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

Principal Component Analysis

Jolliffe, I. T. (2005) · Wiley eBooks · doi:10.1002/0470013192.bsa501 · Cited by 14,522 · see citing works

Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals

Jaenisch, R., & Bird, A. (2003) · Nature Genetics · doi:10.1038/ng1089 · Cited by 6,325 · see citing works

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 · see citing works

The fundamental role of epigenetic events in cancer

Jones, P. A., & Baylin, S. B. (2002) · Nature Reviews Genetics · doi:10.1038/nrg816 · Cited by 5,648 · see citing works

Human DNA methylomes at base resolution show widespread epigenomic differences

Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673 · see citing works

Targeted mutation of the DNA methyltransferase gene results in embryonic lethality

Li, E., Bestor, T. H., & Jaenisch, R. (1992) · Cell · doi:10.1016/0092-8674(92)90611-f · Cited by 3,984 · see citing works

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 · see citing works

CpG islands in vertebrate genomes.

Gardiner-Garden, M., & Frommer, M. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90689-9 · Cited by 3,462 · see citing works

DNA methylation and human disease

Robertson, K. D. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1655 · Cited by 2,864 · see citing works

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 · see citing works

Genome-scale DNA methylation maps of pluripotent and differentiated cells

Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature · doi:10.1038/nature07107 · Cited by 2,536 · see citing works

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

Lister, R., O’Malley, R. C., Tonti‐Filippini, J., Gregory, B. D., Berry, C. C., Millar, A. H., & Ecker, J. R. (2008) · Cell · doi:10.1016/j.cell.2008.03.029 · Cited by 2,424 · see citing works

Cancer-epigenetics comes of age

Jones, P. A., & Laird, P. W. (1999) · Nature Genetics · doi:10.1038/5947 · Cited by 2,334 · see citing works

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

Cokus, S. J., Feng, S.-H., Zhang, X.-Y., Chen, Z., Merriman, B., Haudenschild, C., Pradhan, S., Nelson, S., Pellegrini, M., & Jacobsen, S. (2008) · Nature · doi:10.1038/nature06745 · Cited by 2,278 · see citing works

DNA Modification Mechanisms and Gene Activity During Development

Holliday, R., & Pugh, J. E. (1975) · Science · doi:10.1126/science.187.4173.226 · Cited by 1,973 · see citing works

Continuous base identification for single-molecule nanopore DNA sequencing

Clarke, J., Wu, H., Jayasinghe, L., Patel, A., Reid, S., & Bayley, H. (2009) · Nature Nanotechnology · doi:10.1038/nnano.2009.12 · Cited by 1,813 · see citing works

A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters

Saxonov, S., Berg, P., & Brutlag, D. L. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510310103 · Cited by 1,401 · see citing works

Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations

Levene, M. J., Korlach, J., Turner, S., Foquet, M., Craighead, H. G., & Webb, W. W. (2003) · Science · doi:10.1126/science.1079700 · Cited by 1,380 · see citing works

X inactivation, differentiation, and DNA methylation

Riggs, A. D. (2008) · Cytogenetics and Cell Genetics · doi:10.1159/000130315 · Cited by 1,343 · see citing works

How Are Alkynes Scrambled?

Bunz, U. H. F. (2005) · Science · doi:10.1126/science.1111098 · Cited by 1,252 · see citing works

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

Huang, Y., Pastor, W., Shen, Y.-H., Tahiliani, M., Liu, D. R., & Rao, A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008888 · Cited by 755 · see citing works

Somatic mutations in the neurofibromatosis 1 gene in human tumors

Li, Y., Bollag, G. E., Clark, R., Stevens, J., Conroy, L., Fults, D., Ward, K., Friedman, E., Samowitz, W. S., Robertson, M. A., et al. (1992) · Cell · doi:10.1016/0092-8674(92)90408-5 · Cited by 394 · see citing works

Finding the fifth base: Genome-wide sequencing of cytosine methylationPreprint

Lister, R., & Ecker, J. R. (2009) · Genome Research · doi:10.1101/gr.083451.108 · Cited by 377 · see citing works

An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics

Wong, I., Patel, S. S., & Johnson, K. A. (1991) · Biochemistry · doi:10.1021/bi00216a030 · Cited by 366 · see citing works

