{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T03:41:14Z","timestamp":1790566874530,"version":"4.1.0"},"reference-count":91,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T00:00:00Z","timestamp":1787616000000},"content-version":"vor","delay-in-days":59,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003554","name":"Lundbeck Foundation","doi-asserted-by":"publisher","award":["R413\u20132022\u2013878"],"award-info":[{"award-number":["R413\u20132022\u2013878"]}],"id":[{"id":"10.13039\/501100003554","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ghent University Special Research Fund","award":["BOF20\/GOA\/023"],"award-info":[{"award-number":["BOF20\/GOA\/023"]}]},{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["G071326N"],"award-info":[{"award-number":["G071326N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["W005325N"],"award-info":[{"award-number":["W005325N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Alternative splicing enables a single gene to produce a variety of mRNA transcripts, significantly enhancing protein diversity in higher eukaryotes. Isoform switching refers to the differential usage of a gene\u2019s transcripts and occurs pervasively across physiological and pathological conditions. IsoformSwitchAnalyzeR was developed to identify these isoform switches and analyze their functional consequences. Advances in RNA-seq technology, including long-read and single-cell sequencing, along with state-of-the-art computational tools, enable unprecedented accuracy in isoform switch identification and its functional consequences, necessitating an update to IsoformSwitchAnalyzeR. Here, we present IsoformSwitchAnalyzeR 2.0, with substantial improvements in the robustness of isoform switch detection, the incorporation of new functional annotation types, and interoperability with other bioinformatics tools. We showcase how IsoformSwitchAnalyzeR\u2019s standard workflow is now well-suited for analysis of both long-read RNA-seq and single-cell data through two case studies. Specifically, we analyze long-read data from patients with Alzheimer\u2019s disease and single-cell data from patients with glioblastoma. In both case studies, we find important isoform switches with disease-relevant functional consequences, showcasing the power of IsoformSwitchAnalyzeR v2. Taken together, these findings highlight the versatility and robustness of IsoformSwitchAnalyzeR in handling advanced sequencing technologies, thereby broadening its applicability across diverse research contexts.<\/jats:p>","DOI":"10.1093\/nargab\/lqag098","type":"journal-article","created":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T11:17:15Z","timestamp":1786101435000},"source":"Crossref","is-referenced-by-count":1,"title":["IsoformSwitchAnalyzeR v2: analysis of functional isoform changes in long-read and single-cell sequencing data"],"prefix":"10.1093","volume":"8","author":[{"given":"Chunxu","family":"Han","sequence":"first","affiliation":[{"name":"Section for Bioinformatics, Department of Health Technology, The Technical University of Denmark , DK-2800 Kgs. Lyngby ,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeroen","family":"Gilis","sequence":"additional","affiliation":[{"name":"Detpartment of Mathematics, Computer Science and Statistics, Ghent University , 9000 Ghent ,","place":["Belgium"]},{"name":"Bioinformatics Institute, Ghent University , 9000 Ghent ,","place":["Belgium"]},{"name":"Data Mining and Modeling for Biomedicine, VIB Flemish Institute for Biotechnology , 9052 Ghent ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena Iriondo","family":"Delgado","sequence":"additional","affiliation":[{"name":"Section for Bioinformatics, Department of Health Technology, The Technical University of Denmark , DK-2800 Kgs. Lyngby ,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lieven","family":"Clement","sequence":"additional","affiliation":[{"name":"Detpartment of Mathematics, Computer Science and Statistics, Ghent University , 9000 Ghent ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6450-0608","authenticated-orcid":false,"given":"Kristoffer","family":"Vitting-Seerup","sequence":"additional","affiliation":[{"name":"Section for Bioinformatics, Department of Health