Over the past decade, nanopore sequencing has experienced significant advancements and changes, transitioning from an initially emerging technology to a significant instrument in the field of genomic sequencing. However, as advancements in next-generation sequencing technology persist, nanopore sequencing also improves. This paper reviews the developments, applications, and outlook on nanopore sequencing technology. Currently, nanopore sequencing supports both DNA and RNA sequencing, making it widely applicable in areas such as telomere-to-telomere (T2T) genome assembly, direct RNA sequencing (DRS), and metagenomics. The openness and versatility of nanopore sequencing have established it as a preferred option for an increasing number of research teams, signaling a transformative influence on life science research. As the nanopore sequencing technology advances, it provides a faster, more cost-effective approach with extended read lengths, demonstrating the significant potential for complex genome assembly, pathogen detection, environmental monitoring, and human disease research, offering a fresh perspective in sequencing technologies.
|
Afflerbach, A.-K., Albers, A., Appelt, A., Schweizer, L., Paulus, W., Bockmayr, M., Schuller, U., Thomas, C., 2024. Nanopore sequencing from formalin-fixed paraffin-embedded specimens for copy-number profiling and methylation-based CNS tumor classification. Acta Neuropathol. 147, 1-4.
|
|
Alam, I., Boonkoom, T., Pitakjakpipop, H., Boonbanjong, P., Loha, K., Saeyang, T., Vanichtanankul, J., Japrung, D., 2024. Single-molecule analysis of SRAS-CoV-2 double-stranded polynucleotides using solid-state nanopore with ai-assisted detection and classification: implications for understanding disease severity. ACS Appl. Bio Mater. 7, 1017-1027.
|
|
Albacar, M., Zekhnini, A., Perez-Valle, J., Martinez, J.L., Casamayor, A., Arino, J., 2023. Transcriptomic profiling of the yeast komagataella phaffii in response to environmental alkalinization. Microb. Cell Factories 22, 63.
|
|
Anxuyuan, 2023. AXP100 nanopore sequencer. https://www.axbio.cn/products/45.html.
|
|
Ashton, P.M., Nair, S., Dallman, T., Rubino, S., Rabsch, W., Mwaigwisya, S., Wain, J., O'Grady, J., 2015. Minion nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat. Biotechnol. 33, 296-300.
|
|
Begik, O., Diensthuber, G., Liu, H., Delgado-Tejedor, A., Kontur, C., Niazi, A.M., Valen, E., Giraldez, A.J., Beaudoin, J.-D., Mattick, J.S., et al., 2023. Nano3p-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing. Nat. Methods 20, 75-85.
|
|
Benitez-Paez, A., Portune, K.J., Sanz, Y., 2016. Species-level resolution of 16S rRNA gene amplicons sequenced through the MinionTM portable nanopore sequencer. GigaScience 5, 4.
|
|
Berhanu, S., Majumder, S., Muntener, T., Whitehouse, J., Berner, C., Bera, A.K., Kang, A., Liang, B., Khan, G.N., Sankaran, B., et al., 2023. Sculpting conducting nanopore size and shape through de novo protein design. Science 385, 282-288.
|
|
Bertrand, D., Shaw, J., Kalathiyappan, M., Ng, A.H.Q., Kumar, M.S., Li, C., Dvornicic, M., Soldo, J.P., Koh, J.Y., Tong, C., et al., 2019. Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. Nat. Biotechnol. 37, 937-944.
|
|
Bjoernstad, P.M., Aaloekken, R., Asheim, J., Sundaram, A.Y., Felde, C.N., OEstby, G.H., Dalland, M., Sjursen, W., Carrizosa, C., Vigeland, M.D., et al., 2024. A 39 kb structural variant causing lynch syndrome detected by optical genome mapping and nanopore sequencing. Eur. J. Hum. Genet. 32, 513-520.
|
|
Bloomfield, M., Hutton, S., Velasco, C., Burton, M., Benton, M., Storey, M., 2024. Oxford nanopore next generation sequencing in a front-line clinical microbiology laboratory without on-site bioinformaticians. Pathology 56, 444-447.
|
|
Boileau, E., Li, X., Naarmann-de Vries, I.S., Becker, C., Casper, R., Altmuller, J., Leuschner, F., Dieterich, C., 2022. Full-length spatial transcriptomics reveals the unexplored isoform diversity of the myocardium post-MI. Front. Genet. 13, 912572.
|
|
Brown, C.L., Keenum, I.M., Dai, D., Zhang, L., Vikesland, P.J., Pruden, A., 2021. Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes. Sci. Rep. 11, 3753.
|
|
Bull, R.A., Adikari, T.N., Ferguson, J.M., Hammond, J.M., Stevanovski, I., Beukers, A.G., Naing, Z., Yeang, M., Verich, A., Gamaarachchi, H., et al., 2020. Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis. Nat. Commun. 11, 6272.
|
|
Burton, A.S., Stahl, S.E., John, K.K., Jain, M., Juul, S., Turner, D.J., Harrington, E.D., Stoddart, D., Paten, B., Akeson, M., et al., 2020. Off earth identification of bacterial populations using 16S rDNA nanopore sequencing. Genes 11, 76.
|
|
Charalampous, T., Kay, G.L., Richardson, H., Aydin, A., Baldan, R., Jeanes, C., Rae, D., Grundy, S., Turner, D.J., Wain, J., et al., 2019. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat. Biotechnol. 37, 783-792.
|
|
Ciuffreda, L., Rodriguez-Perez, H., Flores, C., 2021. Nanopore sequencing and its application to the study of microbial communities. Comput. Struct. Biotechnol. J. 19, 1497-1511.
|
|
Community, N., 2024. Dorado 0.7.0. https://community.nanoporetech.com/posts/dorado-0-7-0-release.
|
|
Cretu Stancu, M., Van Roosmalen, M.J., Renkens, I., Nieboer, M.M., Middelkamp, S., De Ligt, J., Pregno, G., Giachino, D., Mandrile, G., Espejo Valle-Inclan, J., et al., 2017. Mapping and phasing of structural variation in patient genomes using nanopore sequencing. Nat. Commun. 8, 1326.
