{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T19:00:01Z","timestamp":1782932401654,"version":"3.54.5"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,3,25]],"date-time":"2025-03-25T00:00:00Z","timestamp":1742860800000},"content-version":"vor","delay-in-days":24,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Ministry of Science and Technology of the People\u2019s Republic of China National Key Research & Development Program","award":["2023YFC3605800"],"award-info":[{"award-number":["2023YFC3605800"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities of China","doi-asserted-by":"publisher","award":["2242023\u00a0K5005"],"award-info":[{"award-number":["2242023\u00a0K5005"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004608","name":"Natural Science Foundation of Jiangsu Province","doi-asserted-by":"publisher","award":["BK20222008"],"award-info":[{"award-number":["BK20222008"]}],"id":[{"id":"10.13039\/501100004608","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Nanjing Science and Technology Bureau Project","award":["202205053"],"award-info":[{"award-number":["202205053"]}]},{"name":"Social Development Plan of the Provincial Department of Science and Technology in Jiangsu Province","award":["BE2023781"],"award-info":[{"award-number":["BE2023781"]}]},{"DOI":"10.13039\/501100018556","name":"Suzhou Science and Technology Project","doi-asserted-by":"publisher","award":["SJC2023005"],"award-info":[{"award-number":["SJC2023005"]}],"id":[{"id":"10.13039\/501100018556","id-type":"DOI","asserted-by":"publisher"}]},{"name":"SEU Innovation Capability Enhancement Plan for Doctoral Students","award":["CXJH_SEU 25145"],"award-info":[{"award-number":["CXJH_SEU 25145"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>DNA methylation plays a crucial role in human diseases pathogenesis. Substantial experimental evidence from clinical and biological studies has confirmed numerous methylation-disease associations, which provide valuable prior knowledge for advancing precision medicine through biomarker discovery and disease subtyping. To systematically mine reliable methylation prior knowledge from known DNA methylation-disease associations and develop robust computational methods for precision medicine applications, we propose MethPriorGCN. By integrating layer attention mechanisms and feature weighting mechanisms, MethPriorGCN not only identified reliable methylation digital biomarkers but also achieved superior disease subtype classification accuracy.<\/jats:p>","DOI":"10.1093\/bib\/bbaf131","type":"journal-article","created":{"date-parts":[[2025,3,29]],"date-time":"2025-03-29T10:13:55Z","timestamp":1743243235000},"source":"Crossref","is-referenced-by-count":5,"title":["MethPriorGCN: a deep learning tool for inferring DNA methylation prior knowledge and guiding personalized medicine"],"prefix":"10.1093","volume":"26","author":[{"given":"Jie","family":"Ni","sequence":"first","affiliation":[{"name":"Institute for Molecular Medical Technology, State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University , No. 2, Southeast University Road, Jiangning District, Nanjing, Jiangsu 211102 ,","place":["China"]},{"name":"Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University , No. 101, Longmian Avenue, Jiangning District, Nanjing, Jiangsu 211166 ,","place":["China"]},{"name":"Institute of Biomedical Devices (Suzhou), Southeast University , No. 8, Jinfeng Road, Suzhou New District, Suzhou, Jiangsu 215163 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Li","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medical Technology, State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University , No. 2, Southeast University Road, Jiangning District, Nanjing, Jiangsu 211102 ,","place":["China"]},{"name":"Institute of Biomedical Devices (Suzhou), Southeast University , No. 8, Jinfeng Road, Suzhou New District, Suzhou, Jiangsu 215163 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shumei","family":"Miao","sequence":"additional","affiliation":[{"name":"Department of Information, The First Affiliated Hospital, Nanjing Medical University , No. 300, Guangzhou Road, Gulou District, Nanjing, Jiangsu 210029 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinting","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medical