DNA methylation: Bisulphite modification and analysis

Clark, S. J., Statham, A. L., Stirzaker, C., Molloy, P. L., & Frommer, M. (2006) · Nature Protocols · doi:10.1038/nprot.2006.324 · Cited by 363 · see citing works

Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase

Hsu, G. W., Ober, M. S., Carell, T., & Beese, L. S. (2004) · Nature · doi:10.1038/nature02908 · Cited by 316 · see citing works

Roles of DNA adenine methylation in host–pathogen interactions: mismatch repair, transcriptional regulation, and more

Marinus, M., & Casadesús, J. (2009) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2008.00159.x · Cited by 305 · see citing works

DNA methylation in early development

Razin, A., & Shemer, R. (1995) · Human Molecular Genetics · doi:10.1093/hmg/4.suppl_1.1751 · Cited by 280 · see citing works

Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures

Korlach, J., Marks, P., Cicero, R. L., Gray, J. J., Murphy, D. L., Roitman, D. B., Pham, T. T., Otto, G. A., Foquet, M., & Turner, S. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0710982105 · Cited by 236 · see citing works

Genome-wide high throughput analysis of DNA methylation in eukaryotes

Pomraning, K., Smith, K., & Freitag, M. (2008) · Methods · doi:10.1016/j.ymeth.2008.09.022 · Cited by 203 · see citing works

Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B‐family polymerases

Berman, A., Kamtekar, S., Goodman, J. L., Lázaro, J., de Vega, M., Blanco, L., Salas, M., & Steitz, T. (2007) · EMBO Journal · doi:10.1038/sj.emboj.7601780 · Cited by 161 · see citing works

Improved fabrication of zero-mode waveguides for single-molecule detection

Foquet, M., Samiee, K. T., Kong, X., Chauduri, B. P., Lundquist, P. M., Turner, S., Freudenthal, J., & Roitman, D. B. (2008) · Journal of Applied Physics · doi:10.1063/1.2831366 · Cited by 104 · see citing works

Parallel confocal detection of single molecules in real time

Lundquist, P. M., Zhong, C. F., Zhao, P., Tomaney, A. B., Peluso, P. S., Dixon, J., Bettman, B., Lacroix, Y., Kwo, D. P., McCullough, E., et al. (2008) · Optics Letters · doi:10.1364/ol.33.001026 · Cited by 102 · see citing works

Solid phase synthesis and restriction endonuclease cleavage of oligodeoxynucleotides containing 5-(hydroxymethyl)-cytosine

Tardy-Planechaud, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.3.553 · Cited by 88 · see citing works

Long, Processive Enzymatic DNA Synthesis Using 100% Dye-Labeled Terminal Phosphate-Linked Nucleotides

Korlach, J., Bibillo, A., Wegener, J., Peluso, P. S., Pham, T. T., Park, I., Clark, S., Otto, G. A., & Turner, S. W. (2008) · Nucleosides Nucleotides & Nucleic Acids · doi:10.1080/15257770802260741 · Cited by 86 · see citing works

Reaction of bisulfite with the 5-hydroxymethyl group in pyrimidines and in phage DNAs

Hayatsu, H., & Shiragami, M. (1979) · Biochemistry · doi:10.1021/bi00571a013 · Cited by 85 · see citing works

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works

Coming of age: ten years of next-generation sequencing technologies

Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352 · see citing works

Opportunities and challenges in long-read sequencing data analysis

Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020) · Genome Biology · doi:10.1186/s13059-020-1935-5 · Cited by 2,530 · see citing works

PacBio Sequencing and its Applications

Rhoads, A., & Au, K. F. (2015) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.08.002 · Cited by 2,338 · see citing works

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

Akalin, A., Kormáksson, M., Li, S., Garrett-Bakelman, F. E., Figueroa, M. E., Melnick, A. M., & Mason, C. E. (2012) · Genome biology · doi:10.1186/gb-2012-13-10-r87 · Cited by 2,205 · see citing works

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

Quail, M., Smith, M. E., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P., & Gu, Y. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-341 · Cited by 2,031 · see citing works

Comparison of Next-Generation Sequencing Systems

Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., Lin, D., Lü, L., & Law, M. (2012) · BioMed Research International · doi:10.1155/2012/251364 · Cited by 1,605 · see citing works

