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For: López-Bigas N, Audit B, Ouzounis C, Parra G, Guigó R. Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett 2005;579:1900-3. [PMID: 15792793 DOI: 10.1016/j.febslet.2005.02.047] [Citation(s) in RCA: 276] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2004] [Revised: 02/09/2005] [Accepted: 02/14/2005] [Indexed: 12/17/2022]
Number Cited by Other Article(s)
1
Baliga N, Stankiewicz K, Valenzuela J, Turkarslan S, Wu WJ, Gomez-Campo K, Locatelli N, Conn T, Radice V, Parker K, Alderdice R, Bay L, Voolstra C, Barshis D, Baums I. Alternative splicing in a coral during heat stress acclimation and recovery. RESEARCH SQUARE 2025:rs.3.rs-6025431. [PMID: 40235473 PMCID: PMC11998799 DOI: 10.21203/rs.3.rs-6025431/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
2
You Q, Liu J, Zhang R, Wang Z, Zhang B, Guo W, Xu N, Bottillo I, Shao L. Splicing Analysis of Exonic TSC1 and TSC2 Gene Variants Causing Tuberous Sclerosis Complex. Hum Mutat 2025;2025:1497712. [PMID: 40226305 PMCID: PMC11978479 DOI: 10.1155/humu/1497712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 03/17/2025] [Indexed: 04/15/2025]
3
Peretto L, D'angiolillo C, Ferraresi P, Balestra D, Pinotti M. Rescue of a panel of Hemophilia A-causing 5'ss splicing mutations by unique Exon-specific U1snRNA variants. Mol Med 2025;31:121. [PMID: 40148820 PMCID: PMC11948882 DOI: 10.1186/s10020-025-01176-8] [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: 09/30/2024] [Accepted: 03/18/2025] [Indexed: 03/29/2025]  Open
4
Lord J, Oquendo CJ, Wai HA, Douglas AGL, Bunyan DJ, Wang Y, Hu Z, Zeng Z, Danis D, Katsonis P, Williams A, Lichtarge O, Chang Y, Bagnall RD, Mount SM, Matthiasardottir B, Lin C, Hansen TVO, Leman R, Martins A, Houdayer C, Krieger S, Bakolitsa C, Peng Y, Kamandula A, Radivojac P, Baralle D. Predicting the impact of rare variants on RNA splicing in CAGI6. Hum Genet 2025;144:243-251. [PMID: 38170232 PMCID: PMC11976748 DOI: 10.1007/s00439-023-02624-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/18/2023] [Indexed: 01/05/2024]
5
Tan H, Gotea V, Jaiswal SK, Seidel NE, Holland DO, Fedkenheuer K, Elkahloun AG, Bang-Christensen SR, Elnitski L. iSoMAs: Finding isoform expression and somatic mutation associations in human cancers. PLoS Comput Biol 2025;21:e1012847. [PMID: 40053523 PMCID: PMC12052144 DOI: 10.1371/journal.pcbi.1012847] [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: 05/15/2024] [Revised: 05/05/2025] [Accepted: 02/03/2025] [Indexed: 03/09/2025]  Open
6
Bak-Gordon P, Manley JL. SF3B1: from core splicing factor to oncogenic driver. RNA (NEW YORK, N.Y.) 2025;31:314-332. [PMID: 39773890 PMCID: PMC11874996 DOI: 10.1261/rna.080368.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Accepted: 12/23/2024] [Indexed: 01/11/2025]
7
Miguel Berenguel L, Gianelli C, Matas Pérez E, del Rosal T, Méndez Echevarría A, Robles Marhuenda Á, Feito Rodríguez M, Caballero Molina MT, Magallares García L, Sánchez Garrido B, Hita Díaz S, Allende Martínez L, Nozal Aranda P, Cámara Hijón C, López Granados E, Rodríguez Pena R, Bravo García-Morato M. Molecular assessment of splicing variants in a cohort of patients with inborn errors of immunity: methodological approach and interpretation remarks. Front Immunol 2025;15:1499415. [PMID: 39944559 PMCID: PMC11814461 DOI: 10.3389/fimmu.2024.1499415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 12/27/2024] [Indexed: 05/09/2025]  Open
8
Zheng H, Cheng C, He M, Zhou W, Li Y, Dai J, Zhang T, Xu K, Zhang X, Tian X, Liu Y. Interpreting Variants of Uncertain Significance in PCD: Abnormal Splicing Caused by a Missense Variant of DNAAF3. Mol Genet Genomic Med 2025;13:e70036. [PMID: 39764684 PMCID: PMC11705539 DOI: 10.1002/mgg3.70036] [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: 02/21/2024] [Revised: 08/16/2024] [Accepted: 11/06/2024] [Indexed: 01/11/2025]  Open
9
Duan C, Rong S, Buerer L, Neil CR, Savatt JM, Strande NT, Fairbrother WG. One-Size-Fits-Many: Antisense oligonucleotides for rescuing splicing mutations in hotspot exons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.07.627366. [PMID: 39677675 PMCID: PMC11643266 DOI: 10.1101/2024.12.07.627366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
10
Ciccolella S, Cozzi D, Della Vedova G, Kuria SN, Bonizzoni P, Denti L. Differential quantification of alternative splicing events on spliced pangenome graphs. PLoS Comput Biol 2024;20:e1012665. [PMID: 39652592 DOI: 10.1371/journal.pcbi.1012665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 12/19/2024] [Accepted: 11/21/2024] [Indexed: 12/21/2024]  Open
11
Zhu L, Chen M, Shi Y, Huang X, Ding H. Prenatal detection of novel compound heterozygous variants of the PLD1 gene in a fetus with congenital heart disease. Front Genet 2024;15:1498485. [PMID: 39553471 PMCID: PMC11564120 DOI: 10.3389/fgene.2024.1498485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Accepted: 10/18/2024] [Indexed: 11/19/2024]  Open
12
Wang Y, Shu M, Wang T, He T, Yuan J, Yang Y. Comprehensive characterization of somatic mutations associated with chimeric RNAs in human cancers. Int J Cancer 2024;155:683-696. [PMID: 38613405 DOI: 10.1002/ijc.34955] [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: 11/03/2023] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024]
13
Vecoli C, Foffa I, Vittorini S, Botto N, Esposito A, Costa S, Piagneri V, Festa P, Ait-Ali L. A novel TGFβR2 splice variant in patient with aortic aneurysm and family history for aortic dissection: a case report. Per Med 2024;21:139-144. [PMID: 38634413 DOI: 10.2217/pme-2023-0135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
14
Speakman E, Gunaratne GH. On a kneading theory for gene-splicing. CHAOS (WOODBURY, N.Y.) 2024;34:043125. [PMID: 38579148 DOI: 10.1063/5.0199364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/05/2024] [Indexed: 04/07/2024]
15
Chafai N, Bonizzi L, Botti S, Badaoui B. Emerging applications of machine learning in genomic medicine and healthcare. Crit Rev Clin Lab Sci 2024;61:140-163. [PMID: 37815417 DOI: 10.1080/10408363.2023.2259466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023]
16
Piron A, Szymczak F, Papadopoulou T, Alvelos MI, Defrance M, Lenaerts T, Eizirik DL, Cnop M. RedRibbon: A new rank-rank hypergeometric overlap for gene and transcript expression signatures. Life Sci Alliance 2024;7:e202302203. [PMID: 38081640 PMCID: PMC10709657 DOI: 10.26508/lsa.202302203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]  Open
17
Knill C, Henderson EJ, Johnson C, Wah VY, Cheng K, Forster AJ, Itasaki N. Defects of the spliceosomal gene SNRPB affect osteo- and chondro-differentiation. FEBS J 2024;291:272-291. [PMID: 37584444 DOI: 10.1111/febs.16934] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/25/2023] [Accepted: 08/14/2023] [Indexed: 08/17/2023]
18
Li K, Xiao J, Ling Z, Luo T, Xiong J, Chen Q, Dong L, Wang Y, Wang X, Jiang Z, Xia L, Yu Z, Hua R, Guo R, Tang D, Lv M, Lian A, Li B, Zhao G, He X, Xia K, Cao Y, Li J. Prioritizing de novo potential non-canonical splicing variants in neurodevelopmental disorders. EBioMedicine 2024;99:104928. [PMID: 38113761 PMCID: PMC10767160 DOI: 10.1016/j.ebiom.2023.104928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]  Open
19
Scheller IF, Lutz K, Mertes C, Yépez VA, Gagneur J. Improved detection of aberrant splicing with FRASER 2.0 and the intron Jaccard index. Am J Hum Genet 2023;110:2056-2067. [PMID: 38006880 PMCID: PMC10716352 DOI: 10.1016/j.ajhg.2023.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/27/2023]  Open
20
