Cited by 370Epigenetics and DNA MethylationRNA modifications and cancerBacterial Genetics and Biotechnology

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 access

Fang, Gang, Munera, Diana, Friedman, David I, Mandlik, Anjali, Chao, Michael C, Banerjee, Onureena, Feng, Zhixing, Losic, Bojan, Mahajan, Milind C, Jabado, Omar J, Deikus, Gintaras, Clark, Tyson A, Luong, Khai, Murray, Iain A, Davis, Brigid M, Keren-Paz, Alona, Chess, Andrew, Roberts, Richard J, Korlach, Jonas, Turner, Steve W, Kumar, Vipin, Waldor, Matthew K, Schadt, Eric E·2012·Nature Biotechnology

DOI 10.1038/nbt.2432PMC PMC3879109

Open this paper in CoChat — free account

Abstract

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.

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

Crossref · 10.1038/nbt.2432

Cites

51 of 51 references verified0 citation errors · 0 not checkable

Statistics

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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
Pathogenic Escherichia coli
Kaper, J. B., Nataro, J. P., & Mobley, H. L. T. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro818 · Cited by 5,583
Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter
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

Flagged first, then by citations

Show all 51 references

Sorted by citations

Items 301–370 of 370

Genome‐Wide 6mA Map Unveils Epigenetic Adaptation in Deep‐Sea Limpet
Chen, C., Liu, J., Zhuang, R., Ni, K., Wang, M., Li, Y., Wang, J., Wang, S., Han, W., & Bao, L. (2026) · Ecology and Evolution · doi:10.1002/ece3.73449 · Cited by 1
Development of an Economic-trait Genetic Marker by Applying Next-generation Sequencing Technologies in a Whole Genome
Gim, J., & Kim, H. (2014) · Journal of Life Science · doi:10.5352/jls.2014.24.11.1258 · Cited by 3
Epigenetic Programming by Microbial Pathogens and Impacts on Acute and Chronic Disease
Mahan, M. J., Heithoff, D. M., Barnes, L., V, & Sinsheimer, R. L. (2017) · Epigenetics and human health · doi:10.1007/978-3-319-55021-3_5 · Cited by 1
Emerging Next-Generation Sequencing Technologies
Anderson, M. W. (2014) · Springer eBooks · doi:10.1007/978-1-4939-0727-4_2 · Cited by 1
A Hidden Markov Model for predicting the methylome of the DNA adenine methyltransferase in bacterial genome
Kasmi, Y., Eladdadi, A., Zeroual, Y., Touzani, A., & Kadmiri, I. M. (2022) · Gene Reports · doi:10.1016/j.genrep.2022.101633 · Cited by 1
Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine
Salava, H., Deák, T., Czepe, C., & Maghuly, F. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3778-4_12 · Cited by 1
Analysing microbial proteins: bioinformatic approaches for molecular structure and function characterization
Sarkar, S., Yadav, M., & Kumar, A. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-31550-3.00002-0 · Cited by 1
Genomic Approaches: an Effective Approach to Determine the Biosynthetic Genes in Actinobacteria
AbuHamdia, A., Riad, D. H., Shaheen, S. I., & Yusuf, W. S. (2025) · Proceedings of the National Academy of Sciences India Section B Biological Sciences · doi:10.1007/s40011-025-01706-8 · Cited by 1
Diversity in genome and epigenome of Helicobacter pylori
Furuta, Y. (2015) · Nippon Saikingaku Zasshi · doi:10.3412/jsb.70.383 · Cited by 1
FastFeatGen: Faster Parallel Feature Extraction from Genome Sequences and Efficient Prediction of DNA $$N^6$$-Methyladenine Sites
Rahman, M. K. (2020) · Lecture notes in computer science · doi:10.1007/978-3-030-46165-2_5 · Cited by 1
Deciphering the Role of Epigenetic Reprogramming in Host-Pathogen Interactions
Kang, A. K., Lynn, A. M., & Dhawan, U. (2021) · Springer eBooks · doi:10.1007/978-981-16-0691-5_3 · Cited by 1
Epigenetic regulatory potential at the metagenomic and genomic scale
Rambo, I. M. (2025) · Library, Museums and Press - UDSpace (University of Delaware) · doi:10.58088/d7ty-z214 · Cited by 1
DNA methylation epigenetically regulates gene expression in Burkholderia cenocepaciaPreprint
Vandenbussche, I., Sass, A. M., Pinto‐Carbó, M., Mannweiler, O., Eberl, L., & Coenye, T. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.21.960518 · Cited by 1
