{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T10:53:52Z","timestamp":1772448832773,"version":"3.50.1"},"reference-count":80,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T00:00:00Z","timestamp":1772409600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF-III2246796"],"award-info":[{"award-number":["NSF-III2246796"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF-III2152030"],"award-info":[{"award-number":["NSF-III2152030"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Understanding how the 3D structure of the genome influences gene regulation is a growing area of interest, particularly in the context of alternative post-transcriptional regulatory events such as alternative splicing (AS) and alternative polyadenylation (APA). These processes are essential for generating transcript and protein diversity, and they are tightly coordinated with transcription. However, despite their biological importance, the relationship between chromatin interactions and alternative pre-messenger RNA regulation remains poorly understood. This gap largely stems from a lack of computational tools capable of integrating structural genomic data with RNA processing dynamics. Exploring how chromatin interactions and epigenetic landscapes shape these events is essential for uncovering the multilayered regulation of gene expression. To bridge this gap, we present EpGAT, a graph attention network-based model that integrates epigenetic read coverage and chromatin interaction data to predict and quantify AS and APA events. By explicitly modeling the spatial organization of the genome, EpGAT captures the regulatory influence of chromatin looping and long-range genomic interactions on RNA processing. The model\u2019s predictions are validated through rigorous cross-cell line and cross-chromosome evaluations, affirming its generalizability and reliability. Beyond prediction, EpGAT offers interpretability by tracing learned parameters back to genomic features, enabling the identification of active enhancers, mapping promoter\u2013enhancer connectivity, and pinpointing the epigenetic factors most critical to specific RNA processing events. These capabilities make EpGAT a powerful tool for dissecting the complex interplay between genome architecture and transcriptomic regulation. More broadly, it provides a generalizable framework for multiple tasks to study the link between 3D genome organization, epigenetic signals, and RNA processing.<\/jats:p>","DOI":"10.1093\/bib\/bbag091","type":"journal-article","created":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T12:43:35Z","timestamp":1770813815000},"source":"Crossref","is-referenced-by-count":0,"title":["EpGAT: integrating epigenetics and 3D genome structure to predict alternative splicing and polyadenylation"],"prefix":"10.1093","volume":"27","author":[{"given":"Sudipto","family":"Baul","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Central Florida , 4328 Scorpius Street, Orlando, FL 32816 ,","place":["United States"]}]},{"given":"Naima","family":"Ahmed Fahmi","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Central Florida , 4328 Scorpius Street, Orlando, FL 32816 ,","place":["United States"]}]},{"given":"Guangyu","family":"Wang","sequence":"additional","affiliation":[{"name":"Houston Methodist Research Institute, Weill Cornell Medical College , 1840 Dynamic Wy, Houston, TX 77030 ,","place":["United States"]}]},{"given":"Hao","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, University of Central Florida , 4328 Scorpius Street, Orlando, FL 32816 ,","place":["United States"]}]},{"given":"Ahmed","family":"Louri","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, George Washington University , 800 22nd Street NW, Washington, DC 20052 ,","place":["United States"]}]},{"given":"Jeongsik","family":"Yong","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities , 420 Washington Ave SE, Minneapolis, MN 55455 ,","place":["United States"]}]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Central Florida , 4328 Scorpius Street, Orlando, FL 32816 ,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2026,3,2]]},"reference":[{"key":"2026030204572592400_ref1","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1016\/j.molcel.2013.02.011","article-title":"The hierarchy of the 3D genome","volume":"49","author":"Gibcus","year":"2013","journal-title":"Mol Cell"},{"key":"2026030204572592400_ref2","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1038\/s41576-018-0060-8","article-title":"Organizational