Ferese R, Scala S, Suppa A, Campopiano R, Asci F, Zampogna A, Chiaravalloti MA, Griguoli A, Storto M, Pardo AD, Giardina E, Zampatti S, Fornai F, Novelli G, Fanelli M, Zecca C, Logroscino G, Centonze D, Gambardella S. Cohort analysis of novel SPAST variants in SPG4 patients and implementation of in vitro and in vivo studies to identify the pathogenic mechanism caused by splicing mutations. Front Neurol 2023;14:1296924. [PMID: 38145127 PMCID: PMC10748595 DOI: 10.3389/fneur.2023.1296924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023]  Open
21
Suzuki Y, Nomura N, Yamada K, Yamada Y, Fukuda A, Hoshino K, Abe S, Kurosawa K, Inaba M, Mizuno S, Wakamatsu N, Hayashi S. Pathogenicity evaluation of variants of uncertain significance at exon-intron junction by splicing assay in patients with Mowat-Wilson syndrome. Eur J Med Genet 2023;66:104882. [PMID: 37944854 DOI: 10.1016/j.ejmg.2023.104882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/20/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
22
Oftedal BE, Berger AH, Bruserud Ø, Goldfarb Y, Sulen A, Breivik L, Hellesen A, Ben-Dor S, Haffner-Krausz R, Knappskog PM, Johansson S, Wolff AS, Bratland E, Abramson J, Husebye ES. A partial form of AIRE deficiency underlies a mild form of autoimmune polyendocrine syndrome type 1. J Clin Invest 2023;133:e169704. [PMID: 37909333 PMCID: PMC10617782 DOI: 10.1172/jci169704] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/29/2023] [Indexed: 11/03/2023]  Open
23
Zeibich R, Kwan P, J. O’Brien T, Perucca P, Ge Z, Anderson A. Applications for Deep Learning in Epilepsy Genetic Research. Int J Mol Sci 2023;24:14645. [PMID: 37834093 PMCID: PMC10572791 DOI: 10.3390/ijms241914645] [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: 08/23/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]  Open
24
Darbinian N, Gallia GL, Darbinyan A, Vadachkoria E, Merabova N, Moore A, Goetzl L, Amini S, Selzer ME. Effects of In Utero EtOH Exposure on 18S Ribosomal RNA Processing: Contribution to Fetal Alcohol Spectrum Disorder. Int J Mol Sci 2023;24:13714. [PMID: 37762017 PMCID: PMC10531167 DOI: 10.3390/ijms241813714] [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: 08/08/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023]  Open
25
Bouvet D, Blondel A, de Sainte Agathe JM, Leroy G, Saint-Martin C, Bellanné-Chantelot C. Evaluation in Monogenic Diabetes of the Impact of GCK, HNF1A, and HNF4A Variants on Splicing through the Combined Use of In Silico Tools and Minigene Assays. Hum Mutat 2023;2023:6661013. [PMID: 40225161 PMCID: PMC11919142 DOI: 10.1155/2023/6661013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 04/15/2025]
26
Liu X, Shi X, Xin Q, Liu Z, Pan F, Qiao D, Chen M, Zhang Y, Guo W, Li C, Zhang Y, Shao L, Zhang R. Identified eleven exon variants in PKD1 and PKD2 genes that altered RNA splicing by minigene assay. BMC Genomics 2023;24:407. [PMID: 37468838 PMCID: PMC10354997 DOI: 10.1186/s12864-023-09444-9] [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: 01/08/2023] [Accepted: 06/11/2023] [Indexed: 07/21/2023]  Open
27
Zheng Z, Song Y, Tan X. Deciphering hERG Mutation in Long QT Syndrome Type 2 Using Antisense Oligonucleotide-Mediated Techniques: Lessons from Cystic Fibrosis. Heart Rhythm 2023:S1547-5271(23)02180-X. [PMID: 37121422 DOI: 10.1016/j.hrthm.2023.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/02/2023]
28
Levacher C, Viennot M, Drouet A, Beaussire L, Coutant S, Théry JC, Baert-Desurmont S, Laé M, Ruminy P, Houdayer C. Disequilibrium between BRCA1 and BRCA2 Circular and Messenger RNAs Plays a Role in Breast Cancer. Cancers (Basel) 2023;15:2176. [PMID: 37046838 PMCID: PMC10093293 DOI: 10.3390/cancers15072176] [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: 03/16/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023]  Open
29
