The DOI matches its Crossref record; 51 of the 51 references it cites were found in a registry or an index.
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
Open accessAbstract
Single-molecule real-time (SMRT) DNA sequencing allows the systematic detection of chemical modifications such as methylation but has not previously been applied on a genome-wide scale. We used this approach to detect 49,311 putative 6-methyladenine (m6A) residues and 1,407 putative 5-methylcytosine (m5C) residues in the genome of a pathogenic Escherichia coli strain. We obtained strand-specific information for methylation sites and a quantitative assessment of the frequency of methylation at each modified position. We deduced the sequence motifs recognized by the methyltransferase enzymes present in this strain without prior knowledge of their specificity. Furthermore, we found that deletion of a phage-encoded methyltransferase-endonuclease (restriction-modification; RM) system induced global transcriptional changes and led to gene amplification, suggesting that the role of RM systems extends beyond protecting host genomes from foreign DNA.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Advanced next generation sequencing platforms such as Single Molecule Real-Time (SMRT) sequencing can be employed to reliably detect certain methylation signatures (Flusberg et al., 2010; Fang et al., 2012) as it has been done for C. autoethanogenum (Utturkar et al., 2015).”
From Gas Fermentation—A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks (2016) · cites this paper as Fang et al., 2012
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.
Datsenko, K., & Wanner, B. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.120163297 · Cited by 15,902
MEME SUITE: tools for motif discovery and searching
Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W., & Noble, W. S. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp335 · Cited by 10,648
A scaling normalization method for differential expression analysis of RNA-seq data
Robinson, M. D., & Oshlack, A. (2010) · Genome Biology · doi:10.1186/gb-2010-11-3-r25 · Cited by 7,876
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
Kaper, J. B., Nataro, J. P., & Mobley, H. L. T. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro818 · Cited by 5,583
Guzman, L., Belin, D., Carson, M. J., & Beckwith, J. (1995) · Journal of Bacteriology · doi:10.1128/jb.177.14.4121-4130.1995 · Cited by 4,942
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
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
Epigenetic Transgenerational Actions of Endocrine Disruptors and Male Fertility
Anway, M. D., Cupp, A. S., Uzumcu, M., & Skinner, M. K. (2005) · Science · doi:10.1126/science.1108190 · Cited by 2,563
Cited by
Sorted by citations
Items 201–300 of 370
Coy, S. R., Gann, E. R., Papoulis, S. E., Holder, M., Ajami, N. J., Petrosino, J. F., Zinser, E. R., Etten, J. L. V., & Wilhelm, S. W. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00887 · Cited by 13
Yi, L., Xu, X., Lin, X., Li, H., Ma, Y., & Lin, J. (2014) · The Analyst · doi:10.1039/c4an00329b · Cited by 13
Forde, B. M., McAllister, L. J., Paton, J. C., Paton, A. W., & Beatson, S. A. (2019) · Scientific Reports · doi:10.1038/s41598-019-45760-5 · Cited by 13
Liu, X., Zheng, J., Ding, J., Wu, J., Zuo, F., & Zhang, G. (2024) · Genes · doi:10.3390/genes15020245 · Cited by 12
Ulrich, R. J., Podkowik, M. M., Tierce, R., Irnov, I., Putzel, G., Samhadaneh, N. M., Lacey, K. A., Boff, D., Morales, S. M., Makita, S., et al. (2025) · Journal of Clinical Investigation · doi:10.1172/jci177872 · Cited by 11
Vitamin B and Vitamin C Affect DNA Methylation and Amino Acid Metabolism in Mycobacterium bovis BCG
Song, N., Zhu, Y., Cui, Y., Lv, M., Tang, Y., Cui, Z., Dang, G., Zheng, H., & Liu, S. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00812 · Cited by 12