Methylation by multiple type I restriction modification systems avoids influencing gene regulation in uropathogenic Escherichia coliPreprint
Mehershahi, K. S., & Chen, S. L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.08.425850 · Cited by 1
Advances in DNA Detection
Song, Y. (2014) · KTH Publication Database DiVA (KTH Royal Institute of Technology) · Cited by 1
Using k-mer Embeddings Learned from a Skip-Gram Based Neural Network as Effective Feature Representation for Building a Cross-Species Prediction Model to Identify DNA N6-Methyladenine Sites in Plant GenomesPreprint
Nguyen, T., Trinh, V.-N., Le, N. Q. K., & Ou, Y. (2021) · Research Square · doi:10.21203/rs.3.rs-553304/v1 · Cited by 1
Community-wide epigenetics provides novel perspectives on the ecology and evolution of marine microbiomePreprint
Seong, H. J., Roux, S., Hwang, C. Y., & Sul, W. J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.30.470565 · Cited by 1
Complete Genome Sequence of Sphingobacterium sp. Strain CZ-2T Isolated from Tobacco Leaves Infected with Wildfire DiseasePreprint
Cai, X., Wang, R., Hu, S., Li, Y., Chen, T., He, J., Tan, S., & Zhou, W. (2019) · Research Square · doi:10.21203/rs.2.15235/v1 · Cited by 1
The streptococcal phase-variable Type I Restriction-Modification system SsuCC20p dictates the methylome of Streptococcus suis and impacts virulencePreprint
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) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.17.533248 · Cited by 1
Coupling DNA processing to early gene expression drives antibiotic resistance plasmid disseminationPreprint
Fraikin, N., Yamaichi, Y., & Lesterlin, C. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.09.698686 · Cited by 1
Next Generation Sequencing for Single-Gene Analysis
Ho, H. H., & Gocke, C. D. (2014) · Springer eBooks · doi:10.1007/978-1-4939-0727-4_14
Predictive Toxicology: Genetics, Genomics, Epigenetics, and Next‐Generation Sequencing in Toxicology
Heckel, T., & Suter‐Dick, L. (2014) · Methods and principles in medicinal chemistry · doi:10.1002/9783527674183.ch08
Playing the 'Next-Generation Game'
Seth-Smith, H. M. B. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro2956
Genomic Analysis Through High-Throughput Sequencing
Hadjithomas, M. (2015) · Springer eBooks · doi:10.1007/978-1-4939-3070-8_12
Measuring CpG Methylation by SMRT Sequencing
Suzuki, Y., Korlach, J., & Morishita, S. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-801596-4.00007-1
Electrophoretic capture of DNA into nanopore-zero-mode waveguides for efficient single-molecule sequencing
Larkin, J. (2015) · Digital Repository Service (Northeastern University) · doi:10.17760/d20200245
Fluorescence Spectroscopy for Cell Membrane Biophysics at the Nanometer and Nanosecond Scales
Rhodes, C. (2012) · eScholarship (California Digital Library)
Characterisation of Streptococcus pneumoniae opacity phase variation
Chai, M. H. C. (2017) · Adelaide Research & Scholarship (AR&S) (University of Adelaide) · doi:10.4225/55/58dc7eaca367a · Cited by 1
Epigenetic Memory via Concordant DNA Methylation is Inversely Correlated to Developmental Potential of Mammalian CellsPreprint
Choi, M., Genereux, D. P., Goodson, J. M., Al-Azzawi, H., Allain, S. Q., Simon, N., Palasek, S., Ware, C. B., Cavanaugh, C., Miller, D. G., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/072488
SMRT sequencing reveals differential patterns of methylation in two O111:H- Shiga toxigenic Escherichia coli isolates from a historic hemolytic uremic syndrome outbreak in AustraliaPreprint
Forde, B. M., McAllister, L. J., Paton, J. C., Paton, A. W., & Beatson, S. A. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/173336
Genomic Surveillance for Antimicrobial Resistance in Mannheimia haemolytica Using Nanopore Single Molecule Sequencing TechnologyPreprint
Lim, A., Naidenov, B., Bates, H., Willyerd, K. L., Snider, T. A., Couger, M. B., Chen, C., & Ramachandran, A. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/395087
『恋する女たち』または『精神性の女たち』(その1)
中村, 嘉. (1979) · Institutional Repositories DataBase (IRDB)
Diversification of the restriction–modification system of Streptococcus pyogenes through its acquisition of mobile elementsPreprint