Technology, State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University , No. 2, Southeast University Road, Jiangning District, Nanjing, Jiangsu 211102 ,","place":["China"]},{"name":"Institute of Biomedical Devices (Suzhou), Southeast University , No. 8, Jinfeng Road, Suzhou New District, Suzhou, Jiangsu 215163 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donghui","family":"Yan","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medical Technology, State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University , No. 2, Southeast University Road, Jiangning District, Nanjing, Jiangsu 211102 ,","place":["China"]},{"name":"Institute of Biomedical Devices (Suzhou), Southeast University , No. 8, Jinfeng Road, Suzhou New District, Suzhou, Jiangsu 215163 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengqi","family":"Jing","sequence":"additional","affiliation":[{"name":"Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University , No. 101, Longmian Avenue, Jiangning District, Nanjing, Jiangsu 211166 ,","place":["China"]},{"name":"Department of Information, The First Affiliated Hospital, Nanjing Medical University , No. 300, Guangzhou Road, Gulou District, Nanjing, Jiangsu 210029 ,","place":["China"]},{"name":"Center for Data Management, The First Affiliated Hospital, Nanjing Medical University , No. 300, Guangzhou Road, Gulou District, Nanjing, Jiangsu 210029 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shan","family":"Lu","sequence":"additional","affiliation":[{"name":"Women and Children Department, The First Affiliated Hospital, Nanjing Medical University , No. 300, Guangzhou Road, Gulou District, Nanjing, Jiangsu 210029 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3534-1924","authenticated-orcid":false,"given":"Zhuoying","family":"Xie","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medical Technology, State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University , No. 2, Southeast University Road, Jiangning District, Nanjing, Jiangsu 211102 ,","place":["China"]},{"name":"Institute of Biomedical Devices (Suzhou), Southeast University , No. 8, Jinfeng Road, Suzhou New District, Suzhou, Jiangsu 215163 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Information, The First Affiliated Hospital, Nanjing Medical University , No. 300, Guangzhou Road, Gulou District, Nanjing, Jiangsu 210029 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Information, The First Affiliated Hospital, Nanjing Medical University , No. 300, Guangzhou Road, Gulou District, Nanjing, Jiangsu 210029 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,3,25]]},"reference":[{"key":"2025032603472858500_ref1","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1038\/nrg3230","article-title":"Functions of DNA methylation: islands, start sites, gene bodies and beyond","volume":"13","author":"Jones","year":"2012","journal-title":"Nat Rev Genet"},{"key":"2025032603472858500_ref2","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1016\/j.tig.2022.03.010","article-title":"DNA methylation: a historical perspective","volume":"38","author":"Mattei","year":"2022","journal-title":"Trends Genet"},{"key":"2025032603472858500_ref3","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1146\/annurev-pathol-042220-022304","article-title":"DNA methylation profiling: an emerging paradigm for cancer diagnosis","volume":"17","author":"Papanicolau-Sengos","year":"2022","journal-title":"Annual Rev Pathol Mech Dis"},{"key":"2025032603472858500_ref4","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1016\/j.tig.2021.05.002","article-title":"Navigating the DNA methylation landscape of cancer","volume":"37","author":"Nishiyama","year":"2021","journal-title":"Trends Genet"},{"key":"2025032603472858500_ref5","doi-asserted-by":"publisher","first-page":"1224","DOI":"10.1056\/NEJM197306072882310","article-title":"Gene De-repression","volume":"288","author":"Frenster John","year":"1973","journal-title":"New Engl J Med"},{"key":"2025032603472858500_ref6","doi-asserted-by":"publisher","first-page":"2405786","DOI":"10.1002\/adfm.202405786","article-title":"A novel approach for tumor-released methylated DNA detection using molecularly imprinted