Sheng, Y., Zhou, M., You, C., & Dai, X. (2021) · Chinese Chemical Letters · doi:10.1016/j.cclet.2021.08.109 · Cited by 12
Pogka, V., Papadopoulou, G., Valiakou, V., Sgouras, D. N., Mentis, A. F., & Karamitros, T. (2022) · Viruses · doi:10.3390/v14061272 · Cited by 13
Fidelity Index Determination of DNA Methyltransferases
Borgaro, J. G., Benner, N., & Zhu, Z. (2013) · PLoS ONE · doi:10.1371/journal.pone.0063866 · Cited by 12
Dziewit, Ł., & Radlińska, M. (2016) · Journal of General Virology · doi:10.1099/jgv.0.000504 · Cited by 12
Potential mechanisms of attenuation for rifampicin-passaged strains of Flavobacterium psychrophilum
Gliniewicz, K., Wildung, M. R., Orfe, L. H., Wiens, G. D., Cain, K. D., Lahmers, K. K., Snekvik, K. R., & Call, D. R. (2015) · BMC Microbiology · doi:10.1186/s12866-015-0518-1 · Cited by 12
Krüger, A., Burgán, J., Friedrich, A. W., Rossen, J. W. A., & Lucchesi, P. M. A. (2018) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2018.02.024 · Cited by 12
Yang, J.-H., Son, Y., Kang, M., & Park, W. (2023) · Microbial Genomics · doi:10.1099/mgen.0.001093 · Cited by 11
The emerging role of DNA methylation in the pathogenicity of bacterial pathogens
Ma, Y., Wang, X., & Li, X.-M. (2025) · Journal of Bacteriology · doi:10.1128/jb.00108-25 · Cited by 11
Tang, F., Xing, X., Chu, J.-M., Yuan, Q., Zhou, X., Feng, Y., & Yuan, B. (2015) · The Analyst · doi:10.1039/c5an00732a · Cited by 11
Fukuyo, M., Nakano, T., Zhang, Y., Furuta, Y., Ishikawa, K., Watanabe‐Matsui, M., Yano, H., Hamakawa, T., Ide, H., & Kobayashi, I. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv116 · Cited by 11
Chen, K., Stephanou, A. S., Roberts, G. A., White, J. H., Cooper, L. P., Houston, P. J., Lindsay, J. A., & Dryden, D. T. F. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-32189-9_7 · Cited by 11
Predominance of N6-Methyladenine-Specific DNA Fragments Enriched by Multiple Immunoprecipitation
Liu, X., Lai, W., Zhang, N., & Wang, H. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b01087 · Cited by 11
N6-Methyladenine DNA modification in Xanthomonas oryzae pv. oryzicola genome
Xiao, C., Xie, S., Xie, Q., Liu, Z., Xing, J.-F., Ji, K.-K., Tao, J., Dai, L., & Luo, F. (2018) · Scientific Reports · doi:10.1038/s41598-018-34559-5 · Cited by 12
Chen, S., Lai, W., Li, Y., Liu, Y., Jiang, J., Li, X., Jiang, G., & Wang, H. (2023) · The EMBO Journal · doi:10.15252/embj.2023113684 · Cited by 10
Genetic Manipulation and Gene Modification Technologies in Bifidobacteria
Fukiya, S., Sakanaka, M., & Yokota, A. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-805060-6.00015-6 · Cited by 12
Long-read metagenomics for strain tracking after faecal microbiota transplant
Fan, Y., Ni, M., Aggarwala, V., Mead, E. A., Ksiezarek, M., Cao, L., Kamm, M. A., Borody, T. J., Paramsothy, S., Kaakoush, N. O., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02164-8 · Cited by 14
Emerging methylation-based approaches in microbiome engineering
Won, C., & Yim, S. S. (2024) · Biotechnology for Biofuels and Bioproducts · doi:10.1186/s13068-024-02529-x · Cited by 10
Breckell, G. L., & Silander, O. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac310 · Cited by 10
Srivastava, A., Murugaiyan, J., Garcia, J. A. L., Corte, D. D., Hoetzinger, M., Eravci, M., Weise, C., Kumar, Y., Roesler, U. H., Hahn, M. W., et al. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.544785 · Cited by 10
Liu, G., Weston, C. Q., Pham, L. K., Waltz, S., Barnes, H., King, P. A., Sphar, D., Yamamoto, R. T., & Forsyth, A. (2016) · PLoS ONE · doi:10.1371/journal.pone.0146064 · Cited by 10
RNA m5C methylation: a potential modulator of innate immune pathways in hepatocellular carcinoma