principles of 3D genome architecture","volume":"19","author":"Jordan Rowley","year":"2018","journal-title":"Nat Rev Genet"},{"key":"2026030204572592400_ref3","doi-asserted-by":"publisher","first-page":"3027","DOI":"10.1101\/gad.1604607","article-title":"Dynamics and interplay of nuclear architecture, genome organization, and gene expression","volume":"21","author":"Schneider","year":"2007","journal-title":"Genes Dev"},{"key":"2026030204572592400_ref4","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1038\/nrm.2016.116","article-title":"Alternative polyadenylation of mRNA precursors","volume":"18","author":"Tian","year":"2017","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2026030204572592400_ref5","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1038\/ng0102-13","article-title":"A genomic view of alternative splicing","volume":"30","author":"Modrek","year":"2002","journal-title":"Nat Genet"},{"key":"2026030204572592400_ref6","doi-asserted-by":"crossref","DOI":"10.1038\/s12276-025-01496-z","article-title":"Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation","volume":"57","author":"Fahmi","year":"2025","journal-title":"Exp Mol Med"},{"key":"2026030204572592400_ref7","doi-asserted-by":"crossref","first-page":"201","DOI":"10.5483\/BMBRep.2017.50.4.019","article-title":"Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies","volume":"50","author":"Yeh","year":"2017","journal-title":"BMB Rep"},{"key":"2026030204572592400_ref8","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.cell.2012.02.018","article-title":"Coding region polyadenylation generates a truncated tRNA synthetase that counters translation repression","volume":"149","author":"Yao","year":"2012","journal-title":"Cell"},{"key":"2026030204572592400_ref9","doi-asserted-by":"publisher","first-page":"e46","DOI":"10.1371\/journal.pgen.0020046","article-title":"Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units","volume":"2","author":"Davis","year":"2006","journal-title":"PLoS Genet"},{"key":"2026030204572592400_ref10","doi-asserted-by":"crossref","first-page":"e1013668","DOI":"10.1371\/journal.pcbi.1013668","article-title":"IPScan: detecting novel intronic PolyAdenylation events with RNA-seq data","volume":"21","author":"Fahmi","year":"2025","journal-title":"PLoS Comput Biol"},{"key":"2026030204572592400_ref11","doi-asserted-by":"publisher","DOI":"10.3390\/ijms22189684","article-title":"Computational methods to study human transcript variants in COVID-19 infected lung cancer cells","volume":"22","author":"Sun","year":"2021","journal-title":"Int J Mol Sci"},{"key":"2026030204572592400_ref12","doi-asserted-by":"publisher","first-page":"152","DOI":"10.3892\/br.2014.407","article-title":"Mechanism of alternative splicing and its regulation","volume":"3","author":"Wang","year":"2015","journal-title":"Biomed Rep"},{"key":"2026030204572592400_ref13","doi-asserted-by":"publisher","first-page":"439","DOI":"10.5483\/BMBRep.2013.46.9.161","article-title":"Splicing and alternative splicing in rice and humans","volume":"46","author":"Zhiguo","year":"2013","journal-title":"BMB Rep"},{"key":"2026030204572592400_ref14","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.tig.2015.01.001","article-title":"Alternative mRNA transcription, processing, and translation: insights from RNA sequencing","volume":"31","author":"de Klerk","year":"2015","journal-title":"Trends Genet"},{"key":"2026030204572592400_ref15","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.ymeth.2012.05.001","article-title":"Hi\u2013C: a comprehensive technique to capture the conformation of genomes","volume":"58","author":"Belton","year":"2012","journal-title":"Methods"},{"key":"2026030204572592400_ref16","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1038\/nrg2641","article-title":"ChIP\u2013seq: advantages and challenges of a maturing technology","volume":"10","author":"Park","year":"2009","journal-title":"Nat Rev Genet"},{"key":"2026030204572592400_ref17","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"ENCODE Project Consortium","year":"2012","journal-title":"Nature"},{"key":"2026030204572592400_ref18","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1038\/nature23884","article-title":"The 4D nucleome project","volume":"549","author":"Dekker","year":"2017","journal-title":"Nature"},{"key":"2026030204572592400_ref19","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/nature14248","article-title":"Integrative