Technology, The Technical University of Denmark , DK-2800 Kgs. Lyngby ,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,25]]},"reference":[{"key":"2026082505004389300_B1","doi-asserted-by":"publisher","first-page":"1413","DOI":"10.1038\/ng.259","article-title":"Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing","volume":"40","author":"Pan","year":"2008","journal-title":"Nat Genet"},{"key":"2026082505004389300_B2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.gene.2012.07.083","article-title":"Function of alternative splicing","volume":"514","author":"Kelemen","year":"2013","journal-title":"Gene"},{"key":"2026082505004389300_B3","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"Wang","year":"2008","journal-title":"Nature"},{"key":"2026082505004389300_B4","doi-asserted-by":"publisher","first-page":"1206","DOI":"10.1158\/1541-7786.MCR-16-0459","article-title":"The landscape of isoform switches in human cancers","volume":"15","author":"Vitting-Seerup","year":"2017","journal-title":"Mol Cancer Res"},{"key":"2026082505004389300_B5","doi-asserted-by":"publisher","first-page":"1843","DOI":"10.1002\/eji.1830220725","article-title":"CD45 isoform expression during T cell development in the thymus","volume":"22","author":"Fujii","year":"1992","journal-title":"Eur J Immunol."},{"key":"2026082505004389300_B6","doi-asserted-by":"publisher","first-page":"18344","DOI":"10.1074\/jbc.M801192200","article-title":"A p120 catenin isoform switch affects rho activity, induces tumor cell invasion, and predicts metastatic disease","volume":"283","author":"Yanagisawa","year":"2008","journal-title":"J Biol Chem"},{"key":"2026082505004389300_B7","doi-asserted-by":"crossref","first-page":"ltac009","DOI":"10.1093\/immadv\/ltac009","article-title":"Target isoforms are an overlooked challenge and opportunity in chimeric antigen receptor cell therapy","volume":"2","author":"Barnkob","year":"2022","journal-title":"Immunother adv"},{"key":"2026082505004389300_B8","doi-asserted-by":"publisher","article-title":"Beyond the gene in genetics: how isoform-resolved analysis empowers the study of both common and rare genetic variation","author":"Mikkelsen","DOI":"10.1101\/2025.03.31.25324931"},{"key":"2026082505004389300_B9","doi-asserted-by":"crossref","first-page":"1356","DOI":"10.12688\/f1000research.8900.2","article-title":"DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics","volume":"5","author":"Robinson","year":"2016","journal-title":"F1000Res"},{"key":"2026082505004389300_B10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-020-01967-8","article-title":"BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty","volume":"21","author":"Tiberi","year":"2020","journal-title":"Genome Biol"},{"key":"2026082505004389300_B11","doi-asserted-by":"publisher","first-page":"3308","DOI":"10.1093\/bioinformatics\/btx411","article-title":"TSIS: an R package to infer alternative splicing isoform switches for time-series data","volume":"33","author":"Guo","year":"2017","journal-title":"Bioinformatics"},{"key":"2026082505004389300_B12","doi-asserted-by":"publisher","first-page":"btac846","DOI":"10.1093\/bioinformatics\/btac846","article-title":"Systematic analysis of alternative splicing in time course data using Spycone","volume":"39","author":"Lio","year":"2023","journal-title":"Bioinformatics"},{"key":"2026082505004389300_B13","doi-asserted-by":"publisher","first-page":"2008","DOI":"10.1101\/gr.133744.111","article-title":"Detecting differential usage of exons from RNA-seq data","volume":"22","author":"Anders","year":"2012","journal-title":"Genome Res"},{"key":"2026082505004389300_B14","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2009","journal-title":"Bioinformatics"},{"key":"2026082505004389300_B15","doi-asserted-by":"publisher","first-page":"374","DOI":"10.12688\/f1000research.51749.2","article-title":"SatuRn: scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications","volume":"10","author":"Gilis","year":"2022","journal-title":"F1000Res"},{"key":"2026082505004389300_B16","doi-asserted-by":"crossref","first-page":"952","DOI":"10.12688\/f1000research.15398.1","article-title":"Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification","volume":"7","author":"Love","year":"2018","journal-title":"F1000Res"},{"key":"2026082505004389300_B17","doi-asserted-by":"crossref","first-page":"1810","DOI":"10.1038\/s41592-023-02026-3","article-title":"Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures","volume":"20","author":"Dong","year":"2023","journal-title":"Nat