polymers","volume":"34","author":"Khawar","year":"2024","journal-title":"Adv Funct Mater"},{"key":"2025032603472858500_ref7","doi-asserted-by":"publisher","first-page":"eaaw3835","DOI":"10.1126\/science.aaw3835","article-title":"Epigenetics as a mediator of plasticity in cancer","volume":"379","author":"Feinberg","year":"2023","journal-title":"Science"},{"key":"2025032603472858500_ref8","doi-asserted-by":"publisher","first-page":"eadf6732","DOI":"10.1126\/scitranslmed.adf6732","article-title":"Targeting DNA methylation and B7-H3 in RB1-deficient and neuroendocrine prostate cancer","volume":"15","author":"Yamada","year":"2023","journal-title":"Sci Transl Med"},{"key":"2025032603472858500_ref9","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1038\/s41598-024-85036-1","article-title":"Galactin-8 DNA methylation mediates macrophage autophagy through the MAPK\/mTOR pathway to alleviate atherosclerosis","volume":"15","author":"Xia","year":"2025","journal-title":"Sci Rep"},{"key":"2025032603472858500_ref10","doi-asserted-by":"publisher","first-page":"4355","DOI":"10.1158\/0008-5472.CAN-20-1379","article-title":"STAT3 and GR cooperate to drive gene expression and growth of basal-like triple-negative breast cancer","volume":"80","author":"Conway","year":"2020","journal-title":"Cancer Res"},{"key":"2025032603472858500_ref11","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1016\/j.semcancer.2020.05.010","article-title":"DNMT1: a key drug target in triple-negative breast cancer","volume":"72","author":"Wong","year":"2021","journal-title":"Semin Cancer Biol"},{"key":"2025032603472858500_ref12","doi-asserted-by":"publisher","first-page":"eabj0264","DOI":"10.1126\/scitranslmed.abj0264","article-title":"Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS","volume":"14","author":"Hop","year":"2022","journal-title":"Sci Transl Med"},{"key":"2025032603472858500_ref13","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1038\/s41392-022-01055-2","article-title":"Epigenetic regulation in cardiovascular disease: mechanisms and advances in clinical trials","volume":"7","author":"Shi","year":"2022","journal-title":"Signal Transduct Target Ther"},{"key":"2025032603472858500_ref14","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1038\/s41392-023-01333-7","article-title":"Epigenetic regulation in metabolic diseases: mechanisms and advances in clinical study","volume":"8","author":"Wu","year":"2023","journal-title":"Signal Transduct Target Ther"},{"key":"2025032603472858500_ref15","doi-asserted-by":"publisher","volume":"22:","DOI":"10.1038\/s41592-024-02568-0"},{"key":"2025032603472858500_ref16","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1038\/s41586-023-06484-9","article-title":"DNA-based programmable gate arrays for general-purpose DNA computing","volume":"622","author":"Lv","year":"2023","journal-title":"Nature"},{"key":"2025032603472858500_ref17","doi-asserted-by":"publisher","first-page":"1666","DOI":"10.1021\/acs.jcim.4c02250","article-title":"Predicting circRNA\u2013disease associations through multisource domain-aware Embeddings and feature projection networks","volume":"65","author":"Liang","year":"2025","journal-title":"J Chem Inf Model"},{"key":"2025032603472858500_ref18","doi-asserted-by":"publisher","first-page":"eadn1870","DOI":"10.1126\/sciadv.adn1870","article-title":"Deep learning predicts DNA methylation regulatory variants in specific brain cell types and enhances fine mapping for brain disorders, science","volume":"11","author":"Zhou","year":"2025","journal-title":"Advances"},{"key":"2025032603472858500_ref19","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/s41746-024-01043-6","article-title":"Informing immunotherapy with multi-omics driven machine learning","volume":"7","author":"Li","year":"2024","journal-title":"NPJ Digital Med"},{"key":"2025032603472858500_ref20","doi-asserted-by":"publisher","first-page":"eabh2724","DOI":"10.1126\/sciadv.abh2724","article-title":"Metabolic detection and systems analyses of pancreatic ductal adenocarcinoma through machine learning, lipidomics, and multi-omics, science","volume":"7","author":"Wang","year":"2021","journal-title":"Advances"},{"key":"2025032603472858500_ref21","doi-asserted-by":"publisher","first-page":"108048","DOI":"10.1016\/j.compbiomed.2024.108048","article-title":"Predicting