analysis of 111 reference human epigenomes","volume":"518","author":"Kundaje","year":"2015","journal-title":"Nature"},{"key":"2026030204572592400_ref20","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34458-4","article-title":"The 4D Nucleome data portal as a resource for searching and visualizing curated nucleomics data","volume":"13","author":"Reiff","year":"2022","journal-title":"Nat Commun"},{"key":"2026030204572592400_ref21","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1016\/j.celrep.2017.10.001","article-title":"Understanding tissue-specific gene regulation cell reports","volume-title":"Cell Reports","author":"Sonawane","year":"2017"},{"key":"2026030204572592400_ref22","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/carcin\/bgp220","article-title":"Epigenetics in cancer","volume":"31","author":"Sharma","year":"2010","journal-title":"Carcinogenesis"},{"key":"2026030204572592400_ref23","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1038\/nature10442","article-title":"CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing","volume":"479","author":"Shukla","year":"2011","journal-title":"Nature"},{"key":"2026030204572592400_ref24","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1016\/j.molcel.2020.03.024","article-title":"DNA methylation regulates alternative polyadenylation via CTCF and the cohesin complex","volume":"78","author":"Nanavaty","year":"2020","journal-title":"Mol Cell"},{"key":"2026030204572592400_ref25","doi-asserted-by":"publisher","first-page":"998","DOI":"10.3389\/fgene.2020.00998","article-title":"The crosstalk between epigenetic mechanisms and alternative RNA processing regulation","volume":"11","author":"Zhang","year":"2020","journal-title":"Front Genet"},{"key":"2026030204572592400_ref26","doi-asserted-by":"publisher","first-page":"3375","DOI":"10.1172\/JCI94292","article-title":"Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesis","volume":"127","author":"Yuan","year":"2017","journal-title":"J Clin Invest"},{"key":"2026030204572592400_ref27","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1126\/science.1184208","article-title":"Regulation of alternative splicing by histone modifications","volume":"327","author":"Luco","year":"2010","journal-title":"Science"},{"key":"2026030204572592400_ref28","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1101\/gad.473408","article-title":"Regulation of alternative polyadenylation by genomic imprinting","volume":"22","author":"Wood","year":"2008","journal-title":"Genes Dev"},{"key":"2026030204572592400_ref29","doi-asserted-by":"publisher","first-page":"701","DOI":"10.1093\/nar\/gkt875","article-title":"Regulation of alternative splicing by local histone modifications: potential roles for RNA-guided mechanisms","volume":"42","author":"Zhou","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2026030204572592400_ref30","article-title":"Graph attention networks","volume-title":"Int Conf Learn Represent","author":"Veli\u010dkovi\u0107","year":"2018"},{"key":"2026030204572592400_ref31","doi-asserted-by":"crossref","first-page":"10220","DOI":"10.3390\/ijms231810220","article-title":"omicsGAT: graph attention network for cancer subtype analyses","volume":"23","author":"Baul","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2026030204572592400_ref32","doi-asserted-by":"crossref","first-page":"bbae316","DOI":"10.1093\/bib\/bbae316","article-title":"Integrating spatial transcriptomics and bulk RNA-seq: predicting gene expression with enhanced resolution through graph attention networks","volume":"25","author":"Baul","year":"2024","journal-title":"Brief Bioinform"},{"key":"2026030204572592400_ref33","article-title":"Hyper-SAGNN: a self-attention based graph neural network for hypergraphs","volume-title":"Int Conf Learn Represent","author":"Zhang","year":"2020"},{"key":"2026030204572592400_ref34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-020-14974-x","article-title":"Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data","volume":"11","author":"Ashoor","year":"2020","journal-title":"Nat Commun"},{"key":"2026030204572592400_ref35","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13104-018-3507-2","article-title":"GrapHi-C: graph-based visualization of Hi-C datasets","volume":"11","author":"MacKay","year":"2018","journal-title":"BMC Res