Meng, S., Bai, J., Wang, H., Mei, L., Long, Z., & Shanfeng, L. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1362159 · Cited by 9
Nurturing gut health: role of m6A RNA methylation in upholding the intestinal barrier
Wang, S., Yang, Y., Jiang, X., Zheng, X., Wei, Q., Dai, W., & Zhang, X. (2024) · Cell Death Discovery · doi:10.1038/s41420-024-02043-x · Cited by 9
SMAC: identifying DNA N6-methyladenine (6mA) at the single-molecule level using SMRT CCS data
Li, H., Niu, J., Sheng, Y., Liu, Y., & Gao, S. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf153 · Cited by 8
Du, S., Cao, K., Yan, Y., Wang, Y., Wang, Z., & Lin, D. (2023) · Journal of Gastroenterology and Hepatology · doi:10.1111/jgh.16416 · Cited by 9
MinION™: New, Long Read, Portable Nucleic Acid Sequencing Device
Ward, A. C., & Kim, W. (2015) · Journal of Bacteriology and Virology · doi:10.4167/jbv.2015.45.4.285 · Cited by 9
Bacterial Epigenomics: Epigenetics in the Age of Population Genomics
Chen, P., Bandoy, D. D. R., & Weimer, B. C. (2020) · Springer eBooks · doi:10.1007/978-3-030-38281-0_11 · Cited by 9
Pacific bioscience sequence technology: Review
Aliy, M. A., Bayeta, S., & Takale, W. (2022) · International Journal of Veterinary Science and Research · doi:10.17352/ijvsr.000108 · Cited by 10
Fully Assembled Genome Sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992
Allard, M. W., Muruvanda, T., Strain, E. A., Timme, R., Luo, Y., Wang, C., Keys, C. E., Payne, J., Cooper, T., Luong, K., et al. (2013) · Genome Announcements · doi:10.1128/genomea.00081-13 · Cited by 9
Fang, G., Munera, D., Friedman, D. I., Mandlik, A., Chao, M. C., Banerjee, O., Feng, Z., Losic, B., Mahajan, M. C., Jabado, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt0613-565f · Cited by 9
SICD6mA: Identifying 6mA Sites using Deep Memory NetworkPreprint
Liu, W., & Li, H. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.02.930776 · Cited by 9
SUPREM: an engineered non-site-specific m6A RNA methyltransferase with highly improved efficiency
Ochiai, Y., Clifton, B. E., Le Coz, M., Terenzio, M., & Laurino, P. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae887 · Cited by 9
Chen, G., Chakraborty, D., & Koudelka, G. B. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1150 · Cited by 8
Riccardi, C., Passeri, I., Cangioli, L., Fagorzi, C., Fondi, M., & Mengoni, A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms24010159 · Cited by 8
Mao, F., Xie, H., Shi, Y., Jiang, S., Wang, S., & Wu, Y. (2023) · Plants · doi:10.3390/plants12122373 · Cited by 8
Phanthunane, C., Pongcharoen, S., Pannarunothai, S., Roboon, J., Phanthunane, P., & Nontarak, J. (2024) · Clinical and Translational Science · doi:10.1111/cts.13868 · Cited by 8
Detecting epigenetic motifs in low coverage and metagenomics settings
Beckmann, N. D., Karri, S., Fang, G., & Bashir, A. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-s9-s16 · Cited by 8
Luan, M., Chen, W., Xing, J.-F., Xiao, C., Chen, Y., & Xie, S. (2019) · BMC Genomics · doi:10.1186/s12864-019-5776-0 · Cited by 8
Liu, G., Jiang, Y., Liu, Y., Han, L.-L., & Feng, H. (2020) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-020-10475-5 · Cited by 8
Distribution Patterns of DNA N6-Methyladenosine Modification in Non-coding RNA Genes
Li, Y., Zhang, X.-M., Luan, M., Xing, J.-F., Chen, J., & Xie, S. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00268 · Cited by 8
Zhang, R., Liu, H., Bai, B., & Wang, H. (2025) · Journal of Separation Science · doi:10.1002/jssc.70159 · Cited by 7
Structures of MPND Reveal the Molecular Recognition of Nucleosomes
Yang, M., Li, X., Tian, Z., Ma, L., Ma, J., Liu, Y., Shang, G., Liang, A., Wu, W., & Chen, Z. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24043368 · Cited by 6
Guo, H., Chen, F., Zhou, M., Lan, W., Zhang, W., Shen, G., Lin, P., Xia, Q., Zhao, P., & Li, Z. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24043468 · Cited by 8