The sequence of sequencers: The history of sequencing DNA

Heather, J. M., & Chain, B. (2016) · Genomics · doi:10.1016/j.ygeno.2015.11.003 · Cited by 1,397 · see citing works

High-Throughput Sequencing Technologies

Reuter, J., Spacek, D. V., & Snyder, M. P. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.05.004 · Cited by 1,330 · see citing works

Epigenome-wide association studies for common human diseases

Rakyan, V. K., Down, T. A., Balding, D. J., & Beck, S. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3000 · Cited by 1,272 · see citing works

Long-read human genome sequencing and its applications

Logsdon, G. A., Vollger, M. R., & Eichler, E. E. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0236-x · Cited by 1,222 · see citing works

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

Chaisson, M., & Tesler, G. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-238 · Cited by 1,183 · see citing works

The Landscape of long noncoding RNA classification

Laurent, G. S., Wahlestedt, C., & Kapranov, P. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.03.007 · Cited by 1,192 · see citing works

The Third Revolution in Sequencing Technology

van Dijk, E., Jaszczyszyn, Y., Naquin, D., & Thermes, C. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.05.008 · Cited by 1,186 · see citing works

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 1,109 · see citing works

DNA sequencing at 40: past, present and future

Shendure, J., Balasubramanian, S., Church, G. M., Gilbert, W., Rogers, J., Schloss, J. A., & Waterston, R. (2017) · Nature · doi:10.1038/nature24286 · Cited by 1,084 · see citing works

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

Song, C., Szulwach, K. E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.-H., Zhang, W., Jian, X., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1732 · Cited by 1,089 · see citing works

Active DNA demethylation: many roads lead to Rome

Wu, S. C., & Zhang, Y. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2950 · Cited by 1,054 · see citing works

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

Roberts, R. J., Vincze, T., Pósfai, J., & Macelis, D. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp874 · Cited by 992 · see citing works

Overview of Next‐Generation Sequencing Technologies

Slatko, B. E., Gardner, A. F., & Ausubel, F. M. (2018) · Current Protocols in Molecular Biology · doi:10.1002/cpmb.59 · Cited by 968 · see citing works

A window into third-generation sequencing

Schadt, E. E., Turner, S., & Kasarskis, A. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq416 · Cited by 960 · see citing works

Next‐generation sequencing technologies for environmental DNA research

Shokralla, S., Spall, J. L., Gibson, J. F., & Hajibabaei, M. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05538.x · Cited by 939 · see citing works

REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.

Roberts, R. J., Vincze, T., Posfai, J., & Macelis, D. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1046 · Cited by 728 · see citing works

Uncovering the role of 5-hydroxymethylcytosine in the epigenome

Branco, M. R., Ficz, G., & Reik, W. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3080 · Cited by 766 · see citing works

Next generation sequencing technology: Advances and applications

Buermans, H. P. J., & den Dunnen, J. T. (2014) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2014.06.015 · Cited by 761 · see citing works

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Ardui, S., Ameur, A., Vermeesch, J. R., & Hestand, M. S. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky066 · Cited by 741 · see citing works

DNA Methylation on N6-Adenine in C. elegans

Greer, E. L., Blanco, M. A., Gu, L., Sendinc, E., Liu, J., Aristizábal-Corrales, D., Hsu, C.-H., Aravind, L., He, C., & Shi, Y. (2015) · Cell · doi:10.1016/j.cell.2015.04.005 · Cited by 702 · see citing works

DNA Methylation Analysis: Choosing the Right Method

Kurdyukov, S., & Bullock, M. (2016) · Biology · doi:10.3390/biology5010003 · Cited by 708 · see citing works

Adaptation genomics: the next generation

Stapley, J., Reger, J., Feulner, P. G. D., Smadja, C. M., Galindo, J., Ekblom, R., Bennison, C., Ball, A. D., Beckerman, A. P., & Slate, J. (2010) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2010.09.002 · Cited by 690 · see citing works

Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidationPreprint

Wu, H., & Zhang, Y. (2011) · Genes & Development · doi:10.17615/800j-yk16 · Cited by 665 · see citing works