Notes"},{"key":"2026030204572592400_ref36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-018-05691-7","article-title":"Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy","volume":"9","author":"Li","year":"2018","journal-title":"Nat Commun"},{"key":"2026030204572592400_ref37","article-title":"Graph convolutional networks for epigenetic state prediction using both sequence and 3D genome data","volume-title":"Bioinformatics","author":"Lanchantin","year":"2020"},{"key":"2026030204572592400_ref38","doi-asserted-by":"publisher","first-page":"930","DOI":"10.1101\/gr.275870.121","article-title":"Chromatin interaction\u2013aware gene regulatory modeling with graph attention networks","volume":"32","author":"Karbalayghareh","year":"2022","journal-title":"Genome Res"},{"key":"2026030204572592400_ref39","doi-asserted-by":"crossref","first-page":"4468","DOI":"10.3390\/ijms22094468","article-title":"AS-Quant: detection and visualization of alternative splicing events with RNA-seq data","volume":"22","author":"Fahmi","year":"2021","journal-title":"Int J Mol Sci"},{"key":"2026030204572592400_ref40","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1186\/s12859-022-04939-w","article-title":"APA-scan: detection and visualization of 3\u2019-UTR alternative polyadenylation with RNA-seq and 3$\\prime $-end-seq data","volume":"23","author":"Fahmi","year":"2022","journal-title":"BMC Bioinformatics"},{"key":"2026030204572592400_ref41","article-title":"PyTorch: an imperative style, high-performance deep learning library","volume":"32","author":"Paszke","year":"2019","journal-title":"Proceedings of the 33rd International Conference on Neural Information Processing Systems"},{"key":"2026030204572592400_ref42","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1007\/978-1-4612-4380-9_35","article-title":"Robust estimation of a location parameter","volume-title":"Breakthroughs in Statistics: Methodology and Distribution","author":"Huber","year":"1992"},{"key":"2026030204572592400_ref43","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1038\/s41588-019-0538-0","article-title":"Activity-by-contact model of enhancer\u2013promoter regulation from thousands of CRISPR perturbations","volume":"51","author":"Fulco","year":"2019","journal-title":"Nat Genet"},{"key":"2026030204572592400_ref44","doi-asserted-by":"publisher","first-page":"e1008006","DOI":"10.1371\/journal.pcbi.1008006","article-title":"Epigenome-based splicing prediction using a recurrent neural network","volume":"16","author":"Lee","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"2026030204572592400_ref45","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1038\/nrg3458","article-title":"Enhancers: five essential questions","volume":"14","author":"Pennacchio","year":"2013","journal-title":"Nat Rev Genet"},{"key":"2026030204572592400_ref46","doi-asserted-by":"publisher","DOI":"10.1098\/rsif.2017.0387","article-title":"Opportunities and obstacles for deep learning in biology and medicine","volume":"15","author":"Ching","year":"2018","journal-title":"J R Soc interface"},{"key":"2026030204572592400_ref47","doi-asserted-by":"publisher","first-page":"727306","DOI":"10.3389\/fonc.2021.727306","article-title":"Calmodulin 2 facilitates angiogenesis and metastasis of gastric cancer via STAT3\/HIF-1A\/VEGF-a mediated macrophage polarization","volume":"11","author":"Ganggang","year":"2021","journal-title":"Front Oncol"},{"key":"2026030204572592400_ref48","doi-asserted-by":"publisher","first-page":"155326","DOI":"10.1016\/j.prp.2024.155326","article-title":"Calmodulin 2 expression is associated with poor prognosis in breast cancer","volume":"258","author":"Yang","year":"2024","journal-title":"Pathol Res Pract"},{"key":"2026030204572592400_ref49","doi-asserted-by":"publisher","DOI":"10.1186\/s40659-020-00310-6","article-title":"Tumor suppressive function of Matrin 3 in the basal-like breast cancer","volume":"53","author":"Yang","year":"2020","journal-title":"Biol Res"},{"key":"2026030204572592400_ref50","doi-asserted-by":"publisher","first-page":"1636","DOI":"10.1038\/s41467-017-01829-1","article-title":"The IKK\/NF-$\\kappa $B signaling pathway requires Morgana to drive breast cancer metastasis","volume":"8","author":"Fusella","year":"2017","journal-title":"Nat Commun"},{"key":"2026030204572592400_ref51","doi-asserted-by":"publisher","DOI":"10.3390\/biomedicines6030082","article-title":"Evidence for the involvement of the master transcription factor NF-$\\kappa $B in cancer initiation and