Methods"},{"key":"2026082505004389300_B18","doi-asserted-by":"publisher","first-page":"1305","DOI":"10.1093\/nar\/gkaf1305","article-title":"Dividing out quantification uncertainty enables assessment of differential transcript usage with limma and edgeR","volume":"53","author":"Baldoni","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026082505004389300_B19","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1093\/nargab\/lqaf117","article-title":"Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing","volume":"7","author":"Lio","year":"2025","journal-title":"NAR Genom Bioinform"},{"key":"2026082505004389300_B20","doi-asserted-by":"publisher","first-page":"4469","DOI":"10.1093\/bioinformatics\/btz247","article-title":"IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences","volume":"35","author":"Vitting-Seerup","year":"2019","journal-title":"Bioinformatics"},{"key":"2026082505004389300_B21","first-page":"1","article-title":"tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing","volume":"21","author":"De\u00a0La\u00a0Fuente","year":"2020","journal-title":"Genome Biol"},{"key":"2026082505004389300_B22","doi-asserted-by":"publisher","first-page":"3070","DOI":"10.1093\/bioinformatics\/btab103","article-title":"IsoTV: processing and visualizing functional features of translated transcript isoforms","volume":"37","author":"Annaldasula","year":"2021","journal-title":"Bioinformatics"},{"key":"2026082505004389300_B23","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1038\/s41514-020-00052-5","article-title":"Differential transcript usage unravels gene expression alterations in Alzheimer\u2019s disease human brains","volume":"7","author":"Marques-Coelho","year":"2021","journal-title":"NPJ Aging Mech Dis"},{"key":"2026082505004389300_B24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s42003-023-05481-y","article-title":"Nanopore long-read RNA sequencing reveals functional alternative splicing variants in human vascular smooth muscle cells","volume":"6","author":"Wu","year":"2023","journal-title":"Commun Biol"},{"key":"2026082505004389300_B25","doi-asserted-by":"publisher","first-page":"3128","DOI":"10.1111\/febs.16723","article-title":"The landscape of differential splicing and transcript alternations in severe COVID-19 infection","volume":"290","author":"Mukherjee","year":"2023","journal-title":"FEBS J"},{"key":"2026082505004389300_B26","doi-asserted-by":"crossref","first-page":"10276","DOI":"10.1038\/s41598-022-14231-9","article-title":"The landscape of isoform switches in sepsis: a multicenter cohort study","volume":"12","author":"Chen","year":"2022","journal-title":"Sci Rep"},{"key":"2026082505004389300_B27","doi-asserted-by":"publisher","first-page":"1554","DOI":"10.1101\/gr.277707.123","article-title":"Comprehensive isoform-level analysis reveals the contribution of alternative isoforms to venom evolution and repertoire diversity","volume":"33","author":"Ye","year":"2023","journal-title":"Genome Res"},{"key":"2026082505004389300_B28","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1016\/j.omtn.2022.08.018","article-title":"Characterizing isoform switching events in esophageal adenocarcinoma","volume":"29","author":"Zhang","year":"2022","journal-title":"Mol Ther Nucleic Acids"},{"key":"2026082505004389300_B29","doi-asserted-by":"publisher","first-page":"4184","DOI":"10.1038\/s41388-021-01849-8","article-title":"The landscape and biological relevance of aberrant alternative splicing events in esophageal squamous cell carcinoma","volume":"40","author":"Wu","year":"2021","journal-title":"Oncogene"},{"key":"2026082505004389300_B30","doi-asserted-by":"publisher","first-page":"e3002505","DOI":"10.1371\/journal.pbio.3002505","article-title":"Single-cell analysis of isoform switching and transposable element expression during preimplantation embryonic development","volume":"22","author":"Wang","year":"2024","journal-title":"PLoS Biol"},{"key":"2026082505004389300_B31","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat Biotechnol"},{"key":"2026082505004389300_B32","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference","volume":"14","author":"Patro","year":"2017","journal-title":"Nat Methods"},{"key":"2026082505004389300_B33","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1038\/s41592-023-01908-w","article-title":"Context-aware transcript quantification from long-read RNA-seq data with Bambu","volume":"20","author":"Chen","year":"2023","journal-title":"Nat Methods"},{"key":"2026082505004389300_B34","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1038\/s41587-022-01565-y","article-title":"Accurate isoform discovery with IsoQuant using long reads","volume":"41","author":"Prjibelski","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2026082505004389300_B35","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1038\/s41592-024-02298-3","article-title":"Systematic assessment of long-read RNA-seq methods for transcript identification and quantification","volume":"21","author":"Pardo-Palacios","year":"2024","journal-title":"Nat Methods"},{"key":"2026082505004389300_B36","doi-asserted-by":"publisher","first-page":"D966","DOI":"10.1093\/nar\/gkae1078","article-title":"GENCODE 2025: reference gene annotation for human and mouse","volume":"53","author":"Mudge","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026082505004389300_B37","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/s41576-019-0150-2","article-title":"RNA sequencing: the teenage years","volume":"20","author":"Stark","year":"2019","journal-title":"Nat Rev Genet."},{"key":"2026082505004389300_B38","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-020-01981-w","article-title":"Obstacles to detecting isoforms using full-length scRNA-seq data","volume":"21","author":"Westoby","year":"2020","journal-title":"Genome Biol"},{"key":"2026082505004389300_B39","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/s41586-021-03969-3","article-title":"Isoform cell-type specificity in the mouse primary motor cortex","volume":"598","author":"Booeshaghi","year":"2021","journal-title":"Nature"},{"key":"2026082505004389300_B40","doi-asserted-by":"crossref","first-page":"eabl4896","DOI":"10.1126\/science.abl4896","article-title":"The Tabula Sapiens: a multiple-organ, single-cell transcriptomic atlas of humans","volume":"376","author":"Jones","year":"2022","journal-title":"Science"},{"key":"2026082505004389300_B41","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1038\/s41593-024-01616-4","article-title":"Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain","volume":"27","author":"Joglekar","year":"2024","journal-title":"Nat Neurosci"},{"key":"2026082505004389300_B42","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/s13059-026-03973-8","article-title":"Juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval","volume":"27","author":"Segers","year":"2026","journal-title":"Genome Biol"},{"key":"2026082505004389300_B43","doi-asserted-by":"publisher","first-page":"e39","DOI":"10.1093\/nar\/gks1026","article-title":"DiffSplice: the genome-wide detection of differential splicing events with RNA-seq","volume":"41","author":"Hu","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2026082505004389300_B44","doi-asserted-by":"crossref","first-page":"lqad084","DOI":"10.1093\/nargab\/lqad084","article-title":"Most protein domains exist as variants with distinct functions across cells, tissues and diseases","volume":"5","author":"Vitting-Seerup","year":"2023","journal-title":"NAR Genom Bioinform"},{"key":"2026082505004389300_B45","doi-asserted-by":"publisher","first-page":"W12","DOI":"10.1093\/nar\/gkx428","article-title":"CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features","volume":"45","author":"Kang","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2026082505004389300_B46","doi-asserted-by":"publisher","first-page":"e74","DOI":"10.1093\/nar\/gkt006","article-title":"CPAT: coding-potential assessment tool using an alignment-free logistic regression model","volume":"41","author":"Wang","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2026082505004389300_B47","doi-asserted-by":"publisher","first-page":"1023","DOI":"10.1038\/s41587-021-01156-3","article-title":"SignalP 6.0 predicts all five types of signal