{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,12]],"date-time":"2026-11-12T08:25:36Z","timestamp":1794471936439,"version":"4.9.1"},"reference-count":60,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T00:00:00Z","timestamp":1784678400000},"content-version":"vor","delay-in-days":202,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018693","name":"Horizon Europe","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100018693","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013209","name":"Hellenic Foundation for Research and Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013209","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Long non-coding RNAs regulate gene expression through chromatin remodeling, transcriptional control, and post-transcriptional modulation, influencing physiological cell homeostasis but also disease onset. Yet most transcriptomic and network-based studies rely on descriptive linear co-expression analyses, missing nonlinear and mechanistic insights. Emerging ML\/DL methods offer promise but remain limited by data sparsity, noise, insufficient biological priors, and poor interpretability, constraining systems-level lncRNA-mRNA motif discovery.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this manuscript, we introduce lncAPNet, an extended version of the APNet workflow, which integrates graph-based nonlinear inference of lncRNA\u2013mRNA interactions using NetBID2\u2019s and scMINERs activity logic within a lncRNA-focused SJARACNe co-expression network, coupled with PASNet, a biologically informed sparse deep learning model. This framework enables explainable identification of lncRNA drivers in three different cancer type case studies, two with bulk RNA-seq datasets [Chronic Lymphocytic Leukemia and Prostate Adenocarcinoma] and one by combining bulk RNA-seq and scRNA-seq omics datasets [Breast Invasive Carcinoma], uncovering lncRNA drivers that illuminate lncRNA-mediated programs in cancer progression.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>lncAPNet\u2019s R scripts, Python scripts, and Nextflow pipeline are available at the GitHub repository: https:\/\/github.com\/BiodataAnalysisGroup\/lncAPNet.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioadv\/vbag204","type":"journal-article","created":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T11:34:02Z","timestamp":1784633642000},"source":"Crossref","is-referenced-by-count":0,"title":["lncAPNet enables the deciphering of lncRNA\u2013mRNA connections in patient transcriptomic data"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0145-033X","authenticated-orcid":false,"given":"Vasileios","family":"Vasileiou","sequence":"first","affiliation":[{"name":"Institute of Applied Biosciences, Center for Research and Technology Hellas , Thessaloniki, 57001,","place":["Greece"]},{"name":"Department of Molecular Biology and Genetics, Democritus University of Thrace , Alexandroupolis, 68100,","place":["Greece"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2575-4354","authenticated-orcid":false,"given":"George I","family":"Gavriilidis","sequence":"additional","affiliation":[{"name":"Institute of Applied Biosciences, Center for Research and Technology Hellas , Thessaloniki, 57001,","place":["Greece"]},{"name":"Center of Digital Health, Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin , Berlin, 10117,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro Faria","family":"Zeni","sequence":"additional","affiliation":[{"name":"Molecular Medicine, Central European Institute of Technology, Masaryk University , Brno, 625 00,","place":["Czech Republic"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marek","family":"Mraz","sequence":"additional","affiliation":[{"name":"Molecular Medicine, Central European Institute of Technology, Masaryk University , Brno, 625 00,","place":["Czech Republic"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evangelos","family":"Karatzas","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridge, CB10 1SD,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonis","family":"Giakountis","sequence":"additional","affiliation":[{"name":"Department of Biochemistry 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