Citations by year
- 2026: 119 · 2025: 160 · 2024: 180 · 2023: 164 · 2022: 161 · 2021: 163 · 2020: 119 · 2019: 85 · 2018: 71 · 2017: 52 · 2016: 16 · 2014: 1
- FWCI
- 5.34
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- University of California, Santa Cruz
- National Institutes of Health
- National Human Genome Research Institute (R01HG007827, R01HG003703, R01HG006321)
- Topics
- Physical Sciences › Engineering › Biomedical Engineering › Nanopore and Nanochannel Transport Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- nanopore sequencing, single-stranded DNA sequencing, sequencing algorithms
- MeSH terms
- Conductometry, DNA, Lipid Bilayers, Sequence Analysis, DNA, Nanopores, High-Throughput Nucleotide Sequencing
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