|
|
Cuenca-Guardiola, J., de la Morena-Barrio, B., Navarro-Manzano, E., Stevens, J., Ouwehand, W.H., Gleadall, N.S., Corral, J., Fernandez-Breis, J.T., 2023. Detection and annotation of transposable element insertions and deletions on the human genome using nanopore sequencing. iScience 26, 108214.
|
|
Curtis-Joseph, N., Peterson, R., Brown, C.E., Beekman, C., Belenky, P., 2024. Mouse diet and vendor impact microbiome perturbation and recovery from early-life pulses of amoxicillin. Front. Microbiomes 3, 1432202.
|
|
Dang, C., Wu, Z., Zhang, M., Li, X., Sun, Y., Wu, R.a., Zheng, Y., Xia, Y., 2022. Microorganisms as bio-filters to mitigate greenhouse gas emissions from high-altitude permafrost revealed by nanopore-based metagenomics. iMeta 1, e24.
|
|
De Meulenaere, K., Cuypers, W.L., Gauglitz, J.M., Guetens, P., Rosanas-Urgell, A., Laukens, K., Cuypers, B., 2024. Selective whole-genome sequencing of plasmodium parasites directly from blood samples by nanopore adaptive sampling. mBio 15, e0196723.
|
|
De Roeck, A., De Coster, W., Bossaerts, L., Cacace, R., De Pooter, T., Van Dongen, J., D'Hert, S., De Rijk, P., Strazisar, M., Van Broeckhoven, C., et al., 2019. Nanosatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on promethion. Genome Biol. 20, 239.
|
|
Deamer, D., Akeson, M., Branton, D., 2016. Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518-524.
|
|
Di Profio, F., Sarchese, V., Fruci, P., Aste, G., Martella, V., Palombieri, A., Di Martino, B., 2023. Exploring the enteric virome of cats with acute gastroenteritis. Vet. Sci. 10, 362.
|
|
Diensthuber, G., Pryszcz, L., Llovera, L., Lucas, M.C., Delgado-Tejedor, A., Cruciani, S., Roignant, J.-Y., Begik, O., Novoa, E.M., 2023. Enhanced detection of RNA modifications and mappability with high-accuracy nanopore RNA basecalling models. bioRxiv, https://doi.org/10.1101/2023.11.28.568965.
|
|
Ferchiou, S., Caza, F., Villemur, R., Betoulle, S., St-Pierre, Y., 2024. From shells to sequences: a proof-of-concept study for on-site analysis of hemolymphatic circulating cell-free DNA from sentinel mussels using nanopore technology. Sci. Total Environ. 934, 172969.
|
|
Fernandez-Suarez, E., Gonzalez-Del Pozo, M., Mendez-Vidal, C., Martin-Sanchez, M., Mena, M., de la Morena-Barrio, B., Corral, J., Borrego, S., Antinolo, G., 2024. Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an alu retrotransposon insertion in the eys gene. Mobile DNA 15, 9.
|
|
Filser, M., Schwartz, M., Merchadou, K., Hamza, A., Villy, M.-C., Decees, A., Frouin, E., Girard, E., Caputo, S.M., Renault, V., et al., 2023. Adaptive nanopore sequencing to determine pathogenicity of BRCA1 exonic duplication. J. Med. Genet. 60, 1206-1209.
|
|
Flack, N., Drown, M., Walls, C., Pratte, J., McLain, A., Faulk, C., 2023. Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul. NAR Genomics Bioinf. 5, lqad033.
|
|
Forquet, R., Jiang, X., Nasser, W., Hommais, F., Reverchon, S., Meyer, S., 2022. Mapping the complex transcriptional landscape of the phytopathogenic bacterium Dickeya dadantii. mBio 13, e0052422.
|
|
Fritch, E.J., Sanders, W., Sims, A.C., Herring, L.E., Barker, N.K., Schepmoes, A.A., Weitz, K.K., Texier, J.R., Dittmer, D.P., Graves, L.M., et al., 2023. Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection. iScience 26, 106780.
|
|
Fu, C., Zhao, Q., Li, Z., Wang, Y., Zhang, S., Lai, Y., Xiao, W., Cui, X., 2017. Complete genome sequence of Halomonas ventosae virulent halovirus QHHSV-1. Arch. Virol. 162, 3215-3219.
|
|
Gallagher, M.D., Matejusova, I., Nguyen, L., Ruane, N.M., Falk, K., Macqueen, D.J., 2018. Nanopore sequencing for rapid diagnostics of salmonid RNA viruses. Sci. Rep. 8, 16307.
|
|
Gamaarachchi, H., Lam, C.W., Jayatilaka, G., Samarakoon, H., Simpson, J.T., Smith, M.A., Parameswaran, S., 2020. GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis. BMC Bioinf. 21, 343.
|
|
Garalde, D.R., Snell, E.A., Jachimowicz, D., Sipos, B., Lloyd, J.H., Bruce, M., Pantic, N., Admassu, T., James, P., Warland, A., et al., 2018. Highly parallel direct RNA sequencing on an array of nanopores. Nat. Methods 15, 201-206.
|
|
Geneus, 2022. Gseq 500 Nanopore Sequencer.
|
|
Geoghegan, J.L., Ren, X., Storey, M., Hadfield, J., Jelley, L., Jefferies, S., Sherwood, J., Paine, S., Huang, S., Douglas, J., et al., 2020. Genomic epidemiology reveals transmission patterns and dynamics of SARS-COV-2 in Aotearoa New Zealand. Nat. Commun. 11, 6351.
|
|
Glinos, D.A., Garborcauskas, G., Hoffman, P., Ehsan, N., Jiang, L., Gokden, A., Dai, X., Aguet, F., Brown, K.L., Garimella, K., et al., 2022. Transcriptome variation in human tissues revealed by long-read sequencing. Nature 608, 353-359.
|
|
Gao, Y., Li, D., Liu, Y.-X. 2023. Microbiome research outlook: past, present, and future. Protein Cell 14, 709-712.
|
|
Goordial, J., Altshuler, I., Hindson, K., Chan-Yam, K., Marcolefas, E., Whyte, L.G., 2017. In situ field sequencing and life detection in remote (79°26'n) canadian high arctic permafrost ice wedge microbial communities. Front. Microbiol. 8, 2594.