peptides using protein language models","volume":"40","author":"Teufel","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2026082505004389300_B48","doi-asserted-by":"publisher","first-page":"W297","DOI":"10.1093\/nar\/gkab408","article-title":"IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation","volume":"49","author":"Erdos","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026082505004389300_B49","doi-asserted-by":"publisher","article-title":"DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks","author":"Hallgren","DOI":"10.1101\/2022.04.08.487609"},{"key":"2026082505004389300_B50","doi-asserted-by":"publisher","first-page":"W228","DOI":"10.1093\/nar\/gkac278","article-title":"DeepLoc 2.0: multi-label subcellular localization prediction using protein language models","volume":"50","author":"Thumuluri","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026082505004389300_B51","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1038\/ng.2653","article-title":"The Genotype-Tissue Expression (GTEx) project","volume":"45","author":"Lonsdale","year":"2013","journal-title":"Nat Genet"},{"key":"2026082505004389300_B52","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-018-03751-6","article-title":"Massive mining of publicly available RNA-seq data from human and mouse","volume":"9","author":"Lachmann","year":"2018","journal-title":"Nat Commun"},{"key":"2026082505004389300_B53","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1038\/nmeth.3805","article-title":"iCOBRA: open, reproducible, standardized and live method benchmarking","volume":"13","author":"Soneson","year":"2016","journal-title":"Nat Methods"},{"key":"2026082505004389300_B54","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/s41587-024-02245-9","article-title":"Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq","volume":"43","author":"Aguzzoli\u00a0Heberle","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2026082505004389300_B55","doi-asserted-by":"publisher","first-page":"1399","DOI":"10.1016\/j.celrep.2017.10.030","article-title":"Single-cell RNA-seq analysis of infiltrating neoplastic cells at the migrating front of human glioblastoma","volume":"21","author":"Darmanis","year":"2017","journal-title":"Cell Rep"},{"key":"2026082505004389300_B56","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2026082505004389300_B57","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026082505004389300_B58","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12915-023-01724-w","article-title":"Expression and splicing mediate distinct biological signals","volume":"21","author":"Dam","year":"2023","journal-title":"BMC Biol"},{"key":"2026082505004389300_B59","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1093\/bioinformatics\/bts034","article-title":"The SVA package for removing batch effects and other unwanted variation in high-throughput experiments","volume":"28","author":"Leek","year":"2012","journal-title":"Bioinformatics"},{"key":"2026082505004389300_B60","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2026082505004389300_B61","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/nmeth.1701","article-title":"SignalP 4.0: discriminating signal peptides from transmembrane regions","volume":"8","author":"Petersen","year":"2011","journal-title":"Nat Methods"},{"key":"2026082505004389300_B62","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1038\/s41587-019-0036-z","article-title":"SignalP 5.0 improves signal peptide predictions using deep neural networks","volume":"37","author":"Almagro\u00a0Armenteros","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026082505004389300_B63","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1038\/s41580-023-00673-0","article-title":"The molecular basis for cellular function of intrinsically disordered protein regions","volume":"25","author":"Holehouse","year":"2024","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2026082505004389300_B64","doi-asserted-by":"publisher","first-page":"5129","DOI":"10.1111\/j.1742-4658.2005.04948.x","article-title":"Flexible nets. The roles of intrinsic disorder in protein interaction networks","volume":"272","author":"Dunker","year":"2005","journal-title":"FEBS