PreprintCited by 384Epigenetics and DNA MethylationGenetic Syndromes and ImprintingGenomics and Chromatin Dynamics

The DOI matches its Crossref record; 24 of the 25 references it cites were found in a registry or an index.

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

Open access

Shoemaker, Robert, Deng, Jie, Wang, Wei, Zhang, Kun·2010·Genome Research

DOI 10.1101/gr.104695.109PMC PMC2892089

Open this paper in CoChat — free account Open PDF

Abstract

In diploid mammalian genomes, parental alleles can exhibit different methylation patterns (allele-specific DNA methylation, ASM), which have been documented in a small number of cases except for the imprinted regions and X chromosomes in females. We carried out a chromosome-wide survey of ASM across 16 human pluripotent and adult cell lines using Illumina bisulfite sequencing. We applied the principle of linkage disequilibrium (LD) analysis to characterize the correlation of methylation between adjacent CpG sites on single DNA molecules, and also investigated the correlation between CpG methylation and single nucleotide polymorphisms (SNPs). We observed ASM on 23% approximately 37% heterozygous SNPs in any given cell line. ASM is often cell-type-specific. Furthermore, we found that a significant fraction (38%-88%) of ASM regions is dependent on the presence of heterozygous SNPs in CpG dinucleotides that disrupt their methylation potential. This study identified distinct types of ASM across many cell types and suggests a potential role for CpG-SNP in connecting genetic variation with the epigenome.

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 · 10.1101/gr.104695.109

Cites

24 of 24 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.

The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
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
SOAP2: an improved ultrafast tool for short read alignment
Li, R., Yu, C., Li, Y., Lam, T., Yiu, S., Kristiansen, K., & Wang, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp336 · Cited by 3,763
DNA methylation and human disease
Robertson, K. D. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1655 · Cited by 2,864
Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays
Drmanac, R., Sparks, A. B., Callow, M. J., Halpern, A. L., Burns, N. L., Kermani, B. G., Carnevali, P., Nazarenko, I., Nilsen, G. B., Yeung, G., et al. (2010) · Science · doi:10.1126/science.1181498 · Cited by 1,212
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
Doi, A., Park, I., Wen, B., Murakami, P. N., Aryee, M. J., Irizarry, R. A., Herb, B. R., Ladd‐Acosta, C., Rho, J., Loewer, S., et al. (2009) · Nature Genetics · doi:10.1038/ng.471 · Cited by 1,201
Glycosylation regulates Notch signalling
Haines, N., & Irvine, K. D. (2003) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1228 · Cited by 643
Allelic Variation in Human Gene Expression
Yan, H., Yuan, W., Velculescu, V. E., Vogelstein, B., & Kinzler, K. W. (2002) · Science · doi:10.1126/science.1072545 · Cited by 625
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming
Deng, J., Shoemaker, R., Xie, B., Gore, A., LeProust, E. M., Antosiewicz‐Bourget, J., Egli, D. M., Maherali, N., Park, I., Yu, J., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1530 · Cited by 502
Self-citation

Flagged first, then by citations

Show all 25 references

1 of the 25 references couldn’t be matched to a known paper.