Roodsant, T. J., van der Putten, B. C. L., Brizuela, J., Coolen, J. P. M., Baltussen, T. J. H., Schipper, K., Pannekoek, Y., van der Ark, K. C. H., & Schultsz, C. (2023) · mBio · doi:10.1128/mbio.02259-23 · Cited by 7
Reducing assembly complexity of microbial genomes with single-molecule sequencing
Koren, S., Harhay, G. P., Smith, T. P. L., Bono, J. L., Harhay, D. M., McVey, S., Radune, D., Bergman, N. H., & Phillippy, A. M. (2013) · Genome biology · doi:10.1186/gb-2013-14-9-r101 · Cited by 21
Epigenomic Landscape of Lyme Disease Spirochetes Reveals Novel Motifs
Wachter, J., Martens, C., Barbian, K., Rego, R. O. M., & Rosa, P. A. (2021) · mBio · doi:10.1128/mbio.01288-21 · Cited by 7
Enam, S. U., Cherry, J. L., Leonard, S. R., Zheludev, I. N., Lipman, D. J., & Fire, A. Z. (2022) · Applied and Environmental Microbiology · doi:10.1128/aem.01670-22 · Cited by 7
Hao, J., Xing, J.-F., Hu, X. W., Wang, Z.-Y., Tang, M.-Q., & Liao, L. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.922152 · Cited by 6
Lefebvre, C. M. J., Pierneef, R., & Reva, O. N. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169307 · Cited by 5
Dam-dependent epigenetic memory regulates prophage reintegration in Salmonella
Yang, J.-H., Son, Y., Park, J.-W., & Park, W. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf951 · Cited by 5
Prophages Preventing Phage Superinfection
Abedon, S. T. (2022) · Springer eBooks · doi:10.1007/978-3-030-94309-7_16 · Cited by 5
Comparison of Yersinia enterocolitica DNA Methylation at Ambient and Host Temperatures
Hofwegen, D. J. V., Hovde, C. J., & Minnich, S. A. (2023) · Epigenomes · doi:10.3390/epigenomes7040030 · Cited by 5
Genome-wide DNA N6-methyladenosine in Aeromonas veronii and Helicobacter pylori
Zhao, H., Ma, J., Tang, Y., Ma, X., Li, J., Li, H., & Liu, Z. (2024) · BMC Genomics · doi:10.1186/s12864-024-10074-y · Cited by 5
Diverse Roles for a Conserved DNA-Methyltransferase in the Entomopathogenic Bacterium Xenorhabdus
Ginibre, N., Legrand, L., Bientz, V., Ogier, J.-C., Lanois, A., Pagès, S., & Brillard, J. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231911981 · Cited by 5
Structural Basis of Nucleic Acid Recognition and 6mA Demethylation by Caenorhabditis elegans NMAD-1A
Shang, G., Yang, M., Li, M., Ma, L., Liu, Y., Ma, J., Chen, Y., Wang, X., Fan, S., Xie, M., et al. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25020686 · Cited by 5
Ferrandi, A., Castani, F., Pitaro, M., Tagliaferri, S., de la Tour, C. B., Alduina, R., Sommer, S., Fasano, M., Barbieri, P., Mancini, M., et al. (2018) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2018.09.020 · Cited by 5
Waters, S. M., Ledford, S. M., Wacker, A. L., Verma, S., Serda, B. M., McKaig, J. M., Varelas, J., Nicoll, P. M., Venkateswaran, K. J., & Smith, D. J. (2021) · International Journal of Astrobiology · doi:10.1017/s1473550421000343 · Cited by 5
Nguyen, T., Trinh, V. N., Le, N. Q. K., & Ou, Y. (2021) · Plant Molecular Biology · doi:10.1007/s11103-021-01204-1 · Cited by 6
Single-Nucleotide-Resolution Sequencing of N6-Methyldeoxyadenosine
Goh, W. S. S. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0876-0_28 · Cited by 5
Advances in whole genome methylomic sequencing
Nordlund, J. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-819414-0.00011-2 · Cited by 5
Role of DNA Methylation in Persister Formation in Uropathogenic E. coliPreprint
Xu, Y., Liu, S., Zhang, Y., & Zhang, W. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.07.897686 · Cited by 5
DNA methylation affects gene expression but not global chromatin structure in Escherichia coli
Morgan, W. J., Amemiya, H. M., & Freddolino, L. (2025) · Journal of Bacteriology · doi:10.1128/jb.00540-24 · Cited by 4