progression","volume":"6","author":"Puar","year":"2018","journal-title":"Biomedicines"},{"key":"2026030204572592400_ref52","doi-asserted-by":"publisher","first-page":"1247","DOI":"10.1093\/jnci\/djn253","article-title":"Identification of chromatin remodeling genes Arid4a and Arid4b as leukemia suppressor genes","volume":"100","author":"Mei-Yi","year":"2008","journal-title":"J Natl Cancer Inst"},{"key":"2026030204572592400_ref53","doi-asserted-by":"crossref","first-page":"D1243","DOI":"10.1093\/nar\/gkae974","article-title":"The UCSC genome browser database: 2025 update","volume":"53","author":"Perez","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026030204572592400_ref54","doi-asserted-by":"crossref","first-page":"1204463","DOI":"10.3389\/fgene.2023.1204463","article-title":"SETD2-H3K36ME3: an important bridge between the environment and tumors","volume":"14","author":"He","year":"2023","journal-title":"Front Genet"},{"key":"2026030204572592400_ref55","doi-asserted-by":"publisher","first-page":"103407","DOI":"10.1016\/j.dnarep.2022.103407","article-title":"The role of histone H3K36me3 writers, readers and erasers in maintaining genome stability","volume":"119","author":"Sharda","year":"2022","journal-title":"DNA Repair"},{"key":"2026030204572592400_ref56","doi-asserted-by":"publisher","first-page":"4709","DOI":"10.1093\/nar\/gkaa248","article-title":"Specific histone modifications associate with alternative exon selection during mammalian development","volume":"48","author":"Qiwen","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2026030204572592400_ref57","doi-asserted-by":"publisher","first-page":"e02482","DOI":"10.7554\/eLife.02482","article-title":"SETD2 is required for DNA double-strand break repair and activation of the p53-mediated checkpoint","volume":"3","author":"Carvalho","year":"2014","journal-title":"eLife"},{"key":"2026030204572592400_ref58","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13578-020-0374-z","article-title":"H3K36me3, message from chromatin to DNA damage repair","volume":"10","author":"Sun","year":"2020","journal-title":"Cell Biosci"},{"key":"2026030204572592400_ref59","doi-asserted-by":"publisher","first-page":"2073","DOI":"10.1080\/15384101.2017.1361064","article-title":"p53 binding sites in normal and cancer cells are characterized by distinct chromatin context","volume":"16","author":"Bao","year":"2017","journal-title":"Cell Cycle"},{"key":"2026030204572592400_ref60","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-32285-1","article-title":"TP53-dependent toxicity of CRISPR\/Cas9 cuts is differential across genomic loci and can confound genetic screening","volume":"13","author":"\u00c1lvarez","year":"2022","journal-title":"Nat Commun"},{"key":"2026030204572592400_ref61","doi-asserted-by":"publisher","first-page":"301","DOI":"10.3389\/fonc.2020.00301","article-title":"Molecular mechanisms of PALB2 function and its role in breast cancer management","volume":"10","author":"Shijie","year":"2020","journal-title":"Front Oncol"},{"key":"2026030204572592400_ref62","doi-asserted-by":"crossref","first-page":"7671","DOI":"10.1073\/pnas.1620208114","article-title":"MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress","volume":"114","author":"Bleuyard","year":"2017","journal-title":"Proc Natl Acad Sci"},{"key":"2026030204572592400_ref63","doi-asserted-by":"publisher","first-page":"495","DOI":"10.3390\/genes11050495","article-title":"Activation of steroidogenesis, anti-apoptotic activity, and proliferation in porcine granulosa cells by RUNX1 is negatively regulated by H3K27me3 transcriptional repression","volume":"11","author":"Zhong","year":"2020","journal-title":"Genes"},{"key":"2026030204572592400_ref64","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1182\/blood-2010-07-295113","article-title":"Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models","volume":"117","author":"Pencovich","year":"2011","journal-title":"Blood"},{"key":"2026030204572592400_ref65","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40364-020-00243-y","article-title":"Recurrent SETD2 mutation in NPM1-mutated acute myeloid leukemia","volume":"8","author":"Sun","year":"2020","journal-title":"Biomark Res"},{"key":"2026030204572592400_ref66","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13058-018-0964-4","article-title":"A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women","volume":"20","author":"Bensen","year":"2018","journal-title":"Breast Cancer