disease-gene associations through self-supervised mutual infomax graph convolution network","volume":"170","author":"Xie","year":"2024","journal-title":"Comput Biol Med"},{"key":"2025032603472858500_ref22","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/s12915-025-02128-8","article-title":"Consensus representation of multiple cell\u2013cell graphs from gene signaling pathways for cell type annotation","volume":"23","author":"Huang","year":"2025","journal-title":"BMC Biol"},{"key":"2025032603472858500_ref23","doi-asserted-by":"publisher","volume":"24","DOI":"10.1093\/bib\/bbac495"},{"key":"2025032603472858500_ref24","doi-asserted-by":"publisher","first-page":"1775","DOI":"10.1016\/j.ymthe.2022.01.041","article-title":"Hierarchical graph attention network for miRNA-disease association prediction","volume":"30","author":"Li","year":"2022","journal-title":"Mol Ther"},{"key":"2025032603472858500_ref25","doi-asserted-by":"publisher","first-page":"2863","DOI":"10.1021\/acs.jcim.3c00856","article-title":"HOPEXGB: a consensual model for predicting miRNA\/lncRNA-disease associations using a heterogeneous disease-miRNA-lncRNA information network","volume":"64","author":"He","year":"2024","journal-title":"J Chem Inf Model"},{"key":"2025032603472858500_ref26","doi-asserted-by":"publisher","volume":"24","DOI":"10.1093\/bib\/bbad212"},{"key":"2025032603472858500_ref27","doi-asserted-by":"publisher","first-page":"3363","DOI":"10.1109\/TCBB.2022.3187739","article-title":"Predicting miRNA-disease associations from miRNA-gene-disease heterogeneous network with multi-relational graph convolutional network model","volume":"20","author":"Peng","year":"2023","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2025032603472858500_ref28","doi-asserted-by":"publisher","first-page":"e1011634","DOI":"10.1371\/journal.pcbi.1011634","article-title":"Predicting lncRNA-disease associations based on heterogeneous graph convolutional generative adversarial network","volume":"19","author":"Lu","year":"2023","journal-title":"PLoS Comput Biol"},{"key":"2025032603472858500_ref29","doi-asserted-by":"publisher","first-page":"e0278817","DOI":"10.1371\/journal.pone.0278817","article-title":"lncRNA-disease association prediction based on the weight matrix and projection score","volume":"18","author":"Wang","year":"2023","journal-title":"PloS One"},{"key":"2025032603472858500_ref30","doi-asserted-by":"publisher","first-page":"1715","DOI":"10.1109\/TCBB.2020.3034910","article-title":"LDICDL: LncRNA-disease association identification based on collaborative deep learning","volume":"19","author":"Lan","year":"2022","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2025032603472858500_ref31","doi-asserted-by":"publisher","first-page":"2839","DOI":"10.1109\/JBHI.2021.3130110","article-title":"Graph triple-attention network for disease-related LncRNA prediction","volume":"26","author":"Xuan","year":"2022","journal-title":"IEEE J Biomed Health Inform"},{"key":"2025032603472858500_ref32","doi-asserted-by":"publisher","first-page":"107833","DOI":"10.1016\/j.compbiolchem.2023.107833","article-title":"BRWMC: predicting lncRNA-disease associations based on bi-random walk and matrix completion on disease and lncRNA networks","volume":"103","author":"Zhang","year":"2023","journal-title":"Comput Biol Chem"},{"key":"2025032603472858500_ref33","doi-asserted-by":"publisher","first-page":"5075","DOI":"10.1109\/JBHI.2022.3199462","article-title":"NSECDA: natural semantic enhancement for CircRNA-disease association prediction","volume":"26","author":"Wang","year":"2022","journal-title":"IEEE J Biomed Health Inform"},{"key":"2025032603472858500_ref34","doi-asserted-by":"publisher","first-page":"3154","DOI":"10.1109\/TCBB.2023.3264466","article-title":"Potential circRNA-disease association prediction using DeepWalk and nonnegative matrix factorization","volume":"20","author":"Qiao","year":"2023","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2025032603472858500_ref35","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab494","article-title":"KGANCDA: predicting circRNA-disease associations based on knowledge graph attention network","volume":"23","author":"Lan","year":"2022","journal-title":"Brief