Ota, A., Nishiuchi, Y., Nakanishi, N., Iijima, Y., Iwamoto, T., Osaki, K., Ogura, Y., Toyoda, A., Suzuki, Y., Hayashi, T., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.30.179317
The deaminase ADAL-pivoted catabolism checkpoint suppresses aberrant DNA N6-methyladenine incorporationPreprint
Chen, S., Lai, W., Zhao, Z., Zhang, N., Liú, Y., Li, X., Jiang, G., & Wang, H. (2021) · Research Square · doi:10.21203/rs.3.rs-374831/v1
『恋する女たち』または『精神性の女たち』(その2)
中村, 嘉. (1979) · 長崎大学教養部紀要人文科学篇
Determination of N6-Methyladenine in DNA of Mammals and Plants by Dpn I Digestion Combined with Size-Exclusion Ultrafiltration and Mass Spectrometry Analysis
Cheng, Q.-Y., & Yuan, B. (2021) · Springer protocols handbooks/Springer protocols · doi:10.1007/978-1-0716-1229-3_11
Bioengineering – Current Applications and Future Perspectives
Kirov, B., & Peykov, S. Z. (2021) · Proceedings of the Technical University of Sofia · doi:10.47978/tus.2021.71.04.003
Extraction and analysis of methylation features from Pacific Biosciences SMRT reads using MeStudioPreprint
Riccardi, C., Passeri, I., Cangioli, L., Fagorzi, C., Mengoni, A., & Fondi, M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.23.485463
Methylation and other Modifications of Nucleic Acids and Proteins☆
Zhang, J.-R., Marinus, M. G., & Deng, H. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.02448-x
Emerging Next-Generation Sequencing Technologies
Anderson, M. W. (2018) · Springer eBooks · doi:10.1007/978-3-319-96830-8_3
ACNN-6mA: Prediction of N6-Methyladenine Loci in Multiple Species Based on Rice Dataset Pre-training ModelPreprint
Bai, J., & Yang, H. (2022) · Research Square · doi:10.21203/rs.3.rs-2268401/v1
A metagenomics approach to identification of eukaryotes in metazoan-associated microbiomesPreprint
Crouch, A. L., Monsey, L., Ramos, C., & Anderson, M. Z. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.16.567323
An Effective Algorithm Based on Sequence and Property Information for N4-methylcytosine Identification in Multiple Species
Zhang, L., Wang, X., Xiao, K., & Kong, L. (2024) · Letters in Organic Chemistry · doi:10.2174/0115701786277281231228093405
Additional file 4 of NT-seq: a chemical-based sequencing method for genomic methylome profiling
Li, X., Guo, S., Cui, Y., Zhang, Z., Luo, X., Angelova, M. T., Landweber, L. F., Wang, Y., & Wu, T. (2022) · Figshare · doi:10.6084/m9.figshare.19933112
Additional file 6 of NT-seq: a chemical-based sequencing method for genomic methylome profiling
Li, X., Guo, S., Cui, Y., Zhang, Z., Luo, X., Angelova, M. T., Landweber, L. F., Wang, Y., & Wu, T. (2022) · Figshare · doi:10.6084/m9.figshare.19933118
Additional file 2 of NT-seq: a chemical-based sequencing method for genomic methylome profiling
Li, X., Guo, S., Cui, Y., Zhang, Z., Luo, X., Angelova, M. T., Landweber, L. F., Wang, Y., & Wu, T. (2022) · Figshare · doi:10.6084/m9.figshare.19933106
Additional file 3 of NT-seq: a chemical-based sequencing method for genomic methylome profiling
Li, X., Guo, S., Cui, Y., Zhang, Z., Luo, X., Angelova, M. T., Landweber, L. F., Wang, Y., & Wu, T. (2022) · Figshare · doi:10.6084/m9.figshare.19933109
Additional file 1 of StableDNAm: towards a stable and efficient model for predicting DNA methylation based on adaptive feature correction learning
Zhuo, L., Wang, R., Fu, X., & Yao, X. (2023) · Figshare · doi:10.6084/m9.figshare.24751223
Additional file 7 of NT-seq: a chemical-based sequencing method for genomic methylome profiling
Li, X., Guo, S., Cui, Y., Zhang, Z., Luo, X., Angelova, M. T., Landweber, L. F., Wang, Y., & Wu, T. (2022) · Figshare · doi:10.6084/m9.figshare.19933124
Additional file 5 of NT-seq: a chemical-based sequencing method for genomic methylome profiling
Li, X., Guo, S., Cui, Y., Zhang, Z., Luo, X., Angelova, M. T., Landweber, L. F., Wang, Y., & Wu, T. (2022) · Figshare · doi:10.6084/m9.figshare.19933115
Detection of DNA N6-Methyladenine Modification through SMRT-seq Features and Machine Learning Model
Guo, Y., Zhang, Y., Liu, X., He, P., Zeng, Y., & Dai, Q. (2024) · Current Bioinformatics · doi:10.2174/0115748936300671240523044154 · Cited by 1
Engineering and laboratory evolution of lactose-utilizing Pseudomonas putida strains
