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Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures.
Dong X, Du MRM, Gouil Q, Tian L, Jabbari JS, Bowden R, Baldoni PL, Chen Y, Smyth GK, Amarasinghe SL, Law CW, Ritchie ME. Dong X, et al. Among authors: gouil q. Nat Methods. 2023 Nov;20(11):1810-1821. doi: 10.1038/s41592-023-02026-3. Epub 2023 Oct 2. Nat Methods. 2023. PMID: 37783886
Opportunities and challenges in long-read sequencing data analysis.
Amarasinghe SL, Su S, Dong X, Zappia L, Ritchie ME, Gouil Q. Amarasinghe SL, et al. Among authors: gouil q. Genome Biol. 2020 Feb 7;21(1):30. doi: 10.1186/s13059-020-1935-5. Genome Biol. 2020. PMID: 32033565 Free PMC article. Review.
The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools.
Dong X, Tian L, Gouil Q, Kariyawasam H, Su S, De Paoli-Iseppi R, Prawer YDJ, Clark MB, Breslin K, Iminitoff M, Blewitt ME, Law CW, Ritchie ME. Dong X, et al. Among authors: gouil q. NAR Genom Bioinform. 2021 Apr 26;3(2):lqab028. doi: 10.1093/nargab/lqab028. eCollection 2021 Jun. NAR Genom Bioinform. 2021. PMID: 33937765 Free PMC article.
Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing.
Tian L, Jabbari JS, Thijssen R, Gouil Q, Amarasinghe SL, Voogd O, Kariyawasam H, Du MRM, Schuster J, Wang C, Su S, Dong X, Law CW, Lucattini A, Prawer YDJ, Collar-Fernández C, Chung JD, Naim T, Chan A, Ly CH, Lynch GS, Ryall JG, Anttila CJA, Peng H, Anderson MA, Flensburg C, Majewski I, Roberts AW, Huang DCS, Clark MB, Ritchie ME. Tian L, et al. Among authors: gouil q. Genome Biol. 2021 Nov 11;22(1):310. doi: 10.1186/s13059-021-02525-6. Genome Biol. 2021. PMID: 34763716 Free PMC article.
Using long-read sequencing to detect imprinted DNA methylation.
Gigante S, Gouil Q, Lucattini A, Keniry A, Beck T, Tinning M, Gordon L, Woodruff C, Speed TP, Blewitt ME, Ritchie ME. Gigante S, et al. Among authors: gouil q. Nucleic Acids Res. 2019 May 7;47(8):e46. doi: 10.1093/nar/gkz107. Nucleic Acids Res. 2019. PMID: 30793194 Free PMC article.
BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation.
Keniry A, Jansz N, Gearing LJ, Wanigasuriya I, Chen J, Nefzger CM, Hickey PF, Gouil Q, Liu J, Breslin KA, Iminitoff M, Beck T, Tapia Del Fierro A, Whitehead L, Jarratt A, Kinkel SA, Taberlay PC, Willson T, Pakusch M, Ritchie ME, Hilton DJ, Polo JM, Blewitt ME. Keniry A, et al. Among authors: gouil q. Nat Commun. 2022 Mar 29;13(1):1658. doi: 10.1038/s41467-022-29333-1. Nat Commun. 2022. PMID: 35351876 Free PMC article.
Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions.
Nahar N, Tram G, Jen FE, Phillips ZN, Weinert LA, Bossé JT, Jabbari JS, Gouil Q, Du MRM, Ritchie ME, Bowden R, Langford PR, Tucker AW, Jennings MP, Turni C, Blackall PJ, Atack JM. Nahar N, et al. Among authors: gouil q. Nucleic Acids Res. 2023 Apr 24;51(7):3240-3260. doi: 10.1093/nar/gkad091. Nucleic Acids Res. 2023. PMID: 36840716 Free PMC article.
37 results