|
|
Gowers, G.-O.F., Vince, O., Charles, J.-H., Klarenberg, I., Ellis, T., Edwards, A., 2019. Entirely off-grid and solar-powered DNA sequencing of microbial communities during an ice cap traverse expedition. Genes 10, 902.
|
|
Gradel, C., Terrazos Miani, M.A., Barbani, M.T., Leib, S.L., Suter-Riniker, F., Ramette, A., 2019. Rapid and cost-efficient enterovirus genotyping from clinical samples using Flongle flow cells. Genes 10, 659.
|
|
Grottoli, A., Beccaccioli, M., Zoppis, E., Fratini, R.S., Schifano, E., Santarelli, M.L., Uccelletti, D., Reverberi, M., 2020. Nanopore sequencing and bioinformatics for rapidly identifying cultural heritage spoilage microorganisms. Front. Mater. 7, 14.
|
|
Grunberger, F., Ferreira-Cerca, S., Grohmann, D., 2022. Nanopore sequencing of RNA and cDNA molecules in Escherichia coli. RNA 28, 400-417.
|
|
Grunberger, F., Knuppel, R., Juttner, M., Fenk, M., Borst, A., Reichelt, R., Hausner, W., Soppa, J., Ferreira-Cerca, S., Grohmann, D., 2020. Exploring prokaryotic transcription, operon structures, rrna maturation and modifications using nanopore-based native RNA sequencing. bioRxiv. https://doi.org/10.1101/2019.12.18.880849.
|
|
Gunter, H.M., Idrisoglu, S., Singh, S., Han, D.J., Ariens, E., Peters, J.R., Wong, T., Cheetham, S.W., Xu, J., Rai, S.K., et al., 2023. mRNA vaccine quality analysis using RNA sequencing. Nat. Commun. 14, 5663.
|
|
Han, X., Zhang, Y., Zhang, Q., Ma, N., Liu, X., Tao, W., Lou, Z., Zhong, C., Deng, X.W., Li, D., et al., 2023. Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit. Mol. Plant 16, 452-470.
|
|
He, X.J., Barron, A.B., Yang, L., Chen, H., He, Y.Z., Zhang, L.Z., Huang, Q., Wang, Z.L., Wu, X.B., Yan, W.Y., et al., 2022. Extent and complexity of RNA processing in honey bee queen and worker caste development. iScience 25, 104301.
|
|
He, Y., Chu, Y., Guo, S., Hu, J., Li, R., Zheng, Y., Ma, X., Du, Z., Zhao, L., Yu, W., 2023. T2T-YAO: a telomere-to-telomere assembled diploid reference genome for Han Chinese. Dev. Reprod. Biol. 21, 1085-1100.
|
|
Heidelbach, S., Dall, S.M., Boejer, J.S., Nissen, J., van der Maas, L.N.L., Sereika, M., Kirkegaard, R., Kousgaard, S.J., Thorlacius-Ussing, O., Jensen, S.I., 2024. Nanomotif: identification and exploitation of DNA methylation motifs in metagenomes using Oxford nanopore sequencing. bioRxiv, https://doi.org/10.1101/2024.04.29.591623.
|
|
Helal, A.A., Saad, B.T., Saad, M.T., Mosaad, G.S., Aboshanab, K.M., 2024. Benchmarking long-read aligners and SV callers for structural variation detection in Oxford nanopore sequencing data. Sci. Rep. 14, 6160.
|
|
Hernandez, R., 2018. Sequencing goes long. Genet. Eng. Biotechnol. N. 38, 1, 14-16.
|
|
Houghtaling, J., List, J., Mayer, M., 2018. Nanopore-based, rapid characterization of individual amyloid particles in solution: concepts, challenges, and prospects. Small 14, 1802412.
|
|
Hu, X.-L., You, C., Zhu, K., Li, X., Gong, J., Ma, H., Sun, X., 2023. Nanopore long-read RNAseq reveals transcriptional variations in citrus species. Front. Plant Sci. 13, 1077797.
|
|
Huang, G., Shi, W., Wang, L., Qu, Q., Zuo, Z., Wang, J., Zhao, F., Wei, F., 2023a. Pandagut provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation. Microbiome 11, 221.
|
|
Huang, H.-R., Liu, X., Arshad, R., Wang, X., Li, W.-M., Zhou, Y., Ge, X.-J., 2023b. Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid cavendish banana. Hortic. Res. 10, uhad153.
|
|
Huang, S., Ouyang, L., Tang, J., Qian, K., Chen, X., Xu, Z., Ming, J., Xi, R., 2024. Spatial transcriptomics: a new frontier in cancer research. Clinical Cancer Bulletin 3, 13.
|
|
Huang, Y.-T., Liu, P.-Y., Shih, P.-W., 2021. Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing. Genome Biol. 22, 95.
|
|
Jain, M., Koren, S., Miga, K.H., Quick, J., Rand, A.C., Sasani, T.A., Tyson, J.R., Beggs, A.D., Dilthey, A.T., Fiddes, I.T., et al., 2018. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat. Biotechnol. 36, 338-345.
|
|
Jain, M., Tyson, J.R., Loose, M., Ip, C.L., Eccles, D.A., O'Grady, J., Malla, S., Leggett, R.M., Wallerman, O., Jansen, H.J., 2017. MinION analysis and reference consortium: phase 2 data release and analysis of R9.0 chemistry. F1000Res. 6, 760.
|
|
Jeanes, C., O'Grady, J., 2016. Diagnosing tuberculosis in the 21st century-dawn of a genomics revolution? Int. J. Mycobacteriol. 5, 384-391.
|
|
Jin, H., Quan, K., He, Q., Kwok, L.-Y., Ma, T., Li, Y., Zhao, F., You, L., Zhang, H., Sun, Z., 2023. A high-quality genome compendium of the human gut microbiome of Inner Mongolians. Nat. Microbiol. 8, 150-161.
|
|
Juul, S., Izquierdo, F., Hurst, A., Dai, X., Wright, A., Kulesha, E., Pettett, R., Turner, D.J., 2015. What's in my pot? Real-time species identification on the MinIONTM. bioRxiv, https://www.biorxiv.org/content/10.1101/030742v1.