Liu, Y., Liu, S., Huang, J., Zhou, J., & He, F. (2024) · Talanta · doi:10.1016/j.talanta.2024.126279 · Cited by 4
Liang, Z., Chen, S., Li, Y., Lai, W., & Wang, H. (2024) · Advanced Science · doi:10.1002/advs.202403376 · Cited by 3
The multifaceted role of m5C RNA methylation in digestive system tumorigenesis
Hu, X., Liu, Y., Zhang, S., Liu, K., & Gu, X. (2025) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2025.1533148 · Cited by 4
Bacterial DNA methylation gets SMRT
Burgess, D. J. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3389 · Cited by 4
Zhao, L., Li, H., Zhu, Z., Wakefield, M. R., Fang, Y., & Ye, Y. (2017) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2017.02.001 · Cited by 4
Nucleotide Metabolism and DNA Replication
Warner, D. F., Evans, J. C., & Mizrahi, V. (2015) · ASM Press eBooks · doi:10.1128/9781555818845.ch30 · Cited by 4
Integrated Production of Butanol from Glycerol
Venkataramanan, K. P., & Scholz, C. (2014) · Elsevier eBooks · doi:10.1016/b978-0-444-59498-3.00011-7 · Cited by 4
New Advances in NGS Technologies
D’Agaro, E. (2017) · InTech eBooks · doi:10.5772/66924 · Cited by 5
Rusk, N. (2012) · Nature Methods · doi:10.1038/nmeth.2320 · Cited by 4
Single-Cell Genomics and Epigenomics
Valdés‐Mora, F., & Lee, H. J. (2016) · Series in bioengineering · doi:10.1007/978-3-662-49118-8_10 · Cited by 4
Zhao, Y., Zhu, R., Wāng, Y., Song, Z., Shan, C., Qiu, J., & Liu, F. (2018) · Journal of Plant Pathology · doi:10.1007/s42161-018-0101-3 · Cited by 4
Rahman, M. K. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/846311 · Cited by 4
Translating genomics research into control of tuberculosis: lessons learned and future prospects
Warner, D. F., & Mizrahi, V. (2014) · Genome biology · doi:10.1186/s13059-014-0514-z · Cited by 3
Wang, Y., Cai, X., Hu, S., Qin, S., Wang, Z., Cao, Y., Hou, C., Yang, J., & Zhou, W. (2022) · Gene · doi:10.1016/j.gene.2022.147118 · Cited by 3
The Role of Whole-Genome Methods in the Industrial Production of Value-Added Compounds
Olymon, K., Dey, U., Abbas, E., & Kumar, A. A. (2023) · Springer eBooks · doi:10.1007/978-981-99-2816-3_6 · Cited by 3
Measuring the Landscape of CpG Methylation of Individual Repetitive ElementsPreprint
Suzuki, Y., Korlach, J., Turner, S. W., Tsukahara, T., Taniguchi, J., Qu, W., Ichikawa, K., Yoshimura, J., Yurino, H., Takahashi, Y., et al. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/018531 · Cited by 3
Epigenetics: Analysis of Cytosine Modifications at Single Base Resolution
Prater, M., & Hamilton, R. S. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20111-8 · Cited by 3
Ashcroft, M. M., Forde, B. M., Phan, M., Peters, K. M., Roberts, L. W., Chan, K., Chong, T. M., Yin, W., Paterson, D. L., Walsh, T. R., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.07.138552 · Cited by 3
A role for N6-methyldeoxyadenosine in C. elegans mitochondrial genome regulationPreprint
Grub, L. K., Held, J. P., Hansen, T. J., Schaffner, S. H., Canter, M. R., Malagise, E. M., & Patel, M. R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.27.534452 · Cited by 3
Epigenetic regulation and antimicrobial resistance: functional roles of DNA methylation
Daaboul, R., Hayek, E. E., Sarraf, F., Yazbek, C., Yazbek, C., Khoury, C. A., & Tokajian, S. T. (2026) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuag017 · Cited by 2
Shi, C., Wang, L., Xu, H., Zhao, Y., Tian, B., & Hua, Y. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25031660 · Cited by 2
Next-Generation Sequencing (NGS) Application in Plant Breeding
Prasad, S. S., Singh, A. K., Patil, K., Ramteke, P. W., Kumar, N., Shukla, P. K., Yashwanth, V., Aakanksha, K., & Srija, M. S. L. (2024) · Advances in plant breeding strategies · doi:10.1007/978-3-031-68586-6_6 · Cited by 2
Yang, W., Wang, X. Q. D., Wenger, A. M., Fan, W., Yu, J., Dou, Y., & Dou, Y. (2025) · Genome biology · doi:10.1186/s13059-025-03592-9 · Cited by 3
