Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L., et al. (2009) · Science · doi:10.1126/science.1170116 · Cited by 5,836

Real-Time DNA Sequencing from Single Polymerase Molecules

Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., et al. (2009) · Science · doi:10.1126/science.1162986 · Cited by 3,732

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

Ito, S., Shen, L., Dai, Q., Wu, S. C., Collins, L. B., Swenberg, J. A., He, C., & Zhang, Y. (2011) · Science · doi:10.1126/science.1210597 · Cited by 3,451

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

Perceptions of epigenetics

Bird, A. (2007) · Nature · doi:10.1038/nature05913 · Cited by 3,011

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

Kriaucionis, S., & Heintz, N. (2009) · Science · doi:10.1126/science.1169786 · Cited by 2,700

The potential and challenges of nanopore sequencing

Branton, D., Deamer, D. W., Marziali, A., Bayley, H., Benner, S. A., Butler, T. J., Ventra, M. D., Garaj, S., Hibbs, A. H., Huang, X. C., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt.1495 · Cited by 2,534

Principles and challenges of genome-wide DNA methylation analysis

Laird, P. W. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2732 · Cited by 1,611

DNA Methylation and Cancer

Das, P. M., & Singal, R. (2004) · Journal of Clinical Oncology · doi:10.1200/jco.2004.07.151 · Cited by 1,469

Direct detection of DNA methylation during single-molecule, real-time sequencing

Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., Korlach, J., & Turner, S. W. (2010) · Nature Methods · doi:10.1038/nmeth.1459 · Cited by 1,460

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

Yu, M., Hon, G. C., Szulwach, K. E., Song, C., Zhang, L., Kim, A., Li, X., Dai, Q., Shen, Y., Park, B., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.027 · Cited by 1,050

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

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

Booth, M. J., Branco, M. R., Ficz, G., Oxley, D., Krueger, F., Reik, W., & Balasubramanian, S. (2012) · Science · doi:10.1126/science.1220671 · Cited by 951

MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system

Mellén, M., Ayata, P., Dewell, S., Kriaucionis, S., & Heintz, N. (2012) · Cell · doi:10.1016/j.cell.2012.11.022 · Cited by 943

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P., et al. (2011) · Nature · doi:10.1038/nature10102 · Cited by 804

DNA methylation profiling in the clinic: applications and challenges

Heyn, H., & Esteller, M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3270 · Cited by 759

Epigenetic transgenerational actions of environmental factors in disease etiology

Skinner, M. K., Manikkam, M., & Guerrero‐Bosagna, C. (2010) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2009.12.007 · Cited by 732

Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine

Iqbal, K., Jin, S., Pfeifer, G. P., & Szabó, P. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1014033108 · Cited by 693

Nanopores: A journey towards DNA sequencing

Wanunu, M. (2012) · Physics of Life Reviews · doi:10.1016/j.plrev.2012.05.010 · Cited by 637

Automated 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

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

Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine

Jin, S.-G., Kadam, S., & Pfeifer, G. P. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq223 · Cited by 437

Comprehensive high-throughput arrays for relative methylation (CHARM)Preprint

Irizarry, R. A., Ladd‐Acosta, C., Carvalho, B. S., Wu, H., Brandenburg, S. A., Jeddeloh, J. A., Wen, B., & Feinberg, A. P. (2008) · Genome Research · doi:10.1101/gr.7301508 · Cited by 433

Comparative isoschizomer profiling of cytosine methylation: The HELP assayPreprint

Khulan, B., Thompson, R. F., Ye, K. Q., Fazzari, M. J., Suzuki, M., Stasiek, E., Figueroa, M. E., Glass, J. L., Chen, Q., Montagna, C., et al. (2006) · Genome Research · doi:10.1101/gr.5273806 · Cited by 400

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

Aran, D., Sivan Sabato, A., & Hellman, A. (2013) · Genome biology · doi:10.1186/gb-2013-14-3-r21 · Cited by 342

Cancer Epigenetics: Modifications, Screening, and Therapy

Gal‐Yam, E. N., Saito, Y., Egger, G., & Jones, P. A. (2007) · Annual Review of Medicine · doi:10.1146/annurev.med.59.061606.095816 · Cited by 270

The Curious Chemical Biology of Cytosine: Deamination, Methylation,and Oxidation as Modulators of Genomic Potential

Nabel, C. S., Manning, S. A., & Kohli, R. M. (2011) · ACS Chemical Biology · doi:10.1021/cb2002895 · Cited by 197

Identification of epigenetic DNA modifications with a protein nanopore

Wallace, E. V. B., Stoddart, D., Heron, A. J., Mikhailova, E., Maglia, G., Donohoe, T. J., & Bayley, H. (2010) · Chemical Communications · doi:10.1039/c0cc02864a · Cited by 176

Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules

Wanunu, M., Cohen-Karni, D., Johnson, R. R., Fields, L. G., Benner, J. S., Peterman, N., Zheng, Y., Klein, M. L., & Drndić, M. (2010) · Journal of the American Chemical Society · doi:10.1021/ja107836t · Cited by 172

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 162

Detection and Quantification of Methylation in DNA using Solid-State Nanopores

Shim, J., Humphreys, G. I., Venkatesan, B. M., Munz, J. M. A., Zou, X., Sathe, C., Schulten, K. J., Kosari, F., Nardulli, A. M., Vasmatzis, G., et al. (2013) · Scientific Reports · doi:10.1038/srep01389 · Cited by 153

Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation

Clark, T. A., Lu, X., Luong, K., Dai, Q., Boitano, M., Turner, S. W., He, C., & Korlach, J. (2013) · BMC Biology · doi:10.1186/1741-7007-11-4 · Cited by 139

Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution

Lluch‐Senar, M., Luong, K., Lloréns‐Rico, V., Delgado, J., Fang, G., Spittle, K. E., Clark, T. A., Schadt, E. E., Turner, S. W., Korlach, J., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003191 · Cited by 107

Nanopore Detection of 8-Oxo-7,8-dihydro-2′-deoxyguanosine in Immobilized Single-Stranded DNA via Adduct Formation to the DNA Damage Site

Schibel, A. E. P., An, N., Jin, Q., Fleming, A. M., Burrows, C. J., & White, H. S. (2010) · Journal of the American Chemical Society · doi:10.1021/ja109501x · Cited by 103

Dynamic changes in 5-hydroxymethylation signatures underpin early and late events in drug exposed liver

Thomson, J. P., Hunter, J. M., Lempiäinen, H., Müller, A., Terranova, R., Moggs, J. G., & Meehan, R. R. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt232 · Cited by 87

Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells

Murphy, P. J., Cipriany, B. R., Wallin, C. B., Ju, C., Szeto, K., Hagarman, J. A., Benítez, J. J., Craighead, H. G., & Soloway, P. D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218495110 · Cited by 81

Mosaic Methylation in Clonal Tissue

Silva, A. J., Ward, K. J., & White, R. L. (1993) · Developmental Biology · doi:10.1006/dbio.1993.1086 · Cited by 63

Reading the second genomic code

Marx, V. (2012) · Nature · doi:10.1038/491143a · Cited by 23

Nanopore sequencing and assembly of a human genome with ultra-long reads

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) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892

Nanopore sequencing technology, bioinformatics and applications

Wang, Y., Zhao, Y., Bollas, A., Wang, Y., & Au, K. F. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-01108-x · Cited by 1,863

Three decades of nanopore sequencing

Deamer, D., Akeson, M., & Branton, D. (2016) · Nature Biotechnology · doi:10.1038/nbt.3423 · Cited by 1,292

Cancer biomarker detection: recent achievements and challenges

Wu, L. J., & Qu, X. (2015) · Chemical Society Reviews · doi:10.1039/c4cs00370e · Cited by 1,252

Detecting DNA cytosine methylation using nanopore sequencing

Simpson, J. T., Workman, R. E., Zuzarte, P. C., David, M., Dursi, L. J., & Timp, W. (2017) · Nature Methods · doi:10.1038/nmeth.4184 · Cited by 1,149

Direct Detection and Mapping of DNA Methylation in Single Molecules using Nanopore MspA

Laszlo, A. H., Derrington, I. M., Brinkerhoff, H. D., Langford, K. W., Nova, I. C., Samson, J. M., Bartlett, J. J., & Gundlach, J. H. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2013.11.1255 · Cited by 1

Detection and Mapping of 5-Methylcytosine and 5-Hydroxymethylcytosine in Short Strands of ssDNA using Nanopore Sequencing with MspA

Laszlo, A. H., Derrington, I. M., Manrao, E. A., & Gundlach, J. H. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2012.11.1194 · Cited by 3

Detection of 5-methylcytosine and 5-hydroxymethylcytosine in DNA via host–guest interactions inside α-hemolysin nanopores

Zeng, T., Liu, L., Li, T., Li, Y., Gao, J., Zhao, Y., & Wu, H. (2015) · Chemical Science · doi:10.1039/c5sc01436k · Cited by 50

Single-Molecule DNA Methylation Quantification Using Electro-optical Sensing in Solid-State Nanopores

Gilboa, T., Torfstein, C., Juhasz, M., Grunwald, A., Ebenstein, Y., Weinhold, E. G., & Meller, A. (2016) · ACS Nano · doi:10.1021/acsnano.6b04748 · Cited by 87

Protein nanopores to detect DNA methylation

de Souza, N. (2013) · Nature Methods · doi:10.1038/nmeth.2798 · Cited by 5