DNA methylation on N6-adenine in mammalian embryonic stem cells

Wu, T. P., Wang, T., Seetin, M. G., Lai, Y., Zhu, S., Lin, K., Liu, Y., Byrum, S. D., Mackintosh, S. G., Zhong, M., et al. (2016) · Nature · doi:10.1038/nature17640 · Cited by 648 · see citing works

Computational solutions to large‐scale data management and analysis

Schadt, E. E., Linderman, M. D., Sorenson, J., Lee, L., & Nolan, G. P. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2857 · Cited by 631 · see citing works

GenBank

Benson, D. A., Cavanaugh, M. L., Clark, K., Karsch‐Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1070 · Cited by 629 · see citing works

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

Sedlazeck, F. J., Lee, H., Darby, C. A., & Schatz, M. C. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0003-4 · Cited by 530 · see citing works

Advancements in Next-Generation Sequencing

Levy, S., & Myers, R. (2016) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022413 · Cited by 598 · see citing works

The advantages of SMRT sequencing

Roberts, R. J., Carneiro, M. O., & Schatz, M. C. (2013) · Genome biology · doi:10.1186/gb-2013-14-6-405 · Cited by 584 · see citing works

Analysing and interpreting DNA methylation data

Bock, C. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3273 · Cited by 580 · see citing works

Mapping Human Epigenomes

Rivera, C. M., & Ren, B. (2013) · Cell · doi:10.1016/j.cell.2013.09.011 · Cited by 550 · see citing works

N6-Methyladenine DNA Modification in the Human Genome

Xiao, C.-L., Zhu, S., He, M., Chen, D., Zhang, Q., Chen, Y., Yu, G., Liu, J., Xie, S.-Q., Luo, F., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.015 · Cited by 531 · see citing works

Mapping DNA methylation with high-throughput nanopore sequencing

Rand, A. C., Jain, M., Eizenga, J. M., Musselman-Brown, A., Olsen, H. E., Akeson, M., & Paten, B. (2017) · Nature Methods · doi:10.1038/nmeth.4189 · Cited by 507 · see citing works

Integrating Artificial Intelligence and Nanotechnology for Precision Cancer Medicine

Adir, O., Poley, M., Chen, G., Froim, S., Krinsky, N., Shklover, J., Shainsky‐Roitman, J., Lammers, T., & Schroeder, A. (2020) · Advanced Materials · doi:10.1002/adma.201901989 · Cited by 496 · see citing works

The birth of the Epitranscriptome: deciphering the function of RNA modifications

Saletore, Y., Meyer, K. D., Korlach, J., Vilfan, I. D., Jaffrey, S. R., & Mason, C. E. (2012) · Genome biology · doi:10.1186/gb-2012-13-10-175 · Cited by 485 · see citing works

Gas Fermentation—A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks

Liew, F., Martin, M. E., Tappel, R. C., Heijstra, B. D., Mihalcea, C., & Köpke, M. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00694 · Cited by 485 · see citing works

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

Liu, Y., Siejka-Zielińska, P., Velikova, G., Bi, Y., Yuan, F., Tomková, M., Bai, C., Chen, L., Schuster‐Böckler, B., & Song, C. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0041-2 · Cited by 474 · see citing works

The advantages of SMRT sequencing

Roberts, R. J., Carneiro, M. O., & Schatz, M. C. (2013) · Genome biology · doi:10.1186/gb-2013-14-7-405 · Cited by 454 · see citing works

Long-Read Sequencing Emerging in Medical Genetics

Mantere, T., Kersten, S., & Hoischen, A. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00426 · Cited by 430 · see citing works

Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease

Ishiura, H., Shibata, S., Yoshimura, J., Suzuki, Y., Qü, W., Doi, K., Almansour, M. A., Kikuchi, J. K., Taira, M., Mitsui, J., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0458-z · Cited by 433 · see citing works

Next generation sequencing and its applications in forensic genetics

Børsting, C., & Morling, N. (2015) · Forensic Science International: Genetics · doi:10.1016/j.fsigen.2015.02.002 · Cited by 460 · see citing works

Landscape of Next-Generation Sequencing Technologies

Niedringhaus, T. P., Milanova, D., Kerby, M. B., Snyder, M. P., & Barron, A. E. (2011) · Analytical Chemistry · doi:10.1021/ac2010857 · Cited by 380 · see citing works

Epigenetic regulation of adaptive responses of forest tree species to the environment