|
|
Kafetzopoulou, L., Pullan, S., Lemey, P., Suchard, M., Ehichioya, D., Pahlmann, M., Thielebein, A., Hinzmann, J., Oestereich, L., Wozniak, D., et al., 2019. Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak. Science 363, 74-77.
|
|
Karst, S.M., Ziels, R.M., Kirkegaard, R.H., Soerensen, E.A., McDonald, D., Zhu, Q., Knight, R., Albertsen, M., 2021. High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nat. Methods 18, 165-169.
|
|
Kasianowicz, J.J., Brandin, E., Branton, D., Deamer, D.W., 1996. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. U.S.A. 93, 13770-13773.
|
|
Kerkhof, L.J., Dillon, K.P., Haggblom, M.M., McGuinness, L.R., 2017. Profiling bacterial communities by minion sequencing of ribosomal operons. Microbiome 5, 116.
|
|
Kim, S.-W., Lee, H.-J., Choi, S., Cho, I.-S., Jeong, R.-D., 2023. Rapid identification of jasmine virus H infecting ixora coccinea by nanopore metatranscriptomics. Plant Pathol. J. 39, 303.
|
|
Kipp, E.J., Lindsey, L.L., Khoo, B., Faulk, C., Oliver, J.D., Larsen, P.A., 2023. Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling. Sci. Rep. 13, 10991.
|
|
Kolmogorov, M., Billingsley, K.J., Mastoras, M., Meredith, M., Monlong, J., Lorig-Roach, R., Asri, M., Alvarez Jerez, P., Malik, L., Dewan, R., et al., 2023. Scalable nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nat. Methods 20, 1483-1492.
|
|
Koster, C.C., Kleefeldt, A.A., van den Broek, M., Luttik, M., Daran, J.M., Daran-Lapujade, P., 2024. Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae reveals condition-dependent intron abundance. Yeast 41, 256-278.
|
|
Krawczyk, P.S., Tudek, A., Mroczek, S., Dziembowski, A., 2023. Transcriptome-wide analysis of mRNA adenylation status in yeast using nanopore sequencing, Deadenylation: Methods and Protocols. Springer, pp. 193-214.
|
|
Kuderna, L.F.K., Lizano, E., Julia, E., Gomez-Garrido, J., Serres-Armero, A., Kuhlwilm, M., Alandes, R.A., Alvarez-Estape, M., Juan, D., Simon, H., et al., 2019. Selective single molecule sequencing and assembly of a human Y chromosome of African origin. Nat. Commun. 10, 4.
|
|
Latorre-Perez, A., Gimeno-Valero, H., Tanner, K., Pascual, J., Vilanova, C., Porcar, M., 2021. A round trip to the desert: in situ nanopore sequencing informs targeted bioprospecting. Front. Microbiol. 12, 768240.
|
|
Laver, T.W., 2014. Evaluating Metagenomic Quantifications from Next-Generation Sequencing Data. University of Exeter (United Kingdom).
|
|
Lebrigand, K., Magnone, V., Barbry, P., Waldmann, R., 2020. High throughput error corrected nanopore single cell transcriptome sequencing. Nat. Commun. 11, 4025.
|
|
Leggett, R.M., Clark, M.D., 2017. A world of opportunities with nanopore sequencing. J. Exp. Bot. 68, 5419-5429.
|
|
Lerminiaux, N., Fakharuddin, K., Mulvey, M.R., Mataseje, L., 2024. Do we still need Illumina sequencing data? Evaluating Oxford Nanopore Technologies R10.4.1 flow cells and the Rapid v14 library prep kit for Gram negative bacteria whole genome assemblies. Can. J. Microbiol. 70, 178-189.
|
|
Li, J., Wang, H., Mao, L., Yu, H., Yu, X., Sun, Z., Qian, X., Cheng, S., Chen, S., Chen, J., et al., 2020. Rapid genomic characterization of SARS-CoV-2 viruses from clinical specimens using nanopore sequencing. Sci. Rep. 10, 17492.
|
|
Li, N., He, Q., Wang, J., Wang, B., Zhao, J., Huang, S., Yang, T., Tang, Y., Yang, S., Aisimutuola, P., et al., 2023. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nat. Genet. 55, 852-860.
|
|
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J.K., Monlong, J., Abel, H.J., et al., 2023. A draft human pangenome reference. Nature 617, 312-324.
|
|
Lin, B., Hui, J., Mao, H., 2021. Nanopore technology and its applications in gene sequencing. Biosensors 11, 214.
|
|
Liu, L., Yang, Y., Deng, Y., Zhang, T., 2022a. Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes. Microbiome 10, 209.
|
|
Liu, S., Ma, X., Wang, Z., Lin, F., Li, M., Li, Y., Yang, L., Rushdi, H.E., Riaz, H., Gao, T., et al., 2023a. MAEL gene contributes to bovine testicular development through the m5C-mediated splicing. iScience 26, 105941.
|
|
Liu, X., Zhang, W., Zhang, Y., Yang, J., Zeng, P., Tian, Z., Sun, W., Cai, J., 2024. Chromosome-scale genomes of Quercus sichourensis and Quercus rex provide insights into the evolution and adaptation of Fagaceae. J. Genet. Genomics 51, 554-565.
|
|
Liu, Y., Lu, F., Wang, J., 2023b. Sequencing of Transcriptome-wide poly(A) Tails by PAIso-Seq, Deadenylation: Methods and Protocols. Springer, pp. 215-232.
|
|
Liu, Y.H., Chou, Y.T., Chang, F.P., Lee, W.J., Guo, Y.C., Chou, C.T., Huang, H.C., Mizuguchi, T., Chou, C.C., Yu, H.Y., et al., 2022b. Neuronal intranuclear inclusion disease in patients with adult-onset non-vascular leukoencephalopathy. Brain 145, 3010-3021.
|
|
Liu, Z., Li, Y., Zhang, X., 2023c. DNA methylation on C5-Cytosine and N6-Adenine in the Bursaphelenchus xylophilus genome. BMC Genom. 24, 671.
|
|
Lu, H., Giordano, F., Ning, Z., 2016. Oxford Nanopore MinION sequencing and genome assembly. Dev. Reprod. Biol. 14, 265-279.