Sorted by citations

Items 201–300 of 384

mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes
Ding, Y., Cai, K., Liu, L., Zhang, Z., Zheng, X., & Shi, J. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac650 · Cited by 15
SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing
Gao, S., Zou, D., Mao, L., Zhou, Q., Jia, W., Huang, Y., Zhao, S., Chen, G., Wu, S., Li, D., et al. (2015) · GigaScience · doi:10.1186/s13742-015-0070-9 · Cited by 14
CpG‐related SNPs in the MS4A region have a dose‐dependent effect on risk of late–onset Alzheimer disease
Ma, Y., Jun, G., Chung, J., Zhang, X., Kunkle, B. W., Naj, A. C., White, C. C., Bennett, D. A., Jager, P. L. D., Mayeux, R. P., et al. (2019) · Aging Cell · doi:10.1111/acel.12964 · Cited by 13
Characterization of Genome-Methylome Interactions in 22 Nuclear Pedigrees
Plongthongkum, N., van Eijk, K. R., de Jong, S., Wang, T., Sul, J. H., Boks, M. P., Kahn, R. S., Fung, H.-L., Ophoff, R. A., & Zhang, K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099313 · Cited by 16
Self-citation
Meta-Analysis of Genome-Wide Association Studies Identifies Novel Functional CpG-SNPs Associated with Bone Mineral Density at Lumbar Spine
Qiu, C., Shen, H., Fu, X., Xu, C., & Deng, H. (2018) · International Journal of Genomics · doi:10.1155/2018/6407257 · Cited by 14
Mapping methylation quantitative trait loci in cardiac tissues nominates risk loci and biological pathways in congenital heart disease
Li, M., Lyu, C., Huang, M., Do, C., Tycko, B., Lupo, P. J., MacLeod, S. L., Randolph, C. E., Liu, N., Witte, J. S., et al. (2021) · BMC Genomic Data · doi:10.1186/s12863-021-00975-2 · Cited by 14
Characterization and machine learning prediction of allele-specific DNA methylation
He, J., Sun, M.-A., Wang, Z., Wang, Q., Li, Q., & Xie, H. (2015) · Genomics · doi:10.1016/j.ygeno.2015.09.007 · Cited by 14
Genetic Determinants of Epigenetic Patterns: Providing Insight into Disease
Cazaly, E., Charlesworth, J., Dickinson, J. L., & Holloway, A. F. (2015) · Molecular Medicine · doi:10.2119/molmed.2015.00001 · Cited by 14
Genome-Wide Investigation of DNA Methylation Marks Associated with FV Leiden Mutation
Aïssi, D., Dennis, J. K., Ladouceur, M., Trương, V., Zwingerman, N., Rocañín-Arjó, A., Germain, M., Paton, T., Morange, P., Gagnon, F., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0108087 · Cited by 14
A CpG-SNP Located within the ARPC3 Gene Promoter Is Associated with Hypertriglyceridemia in Severely Obese Patients
de Toro‐Martín, J., Guénard, F., Tchernof, A., Deshaies, Y., Përusse, L., Biron, S., Lescelleur, O., Biertho, L. D., Marceau, S., & Vohl, M. (2016) · Annals of Nutrition and Metabolism · doi:10.1159/000445358 · Cited by 14
Dual Effects of a RETN Single Nucleotide Polymorphism (SNP) at –420 on Plasma Resistin: Genotype and DNA Methylation
Onuma, H., Tabara, Y., Kawamura, R., Ohashi, J., Nishida, W., Takata, Y., Ochi, M., Nishimiya, T., Ohyagi, Y., Kawamoto, R., et al. (2016) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2016-2417 · Cited by 14
Genetic variants within the second intron of the KCNQ1 gene affect CTCF binding and confer a risk of Beckwith–Wiedemann syndrome upon maternal transmission
Demars, J., Shmela, M. E., Khan, A. W., Lee, K. S., Azzi, S., Déhais, P., Netchine, I., Rossignol, S., Bouc, Y. L., El‐Osta, A., et al. (2014) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2014-102368 · Cited by 14
Familial resemblances in blood leukocyte DNA methylation levels
Tremblay, B. L., Guénard, F., Lamarche, B., Përusse, L., & Vohl, M. (2016) · Epigenetics · doi:10.1080/15592294.2016.1232234 · Cited by 13
The framework for population epigenetic study
Zhao, L., Liu, D., Xu, J., Wang, Z., Chen, Y., Lei, C., Li, Y., Liu, G., & Jiang, Y. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw098 · Cited by 13
Prediction of smoking by multiplex bisulfite PCR with long amplicons considering allele-specific effects on DNA methylation