Bräutigam, K., Vining, K. J., Placette, C. L., Fossdal, C. G., Mirouze, M., Gutierrez‐Marcos, J., Fluch, S., Fraga, M. F., Guevara, M. Á., Abarca, D., et al. (2013) · Ecology and Evolution · doi:10.1002/ece3.461 · Cited by 371 · see citing works

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

Fang, G., Munera, D., Friedman, D. I., Mandlik, A., Chao, M. C., Banerjee, O., Feng, Z., Losic, B., Mahajan, M. C., Jabado, O. J., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2432 · Cited by 360 · see citing works

Long reads: their purpose and place

Pollard, M., Gurdasani, D., Mentzer, A. J., Porter, T., & Sandhu, M. S. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy177 · Cited by 365 · see citing works

Mapping the epigenetic modifications of DNA and RNA

Zhao, L.-Y., Song, J., Liu, Y., Song, C., & Yi, C. (2020) · Protein & Cell · doi:10.1007/s13238-020-00733-7 · Cited by 366 · see citing works

A guide for the diagnosis of rare and undiagnosed disease: beyond the exome

Marwaha, S., Knowles, J. W., & Ashley, E. A. (2022) · Genome Medicine · doi:10.1186/s13073-022-01026-w · Cited by 365 · see citing works

The Epigenomic Landscape of Prokaryotes

Blow, M. J., Clark, T. A., Daum, C. G., Deutschbauer, A. M., Fomenkov, A. I., Fries, R. A., Froula, J. L., Kang, D., Malmstrom, R. R., Morgan, R., et al. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005854 · Cited by 362 · see citing works

A twin approach to unraveling epigenetics

Bell, J. T., & Spector, T. D. (2011) · Trends in Genetics · doi:10.1016/j.tig.2010.12.005 · Cited by 353 · see citing works

Single-Molecule Plasmon Sensing: Current Status and Future Prospects

Taylor, A. B., & Zijlstra, P. (2017) · ACS Sensors · doi:10.1021/acssensors.7b00382 · Cited by 366 · see citing works

Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine

Booth, M. J., Ost, T. W. B., Beraldi, D., Bell, N. M., Branco, M. R., Reik, W., & Balasubramanian, S. (2013) · Nature Protocols · doi:10.1038/nprot.2013.115 · Cited by 348 · see citing works

Biological roles of adenine methylation in RNA

Boulias, K., & Greer, E. L. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00534-0 · Cited by 350 · see citing works

Widespread adenine N6-methylation of active genes in fungi

Mondo, S. J., Dannebaum, R., Kuo, R. C., Louie, K., Bewick, A. J., LaButti, K. M., Haridas, S., Kuo, A., Salamov, A. A., Ahrendt, S. R., et al. (2017) · Nature Genetics · doi:10.1038/ng.3859 · Cited by 334 · see citing works

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

Liu, Q., Li, F., Yu, G., Wang, D., Xiao, C., & Wang, K. (2019) · Nature Communications · doi:10.1038/s41467-019-10168-2 · 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

Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity

Clark, S. J., Lee, H. J., Smallwood, S. A., Kelsey, G., & Reik, W. (2016) · Genome Biology · doi:10.1186/s13059-016-0944-x · Cited by 310 · see citing works

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

Clark, T. A., Murray, I. A., Morgan, R., Kislyuk, A. O., Spittle, K. E., Boitano, M., Fomenkov, A. I., Roberts, R. J., & Korlach, J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1146 · Cited by 315 · see citing works

CRISPR/Cas9-based engineering of the epigenome

Pulecio, J., Verma, N., Mejía-Ramírez, E., Huangfu, D., & Raya, A. (2017) · Cell Stem Cell · doi:10.1016/j.stem.2017.09.006 · Cited by 300 · see citing works

iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC

Feng, P., Yang, H. Q., Ding, H., Lin, H., Chen, W., & Chou, K. (2018) · Genomics · doi:10.1016/j.ygeno.2018.01.005 · Cited by 306 · see citing works

Long walk to genomics: History and current approaches to genome sequencing and assembly

Giani, A. M., Gallo, G. R., Gianfranceschi, L., & Formenti, G. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.11.002 · Cited by 306 · see citing works