Bioinform"},{"key":"2025032603472858500_ref36","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac083","article-title":"iGRLCDA: identifying circRNA-disease association based on graph representation learning","volume":"23","author":"Zhang","year":"2022","journal-title":"Brief Bioinform"},{"key":"2025032603472858500_ref37","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1109\/TCYB.2021.3090756","article-title":"MGRCDA: Metagraph recommendation method for predicting CircRNA-disease association","volume":"53","author":"Wang","year":"2023","journal-title":"IEEE Trans Cybern"},{"key":"2025032603472858500_ref38","doi-asserted-by":"publisher","first-page":"eaan2507","DOI":"10.1126\/science.aan2507","article-title":"A pathology atlas of the human cancer transcriptome","volume":"357","author":"Uhlen","year":"2017","journal-title":"Science"},{"key":"2025032603472858500_ref39","doi-asserted-by":"publisher","first-page":"2780","DOI":"10.1158\/2159-8290.CD-21-0126","article-title":"Comprehensive genomic and transcriptomic analysis for guiding therapeutic decisions in patients with rare cancers","volume":"11","author":"Horak","year":"2021","journal-title":"Cancer Discov"},{"key":"2025032603472858500_ref40","doi-asserted-by":"publisher","first-page":"189104","DOI":"10.1007\/s11432-024-4098-3","article-title":"BioKG-CMI: a multi-source feature fusion model based on biological knowledge graph for predicting circRNA-miRNA interactions","volume":"67","author":"Wei","year":"2024","journal-title":"Sci China Inform Sci"},{"key":"2025032603472858500_ref41","doi-asserted-by":"publisher","first-page":"eadr0036","DOI":"10.1126\/sciadv.adr0036","article-title":"The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA, science","volume":"10","author":"Hardikar","year":"2024","journal-title":"Advances"},{"key":"2025032603472858500_ref42","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1002\/mco2.766","article-title":"Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges","volume":"5","author":"Li","year":"2024","journal-title":"Medcomm"},{"key":"2025032603472858500_ref43","doi-asserted-by":"publisher","DOI":"10.3390\/cancers16112001","article-title":"Current challenges of methylation-based liquid biopsies in cancer diagnostics","volume":"16","author":"Rendek","year":"2024","journal-title":"Cancers (Basel)"},{"key":"2025032603472858500_ref44","doi-asserted-by":"publisher","first-page":"1171","DOI":"10.1038\/s41550-023-02030-9","article-title":"Probing the solar coronal magnetic field with physics-informed neural networks","volume":"7","author":"Jarolim","year":"2023","journal-title":"Nature Astronomy"},{"key":"2025032603472858500_ref45","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1038\/s41377-023-01218-y","article-title":"Recent advances in metasurface design and quantum optics applications with machine learning, physics-informed neural networks, and topology optimization methods","volume":"12","author":"Ji","year":"2023","journal-title":"Light: Sci Appl"},{"key":"2025032603472858500_ref46","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcp.2018.10.045"},{"key":"2025032603472858500_ref47","doi-asserted-by":"publisher","first-page":"23","DOI":"10.3390\/s23218665","article-title":"Gradient statistics-based multi-objective optimization in physics-informed neural networks","volume":"23","author":"Vemuri","year":"2023","journal-title":"Sensors"},{"key":"2025032603472858500_ref48","doi-asserted-by":"publisher","first-page":"111260","DOI":"10.1016\/j.jcp.2022.111260","article-title":"A-PINN: auxiliary physics informed neural networks for forward and inverse problems of nonlinear integro-differential equations","volume":"462","author":"Yuan","year":"2022","journal-title":"J Comput Phys"},{"key":"2025032603472858500_ref49","doi-asserted-by":"publisher","first-page":"113284","DOI":"10.1016\/j.jcp.2024.113284","article-title":"f-PICNN: a physics-informed convolutional neural network for partial differential equations with space-time domain","volume":"515","author":"Yuan","year":"2024","journal-title":"J Comput Phys"},{"key":"2025032603472858500_ref50","doi-asserted-by":"publisher","first-page":"110179","DOI":"10.1016\/j.petrol.2022.110179","article-title":"A physics-informed deep convolutional neural network for