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Features and development of Coot

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Overview of the CCP 4 suite and current developments

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KnowYourCG: Facilitating base-level sparse methylome interpretation

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The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation

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Interplay between circadian and other transcription factors—Implications for cycling transcriptome reprogramming

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Synergistic intragenic epigenetic deregulation by IDH2 and SRSF2 mutations causes mis-splicing of key transcriptional regulators

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Blood-based epigenetic instability linked to human aging and disease

Basrai, S., Nofech-Mozes, I., Detroja, R., Scolari, F. L., Bakhtiari, M., Arruda, A., Murphy, T., Bratman, S. V., Chan, S. M., Minden, M. D., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-69430-z · Cited by 4

The timing of antenatal glucocorticoids determines the receptor sensitivity in preterm infants

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Maternal probiotic and prebiotic supplementation on glucose metabolism in pregnant women and their offspring: effects and related mechanisms

Lin, H., Shao, C., Yu, J., Chen, H., Ren, Y., Ren, J., Zeng, Y., Wu, Y., Zhang, Q., & Xiao, X. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1782361 · Cited by 3

Single-cell profiling of DNA methylation in autism spectrum disorder prefrontal cortex reveals distinct regulatory and aging signatures

Eyring, K. W., Liu, C., Elhajjaoui, N., Abuhanna, K. D., Zhang, Y., von Behren, Z., Tsai, M. J., Eskin, E., Geschwind, D. H., & Luo, C. (2026) · Cell Genomics · doi:10.1016/j.xgen.2026.101278 · Cited by 6

DNA hypomethylation enables the transcriptional repressor SlSPL-CNR to control fruit flavor ester biosynthesis

Zeng, Z., Ma, Y., He, H., Li, L., Peng, Y., Hou, Y., Chai, S., Wang, P., Duan, C., Zhu, J., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-75181-8 · Cited by 3

DNA methylation in heart failure

Anene-Nzelu, C. G., Stenzig, J., & Foo, R. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822258-4.00016-x · Cited by 2

Age-Related Variation in DNA Methylation

Keith, K., Issa, J. J., & Panjarian, S. B. (2022) · Springer eBooks · doi:10.1007/978-3-030-94475-9_10 · Cited by 2

A hypothetical model of skewed DNA methylation balance in the enhancer regions containing differentially methylated cytosines associated with non-malignant complex diseases

Zheng, X., & Zhao, X. (2022) · Medical Hypotheses · doi:10.1016/j.mehy.2022.110950 · Cited by 2

Epigenomic mechanisms and episignature biomarkers in rare diseases

McConkey, H., & Sadiković, B. (2023) · Elsevier eBooks · doi:10.1016/b978-0-443-21863-7.00012-3 · Cited by 2

Identification of Molecular Mechanisms Responsible for the MMP-9-1562C/T Dependent Differential Regulation of Matrix Metalloproteinase-9 Expression in Human Neuron-like Cells

Pabian, S., Ambrożek-Latecka, M., Bragiel-Pieczonka, A. M., Nowicka, K., & Rylski, M. (2023) · Genes · doi:10.3390/genes14112028 · Cited by 2

Loss of DNA methylation disrupts syncytiotrophoblast development: Proposed consequences of aberrant germline gene activation

Lea, G., & Hanna, C. W. (2023) · BioEssays · doi:10.1002/bies.202300140 · Cited by 2

MORA and EnsembleTFpredictor: An ensemble approach to reveal functional transcription factor regulatory networks

Boyer, K., Li, L., Li, T., Zhang, B., & Zhao, G. (2023) · PLoS ONE · doi:10.1371/journal.pone.0294724 · Cited by 2

Transcriptional control of CCAAT/enhancer binding protein zeta gene in chicken adipose tissue

Gao, L., Wang, Y., Gao, Q., Chen, Y., & Zhang, Z. (2024) · Poultry Science · doi:10.1016/j.psj.2024.103540 · Cited by 2

Loci cg06256735 and cg15815843 in the MFAP5 gene regulatory regions are hypomethylated in varicose veins apparently due to active demethylation

Smetanina, M. A., Korolenya, V. A., Sipin, F. A., Oscorbin, I. P., Сергеевна, С. К., Gavrilov, K. A., Shevela, A. I., & Филипенко, М. Л. (2024) · Bioscience Reports · doi:10.1042/bsr20231938 · Cited by 2

A machine learning approach utilizing DNA methylation as a classifier for Pulmonary Tuberculosis screening