Res"},{"key":"2026030204572592400_ref67","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1016\/j.immuni.2014.03.010","article-title":"IL-22+ CD4+ T cells promote colorectal cancer stemness via STAT3 transcription factor activation and induction of the methyltransferase DOT1L","volume":"40","author":"Kryczek","year":"2014","journal-title":"Immunity"},{"key":"2026030204572592400_ref68","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1101\/gr.239053.118","article-title":"A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA","volume":"29","author":"Wang","year":"2019","journal-title":"Genome Res"},{"key":"2026030204572592400_ref69","first-page":"124","article-title":"Histone modification marks strongly regulate CDH1 promoter in prostospheres as a model of prostate cancer stem like cells","volume":"21","author":"Shokraii","year":"2019","journal-title":"Cell J"},{"key":"2026030204572592400_ref70","doi-asserted-by":"publisher","first-page":"65548","DOI":"10.18632\/oncotarget.19214","article-title":"The H3K27me3-demethylase KDM6A is suppressed in breast cancer stem-like cells, and enables the resolution of bivalency during the mesenchymal-epithelial transition","volume":"8","author":"Taube","year":"2017","journal-title":"Oncotarget"},{"key":"2026030204572592400_ref71","first-page":"1827","article-title":"Loss of progesterone receptor through epigenetic regulation is associated with poor prognosis in solid tumors","volume":"10","author":"Li","year":"2020","journal-title":"Am J Cancer Res"},{"key":"2026030204572592400_ref72","volume-title":"BRCA1-and BRCA2-Associated Hereditary Breast and Ovarian Cancer","author":"Petrucelli","year":"1993"},{"key":"2026030204572592400_ref73","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.trecan.2020.01.007","article-title":"TP53 mutations and outcomes in breast cancer: reading beyond the headlines","volume":"6","author":"Shahbandi","year":"2020","journal-title":"Trends Cancer"},{"key":"2026030204572592400_ref74","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1056\/NEJMoa1400382","article-title":"Breast-cancer risk in families with mutations in PALB2","volume":"371","author":"Antoniou","year":"2014","journal-title":"N Engl J Med"},{"key":"2026030204572592400_ref75","doi-asserted-by":"publisher","first-page":"2160","DOI":"10.1038\/leu.2016.126","article-title":"RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features","volume":"30","author":"Gaidzik","year":"2016","journal-title":"Leukemia"},{"key":"2026030204572592400_ref76","doi-asserted-by":"crossref","first-page":"1707","DOI":"10.1182\/blood.2019004226","article-title":"NPM1-mutated acute myeloid leukemia: from bench to bedside","volume":"136","author":"Falini","year":"2020","journal-title":"Blood"},{"key":"2026030204572592400_ref77","doi-asserted-by":"publisher","first-page":"1813","DOI":"10.1101\/gr.136184.111","article-title":"ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia","volume":"22","author":"Landt","year":"2012","journal-title":"Genome Res"},{"key":"2026030204572592400_ref78","doi-asserted-by":"publisher","first-page":"e1003326","DOI":"10.1371\/journal.pcbi.1003326","article-title":"Practical guidelines for the comprehensive analysis of ChIP-seq data","volume":"9","author":"Bailey","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"2026030204572592400_ref79","doi-asserted-by":"crossref","first-page":"e1007287","DOI":"10.1371\/journal.pcbi.1007287","article-title":"DeepHiC: a generative adversarial network for enhancing Hi-C data resolution","volume":"16","author":"Hong","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"2026030204572592400_ref80","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae1267","article-title":"Uncovering topologically associating domains from three-dimensional genome maps with TADGATE","volume":"53","author":"Dang","year":"2025","journal-title":"Nucleic Acids Res"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/2\/bbag091\/67196982\/bbag091.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/2\/bbag091\/67196982\/bbag091.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T09:57:38Z","timestamp":1772445458000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbag091\/8503313"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,1]]},"references-count":80,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbag091","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,3]]},"published":{"date-parts":[[2026,3,1]]},"article-number":"bbag091"}}