Saumaa, S., Ilmjärv, T., Popazova, I., Ets, L., Brauer, A., & Kivisaar, M. (2025) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2025.07.015
Advances in whole genome methylomic sequencing
Nordlund, J. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-26759-8.00030-8
Sequence-independent 6mA methyltransferases for epigenetic profiling and editing
Zhang, J., Zhang, Y., Diao, J., Liu, Y., & Gao, S. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.09.002 · Cited by 1
Additional file 2 of 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) · Figshare · doi:10.6084/m9.figshare.25195111
Additional file 1 of Femtomolar and locus-specific detection of N6-methyladenine in DNA by integrating double-hindered replication and nucleic acid-functionalized MB@Zr-MOF
Zheng, Q., Wang, T., Li, X., Qian, H., Bian, X., Li, X., Bai, H., Ding, S., & Yan, Y. (2021) · Figshare · doi:10.6084/m9.figshare.17140897
Additional file 1 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics
Seong, H. J., Roux, S., Hwang, C. Y., & Sul, W. J. (2022) · Figshare · doi:10.6084/m9.figshare.21220384
Additional file 1 of 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) · Figshare · doi:10.6084/m9.figshare.25194867
Additional file 1 of NT-seq: a chemical-based sequencing method for genomic methylome profiling
Li, X., Guo, S., Cui, Y., Zhang, Z., Luo, X., Angelova, M. T., Landweber, L. F., Wang, Y., & Wu, T. P. (2022) · Figshare · doi:10.6084/m9.figshare.19933103
Additional file 8 of NT-seq: a chemical-based sequencing method for genomic methylome profiling
Li, X., Guo, S., Cui, Y., Zhang, Z., Luo, X., Angelova, M. T., Landweber, L. F., Wang, Y., & Wu, T. P. (2022) · Figshare · doi:10.6084/m9.figshare.19933127
Next-Generation Sequence (NGS) Analysis: Current Trends, Techniques, and Applications
Narayanasamy, S., Kumar, U. V., Lakshmanan, S., & Uthandi, S. (2025) · Springer handbooks · doi:10.1007/978-3-031-81728-1_35
Host-Filtered Blood Nucleic Acids for Pathogen Detection: Shared Background, Sparse Signal, and Methodological Limits
Wang, Z., Chen, G., Yang, M., Wang, S., Fang, J., Shi, C., Gu, Y., & Ning, Z. (2026) · Pathogens · doi:10.3390/pathogens15010055
Long-read metagenomics and methylation-based binning allow the description of the emerging high-risk antibiotic resistance genes and their hidden hosts in complex communitiesPreprint
Markkanen, M. A., Putkuri, H., Kičiatovas, D., Mustonen, V., Virta, M., & Karkman, A. (2026) · medRxiv · doi:10.64898/2026.02.18.26346558
Etude de la méthylation de l'ADN chez la bactérie pathogène d'insectes Photorhabdus luminescens
Payelleville, A. (2018) · theses.fr (ABES) · doi:10.70675/e9c45763z861az4e61zbfcdzf5ec68e729e4
Identification and characterization of Polycomb repressed gene-enhancer loops
Souaid, C. (2019) · theses.fr (ABES) · doi:10.70675/ad8a4539z2325z46aazbc1fza812d4b02626
Molecular determinants of host adaptation in the plant pathogen Ralstonia solanacearum
Gopalan-Nair, R. (2020) · theses.fr (ABES) · doi:10.70675/f734aceez2507z448az8656z36d80de55b36
Yeast nuclei–mediated precise delivery of synthetic megabase-scale human DNA into mammalian embryos
Liu, Y., Zhou, J., Liu, Z., & Yuan, Y. (2026) · Nature Protocols · doi:10.1038/s41596-026-01374-6
A review on revolutionizing DNA sequence classification with machine learning and deep learning technique
Bavankumar, S., Rathikarani, V., & Santhoshkumar, R. (2026) · AIP conference proceedings · doi:10.1063/5.0330827
『恋する女たち』または『精神性の女たち』(その2)
中村, 嘉. (1979) · Institutional Repositories DataBase (IRDB)
Nanodisco: validation datasets
Tourancheau, A. (2024) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.14518354

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: Fang, Gang
Friedman, David I
Chao, Michael C
Feng, Zhixing
Losic, Bojan
Deikus, Gintaras
Clark, Tyson A
Murray, Iain A
Chess, Andrew
Roberts, Richard J
Korlach, Jonas
Turner, Steve W
Kumar, Vipin
Waldor, Matthew K
Schadt, Eric E
Venue: Nature Biotechnology
Publisher: Springer Science and Business Media LLC
Published: 2012-11-08
Volume: 30
Issue: 12
Pages: 1232-1239
ISSN: 0733-222X (ISSN-L)
1087-0156
1546-1696
DOI: 10.1038/nbt.2432
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
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks