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For: de la Fuente L, Arzalluz-Luque Á, Tardáguila M, Del Risco H, Martí C, Tarazona S, Salguero P, Scott R, Lerma A, Alastrue-Agudo A, Bonilla P, Newman JRB, Kosugi S, McIntyre LM, Moreno-Manzano V, Conesa A. tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing. Genome Biol 2020;21:119. [PMID: 32423416 PMCID: PMC7236505 DOI: 10.1186/s13059-020-02028-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/23/2020] [Indexed: 12/26/2022]  Open
Number Cited by Other Article(s)
1
Leung SK, Bamford RA, Jeffries AR, Castanho I, Chioza B, Flaxman CS, Moore K, Dempster EL, Harvey J, Brown JT, Ahmed Z, O'Neill P, Richardson SJ, Hannon E, Mill J. Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology. Nat Commun 2024;15:6458. [PMID: 39095344 PMCID: PMC11297290 DOI: 10.1038/s41467-024-50486-8] [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: 10/04/2023] [Accepted: 07/10/2024] [Indexed: 08/04/2024]  Open
2
Abood A, Mesner LD, Jeffery ED, Murali M, Lehe MD, Saquing J, Farber CR, Sheynkman GM. Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease. Am J Hum Genet 2024:S0002-9297(24)00227-1. [PMID: 39079539 DOI: 10.1016/j.ajhg.2024.07.003] [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: 02/19/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 08/07/2024]  Open
3
Pardo-Palacios FJ, Arzalluz-Luque A, Kondratova L, Salguero P, Mestre-Tomás J, Amorín R, Estevan-Morió E, Liu T, Nanni A, McIntyre L, Tseng E, Conesa A. SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms. Nat Methods 2024;21:793-797. [PMID: 38509328 PMCID: PMC11093726 DOI: 10.1038/s41592-024-02229-2] [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: 06/01/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
4
Kato Y, Nitta JH, Perez CAG, Adhitama N, Religia P, Toyoda A, Iwasaki W, Watanabe H. Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna. Sci Rep 2024;14:9407. [PMID: 38688940 PMCID: PMC11061156 DOI: 10.1038/s41598-024-59774-1] [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: 01/30/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]  Open
5
Murali M, Saquing J, Lu S, Gao Z, Jordan B, Wakefield ZP, Fiszbein A, Cooper DR, Castaldi PJ, Korkin D, Sheynkman G. Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585320. [PMID: 38559226 PMCID: PMC10980011 DOI: 10.1101/2024.03.15.585320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
6
Xu F, Liu S, Zhao A, Shang M, Wang Q, Jiang S, Cheng Q, Chen X, Zhai X, Zhang J, Wang X, Yan J. iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize. THE NEW PHYTOLOGIST 2024;241:2606-2620. [PMID: 38291701 DOI: 10.1111/nph.19554] [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: 10/24/2023] [Accepted: 01/06/2024] [Indexed: 02/01/2024]
7
Boti MA, Adamopoulos PG, Vassilacopoulou D, Scorilas A. Unraveling the Concealed Transcriptomic Landscape of PTEN in Human Malignancies. Curr Genomics 2023;24:250-262. [PMID: 38169628 PMCID: PMC10758127 DOI: 10.2174/0113892029265367231013113304] [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: 06/22/2023] [Revised: 07/29/2023] [Accepted: 09/19/2023] [Indexed: 01/05/2024]  Open
8
Nguyen LAC, Mori M, Yasuda Y, Galipon J. Functional Consequences of Shifting Transcript Boundaries in Glucose Starvation. Mol Cell Biol 2023;43:611-628. [PMID: 37937348 PMCID: PMC10761120 DOI: 10.1080/10985549.2023.2270406] [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: 07/11/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023]  Open
9
Al-Dossary O, Furtado A, KharabianMasouleh A, Alsubaie B, Al-Mssallem I, Henry RJ. Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows. PLANT METHODS 2023;19:112. [PMID: 37865785 PMCID: PMC10589961 DOI: 10.1186/s13007-023-01091-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
10
Xia Y, Jin Z, Zhang C, Ouyang L, Dong Y, Li J, Guo L, Jing B, Shi Y, Miao S, Xi R. TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing. Nat Commun 2023;14:5935. [PMID: 37741817 PMCID: PMC10518008 DOI: 10.1038/s41467-023-41649-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 09/13/2023] [Indexed: 09/25/2023]  Open
11
Pardo-Palacios FJ, Arzalluz-Luque A, Kondratova L, Salguero P, Mestre-Tomás J, Amorín R, Estevan-Morió E, Liu T, Nanni A, McIntyre L, Tseng E, Conesa A. SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541248. [PMID: 37398077 PMCID: PMC10312485 DOI: 10.1101/2023.05.17.541248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
12
McCabe SD, Nobel AB, Love MI. ACTOR: a latent Dirichlet model to compare expressed isoform proportions to a reference panel. Biostatistics 2023;24:388-405. [PMID: 33948626 PMCID: PMC10102900 DOI: 10.1093/biostatistics/kxab013] [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: 01/23/2020] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 11/13/2022]  Open
13
Abood A, Mesner LD, Jeffery ED, Murali M, Lehe M, Saquing J, Farber CR, Sheynkman GM. Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.531557. [PMID: 36993769 PMCID: PMC10055087 DOI: 10.1101/2023.03.17.531557] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
14
Prjibelski AD, Mikheenko A, Joglekar A, Smetanin A, Jarroux J, Lapidus AL, Tilgner HU. Accurate isoform discovery with IsoQuant using long reads. Nat Biotechnol 2023:10.1038/s41587-022-01565-y. [PMID: 36593406 DOI: 10.1038/s41587-022-01565-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/13/2022] [Indexed: 01/04/2023]
15
Weber R, Ghoshdastider U, Spies D, Duré C, Valdivia-Francia F, Forny M, Ormiston M, Renz PF, Taborsky D, Yigit M, Bernasconi M, Yamahachi H, Sendoel A. Monitoring the 5'UTR landscape reveals isoform switches to drive translational efficiencies in cancer. Oncogene 2023;42:638-650. [PMID: 36550360 PMCID: PMC9957725 DOI: 10.1038/s41388-022-02578-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
16
Wu S, Schmitz U. Single-cell and long-read sequencing to enhance modelling of splicing and cell-fate determination. Comput Struct Biotechnol J 2023;21:2373-2380. [PMID: 37066125 PMCID: PMC10091034 DOI: 10.1016/j.csbj.2023.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023]  Open
17
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: 0.5] [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
18
Miller AR, Wijeratne S, McGrath SD, Schieffer KM, Miller KE, Lee K, Mathew M, LaHaye S, Fitch JR, Kelly BJ, White P, Mardis ER, Wilson RK, Cottrell CE, Magrini V. Pacific Biosciences Fusion and Long Isoform Pipeline for Cancer Transcriptome-Based Resolution of Isoform Complexity. J Mol Diagn 2022;24:1292-1306. [PMID: 36191838 DOI: 10.1016/j.jmoldx.2022.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 08/05/2022] [Accepted: 09/13/2022] [Indexed: 01/13/2023]  Open
19
Castaldi PJ, Abood A, Farber CR, Sheynkman GM. Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease. Hum Mol Genet 2022;31:R123-R136. [PMID: 35960994 PMCID: PMC9585682 DOI: 10.1093/hmg/ddac196] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023]  Open
20
Zhou D, Tran Y, Abou Elela S, Scott MS. SAPFIR: A webserver for the identification of alternative protein features. BMC Bioinformatics 2022;23:250. [PMID: 35751026 PMCID: PMC9229502 DOI: 10.1186/s12859-022-04804-w] [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: 03/10/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022]  Open
21
Nanni AV, Morse AM, Newman JRB, Choquette NE, Wedow JM, Liu Z, Leakey ADB, Conesa A, Ainsworth EA, McIntyre LM. Variation in leaf transcriptome responses to elevated ozone corresponds with physiological sensitivity to ozone across maize inbred lines. Genetics 2022;221:6586798. [PMID: 35579358 DOI: 10.1093/genetics/iyac080] [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: 03/30/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022]  Open
22
Arzalluz-Luque A, Salguero P, Tarazona S, Conesa A. acorde unravels functionally interpretable networks of isoform co-usage from single cell data. Nat Commun 2022;13:1828. [PMID: 35383181 PMCID: PMC8983708 DOI: 10.1038/s41467-022-29497-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 03/16/2022] [Indexed: 12/13/2022]  Open
23
Tseng E, Underwood JG, Evans Hutzenbiler BD, Trojahn S, Kingham B, Shevchenko O, Bernberg E, Vierra M, Robbins CT, Jansen HT, Kelley JL. Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos). G3 (BETHESDA, MD.) 2022;12:6472356. [PMID: 35100340 PMCID: PMC9210309 DOI: 10.1093/g3journal/jkab422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022]
24
Katsoula G, Steinberg J, Tuerlings M, de Almeida RC, Southam L, Swift D, Meulenbelt I, Wilkinson JM, Zeggini E. A molecular map of long non-coding RNA expression, isoform switching and alternative splicing in osteoarthritis. Hum Mol Genet 2022;31:2090-2105. [PMID: 35088088 PMCID: PMC9239745 DOI: 10.1093/hmg/ddac017] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/22/2021] [Accepted: 01/10/2022] [Indexed: 11/30/2022]  Open
25
Reixachs-Solé M, Eyras E. Uncovering the impacts of alternative splicing on the proteome with current omics techniques. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022;13:e1707. [PMID: 34979593 PMCID: PMC9542554 DOI: 10.1002/wrna.1707] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022]
26
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] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/10/2021] [Indexed: 01/27/2023]  Open
27
Stephenson M, Nip KM, HafezQorani S, Gagalova KK, Yang C, Warren RL, Birol I. RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes. NAR Genom Bioinform 2021;3:lqab105. [PMID: 34859209 PMCID: PMC8633890 DOI: 10.1093/nargab/lqab105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/21/2021] [Accepted: 11/26/2021] [Indexed: 11/12/2022]  Open
28
Altered cell and RNA isoform diversity in aging Down syndrome brains. Proc Natl Acad Sci U S A 2021;118:2114326118. [PMID: 34795060 PMCID: PMC8617492 DOI: 10.1073/pnas.2114326118] [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] [Accepted: 10/08/2021] [Indexed: 12/11/2022]  Open
29
Karakulak T, Moch H, von Mering C, Kahraman A. Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies. Front Mol Biosci 2021;8:726902. [PMID: 34888349 PMCID: PMC8650491 DOI: 10.3389/fmolb.2021.726902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/01/2021] [Indexed: 12/03/2022]  Open
30
Lorenzi C, Barriere S, Arnold K, Luco RF, Oldfield AJ, Ritchie W. IRFinder-S: a comprehensive suite to discover and explore intron retention. Genome Biol 2021;22:307. [PMID: 34749764 PMCID: PMC8573998 DOI: 10.1186/s13059-021-02515-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022]  Open
31
A global map of associations between types of protein posttranslational modifications and human genetic diseases. iScience 2021;24:102917. [PMID: 34430807 PMCID: PMC8365368 DOI: 10.1016/j.isci.2021.102917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/27/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022]  Open
32
Ye C, Zhao D, Ye W, Wu X, Ji G, Li QQ, Lin J. QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering. Brief Bioinform 2021;22:6319934. [PMID: 34255024 DOI: 10.1093/bib/bbab268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 01/09/2023]  Open
33
Alternative mRNA Processing of Innate Response Pathways in Respiratory Syncytial Virus (RSV) Infection. Viruses 2021;13:v13020218. [PMID: 33572560 PMCID: PMC7912025 DOI: 10.3390/v13020218] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022]  Open
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