Kondratyev, N. V., Golov, A. K., Алфимова, М. В., Лежейко, Т. В., & Голимбет, В. Е. (2018) · Clinical Epigenetics · doi:10.1186/s13148-018-0565-1 · Cited by 13
NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule
Fu, H., Zheng, H., Chen, X., Weirauch, M. T., Muglia, L. J., Wang, L., & Liu, Y. (2023) · Genome biology · doi:10.1186/s13059-023-02889-x · Cited by 12
Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer
Halabi, N. M., Martínez, A., Farsi, H. F. A., Mery-Lamarche, E., Puydenus, L., Pujol, P., Khalak, H. G., McLurcan, C., Ferron, G., Querleu, D., et al. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005755 · Cited by 13
A genome-wide analysis of DNA methylation identifies a novel association signal for Lp(a) concentrations in the LPA promoter
Coassin, S., Hermann‐Kleiter, N., Haun, M., Wahl, S., Wilson, R., Paulweber, B., Kunze, S., Meitinger, T., Strauch, K., Peters, A., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0232073 · Cited by 13
Interferon-Gamma DNA Methylation Is Affected by Mycophenolic Acid but Not by Tacrolimus after T-Cell Activation
Peters, F. S., Peeters, A. M. A., Hofland, L. J., Betjes, M. G. H., Boer, K., & Baan, C. C. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00822 · Cited by 13
Variation within the non-coding genome influences genetic and epigenetic regulation of the human leukocyte antigen genes
Arumugam, T., Adimulam, T., Gokul, A., & Ramsuran, V. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1422834 · Cited by 13
MeSiC: A Model-Based Method for Estimating 5 mC Levels at Single-CpG Resolution from MeDIP-seq
Xiao, Y., Yu, F., Pang, L., Zhao, H., Liu, L., Zhang, G., Liu, T., Zhang, H., Fan, H., Zhang, Y., et al. (2015) · Scientific Reports · doi:10.1038/srep14699 · Cited by 12
The DNA methylation haplotype (mHap) format and mHapTools
Zhang, Z., Dan, Y., Xu, Y., Zhang, J., Zheng, X., & Shi, J. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab458 · Cited by 13
Integrating whole genome sequencing, methylation, gene expression, topologically associated domain information in regulatory mutation prediction: A study of follicular lymphoma
Farooq, A., Trøen, G., Delabie, J., & Wang, J. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.03.023 · Cited by 11
Bioinformatics Tools for Discovery and Functional Analysis of Single Nucleotide Polymorphisms
Li, L., & Wei, D. (2014) · Advances in experimental medicine and biology · doi:10.1007/978-94-017-9245-5_17 · Cited by 11
Functional Genomics- and Network-driven Systems Biology Approaches for Pharmacogenomics and Toxicogenomics
Yang, X., Zhang, B., & Zhu, J. (2012) · Current Drug Metabolism · doi:10.2174/138920012802138633 · Cited by 11
Deconvolution of the Genomic and Epigenomic Interaction Landscape of Triple-Negative Breast Cancer
Wu, J., Mamidi, T. K. K., Zhang, L., & Hicks, C. (2019) · Cancers · doi:10.3390/cancers11111692 · Cited by 11
Allele-specific RNAN6-methyladenosine modifications reveal functional genetic variants in human tissuesPreprint
Cao, S., Zhu, H., Cui, J. J., Liu, S., Li, Y., Shi, J., Mo, J., Wang, Z., Wang, H., Hu, J., et al. (2023) · Genome Research · doi:10.1101/gr.277704.123 · Cited by 11
Methylation of Immune-Related Genes in Peripheral Blood Leukocytes and Breast Cancer
Tian, T., Fu, J., Li, D., Liu, Y., Sun, H., Wang, X., Zhang, X., Zhang, D., Zheng, T., Zhao, Y., et al. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.817565 · Cited by 10
DNA Methylation in Honey Bees and the Unresolved Questions in Insect Methylomics
Wedd, L., Kucharski, R., & Maleszka, R. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-11454-0_7 · Cited by 10
Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model
Wang, F., Zhang, S., Wen, Y., Wei, Y., Yan, H., Liu, H., Su, J., Zhang, Y., & Che, J. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbt076 · Cited by 10
epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data
Vincent, M., Mundbjerg, K., Pedersen, J. S., Liang, G., Jones, P. A., Orntoft, T. F., Sørensen, K. D., & Wiuf, C. (2017) · Genome biology · doi:10.1186/s13059-017-1168-4 · Cited by 10
Association of two synonymous splicing-associated CpG single nucleotide polymorphisms in calpain 10 and solute carrier family 2 member 2 with type 2 diabetes
Karambataki, M., Malousi, A., Tzimagiorgis, G., Haitoglou, C., Fragou, A., Georgiou, E., Papadopoulou, F., Krassas, G. E., & Kouidou, S. (2016) · Biomedical Reports · doi:10.3892/br.2016.833 · Cited by 10
Emerging Advances in Computational Omics Tools for Systems Analysis of Gramineae Family Grass Species and Their Abiotic Stress Responsive Functions
Muthuramalingam, P., Jeyasri, R., Dhamodharan, K., Pandian, S., Krishnan, S. R., Krishnan, S. R., Satish, L., Satish, L., Satish, L., Pandian, S. K., et al. (2019) · doi:10.1002/9781119509967.ch10 · Cited by 10
Common epigenetic variation in a European population of mentally healthy young adults
Milnik, A., Vogler, C., Demougin, P., Egli, T., Freytag, V., Hartmann, F., Heck, A., Peter, F., Spalek, K., Steták, A., et al. (2016) · Journal of Psychiatric Research · doi:10.1016/j.jpsychires.2016.08.012 · Cited by 9
Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome
Welsh, L., Maleszka, R., & Forêt, S. (2017) · Royal Society Open Science · doi:10.1098/rsos.170248 · Cited by 10
Causal modeling in a multi-omic setting: insights from GAW20
Auerbach, J., Howey, R. A. J., Jiang, L., Justice, A. E., Li, L., Oualkacha, K., Sayols-Baixeras, S., & Aslibekyan, S. W. (2018) · BMC Genetics · doi:10.1186/s12863-018-0645-4 · Cited by 9
Mediators and dynamics of DNA methylation
Shoemaker, R., Wang, W. T., & Zhang, K. (2010) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.124 · Cited by 9
Self-citation
MIRA-SNuPE, a quantitative, multiplex method for measuring allele-specific DNA methylation
Lee, D., Tran, D. A., Singh, P., Oates, N., Rivas, G. E., Larson, G. P., Pfeifer, G. P., & Szabó, P. E. (2011) · Epigenetics · doi:10.4161/epi.6.2.13699 · Cited by 8
Bioinformatics and Translation Elongation
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-032-18842-7_11 · Cited by 9
Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant
Correia, L., Magno, R., Xavier, J., de Almeida, B. P., Duarte, I., Esteves, F., Ghezzo, M. N., Eldridge, M., Sun, C., Bosma, A., et al. (2021) · npj Breast Cancer · doi:10.1038/s41523-022-00435-9 · Cited by 9
Putting the ‘epi’ into epigenetics research in psychiatry
El‐Sayed, A. M., Koenen, K. C., & Galea, S. (2013) · Journal of Epidemiology & Community Health · doi:10.1136/jech-2013-202430 · Cited by 8
Analyzing the Effects of Genetic Variation in Noncoding Genomic Regions
Mansur, Y. A., Rojano, E., Ranea, J. A. G., & Perkins, J. R. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-805364-5.00007-x · Cited by 9
Advancement in Sustainable Agriculture: Computational and Bioinformatics Tools
Parray, J. A., Mir, M. Y., & Shameem, N. (2019) · Springer eBooks · doi:10.1007/978-981-13-8840-8_10 · Cited by 8
Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichmentPreprint
Yan, B., Wang, D., Vaisvila, R., Sun, Z., & Ettwiller, L. M. (2022) · Genome Research · doi:10.1101/gr.277080.122 · Cited by 8
The effect of type 1 diabetes protection and susceptibility associated HLA class II genotypes on DNA methylation in immune cells
Pahkuri, S., Katayama, S., Valta, M., Nygård, L., Knip, M., Kere, J., Ilonen, J., & Lempainen, J. (2024) · HLA · doi:10.1111/tan.15548 · Cited by 8
Promoter Methylation of QKI as a Potential Specific Biomarker for Early Detection of Colorectal Cancer
Zhang, L., Li, D., Gao, L., Fu, J., Sun, S., Huang, H., Zhang, D., Jia, C., Zheng, T., Cui, B., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.928150 · Cited by 7