J"},{"key":"2026082505004389300_B65","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12964-022-00821-7","article-title":"Intrinsically disordered proteins play diverse roles in cell signaling","volume":"20","author":"Bondos","year":"2022","journal-title":"Cell Commun Signal"},{"key":"2026082505004389300_B66","doi-asserted-by":"publisher","first-page":"9045","DOI":"10.3390\/ijms21239045","article-title":"Liquid\u2013liquid phase separation by intrinsically disordered protein regions of viruses: roles in viral life cycle and control of virus\u2013host interactions","volume":"21","author":"Brocca","year":"2020","journal-title":"Int J Mol Sci"},{"key":"2026082505004389300_B67","doi-asserted-by":"crossref","first-page":"W510","DOI":"10.1093\/nar\/gkac439","article-title":"NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning","volume":"50","author":"H\u00f8ie","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026082505004389300_B68","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2026082505004389300_B69","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026082505004389300_B70","doi-asserted-by":"crossref","first-page":"2117","DOI":"10.1038\/s41588-023-01560-2","article-title":"Isoform-level transcriptome-wide association uncovers genetic risk mechanisms for neuropsychiatric disorders in the human brain","volume":"55","author":"Bhattacharya","year":"2023","journal-title":"Nat Genet"},{"key":"2026082505004389300_B71","doi-asserted-by":"publisher","first-page":"1191680","DOI":"10.3389\/fnagi.2023.1191680","article-title":"Comprehensive transcript-level analysis reveals transcriptional reprogramming during the progression of Alzheimer\u2019s disease","volume":"15","author":"Wu","year":"2023","journal-title":"Front Aging Neurosci"},{"key":"2026082505004389300_B72","doi-asserted-by":"crossref","first-page":"2407","DOI":"10.1038\/s41588-024-01939-9","article-title":"GWAS of multiple neuropathology endophenotypes identifies new risk loci and provides insights into the genetic risk of dementia","volume":"56","author":"Shade","year":"2024","journal-title":"Nat Genet"},{"key":"2026082505004389300_B73","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1126\/science.1074069","article-title":"Alzheimer\u2019s disease is a synaptic failure","volume":"298","author":"Selkoe","year":"2002","journal-title":"Science"},{"key":"2026082505004389300_B74","doi-asserted-by":"publisher","first-page":"1129036","DOI":"10.3389\/fnsyn.2023.1129036","article-title":"Alzheimer\u2019s disease as a synaptopathy: evidence for dysfunction of synapses during disease progression","volume":"15","author":"Meftah","year":"2023","journal-title":"Front Synaptic Neurosci"},{"key":"2026082505004389300_B75","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1016\/j.tins.2008.06.005","article-title":"Neuronal calcium mishandling and the pathogenesis of Alzheimer\u2019s disease","volume":"31","author":"Bezprozvanny","year":"2008","journal-title":"Trends Neurosci"},{"key":"2026082505004389300_B76","doi-asserted-by":"publisher","first-page":"5","DOI":"10.3389\/fphys.2017.00005","article-title":"The multifaceted role of SNARE proteins in membrane fusion","volume":"8","author":"Han","year":"2017","journal-title":"Front Physiol"},{"key":"2026082505004389300_B77","doi-asserted-by":"publisher","first-page":"4525","DOI":"10.1523\/JNEUROSCI.3352-16.2017","article-title":"Early Golgi abnormalities and neurodegeneration upon loss of presynaptic proteins Munc18-1, syntaxin-1, or SNAP-25","volume":"37","author":"Santos","year":"2017","journal-title":"J Neurosci"},{"key":"2026082505004389300_B78","doi-asserted-by":"publisher","first-page":"1244","DOI":"10.1016\/j.celrep.2015.07.044","article-title":"Amyloid-\u03b2 oligomers may impair SNARE-mediated exocytosis by direct binding to syntaxin 1a","volume":"12","author":"Yang","year":"2015","journal-title":"Cell Rep"},{"key":"2026082505004389300_B79","doi-asserted-by":"publisher","first-page":"7911","DOI":"10.1523\/JNEUROSCI.1314-16.2016","article-title":"Distinct functions of syntaxin-1 in neuronal maintenance, synaptic vesicle docking, and fusion in mouse neurons","volume":"36","author":"Vardar","year":"2016","journal-title":"J Neurosci"},{"key":"2026082505004389300_B80","doi-asserted-by":"publisher","first-page":"3046","DOI":"10.1073\/pnas.94.7.3046","article-title":"A