Scheller IF, Lutz K, Mertes C, Yépez VA, Gagneur J. Improved detection of aberrant splicing using the Intron Jaccard Index. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.31.23287997. [PMID: 37066374 PMCID: PMC10104204 DOI: 10.1101/2023.03.31.23287997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
30
Fackenthal JD. Alternative mRNA Splicing and Promising Therapies in Cancer. Biomolecules 2023;13:biom13030561. [PMID: 36979496 PMCID: PMC10046298 DOI: 10.3390/biom13030561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/09/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023]  Open
31
de Sainte Agathe JM, Filser M, Isidor B, Besnard T, Gueguen P, Perrin A, Van Goethem C, Verebi C, Masingue M, Rendu J, Cossée M, Bergougnoux A, Frobert L, Buratti J, Lejeune É, Le Guern É, Pasquier F, Clot F, Kalatzis V, Roux AF, Cogné B, Baux D. SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation. Hum Genomics 2023;17:7. [PMID: 36765386 PMCID: PMC9912651 DOI: 10.1186/s40246-023-00451-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/18/2023] [Indexed: 02/12/2023]  Open
32
Dawes R, Bournazos AM, Bryen SJ, Bommireddipalli S, Marchant RG, Joshi H, Cooper ST. SpliceVault predicts the precise nature of variant-associated mis-splicing. Nat Genet 2023;55:324-332. [PMID: 36747048 PMCID: PMC9925382 DOI: 10.1038/s41588-022-01293-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/15/2022] [Indexed: 02/08/2023]
33
Lightfoot HL, Smith GF. Targeting RNA with small molecules-A safety perspective. Br J Pharmacol 2023. [PMID: 36631428 DOI: 10.1111/bph.16027] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/30/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]  Open
34
Leman R, Parfait B, Vidaud D, Girodon E, Pacot L, Le Gac G, Ka C, Ferec C, Fichou Y, Quesnelle C, Aucouturier C, Muller E, Vaur D, Castera L, Boulouard F, Ricou A, Tubeuf H, Soukarieh O, Gaildrat P, Riant F, Guillaud‐Bataille M, Caputo SM, Caux‐Moncoutier V, Boutry‐Kryza N, Bonnet‐Dorion F, Schultz I, Rossing M, Quenez O, Goldenberg L, Harter V, Parsons MT, Spurdle AB, Frébourg T, Martins A, Houdayer C, Krieger S. SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing. Hum Mutat 2022;43:2308-2323. [PMID: 36273432 PMCID: PMC10946553 DOI: 10.1002/humu.24491] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 10/06/2022] [Accepted: 10/18/2022] [Indexed: 01/25/2023]
35
Identification of Novel mRNA Isoforms Associated with Acute Heat Stress Response Using RNA Sequencing Data in Sprague Dawley Rats. BIOLOGY 2022;11:biology11121740. [PMID: 36552250 PMCID: PMC9774719 DOI: 10.3390/biology11121740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022]
36
Zhou YQ, Wang XQ, Jiang J, Huang SL, Dai ZJ, Kong QQ. Novel hydroxymethylbilane synthase gene mutation identified and confirmed in a woman with acute intermittent porphyria: A case report. World J Clin Cases 2022;10:12319-12327. [PMID: 36483813 PMCID: PMC9724524 DOI: 10.12998/wjcc.v10.i33.12319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/10/2022] [Accepted: 11/02/2022] [Indexed: 11/23/2022]  Open
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Cormier MJ, Pedersen BS, Bayrak-Toydemir P, Quinlan AR. Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies. BMC Bioinformatics 2022;23:482. [PMID: 36376793 PMCID: PMC9664736 DOI: 10.1186/s12859-022-05041-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]  Open
38
Caceres M, Mumey B, Husic E, Rizzi R, Cairo M, Sahlin K, Tomescu AI. Safety in Multi-Assembly via Paths Appearing in All Path Covers of a DAG. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3673-3684. [PMID: 34847041 DOI: 10.1109/tcbb.2021.3131203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
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Skryabin NA, Zhigalina DI, Stepanov VA. The Role of Splicing in the Pathogenesis of Monogenic Diseases. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