Integration of Genomic and Epigenomic DNA Methylation Data in Common Complex Diseases by Haplotype-Specific Methylation Analysis
Bell, C. G. (2011) · Personalized Medicine · doi:10.2217/pme.11.14 · Cited by 7
Integrating genomic and epigenomic information: a promising strategy for identifying functional DNA variants of human disease
Zaina, S., & Lund, G. (2012) · Clinical Genetics · doi:10.1111/j.1399-0004.2011.01840.x · Cited by 7
Distance-Based Phylogenetic Methods
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-319-90684-3_15 · Cited by 7
A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patternsPreprint
Feng, Y., Zhang, Z., Hong, Y., Ding, Y., Liu, L., Gao, S., Fang, H., & Shi, J. (2023) · Genome Research · doi:10.1101/gr.278146.123 · Cited by 7
Profiling haplotype specific CpG and CpH methylation within a schizophrenia GWAS locus on chromosome 14 in schizophrenia and healthy subjects
Алфимова, М. В., Kondratyev, N. V., Golov, A. K., & Голимбет, В. Е. (2020) · Scientific Reports · doi:10.1038/s41598-020-61671-2 · Cited by 6
Role of Bioinformatics in Drug Design and Discovery
Patel, P. H., JHA, A. N., & Chakraborthy, G. S. (2023) · Interdisciplinary biotechnological advances · doi:10.1007/978-981-99-1316-9_1 · Cited by 6
Programming of DNA methylation in type 2 diabetes
Simmons, R. A. (2013) · Diabetologia · doi:10.1007/s00125-013-2866-4 · Cited by 6
SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data
Steyaert, S., Criekinge, W. V., Paepe, A. D., Denil, S. L. I. J., Mensaert, K., Vandepitte, K., Berghe, W. V., Trooskens, G., & Meyer, T. D. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku847 · Cited by 6
Quantitative Trait Loci Identify Functional Noncoding Variation in Cancer
Heyn, H. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005826 · Cited by 6
Polymorphisms in JAK2 Gene are Associated with Production Traits and Mastitis Resistance in Dairy Cattle
Ali, N., Niaz, S., Khan, N. U., Gohar, A., Khattak, I., Dong, Y., Khattak, T., Ahmad, I., Wang, Y., & Usman, Τ. (2019) · Annals of Animal Science · doi:10.2478/aoas-2019-0082 · Cited by 6
Relationship between Alzheimer's disease-associated SNPs within the CLU gene, local DNA methylation and episodic verbal memory in healthy and schizophrenia subjects
Алфимова, М. В., Kondratyev, N. V., Golov, A. K., & Голимбет, В. Е. (2018) · Psychiatry Research · doi:10.1016/j.psychres.2018.12.134 · Cited by 6
Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensationPreprint
Metzger, D. C. H., Porter, I., Mobley, B., Sandkam, B. A., Fong, L. J. M., Anderson, A. P., & Mank, J. E. (2023) · Genome Research · doi:10.1101/gr.278127.123 · Cited by 9
Investigating the potential of single-cell DNA methylation data to detect allele-specific methylation and imprinting
Johnson, N. D., Cutler, D. J., & Conneely, K. N. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.02.009 · Cited by 5
Intergenerational association of DNA methylation between parents and offspring
Jiang, Y., Zhang, H., Chen, S., Ewart, S., Holloway, J. W., Arshad, S. H., & Karmaus, W. (2024) · Scientific Reports · doi:10.1038/s41598-024-69317-3 · Cited by 5
Rare genetic variants underlie outlying levels of DNA methylation and gene-expression
Chundru, V. K., Marioni, R. E., Prendergast, J. G. D., Lin, T., Beveridge, A. J., Martin, N. G., Montgomery, G. W., Hume, D. A., Deary, I. J., Visscher, P. M., et al. (2023) · Human Molecular Genetics · doi:10.1093/hmg/ddad028 · Cited by 5
Nucleotide Substitution Models and Evolutionary Distances
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-319-90684-3_12 · Cited by 5
CTCF-Mediated Genome Architecture Regulates the Dosage of Mitotically Stable Mono-allelic Expression of Autosomal Genes
Chandradoss, K. R., Chawla, B., Dhuppar, S., Nayak, R., Ramachandran, R., Kurukuti, S., Mazumder, A., & Sandhu, K. S. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108302 · Cited by 5
