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SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation.
BMC Genomics. 2023 Jun 6;24(1):305. doi: 10.1186/s12864-023-09391-5.
BMC Genomics. 2023.
PMID: 37280537
Free PMC article.
Ensembl 2023.
Martin FJ, Amode MR, Aneja A, Austine-Orimoloye O, Azov AG, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji SK, Bignell A, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Charkhchi M, Cockburn A, Da Rin Fiorretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Ghattaoraya GS, Martinez JG, Guijarro C, Hardy M, Hollis Z, Hourlier T, Hunt T, Kay M, Kaykala V, Le T, Lemos D, Marques-Coelho D, Marugán JC, Merino GA, Mirabueno LP, Mushtaq A, Hossain SN, Ogeh DN, Sakthivel MP, Parker A, Perry M, Piližota I, Prosovetskaia I, Pérez-Silva JG, Salam AIA, Saraiva-Agostinho N, Schuilenburg H, Sheppard D, Sinha S, Sipos B, Stark W, Steed E, Sukumaran R, Sumathipala D, Suner MM, Surapaneni L, Sutinen K, Szpak M, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Walts B, Wass E, Willhoft N, Allen J, Alvarez-Jarreta J, Chakiachvili M, Flint B, Giorgetti S, Haggerty L, Ilsley GR, Loveland JE, Moore B, Mudge JM, Tate J, Thybert D, Trevanion SJ, Winterbottom A, Frankish A, Hunt SE, Ruffier M, Cunningham F, Dyer S, Finn RD, Howe KL, Harrison PW, Yates AD, Flicek P.
Martin FJ, et al. Among authors: saraiva agostinho n.
Nucleic Acids Res. 2023 Jan 6;51(D1):D933-D941. doi: 10.1093/nar/gkac958.
Nucleic Acids Res. 2023.
PMID: 36318249
Free PMC article.
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Ensembl 2024.
Harrison PW, Amode MR, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji SK, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Campbell LI, Martinez MC, Charkhchi M, Chougule K, Cockburn A, Davidson C, De Silva NH, Dodiya K, Donaldson S, El Houdaigui B, Naboulsi TE, Fatima R, Giron CG, Genez T, Grigoriadis D, Ghattaoraya GS, Martinez JG, Gurbich TA, Hardy M, Hollis Z, Hourlier T, Hunt T, Kay M, Kaykala V, Le T, Lemos D, Lodha D, Marques-Coelho D, Maslen G, Merino GA, Mirabueno LP, Mushtaq A, Hossain SN, Ogeh DN, Sakthivel MP, Parker A, Perry M, Piližota I, Poppleton D, Prosovetskaia I, Raj S, Pérez-Silva JG, Salam AIA, Saraf S, Saraiva-Agostinho N, Sheppard D, Sinha S, Sipos B, Sitnik V, Stark W, Steed E, Suner MM, Surapaneni L, Sutinen K, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Ware D, Wass E, Willhoft NL, Allen J, Alvarez-Jarreta J, Chakiachvili M, Flint B, Giorgetti S, Haggerty L, Ilsley GR, Keatley J, Loveland JE, Moore B, Mudge JM, Naamati G, Tate J, Trevanion SJ, Winterbottom A, Frankish A, Hunt SE, Cunningham F, Dyer S, Finn RD, Martin FJ, Yates AD.
Harrison PW, et al. Among authors: saraiva agostinho n.
Nucleic Acids Res. 2024 Jan 5;52(D1):D891-D899. doi: 10.1093/nar/gkad1049.
Nucleic Acids Res. 2024.
PMID: 37953337
Free PMC article.
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voyAGEr, a free web interface for the analysis of age-related gene expression alterations in human tissues.
Schneider AL, Martins-Silva R, Kaizeler A, Saraiva-Agostinho N, Barbosa-Morais NL.
Schneider AL, et al. Among authors: saraiva agostinho n.
Elife. 2024 Mar 28;12:RP88623. doi: 10.7554/eLife.88623.
Elife. 2024.
PMID: 38546191
Free PMC article.
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betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions.
Ascensão-Ferreira M, Martins-Silva R, Saraiva-Agostinho N, Barbosa-Morais NL.
Ascensão-Ferreira M, et al. Among authors: saraiva agostinho n.
RNA. 2024 Mar 18;30(4):337-353. doi: 10.1261/rna.079764.123.
RNA. 2024.
PMID: 38278530
Free PMC article.
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Interactive Alternative Splicing Analysis of Human Stem Cells Using psichomics.
Saraiva-Agostinho N, Barbosa-Morais NL.
Saraiva-Agostinho N, et al.
Methods Mol Biol. 2020;2117:179-205. doi: 10.1007/978-1-0716-0301-7_10.
Methods Mol Biol. 2020.
PMID: 31960379
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psichomics: graphical application for alternative splicing quantification and analysis.
Saraiva-Agostinho N, Barbosa-Morais NL.
Saraiva-Agostinho N, et al.
Nucleic Acids Res. 2019 Jan 25;47(2):e7. doi: 10.1093/nar/gky888.
Nucleic Acids Res. 2019.
PMID: 30277515
Free PMC article.
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Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems.
Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL.
Gallego-Paez LM, et al. Among authors: saraiva agostinho n.
Hum Genet. 2017 Sep;136(9):1015-1042. doi: 10.1007/s00439-017-1790-y. Epub 2017 Apr 3.
Hum Genet. 2017.
PMID: 28374191
Free PMC article.
Review.
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FirebrowseR: an R client to the Broad Institute's Firehose Pipeline.
Deng M, Brägelmann J, Kryukov I, Saraiva-Agostinho N, Perner S.
Deng M, et al. Among authors: saraiva agostinho n.
Database (Oxford). 2017 Jan 6;2017:baw160. doi: 10.1093/database/baw160. Print 2017.
Database (Oxford). 2017.
PMID: 28062517
Free PMC article.
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