40
Valenzuela-Palomo A, Sanoguera-Miralles L, Bueno-Martínez E, Esteban-Sánchez A, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Gómez-Barrero S, de la Hoya M, Velasco-Sampedro EA. Splicing Analysis of 16 PALB2 ClinVar Variants by Minigene Assays: Identification of Six Likely Pathogenic Variants. Cancers (Basel) 2022;14:cancers14184541. [PMID: 36139699 PMCID: PMC9496955 DOI: 10.3390/cancers14184541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022]  Open
41
Hatch ST, Smargon AA, Yeo GW. Engineered U1 snRNAs to modulate alternatively spliced exons. Methods 2022;205:140-148. [PMID: 35764245 PMCID: PMC11185844 DOI: 10.1016/j.ymeth.2022.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022]  Open
42
Poly(A) capture full length cDNA sequencing improves the accuracy and detection ability of transcript quantification and alternative splicing events. Sci Rep 2022;12:10599. [PMID: 35732903 PMCID: PMC9217819 DOI: 10.1038/s41598-022-14902-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/14/2022] [Indexed: 11/08/2022]  Open
43
CI-SpliceAI—Improving machine learning predictions of disease causing splicing variants using curated alternative splice sites. PLoS One 2022;17:e0269159. [PMID: 35657932 PMCID: PMC9165884 DOI: 10.1371/journal.pone.0269159] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/16/2022] [Indexed: 11/23/2022]  Open
44
Gu H, Hong J, Lee W, Kim SB, Chun S, Min WK. RNA Sequencing for Elucidating an Intronic Variant of Uncertain Significance (SDHD c.314+3A>T) in Splicing Site Consensus Sequences. Ann Lab Med 2022;42:376-379. [PMID: 34907111 PMCID: PMC8677484 DOI: 10.3343/alm.2022.42.3.376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/02/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022]  Open
45
Empirical prediction of variant-activated cryptic splice donors using population-based RNA-Seq data. Nat Commun 2022;13:1655. [PMID: 35351883 PMCID: PMC8964760 DOI: 10.1038/s41467-022-29271-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 03/01/2022] [Indexed: 11/24/2022]  Open
46
Wu T, Deme L, Zhang Z, Huang X, Xu S, Yang G. Decay of TRPV3 as the genomic trace of epidermal structure changes in the land-to-sea transition of mammals. Ecol Evol 2022;12:e8731. [PMID: 35342611 PMCID: PMC8931706 DOI: 10.1002/ece3.8731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 11/09/2022]  Open
47
He WB, Xiao WJ, Dai CL, Wang YR, Li XR, Gong F, Meng LL, Tan C, Zeng SC, Lu GX, Lin G, Tan YQ, Hu H, Du J. RNA splicing analysis contributes to reclassifying variants of uncertain significance and improves the diagnosis of monogenic disorders. J Med Genet 2022;59:1010-1016. [PMID: 35121647 DOI: 10.1136/jmedgenet-2021-108013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/06/2022] [Indexed: 11/04/2022]
48
Anthony K. RNA-based therapeutics for neurological diseases. RNA Biol 2022;19:176-190. [PMID: 35067193 PMCID: PMC8786337 DOI: 10.1080/15476286.2021.2021650] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
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Liu L, Yu C, Yan G. Identification of a novel heterozygous TSC2 splicing variant in a patient with Tuberous sclerosis complex: A case report. Medicine (Baltimore) 2022;101:e28666. [PMID: 35060563 PMCID: PMC8772658 DOI: 10.1097/md.0000000000028666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/05/2022] [Indexed: 01/05/2023]  Open
50
Lai HC, Ho UY, James A, De Souza P, Roberts TL. RNA metabolism and links to inflammatory regulation and disease. Cell Mol Life Sci 2021;79:21. [PMID: 34971439 PMCID: PMC11072290 DOI: 10.1007/s00018-021-04073-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 09/29/2021] [Accepted: 10/22/2021] [Indexed: 11/29/2022]
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