conserved domain is present in different families of vesicular fusion proteins: a\u2009new\u2009superfamily","volume":"94","author":"Weimbs","year":"1997","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026082505004389300_B81","doi-asserted-by":"publisher","first-page":"319","DOI":"10.4161\/viru.1.4.12195","article-title":"SNARE motif: a common motif used by pathogens to manipulate membrane fusion","volume":"1","author":"Wesolowski","year":"2010","journal-title":"Virulence"},{"key":"2026082505004389300_B82","doi-asserted-by":"publisher","first-page":"e14057","DOI":"10.1200\/JCO.2023.41.16_suppl.e14057","article-title":"Overall survival in patients with recurrent glioblastomas with combination chemotherapy and tumor treating fields (TTF)","volume":"41","author":"Nahm","year":"2023","journal-title":"J Clin Oncol"},{"key":"2026082505004389300_B83","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1007\/s00401-007-0293-7","article-title":"Diffuse glioma growth: a guerilla war","volume":"114","author":"Claes","year":"2007","journal-title":"Acta Neuropathol"},{"key":"2026082505004389300_B84","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-024-52167-y","article-title":"Glioblastoma cells increase expression of notch signaling and synaptic genes within infiltrated brain tissue","volume":"15","author":"Harwood","year":"2024","journal-title":"Nat Commun"},{"key":"2026082505004389300_B85","doi-asserted-by":"publisher","first-page":"1932","DOI":"10.3390\/ijms21061932","article-title":"Tumor cell invasion in glioblastoma","volume":"21","author":"Vollmann-Zwerenz","year":"2020","journal-title":"Int J Mol Sci"},{"key":"2026082505004389300_B86","doi-asserted-by":"publisher","first-page":"806","DOI":"10.3390\/biomedicines10040806","article-title":"The hallmarks of glioblastoma: heterogeneity, intercellular crosstalk and molecular signature of invasiveness and progression","volume":"10","author":"Torrisi","year":"2022","journal-title":"Biomedicines"},{"key":"2026082505004389300_B87","doi-asserted-by":"publisher","first-page":"1440409","DOI":"10.3389\/fncel.2024.1440409","article-title":"Discovery of GJC1 as a prognostic biomarker in glioma cells: insights into its cell-cycle relationship and differential expression in non-neuronal cells","volume":"18","author":"Ji","year":"2024","journal-title":"Front Cell Neurosci"},{"key":"2026082505004389300_B88","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1007\/s10616-022-00563-x","article-title":"Connexin 45 is a novel suppressor of melanoma metastasis","volume":"75","author":"Saito","year":"2023","journal-title":"Cytotechnology"},{"key":"2026082505004389300_B89","doi-asserted-by":"publisher","first-page":"116303","DOI":"10.1016\/j.celrep.2025.116303","article-title":"Connexin 43 drives glioblastoma cancer stem cell phenotypes through a WNK lysine-deficient protein kinase 1-c-MYC signaling axis","volume":"44","author":"Mulkearns-Hubert","year":"2025","journal-title":"Cell Reports"},{"key":"2026082505004389300_B90","doi-asserted-by":"publisher","first-page":"711733","DOI":"10.3389\/fmolb.2021.711733","article-title":"Isoform age\u2014splice isoform profiling using long-read technologies","volume":"8","author":"De\u00a0Paoli-Iseppi","year":"2021","journal-title":"Front Mol Biosci"},{"key":"2026082505004389300_B91","doi-asserted-by":"publisher","article-title":"The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity","author":"Reese","DOI":"10.1101\/2023.05.15.540865"}],"container-title":["NAR Genomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/3\/lqag098\/70775769\/lqag098.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/3\/lqag098\/70775769\/lqag098.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T09:00:54Z","timestamp":1787648454000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nargab\/article\/doi\/10.1093\/nargab\/lqag098\/8769948"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,27]]},"references-count":91,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,6,27]]}},"URL":"https:\/\/doi.org\/10.1093\/nargab\/lqag098","relation":{},"ISSN":["2631-9268"],"issn-type":[{"value":"2631-9268","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,6,27]]},"article-number":"lqag098"}}