Le, N. T., Do, T. T. H., Duong, D. M. T., Tran, D. H. N., Huynh, T. Q., Huynh, K., Nguyen, P. T., Le, M. T., & Nguyen, T. T. H. (2024) · Gene Reports · doi:10.1016/j.genrep.2024.101939 · Cited by 2

A plant virus differentially alters DNA methylation in two cryptic species of a hemipteran vector

Catto, M. A., Ghosh, S., Pandey, S., Mondal, B., Simmons, A. M., Hunt, B. G., & Srinivasan, R. (2024) · npj Viruses · doi:10.1038/s44298-024-00044-2 · Cited by 2

DNA Methylation Negatively Regulates Gene Expression of Key Cytokines Secreted by BMMCs Recognizing FMDV-VLPs

Li, M., Ning, P., Bai, R., Tian, Z., Liu, S., & Li, L. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms251910849 · Cited by 2

CpG hypomethylation at proximal promoter and 5’UTR along with IL6 signaling loop associates with MYD88 upregulation in epithelial ovarian cancer

Li, J., Mei, B., Zhu, Y., Huang, J., Li, M., Wang, D., Huang, J., & Zhang, G. (2024) · Scientific Reports · doi:10.1038/s41598-024-81975-x · Cited by 2

Bisphenol A diglycidyl ether-induced DNA methylation abnormalities may disrupt testis development in adult male zebrafish

Lee, E. J., Lee, H., Kang, J., Kim, K., & Yang, Y.-J. (2025) · Environmental Analysis Health and Toxicology · doi:10.5620/eaht.2025s05 · Cited by 2

PAX3 Regulatory Signatures and Gene Targets in Melanoma Cells

Moore, S. P. G., Krishnan, S. G., Kothari, R. J., Prince, N. B., Kenny, C., Zhang, C., & Lang, D. (2025) · Genes · doi:10.3390/genes16050577 · Cited by 3

AMHY and sex determination in egg-laying mammals

Shearwin‐Whyatt, L., Fenelon, J. C., Yu, H., Major, A. T., Qu, Z., Zhou, Y., Shearwin, K. E., Galbraith, J. D., Stuart, A., Adelson, D. L., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03546-1 · Cited by 2

Chemical Control of Genes: Synthetic Genome Readers and Gene Regulators

Ansari, A. Z., Mohammed, A., Achari, A., Danda, A., Philips, S. J., Deane, C. D., & Kandikonda, S. (2025) · Chemical Reviews · doi:10.1021/acs.chemrev.5c00112 · Cited by 2

Building a bovine blood DNA methylation epimap related to disease phenotypes

Bouzeraa, L., Martin, H., Marques, J. C. S., Cerri, R. L. A., & Sirard, M. (2025) · BMC Genomics · doi:10.1186/s12864-025-12112-9 · Cited by 2

Epigenome-Wide Analysis of DNA Methylation in Colorectal Cancer

Mutalib, N. A., Baharuddin, R., & Jamal, R. (2019) · Computational Epigenetics and Diseases · doi:10.1016/b978-0-12-814513-5.00018-0 · Cited by 3

Methods in epigenetics-based systems biology and their applications

Jung, S., Ali, M., & del Sol, A. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-819414-0.00030-6 · Cited by 3

Prospects for Use of Single-Cell Sequencing to Assess DNA Methylation in Asthma

Men, S., & Yu, Y. (2020) · Medical Science Monitor · doi:10.12659/msm.925514 · Cited by 2

Targeting epigenetic alterations in the treatment of glioma

Okechukwu, C. E. (2021) · MGM Journal of Medical Sciences · doi:10.4103/mgmj.mgmj_3_21 · Cited by 2

Direct and Base Excision Repair-Mediated Regulation of a GC-Rich cis-Element in Response to 5-Formylcytosine and 5-Carboxycytosine

Müller, N., Ponkkonen, E., Carell, T., & Khobta, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222011025 · Cited by 2

Novel gross deletion at the LHX4 gene locus in a child with growth hormone deficiency

Samarasinghe, S. M., Sundralingam, T., Hewage, A. S., de Silva, K. S. H., & Tennekoon, K. H. (2021) · Growth Hormone & IGF Research · doi:10.1016/j.ghir.2021.101443 · Cited by 2

The X-factor in ART: does the use of assisted reproductive technologies influence DNA methylation on the X chromosome?

