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For: Louadi Z, Elkjaer ML, Klug M, Lio CT, Fenn A, Illes Z, Bongiovanni D, Baumbach J, Kacprowski T, List M, Tsoy O. Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. Genome Biol 2021;22:327. [PMID: 34857024 PMCID: PMC8638120 DOI: 10.1186/s13059-021-02538-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/10/2021] [Indexed: 01/27/2023]  Open
Number Cited by Other Article(s)
1
Crowl S, Coleman MB, Chaphiv A, Jordan BT, Naegle KM. Systematic analysis of the effects of splicing on the diversity of post-translational modifications in protein isoforms using PTM-POSE. Cell Syst 2025:101318. [PMID: 40513562 DOI: 10.1016/j.cels.2025.101318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 01/17/2025] [Accepted: 05/16/2025] [Indexed: 06/16/2025]
2
Albrecht E, Pelz K, Gress A, Trung HN, Kalinina OV, Kacprowski T, Baumbach J, List M, Tsoy O. DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders. Nucleic Acids Res 2025:gkaf384. [PMID: 40337913 DOI: 10.1093/nar/gkaf384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 04/11/2025] [Accepted: 04/25/2025] [Indexed: 05/09/2025]  Open
3
Yuasa T, Tokuda Y, Nakano M, Tashiro K, Tourtas T, Schlötzer-Schrehardt U, Kruse F, Koizumi N, Okumura N. Comprehensive analysis of splicing variants in corneal endothelial cells of patients with Fuchs endothelial corneal dystrophy. Sci Rep 2025;15:14664. [PMID: 40287469 PMCID: PMC12033338 DOI: 10.1038/s41598-025-92119-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Accepted: 02/25/2025] [Indexed: 04/29/2025]  Open
4
Ke L, Liu J, Feng G, Li X, Zhang Y, Zhang S, Ma X, Di Q. Effects of acute PM2.5 purification on cognitive function and underlying mechanisms: Evidence from integrating alternative splicing into multi-omics. JOURNAL OF HAZARDOUS MATERIALS 2025;487:137214. [PMID: 39823879 DOI: 10.1016/j.jhazmat.2025.137214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 01/07/2025] [Accepted: 01/12/2025] [Indexed: 01/20/2025]
5
Monzó C, Liu T, Conesa A. Transcriptomics in the era of long-read sequencing. Nat Rev Genet 2025:10.1038/s41576-025-00828-z. [PMID: 40155769 DOI: 10.1038/s41576-025-00828-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2025] [Indexed: 04/01/2025]
6
Dery KJ, Wong Z, Wei M, Kupiec-Weglinski JW. Mechanistic Insights into Alternative Gene Splicing in Oxidative Stress and Tissue Injury. Antioxid Redox Signal 2024;41:890-909. [PMID: 37776178 PMCID: PMC11631805 DOI: 10.1089/ars.2023.0437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023]
7
Kiseleva OI, Arzumanian VA, Kurbatov IY, Poverennaya EV. In silico and in cellulo approaches for functional annotation of human protein splice variants. BIOMEDITSINSKAIA KHIMIIA 2024;70:315-328. [PMID: 39324196 DOI: 10.18097/pbmc20247005315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
8
Tan C, Sim D, Zhen Y, Tian H, Koh J, Roca X. PRPF40A induces inclusion of exons in GC-rich regions important for human myeloid cell differentiation. Nucleic Acids Res 2024;52:8800-8814. [PMID: 38943321 PMCID: PMC11347146 DOI: 10.1093/nar/gkae557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024]  Open
9
Arora C, De Oliveira Rosa N, Matic M, Cascone M, Miglionico P, Raimondi F. EXPANSION: a webserver to explore the functional consequences of protein-coding alternative splice variants in cancer genomics. BIOINFORMATICS ADVANCES 2023;3:vbad135. [PMID: 37810457 PMCID: PMC10560094 DOI: 10.1093/bioadv/vbad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/10/2023]
10
Hackl LM, Fenn A, Louadi Z, Baumbach J, Kacprowski T, List M, Tsoy O. Alternative splicing impacts microRNA regulation within coding regions. NAR Genom Bioinform 2023;5:lqad081. [PMID: 37705830 PMCID: PMC10495541 DOI: 10.1093/nargab/lqad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/04/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]  Open
11
Gjerga E, Naarmann-de Vries IS, Dieterich C. Characterizing alternative splicing effects on protein interaction networks with LINDA. Bioinformatics 2023;39:i458-i464. [PMID: 37387163 DOI: 10.1093/bioinformatics/btad224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]  Open
12
Cimmino G, Conte S, Palumbo D, Sperlongano S, Torella M, Della Corte A, Golino P. The Novel Role of Noncoding RNAs in Modulating Platelet Function: Implications in Activation and Aggregation. Int J Mol Sci 2023;24:7650. [PMID: 37108819 PMCID: PMC10144470 DOI: 10.3390/ijms24087650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]  Open
13
Rogalska ME, Vivori C, Valcárcel J. Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects. Nat Rev Genet 2023;24:251-269. [PMID: 36526860 DOI: 10.1038/s41576-022-00556-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 12/23/2022]
14
Lio CT, Grabert G, Louadi Z, Fenn A, Baumbach J, Kacprowski T, List M, Tsoy O. Systematic analysis of alternative splicing in time course data using Spycone. Bioinformatics 2022;39:6965022. [PMID: 36579860 PMCID: PMC9831059 DOI: 10.1093/bioinformatics/btac846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022]  Open
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