simulating and predicting transient Darcy flows in heterogeneous reservoirs without labeled data","volume":"211","author":"Zhang","year":"2022","journal-title":"J Petrol Sci Eng"},{"key":"2025032603472858500_ref51","doi-asserted-by":"publisher","first-page":"23836","DOI":"10.1038\/s41598-024-74711-y","article-title":"Enhancing convergence speed with feature enforcing physics-informed neural networks using boundary conditions as prior knowledge","volume":"14","author":"Jahani-nasab","year":"2024","journal-title":"Sci Rep"},{"key":"2025032603472858500_ref52","doi-asserted-by":"publisher","first-page":"15015","DOI":"10.1038\/s41598-024-65304-w","article-title":"Application of physics encoded neural networks to improve predictability of properties of complex multi-scale systems","volume":"14","author":"Meinders","year":"2024","journal-title":"Sci Rep"},{"key":"2025032603472858500_ref53","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1038\/s43588-022-00215-2","article-title":"Physics-informed recurrent neural network for time dynamics in optical resonances","volume":"2","author":"Tang","year":"2022","journal-title":"Nat Comput Sci"},{"key":"2025032603472858500_ref54","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41586-024-08469-8","article-title":"Precise modelling of mitochondrial diseases using optimized mitoBEs","volume":"639","author":"Zhang","year":"2025","journal-title":"Nature"},{"key":"2025032603472858500_ref55","doi-asserted-by":"publisher","first-page":"1562","DOI":"10.1016\/j.cell.2018.05.056","article-title":"Visible machine learning for biomedicine","volume":"173","author":"Yu","year":"2018","journal-title":"Cell"},{"key":"2025032603472858500_ref56","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1038\/s43586-024-00294-7","article-title":"Graph neural networks","volume":"4","author":"Corso","year":"2024","journal-title":"Nat Rev Methods Primers"},{"key":"2025032603472858500_ref57","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1109\/RBME.2021.3122522","article-title":"Graph signal processing, graph neural network and graph learning on biological data: a systematic review, Ieee reviews in biomedical","volume":"16","author":"Li","year":"2023","journal-title":"Engineering"},{"key":"2025032603472858500_ref58","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1038\/nrg.2017.86","article-title":"Statistical and integrative system-level analysis of DNA methylation data","volume":"19","author":"Teschendorff","year":"2018","journal-title":"Nat Rev Genet"},{"key":"2025032603472858500_ref59","doi-asserted-by":"publisher","first-page":"D1208","DOI":"10.1093\/nar\/gkab1088","article-title":"DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database","volume":"50","author":"Xing","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025032603472858500_ref60","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1093\/bib\/bbad378","article-title":"Multiomics dynamic learning enables personalized diagnosis and prognosis for pancancer and cancer subtypes","volume":"24","author":"Lu","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025032603472858500_ref61","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1093\/bioinformatics\/btw715","article-title":"A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases","volume":"33","author":"Chen","year":"2017","journal-title":"Bioinformatics"},{"key":"2025032603472858500_ref62","doi-asserted-by":"publisher","first-page":"3036","DOI":"10.1093\/bioinformatics\/btr500","article-title":"Gaussian interaction profile kernels for predicting drug-target interaction","volume":"27","author":"Laarhoven","year":"2011","journal-title":"Bioinformatics"},{"key":"2025032603472858500_ref63","doi-asserted-by":"publisher","first-page":"2617","DOI":"10.1093\/bioinformatics\/btt426","article-title":"Novel human lncRNA-disease association inference based on lncRNA expression profiles","volume":"29","author":"Chen","year":"2013","journal-title":"Bioinformatics"},{"key":"2025032603472858500_ref64","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.1406.6247","article-title":"Recurrent models of visual attention","volume":"3","author":"Mnih","year":"2014","journal-title":"Adv Neural Inform Processing