Next-Generation Sequencing and Emerging Technologies

Kumar, K. R., Cowley, M. J., & Davis, R. L. (2019) · Seminars in Thrombosis and Hemostasis · doi:10.1055/s-0039-1688446 · Cited by 299 · see citing works

Single-cell epigenomics: techniques and emerging applications

Schwartzman, O., & Tanay, A. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3980 · Cited by 282 · see citing works

Marine Environmental Epigenetics

Eirin-Lopez, J. M., & Putnam, H. M. (2018) · Annual Review of Marine Science · doi:10.1146/annurev-marine-010318-095114 · Cited by 284 · see citing works

DNA methylation in bacteria: from the methyl group to the methylome

Sánchez-Romero, M. A., Cota, I., & Casadesús, J. (2015) · Current Opinion in Microbiology · doi:10.1016/j.mib.2015.03.004 · Cited by 284 · see citing works

The bacterial epigenome

Sánchez-Romero, M. A., & Casadesús, J. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0286-2 · Cited by 284 · see citing works

Decoding the epitranscriptional landscape from native RNA sequences

Jenjaroenpun, P., Wongsurawat, T., Wadley, T. D., Wassenaar, T. M., Liu, J., Dai, Q., Wanchai, V., Akel, N. S., Jamshidi‐Parsian, A., Franco, A. T., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa620 · Cited by 279 · see citing works

iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties

Chen, W., Yang, H. Q., Feng, P., Ding, H., & Lin, H. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx479 · Cited by 276 · see citing works

De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal ProcessingPreprint

Stoiber, M. H., Quick, J., Egan, R. S., Lee, J. E., Celniker, S., Neely, R. K., Loman, N. J., Pennacchio, L. A., & Brown, J. B. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/094672 · Cited by 276 · see citing works

Epigenetics of Host–Pathogen Interactions: The Road Ahead and the Road Behind

Gómez-Díaz, E., Jordà, M., Peinado, M., & Rivero, A. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1003007 · Cited by 259 · see citing works

The Dynamics of DNA Methylation in Schizophrenia and Related Psychiatric Disorders

Grayson, D. R., & Guidotti, A. (2012) · Neuropsychopharmacology · doi:10.1038/npp.2012.125 · Cited by 267 · see citing works

Epigenetic modification of nucleic acids: from basic studies to medical applications

Chen, Y., Hong, T., Wang, S., Mo, J., Tian, T., & Zhou, X. (2017) · Chemical Society Reviews · doi:10.1039/c6cs00599c · Cited by 266 · see citing works

Mutagenesis as a Tool in Plant Genetics, Functional Genomics, and Breeding

Sikora, P., Chawade, A., Larsson, M., Olsson, J., & Olsson, O. (2011) · International Journal of Plant Genomics · doi:10.1155/2011/314829 · Cited by 265 · see citing works

Advances in the profiling of DNA modifications: cytosine methylation and beyond

Plongthongkum, N., Diep, D. H., & Zhang, K. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3772 · Cited by 259 · see citing works

The methylomes of six bacteria

Murray, I. A., Clark, T. A., Morgan, R., Boitano, M., Anton, B. P., Luong, K., Fomenkov, A. I., Turner, S. W., Korlach, J., & Roberts, R. J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks891 · Cited by 253 · see citing works

DNA N-Adenine Methylation in Arabidopsis thaliana

Liang, Z., Shen, L., Cui, X., Bao, S., Geng, Y., Yu, G., Liang, F., Xie, S. B., Lu, T., Gu, X., et al. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.03.012 · Cited by 259 · see citing works

DNA N6-methyladenine: a new epigenetic mark in eukaryotes?

Luo, G.-Z., Blanco, M. A., Greer, E. L., He, C., & Shi, Y. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4076 · Cited by 252 · see citing works

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

Ni, P., Huang, N., Zhang, Z., Wang, D., Liang, F., Yu, M., Xiao, C., Luo, F., & Wang, J. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz276 · Cited by 252 · see citing works

Type I restriction enzymes and their relatives

Loenen, W. A., Dryden, D., Raleigh, E., & Wilson, G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt847 · Cited by 250 · see citing works

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine

Yu, M., Hon, G. C., Szulwach, K. E., Song, C., Jin, P., Ren, B., & He, C. (2012) · Nature Protocols · doi:10.1038/nprot.2012.137 · Cited by 250 · see citing works