|
|
Lu, X., Peng, Y., Geng, Y., Zhao, H., Shen, X., Li, D., Li, Z., Lu, L., Fan, M., Xu, W., et al., 2022. Co-localization of sampling and sequencing for zoonotic pathogen identification in the field monitoring using mobile laboratories. China CDC Wkly. 4, 259-263.
|
|
Magi, A., Semeraro, R., Mingrino, A., Giusti, B., D'Aurizio, R., 2017. Nanopore sequencing data analysis: state of the art, applications and challenges. Briefings Bioinf. 19, 1256-1272.
|
|
Magome, T.G., Ramatla, T., Mokgokong, P., Thekisoe, O., Lekota, K.E., 2023. The draft genome and pan-genome structure of Paraclostridium bifermentans strain T2 isolated from sheep faeces. Data Brief 51, 109660.
|
|
Martignano, F., Munagala, U., Crucitta, S., Mingrino, A., Semeraro, R., Del Re, M., Petrini, I., Magi, A., Conticello, S.G., 2021. Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients. Mol. Cancer 20, 32.
|
|
Marx, V., 2023. Method of the year: long-read sequencing. Nat. Methods 20, 6-11.
|
|
Menegon, M., Cantaloni, C., Rodriguez-Prieto, A., Centomo, C., Abdelfattah, A., Rossato, M., Bernardi, M., Xumerle, L., Loader, S., Delledonne, M., 2017. On site DNA barcoding by nanopore sequencing. PLoS One 12, e0184741.
|
|
Meyer, A., Schloissnig, S., Franchini, P., Du, K., Woltering, J.M., Irisarri, I., Wong, W.Y., Nowoshilow, S., Kneitz, S., Kawaguchi, A., et al., 2021. Giant lungfish genome elucidates the conquest of land by vertebrates. Nature 590, 284-289.
|
|
Miga, K.H., Koren, S., Rhie, A., Vollger, M.R., Gershman, A., Bzikadze, A., Brooks, S., Howe, E., Porubsky, D., Logsdon, G.A., et al., 2020. Telomere-to-telomere assembly of a complete human X chromosome. Nature 585, 79-84.
|
|
Mikheyev, A.S., Tin, M.M., 2014. A first look at the Oxford Nanopore MinION sequencer. Mol. Ecol. Resour. 14, 1097-1102.
|
|
Minei, R., Hoshina, R., Ogura, A., 2018. De novo assembly of middle-sized genome using MinION and Illumina sequencers. BMC Genom. 19, 700.
|
|
Mock, A., Braun, M., Scholl, C., Frohling, S., Erkut, C., 2023. Transcriptome profiling for precision cancer medicine using shallow nanopore cDNA sequencing. Sci. Rep. 13, 2378.
|
|
Muller, C.A., Boemo, M.A., Spingardi, P., Kessler, B.M., Kriaucionis, S., Simpson, J.T., Nieduszynski, C.A., 2019. Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. Nat. Methods 16, 429-436.
|
|
Murakami, K., Kubota, S.I., Tanaka, K., Tanaka, H., Akabane, K., Suzuki, R., Shinohara, Y., Takei, H., Hashimoto, S., Tanaka, Y., et al., 2023. High-precision rapid testing of omicron SARS-CoC-2 variants in clinical samples using AI-nanopore. Lab Chip 23, 4909-4918.
|
|
Nanopore, O., 2019. New ‘R10’ nanopore released into early access. https://nanoporetech.com/news/news-new-r10-nanopore-released-early-access.
|
|
Negri, T., Mantri, S., Angelov, A., Peter, S., Muth, G., Eustaquio, A.S., Ziemert, N., 2022. A rapid and efficient strategy to identify and recover biosynthetic gene clusters from soil metagenomes. Appl. Microbiol. Biotechnol. 106, 3293-3306.
|
|
Neumann, D., Reddy, A.S., Ben-Hur, A., 2022. Rodan: a fully convolutional architecture for basecalling nanopore RNA sequencing data. BMC Bioinf. 23, 142.
|
|
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A.V., Mikheenko, A., Vollger, M.R., Altemose, N., Uralsky, L., Gershman, A., et al., 2022. The complete sequence of a human genome. Science 376, 44-53.
|
|
Padilla, J.-C.A., Barutcu, S., Malet, L., Deschamps-Francoeur, G., Calderon, V., Kwon, E., Lecuyer, E., 2023. Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing. BMC Genom. 24, 564.
|
|
Pages-Gallego, M., de Ridder, J., 2023. Comprehensive benchmark and architectural analysis of deep learning models for nanopore sequencing basecalling. Genome Biol. 24, 71.
|
|
Papetti, D.M., Spolaor, S., Nazari, I., Tirelli, A., Leonardi, T., Caprioli, C., Besozzi, D., Vlachou, T., Pelicci, P.G., Cazzaniga, P., et al., 2023. Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning. Front. Bioinf. 3, 1067113.
|
|
Pater, A.A., Bosmeny, M.S., White, A.A., Sylvain, R.J., Eddington, S.B., Parasrampuria, M., Ovington, K.N., Metz, P.E., Yinusa, A.O., Barkau, C.L., et al., 2021. High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples. J. Biol. Methods 8(COVID 19 Spec Iss), e155.
|
|
Payne, A., Holmes, N., Clarke, T., Munro, R., Debebe, B.J., Loose, M., 2021. Readfish enables targeted nanopore sequencing of gigabase-sized genomes. Nat. Biotechnol. 39, 442-450.
|
|
Payne, A., Holmes, N., Rakyan, V., Loose, M., 2019. Bulkvis: a graphical viewer for Oxford nanopore bulk FAST5 files. Bioinformatics 35, 2193-2198.
|
|
Peng, K., Liu, Y.-X., Sun, X., Wang, Q., Du, P., Zhang, Y., Wang, M., Wang, Z., Li, R., 2023. Long-read metagenomic sequencing reveals that high-copy small plasmids shape the highly prevalent antibiotic resistance genes in animal fecal microbiome. Sci. Total Environ. 893, 164585.