Illumina HumanMethylation BeadChip for Genome-Wide DNA Methylation Profiling: Advantages and Limitations
Nakabayashi, K. (2017) · Springer eBooks · doi:10.1007/978-3-319-31143-2_89-1 · Cited by 5
Examining the Impact of Imputation Errors on Fine-Mapping Using DNA Methylation QTL as a Model Trait
Chundru, V. K., Marioni, R. E., Prendergast, J. G. D., Vallerga, C. L., Lin, T., Beveridge, A. J., Gratten, J., Hume, D. A., Deary, I. J., Wray, N. R., et al. (2019) · Genetics · doi:10.1534/genetics.118.301861 · Cited by 6
pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions
Chung, R., & Kang, C.-Y. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz635 · Cited by 5
Genomic region detection via Spatial Convex Clustering
Nagorski, J., & Allen, G. I. (2018) · PLoS ONE · doi:10.1371/journal.pone.0203007 · Cited by 5
Forensic applications of compound genetic markers: trends and future directions
Shabalala, S., Ismail, N., & Ghai, M. (2025) · Science & Justice · doi:10.1016/j.scijus.2025.101301 · Cited by 5
Regulation of glutamate transport and neuroinflammation in a term newborn rat model of hypoxic–ischaemic brain injury
Pregnolato, S., Sabir, H., Luyt, K., Rienecker, K. D. A., Isles, A. R., & Chakkarapani, E. (2022) · Brain and Neuroscience Advances · doi:10.1177/23982128221097568 · Cited by 4
Epigenetic structure and the role of polymorphism in the shaping of DNA methylation patterns of equine OAS1 locus
Ząbek, T., Semik, E., Wnuk, M., Fornal, A., Gurgul, A., & Bugno‐Poniewierska, M. (2014) · Journal of Applied Genetics · doi:10.1007/s13353-014-0244-7 · Cited by 4
A Statistical Method for Observing Personal Diploid Methylomes and Transcriptomes with Single-Molecule Real-Time Sequencing
Suzuki, Y., Wang, Y., Au, K. F., & Morishita, S. (2018) · Genes · doi:10.3390/genes9090460 · Cited by 4
Epigenetic marks in suicide: a review
Ramos-Rosales, D. F., Vázquez-Alaníz, F., Urtiz-Estrada, N., Ramirez-Valles, E. G., Méndez-Hernández, E. M., Salas-Leal, A. C., & Barraza-Salas, M. (2021) · Psychiatric Genetics · doi:10.1097/ypg.0000000000000297 · Cited by 5
Epigenetic regulation of monoallelic gene expression
Shiba, H., & Takayama, S. (2012) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2011.01317.x · Cited by 4
Epigenetics of Psychopathology
Smith, A. K., Parets, S. E., & Kim, A. W. (2014) · Springer eBooks · doi:10.1007/978-1-4614-9509-3_10 · Cited by 4
Directional X Chromosome Skewing of White Blood Cells from Subjects with Heterozygous Mosaicism for the Variant IRAK1 Haplotype
Morcillo, P., Qin, Y., Peña, G., Mosenthal, A. C., Livingston, D. H., & Spolarics, Z. (2019) · Inflammation · doi:10.1007/s10753-019-01127-6 · Cited by 4
Simultaneous profiling of DNA methylation and chromatin architecture in mixed populations and in single cellsPreprint
Li, G., Liu, Y., Zhang, Y., Fang, R., Kellis, M., & Ren, B. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/470963 · Cited by 4
Genetic/epigenetic DNA markers for linking suspects and tissues in complex crime scenes
Mizrachi, R., Neiman, D., Rosenski, J., Loyfer, N., Share, D., Adjedj, C., Gläser, B., Shpitzen, M., Dor, Y., Shemer, R., et al. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf395 · Cited by 4
Expanding Upon Genomics in Rare Diseases: Epigenomic Insights
Tan, J. W., Blake, E. J., Farris, J. D., & Klee, E. W. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms26010135 · Cited by 3
Epigenomic Factors in Human Obesity
Bell, C. G. (2012) · Elsevier eBooks · doi:10.1016/b978-0-12-388415-2.00014-7 · Cited by 3
Genomic Features: Content Sensors, Nucleotide Skew Plot, Strand Asymmetry, and DNA Methylation
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-319-90684-3_11 · Cited by 3
Bioinformatics and Translation Initiation
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-032-18842-7_10 · Cited by 3
Different Methylation of CpG-SNPs in Behcet’s Disease
