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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: clark mb. 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.
Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection.
Chang JJ, Rawlinson D, Pitt ME, Taiaroa G, Gleeson J, Zhou C, Mordant FL, De Paoli-Iseppi R, Caly L, Purcell DFJ, Stinear TP, Londrigan SL, Clark MB, Williamson DA, Subbarao K, Coin LJM. Chang JJ, et al. Among authors: clark mb. Cell Rep. 2021 May 11;35(6):109108. doi: 10.1016/j.celrep.2021.109108. Epub 2021 Apr 23. Cell Rep. 2021. PMID: 33961822 Free PMC article.
Isoform Age - Splice Isoform Profiling Using Long-Read Technologies.
De Paoli-Iseppi R, Gleeson J, Clark MB. De Paoli-Iseppi R, et al. Among authors: clark mb. Front Mol Biosci. 2021 Aug 2;8:711733. doi: 10.3389/fmolb.2021.711733. eCollection 2021. Front Mol Biosci. 2021. PMID: 34409069 Free PMC article. Review.
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: clark mb. Genome Biol. 2021 Nov 11;22(1):310. doi: 10.1186/s13059-021-02525-6. Genome Biol. 2021. PMID: 34763716 Free PMC article.
Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.
Chang JJ, Gleeson J, Rawlinson D, De Paoli-Iseppi R, Zhou C, Mordant FL, Londrigan SL, Clark MB, Subbarao K, Stinear TP, Coin LJM, Pitt ME. Chang JJ, et al. Among authors: clark mb. Front Immunol. 2022 Apr 6;13:832223. doi: 10.3389/fimmu.2022.832223. eCollection 2022. Front Immunol. 2022. PMID: 35464437 Free PMC article.
Pervasive effects of RNA degradation on Nanopore direct RNA sequencing.
Prawer YDJ, Gleeson J, De Paoli-Iseppi R, Clark MB. Prawer YDJ, et al. Among authors: clark mb. NAR Genom Bioinform. 2023 Jun 9;5(2):lqad060. doi: 10.1093/nargab/lqad060. eCollection 2023 Jun. NAR Genom Bioinform. 2023. PMID: 37305170 Free PMC article.
133 results