|
|
Philpott, M., Watson, J., Thakurta, A., Brown Jr, T., Brown Sr, T., Oppermann, U., Cribbs, A.P., 2021. Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq. Nat. Biotechnol. 39, 1517-1520.
|
|
Pichler, I., Schmutz, S., Ziltener, G., Zaheri, M., Kufner, V., Trkola, A., Huber, M., 2023. Rapid and sensitive single-sample viral metagenomics using nanopore Flongle sequencing. J. Virol. Methods 320, 114784.
|
|
Pitt, M.E., Nguyen, S.H., Duarte, T.P.S., Teng, H., Blaskovich, M.A.T., Cooper, M.A., Coin, L.J.M., 2020. Evaluating the genome and resistome of extensively drug-resistant Klebsiella pneumoniae using native DNA and RNA nanopore sequencing. GigaScience 9, giaa002.
|
|
Polyseq, 2024. Polyseqone nanopore sequencer. https://www.polyseq.com/products.
|
|
Poursalavati, A., Javaran, V.J., Laforest-Lapointe, I., Fall, M.L., 2023. Soil metatranscriptomics: an improved RNA extraction method toward functional analysis using nanopore direct RNA sequencing. Phytobiomes J. 7, 42-54.
|
|
Pust, M.-M., Davenport, C.F., Wiehlmann, L., Tummler, B., 2022. Direct RNA nanopore sequencing of Pseudomonas aeruginosa clone C transcriptomes. J. Bacteriol. 204, e0041821.
|
|
Qiu, Z., Yuan, L., Lian, C.-A., Lin, B., Chen, J., Mu, R., Qiao, X., Zhang, L., Xu, Z., Fan, L., 2024. BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis. Nat. Commun. 15, 2179.
|
|
Quick, J., Quinlan, A.R., Loman, N.J., 2014. A reference bacterial genome dataset generated on the MinIONTM portable single-molecule nanopore sequencer. GigaScience 3, 22.
|
|
Reggiardo, R.E., Maroli, S.V., Peddu, V., Davidson, A.E., Hill, A., LaMontagne, E., Aaraj, Y.A., Jain, M., Chan, S.Y., Kim, D.H., 2023. Profiling of repetitive RNA sequences in the blood plasma of patients with cancer. Nat. Biomed. Eng. 7, 1627-1635.
|
|
Ren, Y., Huang, Z., Zhou, L., Xiao, P., Song, J., He, P., Xie, C., Zhou, R., Li, M., Dong, X., et al., 2023. Spatial transcriptomics reveals niche-specific enrichment and vulnerabilities of radial glial stem-like cells in malignant gliomas. Nat. Commun. 14, 1028.
|
|
Romagnoli, S., Bartalucci, N., Vannucchi, A.M., 2023. Resolving complex structural variants via nanopore sequencing. Front. Genet. 14, 1213917.
|
|
Samarakoon, H., Ferguson, J.M., Gamaarachchi, H., Deveson, I.W., 2023. Accelerated nanopore basecalling with SLOW5 data format. Bioinformatics 39, btad352.
|
|
Sanchez-Navarro, R., Nuhamunada, M., Mohite, O.S., Wasmund, K., Albertsen, M., Gram, L., Nielsen, P.H., Weber, T., Singleton, C.M., 2022. Long-read metagenome-assembled genomes improve identification of novel complete biosynthetic gene clusters in a complex microbial activated sludge ecosystem. mSystems 7, e0063222.
|
|
Schmidt, M.H., Vogel, A., Denton, A.K., Istace, B., Wormit, A., van de Geest, H., Bolger, M.E., Alseekh, S., Mass, J., Pfaff, C., et al., 2017. De novo assembly of a new Solanum pennellii accession using nanopore sequencing. Plant Cell 29, 2336-2348.
|
|
Sereika, M., Kirkegaard, R.H., Karst, S.M., Michaelsen, T.Y., Soerensen, E.A., Wollenberg, R.D., Albertsen, M., 2022. Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. Nat. Methods 19, 823-826.
|
|
Shafin, K., Pesout, T., Lorig-Roach, R., Haukness, M., Olsen, H.E., Bosworth, C., Armstrong, J., Tigyi, K., Maurer, N., Koren, S., et al., 2020. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat. Biotechnol. 38, 1044-1053.
|
|
Sheka, D., Alabi, N., Gordon, P.M., 2021. Oxford Nanopore sequencing in clinical microbiology and infection diagnostics. Briefings Bioinf. 22, bbaa403.
|
|
Shiau, C.-K., Lu, L., Kieser, R., Fukumura, K., Pan, T., Lin, H.-Y., Yang, J., Tong, E.L., Lee, G., Yan, Y., et al., 2023a. High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors. Nat. Commun. 14, 4124.
|
|
Shiau, C.-K., Lu, L., Kieser, R., Fukumura, K., Pan, T., Lin, H.-Y., Yang, J., Tong, E.L., Lee, G., Yan, Y., 2023b. scNanoGPS: a robust tool for simultaneous calculation of same-cell genotypes and phenotypes from single cell long read transcriptomes. Cancer Res. 83(7_Suppl. ment), 2069-2069.
|
|
Shin, J., Lee, S., Go, M.-J., Lee, S.Y., Kim, S.C., Lee, C.-H., Cho, B.-K., 2016. Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing. Sci. Rep. 6, 29681.
|
|
Singh, M., Al-Eryani, G., Carswell, S., Ferguson, J.M., Blackburn, J., Barton, K., Roden, D., Luciani, F., Giang Phan, T., Junankar, S., et al., 2019. High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes. Nat. Commun. 10, 3120.
|
|
Song, C., Liu, Y., Song, A., Dong, G., Zhao, H., Sun, W., Ramakrishnan, S., Wang, Y., Wang, S., Li, T., et al., 2018. The Chrysanthemum nankingense genome provides insights into the evolution and diversification of chrysanthemum flowers and medicinal traits. Mol. Plant 11, 1482-1491.
|
|
Sovic, I., Sikic, M., Wilm, A., Fenlon, S.N., Chen, S., Nagarajan, N., 2016. Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Nat. Commun. 7, 11307.