Huang, Y., Tan, H., Cao, Q., Yuan, G., Su, G., & Yang, P. (2019) · BioMed Research International · doi:10.1155/2019/3489305 · Cited by 3
Mapping eQTL by leveraging multiple tissues and DNA methylation
Acharya, C. R., Owzar, K., & Allen, A. S. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1856-9 · Cited by 3
Elucidation of the Genomic‐Epigenomic Interaction Landscape of Aggressive Prostate Cancer
Mamidi, T. K. K., Wu, J., & Hicks, C. (2021) · BioMed Research International · doi:10.1155/2021/6641429 · Cited by 3
Pharmaco-epigenetics: Histone modification and personalized medicine
Sabi, S. H., Qnais, E. Y. A., Tall, Y. R. A., Almaaytah, A. M., & Masaadeh, M. M. (2023) · Pharmacia · doi:10.3897/pharmacia.70.e104097 · Cited by 3
Epigenome-Wide Association Studies: Potential Insights into Human Disease
Bell, C. G. (2013) · Springer eBooks · doi:10.1007/978-1-4614-8078-5_13 · Cited by 3
Illumina HumanMethylation BeadChip for Genome-Wide DNA Methylation Profiling: Advantages and Limitations
Nakabayashi, K. (2019) · Springer eBooks · doi:10.1007/978-3-319-55530-0_89 · Cited by 3
Protein Isoelectric Point and Helicobacter pylori
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-032-18842-7_14 · Cited by 3
Investigation of DNA variants specific to ROBO2 Isoform ‘a’ in Irish vesicoureteric reflux patients reveals marked CpG island variation
Darlow, J. M., Dobson, M. G., Green, A., Puri, P., & Barton, D. E. (2020) · Scientific Reports · doi:10.1038/s41598-020-58818-6 · Cited by 3
Noninvasive Lung Cancer Early Detection via Deep Methylation Representation Learning
Cai, X., Tao, J., Wang, S., Wang, Z., Wang, J., Li, M., Wang, H., Tu, X., Yang, H., Fan, J., et al. (2022) · Proceedings of the AAAI Conference on Artificial Intelligence · doi:10.1609/aaai.v36i11.21439 · 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
Analysis of Allele‐Specific Expression
Li, Y., Chen, A., & Liu, Z. (2017) · Wiley eBooks · doi:10.1002/9781118782392.ch14 · 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
DNA co-methylation networks outline the structure and remodeling dynamics of colorectal cancer epigenomePreprint
Mallona, I., Aussó, S., Díez-Villanueva, A., Moreno, V. R., & Peinado, M. A. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/428730 · Cited by 3
Sequencing-based methods for single-cell multi-omics studies
Qin, S., Liu, S., & Weng, X. (2023) · Science China Chemistry · doi:10.1007/s11426-023-1793-7 · Cited by 2
Defining bovine CpG epigenetic diversity by analyzing RRBS data from sperm of Montbéliarde and Holstein bulls
Capra, E., Lazzari, B., Cozzi, P., Turri, F., Negrini, R., Ajmone‐Marsan, P., & Stella, A. (2025) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2025.1532711 · Cited by 2
Integrating plasticity into conservation practice: Harnessing genetic estimates of epigenetic potential to study phenotypic plasticity in wild populations
Sheldon, E. L., Martin, L. B., & Schrey, A. W. (2025) · Journal of Applied Ecology · doi:10.1111/1365-2664.70019 · Cited by 2
The interaction between a leflunomide-response methylation site (cg17330251) and variant (rs705379) on response to leflunomide in patients with rheumatoid arthritis
Zhao, F., Chen, Y., Liu, H., Jin, L., Feng, X., Dai, B., Chen, M., Wang, Q., Yao, Y., Liao, R., et al. (2025) · Frontiers in Pharmacology · doi:10.3389/fphar.2025.1499723 · Cited by 2
Integrative Omics Analysis Reveals the Regulation of Hypoxia Tolerance in Large Yellow Croaker ( Larimichthys crocea ) via the Lipoic Acid Synthase ( lias ) Gene
Ding, J., Jia, S., Meng, R., Wang, X., Wu, X., Weiliang, S. H. E. N., ZHANG, Y., & Zhu, J. (2026) · Advanced Science · doi:10.1002/advs.76310 · Cited by 2
Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock Probes
Diep, D. H., Plongthongkum, N., & Zhang, K. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7481-8_19 · Cited by 2
Self-citation