5‐Hydroxymethylcytosine, the Sixth Base of the Genome

Münzel, M., Globisch, D., & Carell, T. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.201101547 · Cited by 252 · see citing works

TET proteins and the control of cytosine demethylation in cancer

Scourzic, L., Mouly, E., & Bernard, O. (2015) · Genome Medicine · doi:10.1186/s13073-015-0134-6 · Cited by 251 · see citing works

Third Generation DNA Sequencing: Pacific Biosciences' Single Molecule Real Time Technology

McCarthy, A. A. (2010) · Chemistry & Biology · doi:10.1016/j.chembiol.2010.07.004 · Cited by 244 · see citing works

New Technologies for Studying Biofilms

Franklin, M. J., Chang, C. B., Akiyama, T., & Bothner, B. B. (2015) · Microbiology Spectrum · doi:10.1128/microbiolspec.mb-0016-2014 · Cited by 238 · see citing works

DNA methylation in higher plants: Past, present and future

Vanyushin, B. F., & Ashapkin, V. V. (2011) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2011.04.006 · Cited by 238 · see citing works

Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond

Guo, J. U., Su, Y., Zhong, C., Ming, G.-L., & Song, H. (2011) · Cell Cycle · doi:10.4161/cc.10.16.17093 · Cited by 235 · see citing works

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine

Song, C., Clark, T. A., Lu, X., Kislyuk, A. O., Dai, Q., Turner, S. W., He, C., & Korlach, J. (2011) · Nature Methods · doi:10.1038/nmeth.1779 · Cited by 235 · see citing works

Deciphering bacterial epigenomes using modern sequencing technologies

Beaulaurier, J., Schadt, E. E., & Fang, G. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0081-3 · Cited by 228 · see citing works

Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses

Weigele, P., & Raleigh, E. A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00114 · Cited by 212 · see citing works

Meta-4mCpred: A Sequence-Based Meta-Predictor for Accurate DNA 4mC Site Prediction Using Effective Feature Representation

Manavalan, B., Basith, S., Shin, T. H., Wei, L., & Lee, G. (2019) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2019.04.019 · Cited by 219 · see citing works

DNA methyltransferases and epigenetic regulation in bacteria

Adhikari, S., & Curtis, P. D. (2016) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuw023 · Cited by 218 · see citing works

DNA methylation methods: Global DNA methylation and methylomic analyses

Li, S., & Tollefsbol, T. O. (2020) · Methods · doi:10.1016/j.ymeth.2020.10.002 · Cited by 219 · see citing works

Identification and analysis of adenine N6-methylation sites in the rice genome

Zhou, C., Wang, C., Liu, H., Zhou, Q., Liu, Q., Guo, Y., Peng, T., Song, J., Zhang, J., Chen, L., et al. (2018) · Nature Plants · doi:10.1038/s41477-018-0214-x · Cited by 216 · see citing works

i6mA-Pred: identifying DNA N6-methyladenine sites in the rice genome

Chen, W., Lv, H., Nie, F., & Lin, H. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz015 · Cited by 212 · see citing works

High‐Throughput DNA Sequencing Beyond the Four‐Letter Code: Epigenetic Modifications Revealed by Single‐Molecule Bypass Kinetics

Summerer, D. (2010) · ChemBioChem · doi:10.1002/cbic.201000569 · Cited by 9 · see citing works

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

Clark, T. A., Murray, I. A., Morgan, R., Kislyuk, A. O., Spittle, K. E., Boitano, M., Fomenkov, A. I., Roberts, R. J., & Korlach, J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1146 · Cited by 315 · see citing works

Zeroing in on DNA methylomes with no BS

Ecker, J. R. (2010) · Nature Methods · doi:10.1038/nmeth0610-435 · Cited by 7 · see citing works

Genome-wide detection of cytosine methylation by single molecule real-time sequencing

Tse, O. Y. O., Jiang, P., Cheng, S. H., Peng, W., Shang, H., Wong, J., Chan, S. L., Poon, L. C., Leung, T. Y., Chan, K. C. A., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2019768118 · Cited by 139 · see citing works

DNA methylation while you sequence

Muers, M. R. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2817 · Cited by 1 · see citing works