Syst"},{"key":"2025032603472858500_ref65","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1093\/bib\/bbaa243","article-title":"Predicting drug-disease associations through layer attention graph convolutional network","volume":"22","author":"Yu","year":"2021","journal-title":"Brief Bioinform"},{"key":"2025032603472858500_ref66","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/s12911-022-01807-8","article-title":"Predicting miRNA-disease associations via layer attention graph convolutional network model","volume":"22","author":"Han","year":"2022","journal-title":"BMC Med Inform Decis Mak"},{"key":"2025032603472858500_ref67","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab074","article-title":"NMCMDA: neural multicategory MiRNA-disease association prediction","volume":"22","author":"Wang","year":"2021","journal-title":"Brief Bioinform"},{"key":"2025032603472858500_ref68","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad524","article-title":"MHCLMDA: multihypergraph contrastive learning for miRNA-disease association prediction","volume":"25","author":"Peng","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025032603472858500_ref69","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1093\/bib\/bbad118","article-title":"End-to-end interpretable disease-gene association prediction","volume":"24","author":"Li","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025032603472858500_ref70","doi-asserted-by":"publisher","first-page":"e18345","DOI":"10.1111\/jcmm.18345","article-title":"SCPLPA: an miRNA-disease association prediction model based on spatial consistency projection and label propagation algorithm","volume":"28","author":"Chen","year":"2024","journal-title":"J Cell Mol Med"},{"key":"2025032603472858500_ref71","doi-asserted-by":"publisher","first-page":"625612","DOI":"10.3389\/fonc.2021.625612","article-title":"Upregulation of PEDF predicts a poor prognosis and promotes esophageal squamous cell carcinoma progression by modulating the MAPK\/ERK signaling pathway","volume":"11","author":"Chen","year":"2021","journal-title":"Front Oncol"},{"key":"2025032603472858500_ref72","doi-asserted-by":"publisher","first-page":"bbae080","DOI":"10.1093\/bib\/bbae080","article-title":"IBPGNET: lung adenocarcinoma recurrence prediction based on neural network interpretability","volume":"25","author":"Xu","year":"2024","journal-title":"Brief Bioinform"},{"key":"2025032603472858500_ref73","doi-asserted-by":"publisher","first-page":"790433","DOI":"10.3389\/fmolb.2021.790433","article-title":"The involvement of TRIB3 and FABP1 and their potential functions in the dynamic process of gastric cancer","volume":"8","author":"Liu","year":"2021","journal-title":"Front Mol Biosci"},{"key":"2025032603472858500_ref74","doi-asserted-by":"publisher","first-page":"1354195","DOI":"10.3389\/fgene.2024.1354195","article-title":"DNA methylation markers in esophageal cancer","volume":"15","author":"Xu","year":"2024","journal-title":"Front Genet"},{"key":"2025032603472858500_ref75","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1186\/s13046-018-0699-1","article-title":"CADM2, as a new target of miR-10b, promotes tumor metastasis through FAK\/AKT pathway in hepatocellular carcinoma","volume":"37","author":"Li","year":"2018","journal-title":"J Exp Clin Cancer Res"},{"key":"2025032603472858500_ref76","doi-asserted-by":"publisher","first-page":"3214","DOI":"10.1158\/2159-8290.CD-21-0441","article-title":"Rlf-Mycl gene fusion drives tumorigenesis and metastasis in a mouse model of small cell lung cancer","volume":"11","author":"Ciampricotti","year":"2021","journal-title":"Cancer Discov"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/2\/bbaf131\/62699988\/bbaf131.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/2\/bbaf131\/62699988\/bbaf131.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,29]],"date-time":"2025-03-29T10:14:06Z","timestamp":1743243246000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaf131\/8093115"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3]]},"references-count":76,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2025,3,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaf131","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,3]]},"published":{"date-parts":[[2025,3]]},"article-number":"bbaf131"}}