Romanowska, J., Nustad, H. E., Page, C. M., Denault, W. R. P., Bohlin, J., Magnus, M. C., Magnus, M. C., Gjerdevik, M., Novakovic, B., Saffery, R., et al. (2023) · Human Genomics · doi:10.1186/s40246-023-00484-6 · Cited by 3

Relative expression of key genes involved in nucleic acids methylation in Anopheles gambiae sensu stricto

Djihinto, O., Meacci, D., Medjigbodo, A. A., Bernardini, F., & Djogbénou, L. (2023) · Medical and Veterinary Entomology · doi:10.1111/mve.12681 · Cited by 2

The genomic landscape of mammal domestication might be orchestrated by selected transcription factors regulating brain and craniofacial development

Benítez‐Burraco, A., Uriagereka, J., & Nataf, S. (2023) · Development Genes and Evolution · doi:10.1007/s00427-023-00709-7 · Cited by 5

The transcription activity of OTX2 on p16 expression is significantly blocked by methylation of CpG shore in non-promoter of lung cancer cell lines

Peng, H., Fu, W., Chang, C. H., Gao, H., He, Q., Liu, Z., Cui, M., Wang, H., Yu, Y., Wu, Y., et al. (2023) · Translational Cancer Research · doi:10.21037/tcr-23-909 · Cited by 2

Predisposition to atrioventricular septal defects may be caused by SOX7 variants that impair interaction with GATA4

Li, B., Li, Z., Yang, J., Hong, N., Jin, L., Xu, Y., Fu, Q., Sun, K., Yu, Y., Lu, Y., et al. (2022) · Molecular Genetics and Genomics · doi:10.1007/s00438-022-01859-5 · Cited by 2

Zbtb24 binding protects promoter activity by antagonizing DNA methylation in mESCsPreprint

Wu, H., León, D. S., Vukić, M., Vonk, K. K. D., Breukel, C., Chouaref, J., Laros, J. F. J., & Daxinger, L. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/858662 · Cited by 2

Distinct Contribution of DNA Methylation and Histone Acetylation to the Genomic Occupancy of Transcription FactorsPreprint

Cusack, M., King, H. W., Spingardi, P., Kessler, B. M., Klose, R. J., & Kriaučionis, S. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/670307 · Cited by 2

The landscape of accessible chromatin in quiescent and post-myocardial infarction cardiac fibroblastsPreprint

Li, C., Sun, J., Liu, Q., Dodlapati, S., Ming, H., Wang, L., Li, Y., Li, R., Jiang, Z., Francis, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.03.433814 · Cited by 2

Emergence of an adaptive epigenetic cell state in human bladder urothelial carcinoma evolutionPreprint

Xiao, Y., Wan, J., Qian, K., Wu, K., Wang, G., Jiang, W. I., Cao, R., Ju, L., Zhao, Y., Zheng, H., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.30.466556 · Cited by 2

DNA co-methylation has a stable structure and is related to specific aspects of genome regulationPreprint

Watkins, S., Suderman, M. J., Hemani, G., Burrows, K., Lawlor, D. A., West, J., Willan, K., Timpson, N. J., Min, J. L., & Gaunt, T. R. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.16.484648 · Cited by 3

Two MADS-box transcription factors mediate epigenetic control of tomato fruit ripeningPreprint

Niu, Q., Xu, Y., Huang, H., Li, L., Tang, D., Wu, S., Liu, P., Liu, R., Ma, Y., Ni, J., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-2003863/v1 · Cited by 2

Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localizationPreprint

Nguyen, V. T. C., Nguyen, T. H., Doan, N. N. T., Pham, T. M. Q., Nguyen, G. T. H., Nguyen, T. D., Tran, T. T. T., Long, V. D., Phan, T. H., Jasmine, T. X., et al. (2023) · eLife · doi:10.7554/elife.89083.1 · Cited by 2

The pioneer transcription factor ELF2 remodels the nucleosome near transcription start sitesPreprint

Xiao, T., Crowe‐McAuliffe, C., Ochmann, M., Du, Y., Hou, T., Chen, Y., Zhu, F., Seyednasrollah, F. S., Osmala, M., Vanharanta, S., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.24.595749 · Cited by 2

Oncometabolite-driven enhancer hypermethylation promotes a hyporesponsive microglial state in IDH-mutant gliomasPreprint

Laurenge, A., Pugliese, P., Scuderi, S., Mathon, B., Drouiche, L., Richard, Q., Jouannet, S., Benmohamed, C., Smirnov, K., Sakr, L. H. D., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.23.608811 · Cited by 2

A Single-Cell Atlas of DNA Methylation in Autism Spectrum Disorder Reveals Distinct Regulatory and Aging SignaturesPreprint

Eyring, K. W., Liu, C., Elhajjaoui, N., Abuhanna, K. D., Zhang, Y., von Behren, Z., Eskin, E., Geschwind, D. H., & Luo, C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.17.660162 · Cited by 2

A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interestPreprint

Bates, A. D., Grzela, D. P., Studzian, M., Brennan, L., Williams, M., Fawcett, C. J., Hammond, B., Grewal, M., Ratajewski, M., Pułaski, Ł., et al. (2026) · Genome Research · doi:10.1101/gr.281154.125 · Cited by 2

Genetic and epigenetic control of life cycle transitions in the brown alga Ectocarpus sp.