|
|
Stahl-Rommel, S., Jain, M., Nguyen, H.N., Arnold, R.R., Aunon-Chancellor, S.M., Sharp, G.M., Castro, C.L., John, K.K., Juul, S., Turner, D.J., et al., 2021. Real-time culture-independent microbial profiling onboard the international space station using nanopore sequencing. Genes 12, 106.
|
|
Stanojevic, D., Lin, D., Florez De Sessions, P., Sikic, M., 2024. Telomere-to-telomere phased genome assembly using error-corrected simplex nanopore reads. bioRxiv, 2024.2005. 2018.594796.
|
|
Stark, R., Grzelak, M., Hadfield, J., 2019. Rna sequencing: the teenage years. Nat. Rev. Genet. 20, 631-656.
|
|
Stockton, J.D., Nieto, T., Wroe, E., Poles, A., Inston, N., Briggs, D., Beggs, A.D., 2020. Rapid, highly accurate and cost-effective open-source simultaneous complete HLA typing and phasing of class I and II alleles using nanopore sequencing. HLA 96, 163-178.
|
|
Sun, Y., Cheng, Z., Li, X., Yang, Q., Zhao, B., Wu, Z., Xia, Y., 2023. Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing. Genome Res. 33, 612-621.
|
|
Technoligies, O.N., 2020. Metapore-c: using chromatin conformation capture and long nanopore reads for metagenomic analysis. https://ftp.nanoporetech.com/resource-centre/metaporec.
|
|
Tian, L., Jabbari, J.S., Thijssen, R., Gouil, Q., Amarasinghe, S.L., Voogd, O., Kariyawasam, H., Du, M.R., Schuster, J., Wang, C., et al., 2021. Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing. Genome Biol. 22, 310.
|
|
Tourancheau, A., Mead, E.A., Zhang, X.-S., Fang, G., 2021. Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing. Nat. Methods 18, 491-498.
|
|
Ulahannan, N., Pendleton, M., Deshpande, A., Schwenk, S., Behr, J.M., Dai, X., Tyer, C., Rughani, P., Kudman, S., Adney, E., et al., 2019. Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure. bioRxiv, 833590.
|
|
Ulrich, J.-U., Epping, L., Pilz, T., Walther, B., Stingl, K., Semmler, T., Renard, B.Y., 2024. Nanopore adaptive sampling effectively enriches bacterial plasmids. mSystems, 9, e00945-00923.
|
|
Van Dijk, E.L., Jaszczyszyn, Y., Naquin, D., Thermes, C., 2018. The third revolution in sequencing technology. Trends Genet. 34, 666-681.
|
|
van Dijk, E.L., Naquin, D., Gorrichon, K., Jaszczyszyn, Y., Ouazahrou, R., Thermes, C., Hernandez, C., 2023. Genomics in the long-read sequencing era. Trends Genet. 39, 649-671.
|
|
Vereecke, N., Zwickl, S., Gumbert, S., Graaf, A., Harder, T., Ritzmann, M., Lillie-Jaschniski, K., Theuns, S., Stadler, J., 2023. Viral and bacterial profiles in endemic influenza A virus infected swine herds using nanopore metagenomic sequencing on tracheobronchial swabs. Microbiol. Spectr. 11, e0009823.
|
|
Vermeulen, C., Pages-Gallego, M., Kester, L., Kranendonk, M.E.G., Wesseling, P., Verburg, N., de Witt Hamer, P., Kooi, E.J., Dankmeijer, L., van der Lugt, J., et al., 2023. Ultra-fast deep-learned CNS tumour classification during surgery. Nature 622, 842-849.
|
|
Wang, G., Li, S., Yan, Q., Guo, R., Zhang, Y., Chen, F., Tian, X., Lv, Q., Jin, H., Ma, X., et al., 2023. Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome. J. Adv. Res. 48, 75-86.
|
|
Wang, J., Yang, L., Cheng, A., Tham, C.-Y., Tan, W., Darmawan, J., de Sessions, P.F., Wan, Y., 2024. Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome. Nat. Commun. 15, 481.
|
|
Wang, M., Fu, A., Hu, B., Tong, Y., Liu, R., Liu, Z., Gu, J., Xiang, B., Liu, J., Jiang, W., et al., 2020. Nanopore targeted sequencing for the accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses. Small 16, e2002169.
|
|
Wang, Y., Zhao, Y., Bollas, A., Wang, Y., Au, K.F., 2021. Nanopore sequencing technology, bioinformatics and applications. Nat. Biotechnol. 39, 1348-1365.
|
|
Wang, Z., Qin, L., Liu, J., Jiang, L., Zou, X., Chen, X., Song, F., Dai, H., Hou, Y., 2022. Forensic nanopore sequencing of microhaplotype markers using QitanTech's QNome. Forensic Sci. Int. Genet. 57, 102657.
|
|
Waschulin, V., Borsetto, C., James, R., Newsham, K.K., Donadio, S., Corre, C., Wellington, E., 2022. Biosynthetic potential of uncultured antarctic soil bacteria revealed through long-read metagenomic sequencing. ISME J. 16, 101-111.
|
|
Weilguny, L., De Maio, N., Munro, R., Manser, C., Birney, E., Loose, M., Goldman, N., 2023. Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design. Nat. Biotechnol. 41, 1018-1025.
|
|
Wen, T., Niu, G., Chen, T., Shen, Q., Yuan, J., Liu, Y.-X. 2023. The best practice for microbiome analysis using R. Protein Cell 14, 713-725.
|
|
White, L.K., Hesselberth, J.R., 2022. Modification mapping by nanopore sequencing. Front. Genet. 13, 1037134.
|
|
Wick, R.R., Judd, L.M., Gorrie, C.L., Holt, K.E., 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595.
|
|
Wick, R.R., Judd, L.M., Holt, K.E., 2023. Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLoS Comput. Biol. 19, e1010905.
|
|
Wongsurawat, T., Jenjaroenpun, P., Wanchai, V., Nookaew, I., 2022. Native RNA or cDNA sequencing for transcriptomic analysis: a case study on Saccharomyces cerevisiae. Front. Bioeng. Biotechnol. 10, 842299.
|
|
Wrenn, D.C., Drown, D.M., 2023. Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities. GigaByte 2023, gigabyte103.
|
|
Wu, H., Lu, Y., Duan, Z., Wu, J., Lin, M., Wu, Y., Han, S., Li, T., Fan, Y., Hu, X., et al., 2023. Nanopore long-read RNA sequencing reveals functional alternative splicing variants in human vascular smooth muscle cells. Commun. Biol. 6, 1104.
|
|
Wu, K., Zhou, L., Tahon, G., Liu, L., Li, J., Zhang, J., Zheng, F., Deng, C., Han, W., Bai, L., et al., 2024. Isolation of a methyl-reducing methanogen outside the Euryarchaeota. Nature 632, 1124-1130.
|
|
Xia, Q., Ding, T., Chang, T., Ruan, J., Yang, J., Ma, M., Liu, J., Liu, Z., Jiao, S., Wu, J., et al., 2024. Nanopore sequencing with T2T-CHM13 for accurate detection and preventing the transmission of structural rearrangements in highly repetitive heterochromatin regions in human embryos. Clin. Transl. Med. 14, e1612.
|
|
Xia, Y., Li, X., Wu, Z., Nie, C., Cheng, Z., Sun, Y., Liu, L., Zhang, T., 2023. Strategies and tools in Illumina and nanopore-integrated metagenomic analysis of microbiome data. iMeta 2, e72.
|
|
Xie, S., Leung, A.W.-S., Zheng, Z., Zhang, D., Xiao, C., Luo, R., Luo, M., Zhang, S., 2021. Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era. Innov. 2, 100153.
|
|
Xu, X., Bhalla, N., Stahl, P., Jalden, J., 2023. Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network. BMC Bioinf. 24, 461.
|
|
Yang, Z., Guarracino, A., Biggs, P.J., Black, M.A., Ismail, N., Wold, J.R., Merriman, T.R., Prins, P., Garrison, E., de Ligt, J., 2023. Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads. Front. Genet. 14, 1225248.
|
|
Ye, L., Dong, N., Xiong, W., Li, J., Li, R., Heng, H., Chan, E.W.C., Chen, S., 2022. High-resolution metagenomics of human gut microbiota generated by nanopore and Illumina hybrid metagenome assembly. Front. Microbiol. 13, 801587.
|
|
Ye, L., Liu, X., Ni, Y., Xu, Y., Zheng, Z., Chen, K., Hu, Q., Tan, L., Guo, Z., Wai, C.K., et al., 2024. Comprehensive genomic and plasmid characterization of multidrug-resistant bacterial strains by R10.4.1 nanopore sequencing. Microbiol. Res. 283, 127666.
|
|
Yeh, Y.-M., Lu, Y.-C., 2022. MSRCall: a multi-scale deep neural network to basecall Oxford Nanopore sequences. Bioinformatics 38, 3877-3884.
|
|
Yu, F., Qi, H., Gao, L., Luo, S., Njeri Damaris, R., Ke, Y., Wu, W., Yang, P., 2023. Identifying RNA modifications by direct RNA sequencing reveals complexity of epitranscriptomic dynamics in rice. Dev. Reprod. Biol. 21, 788-804.
|
|
Zeglinski, K., Montellese, C., Ritchie, M.E., Alhamdoosh, M., Vonarburg, C., Bowden, R., Jordi, M., Gouil, Q., Aeschimann, F., Hsu, A., 2023. An optimised protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing. bioRxiv, 2023.2012. 2003.569756.
|
|
Zhang, J.-Y., Zhang, Y., Wang, L., Guo, F., Yun, Q., Zeng, T., Yan, X., Yu, L., Cheng, L., Wu, W., 2024. A single-molecule nanopore sequencing platform. bioRxiv, 2024.2008. 2019.608720.
|
|
Zhang, L., Rong, W., Ma, J., Li, H., Tang, X., Xu, S., Wang, L., Wan, L., Zhu, Q., Jiang, B., et al., 2022a. Comprehensive analysis of DNA 5-methylcytosine and N6-adenine methylation by nanopore sequencing in hepatocellular carcinoma. Front. Cell Dev. Biol. 10, 827391.
|
|
Zhang, T., Li, H., Ma, S., Cao, J., Liao, H., Huang, Q., Chen, W., 2023a. The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling. Appl. Environ. Microbiol. 89, e0060523.
|
|
Zhang, X.X., Lv, Q.B., Yan, Q.L., Zhang, Y., Guo, R.C., Meng, J.X., Ma, H., Qin, S.Y., Zhu, Q.H., Li, C.Q., et al., 2022b. A catalog of over 5,000 metagenome-assembled microbial genomes from the Caprinae gut microbiota. Microbiol. Spectr. 10, e0221122.
|
|
Zhang, Y., Zhang, Q., Yang, X., Gu, X., Chen, J., Shi, T., 2023b. 6mA DNA methylation on genes in plants is associated with gene complexity, expression and duplication. Plants 12, 1949.
|
|
Zhao, W., Zeng, W., Pang, B., Luo, M., Peng, Y., Xu, J., Kan, B., Li, Z., Lu, X., 2023. Oxford nanopore long-read sequencing enables the generation of complete bacterial and plasmid genomes without short-read sequencing. Front. Microbiol. 14, 1179966.
|
|
Zheng, H., Xu, J., Chu, Y., Jiang, W., Yao, W., Mo, S., Song, X., Zhou, J., 2022. A global regulatory network for dysregulated gene expression and abnormal metabolic signaling in immune cells in the microenvironment of Graves' disease and Hashimoto's thyroiditis. Front. Immunol. 13, 879824.
|
|
Zhong, S., Sun, Y.Q., Huo, J.X., Xu, W.Y., Yang, Y.N., Yang, J.B., Wu, W.J., Liu, Y.X., Wu, C.M., Li, Y.G., 2024. The gut microbiota-aromatic hydrocarbon receptor (AhR) axis mediates the anticolitic effect of polyphenol-rich extracts from Sanghuangporus. iMeta 3, e180.
|
|
Zhou, D., Guo, S., Wang, Y., Zhao, J., Liu, H., Zhou, F., Huang, Y., Gu, Y., Jin, G., Zhang, Y., 2023. Functional characteristics of DNA N6-methyladenine modification based on long-read sequencing in pancreatic cancer. Brief. Funct. Genomics 23, 150-162.
|
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