Recent Advances in The Bioanalysis of Modified Nucleotides in Epigenetic Studies
Fragou, D., Fragou, A., Samanidou, V., Kouidou, S., Njau, S. N., & Kovatsi, L. (2013) · Bioanalysis · doi:10.4155/bio.13.270 · Cited by 2
Korlach, J. (2012) · Industrial Biotechnology · doi:10.1089/ind.2012.1546 · Cited by 2
Forward and Reverse Genetics to Model Human Diseases in the Mouse
Gondo, Y., Makino, S., & Fukumura, R. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-809468-6.00028-0 · Cited by 3
Genomics of LAB and dairy‐associated species
Poltronieri, P., Rossi, F., Cammà, C., Pomilio, F., & Randazzo, C. L. (2017) · Wiley eBooks · doi:10.1002/9781119115007.ch5 · Cited by 2
Oliveira, P. H., Ribis, J. W., Garrett, E. M., Trzilova, D., Kim, A., Sekulović, O., Mead, E. A., Pak, T., Zhu, S., Deikus, G. Y., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/398891 · Cited by 2
Sullivan, M. J., Altman, D. R., Chacko, K., Ciferri, B., Webster, E., Pak, T. R., Deikus, G. Y., Lewis-Sandari, M., Khan, Z., Beckford, C., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/522078 · Cited by 2
MeStudio: crossing methylation and genomic features for comparative epigenomic analysesPreprint
Riccardi, C., Passeri, I., Cangioli, L., Fagorzi, C., Mengoni, A., & Fondi, M. (2022) · doi:10.22541/au.165486096.67697546/v1 · Cited by 2
Sizmur, T. P., & Larionov, A. A. (2025) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2025.109712 · Cited by 1
Decoding the genome and epigenome of avian Escherichia coli strains by R10.4.1 nanopore sequencing
Wang, J., Liu, X., Shao, Y., Li, R., & Paudel, S. (2025) · Frontiers in Veterinary Science · doi:10.3389/fvets.2025.1541964 · Cited by 1
Metadata
- Authors
- Fang, G., Munera, D., Friedman, D. I., Mandlik, A., Chao, M. C., Banerjee, O., Feng, Z., Losic, B., Mahajan, M. C., Jabado, O. J., Deikus, G., Clark, T. A., Luong, K., Murray, I. A., Davis, B. M., Keren-Paz, A., Chess, A., Roberts, R. J., Korlach, J., Turner, S. W., Kumar, V., Waldor, M. K., & Schadt, E. E.
- Affiliations
- University of Minnesota (US)
- Brigham and Women's Hospital (US)
- University of Michigan (US)
- Pacific Biosciences (United States) (US)
- Stanford University (US)
- Icahn School of Medicine at Mount Sinai (US)
- New England Biolabs (United States) (US)
- Corresponding author
- Waldor, Matthew K
- Schadt, Eric E
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2012-11-08
- Volume
- 30
- Issue
- 12
- Pages
- 1232-1239
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC3879109
- OpenAlex
- W2025361601
- Cited by
- 360
- References
- 51
- Citations by year
- 2026: 7 · 2025: 21 · 2024: 19 · 2023: 19 · 2022: 24 · 2021: 24 · 2020: 29 · 2019: 30 · 2018: 36 · 2017: 19 · 2016: 25 · 2015: 44 · 2014: 31 · 2013: 25 · 2012: 4
- FWCI
- 13.38
- Type
- journal article
- Language
- en
- Update notices
- erratum (2013-06-10)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation (0916439)
- Howard Hughes Medical Institute
- National Institutes of Health
- National Institute of General Medical Sciences (R44GM100560, R44GM105125)
- National Institute of Allergy and Infectious Diseases (R37AI-42347, R37AI042347)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- DNA methylation, 6-methyladenine, 5-methylcytosine, Escherichia coli, single-molecule real-time sequencing, restriction-modification systems, gene amplification, gene expression changes, genome-wide methylation mapping
- MeSH terms
- Adenine, Biotechnology, Chromosome Mapping, DNA, Bacterial, Escherichia coli, Gene Amplification, Spiro Compounds, Substrate Specificity, DNA Restriction-Modification Enzymes, Genome, Bacterial, Gene Deletion, Sequence Analysis, DNA, DNA Methylation, 5-Methylcytosine
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