Bourdareau, S. (2018) · theses.fr (ABES) · doi:10.70675/78884081zb539z4200z8bd7zc2774b41cca6 · Cited by 3

5-Methylcytosine and Its Oxidized Derivatives

Pfeifer, G. P. (2019) · Springer eBooks · doi:10.1007/978-981-13-8958-0_3 · Cited by 1

Hybridization-based CpG methylation level detection using methyl-CpG-binding domain–fused luciferase

Goto, A., & Yoshida, W. (2023) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-023-04657-z · Cited by 1

Aspirin Challenge–Induced Genome-Wide DNA Methylation Profile of Peripheral Blood Lymphocytes in Aspirin-Exacerbated Respiratory Disease

Lee, J.-U., Chang, H. S., Shim, J., Kim, M., Cho, Y.-J., Kim, M. K., Park, S.-L., Lee, S. J., Park, J., & Park, C. (2024) · DNA and Cell Biology · doi:10.1089/dna.2023.0218 · Cited by 1

Changes in hippocampal volume, synaptic plasticity and amylin sensitivity in an animal model of type 2 diabetes are associated with increased vulnerability to amyloid-beta in advancing age

Tarhan, M., Hartl, T., Shchyglo, O., Colitti-Klausnitzer, J., Kuhla, A., Breuer, T. M., & Manahan‐Vaughan, D. (2024) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2024.1373477 · Cited by 2

Multicenter study of OPRM1 A118G and promoter-region DNA methylation associations with opioid outcomes and chronic postsurgical pain after pediatric musculoskeletal surgery

Upton, B. A., Krolick, K. N., Zhang, X., Pilipenko, V. V., Martin, L. J., Ji, H., Glynn, S. M., Barnett, K., Ganesh, A., Monitto, C. L., et al. (2024) · PAIN Reports · doi:10.1097/pr9.0000000000001201 · Cited by 1

DNA methylation at birth and IgE trajectories from birth to adolescence, different patterns between White and Asian

Zhang, H., Duan, J., Han, L., Alam, N., Ray, M. A., Yang, F., Jiang, Y., Ewart, S., Holloway, J. W., Karmaus, W. J. J., et al. (2025) · Epigenomics · doi:10.1080/17501911.2025.2453412 · Cited by 1

Analysis of the Transcriptional Control of Bcl11b in Chicken: IRF1 and GATA1 as Negative Regulators

Qiu, L., Wang, H., Li, W., Yang, T., Bai, H., & Chang, G. (2025) · Animals · doi:10.3390/ani15050665 · Cited by 1

DNMT1 ‐Induced Downregulation of CBX7 Inhibits ERK Phosphorylation and Promotes Pancreatic Ductal Adenocarcinoma Progression

Shi, H., Liu, X., Cheng, X., Guo, S., Zheng, Y., Tan, W., Ge, Y., Xu, J., Li, Y., & Song, J. (2025) · The FASEB Journal · doi:10.1096/fj.202402903r · Cited by 1

The TET protein family interactor PROSER1 sustains hematopoietic stem cell function

Knatko, E. V., Fleming, A., Li, X., Crawley, P. E., Budriunaite, I., & Rasmussen, K. D. (2025) · Blood Advances · doi:10.1182/bloodadvances.2024015683 · Cited by 1

DNA methylation in normal-appearing tissue associated with prostate cancer recurrence and metastasis

Pedersen, C. A., Fleischer, T., Wess, M., Midtbust, E., Andersen, M. K., Viset, T., Størkersen, Ø., Rye, M. B., & Tessem, M. (2025) · Clinical Epigenetics · doi:10.1186/s13148-025-01932-x · Cited by 1

Transcription factor degraders

Wang, M., Wei, Y., & Ma, X. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-21816-3.00006-3 · Cited by 1

Aldehyde or Hydrate? Investigation into the Oxidation of 5‐Formylcytosine Derivatives Using a Computational and Experimental Approach

Liu, K., Menke, A., Zott, F. L., Mayer, D., Daumann, L. J., & Zipse, H. (2025) · ChemBioChem · doi:10.1002/cbic.202500480 · Cited by 1