Authors: Shoemaker, R., Deng, J., Wang, W., & Zhang, K.
Affiliations: University of California San Diego (US)
ORCID: Deng, Jie
Wang, Wei
Zhang, Kun
Venue: Genome Research
Publisher: Cold Spring Harbor Laboratory
Published: 2010-04-23
Volume: 20
Issue: 7
Pages: 883-889
ISSN: 1088-9051 (ISSN-L)
DOI: 10.1101/gr.104695.109
PMC: PMC2892089
OpenAlex: W2155471840
Cited by: 380
References: 25
Citations by year: 2026: 7 · 2025: 15 · 2024: 13 · 2023: 14 · 2022: 22 · 2021: 17 · 2020: 16 · 2019: 23 · 2018: 29 · 2017: 33 · 2016: 31 · 2015: 43 · 2014: 33 · 2013: 25 · 2012: 30
Type: posted content
Language: en
Open access: bronze
doi.org
Locations: Genome Research (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: National Institutes of Health
University of California, San Diego
National Institute on Drug Abuse (R01DA025779)
National Institute of General Medical Sciences (R01GM072856)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords: allele-specific methylation, DNA methylation, heterozygous SNPs, linkage disequilibrium, cell type-specific methylation, epigenome, genetic variation, human genome
MeSH terms: Adult, Alleles, Base Sequence, Cell Line, DNA Mutational Analysis, Female, Gene Frequency, Humans, Linkage Disequilibrium, Genome, Human, CpG Islands, DNA Methylation, Polymorphism, Single Nucleotide

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

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

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