Identification of blood-derived DNA methylation biomarkers of glaucoma and intraocular pressure measurements in three European ancestry cohorts including the Canadian longitudinal study on aging

Jiang, X., Mahroo, O. A., Khawaja, A. P., Skowronska‐Krawczyk, D., Mackey, D. A., Wiggs, J. L., Hammond, C. J., Hysi, P. G., & Bell, C. G. (2025) · Epigenetics · doi:10.1080/15592294.2025.2566496 · Cited by 1

TKI resistance related genes in LUAD predict patient prognosis and tumor immune microenvironment with LHX2 as a hub gene

Huang, R., Liang, Q., Wang, H., Qian, H., & Guo, R. (2025) · Discover Oncology · doi:10.1007/s12672-025-03959-1 · Cited by 1

Coordinated epigenetic dysregulation of CNR1 and FAAH genes drives endocannabinoid system dysfunction in anorexia nervosa

Gilardini, F., Mercante, F., Sabatucci, A., Pucci, M., Cifani, C., Segura‐Garcìa, C., Rania, M., & D’Addario, C. (2025) · Journal of Eating Disorders · doi:10.1186/s40337-025-01472-y · Cited by 1

Quantifying transcription factor specificity with advanced DNA universal microarrays featuring long and modified binding sites

Bayer, Y., O’Hagan, M., Miodownik, I., & Afek, A. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1382 · Cited by 1

Triphenyl phosphate induces coordinated DNA methylation and gene expression changes in aquatic embryonic cells

Germain, L., Ott, B. P., Hindmarch, C. C. T., & Winn, L. M. (2026) · Current Zoology · doi:10.1093/eep/dvag003 · Cited by 1

Systematic analysis of functional genetic and epigenetic variants in colorectal cancer

Chen, E., Yang, Q., Dai, H., Chen, Y., Zhang, Y., Wang, Q., Hou, R., Chen, M., Wang, J., Xie, Q., et al. (2026) · Science Advances · doi:10.1126/sciadv.aeb2473 · Cited by 1

Epigenetic dysregulation of IRF9 drives excessive interferon signaling in COPD

Prada, M. L., Schwartz, U., Pease, D. F., Pohl, S. T., Ackesson, D., Li, R., Behrendt, A., Tamas, R., Stammler, V., Richter, M., et al. (2026) · EMBO Molecular Medicine · doi:10.1038/s44321-026-00386-9 · Cited by 4

A Novel mechanism for depot-specific leptin gene expression regulation and its persistence after weight loss

Taege, N., Britsemmer, J. H., Israel, A., Krause, C., Junge, S., Feuchtinger, A., Ussar, S., Pfluger, P. T., Gemoll, T., Schriever, S. C., et al. (2026) · iScience · doi:10.1016/j.isci.2026.115101 · Cited by 1

PAX3: A Driver of Normal Development and Disease

Prince, N. B., Liang, J. H., Rosato, T. M., & Lang, D. (2026) · Biomolecules · doi:10.3390/biom16030450 · Cited by 1

Leveraging Auxiliary Potentials in RFDiffusion for the Design of NA-Binding Proteins

Geraseva, E., Bokov, G. V., Polovnikov, V., & Golovin, A. V. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c00109 · Cited by 1

Loss of DNA methyltransferase 3a enhances Caspase-8 transcription and promotes cardiomyocyte pyroptosis during myocardial infarction

Wang, N., Gong, L., Zhao, X., Zhao, W., Xu, N., Chen, X., Zhang, Q., Li, M., Yao, Y., Yu, H., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-71941-8 · Cited by 1

Miniaturized HOXB13 Mimetics Are Sequence-Specific, Methyl-Sensitive DNA Binders

Wong, C., & Chow, S. Y. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.6c01290 · Cited by 1

Cooperative care influences genome-wide levels of DNA methylation in nestling chestnut-crowned babblers

Liebl, A. L., Anderson, S., Russell, A. F., Wesner, J. S., & Petersen, J. L. (2026) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2025.0014 · Cited by 1

Long-read sequencing for epigenomic studies in the fields of ecology and evolution

de Carvalho, C. F., Ord, J., Escuer, P., Fox, J. A., Li‐Byarlay, H., Peck, L. D., Planidin, N. P., Venney, C. J., & Marshall, H. (2026) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2025.0099 · Cited by 1

Alpha-ketoglutarate ameliorates diabetes-associated skeletal muscle fibrosis by restoring TET2-dependent epigenetic remodeling in CD90 positive fibro-adipogenic progenitors

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