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scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor.
NAR Genom Bioinform. 2023 Nov 30;5(4):lqad105. doi: 10.1093/nargab/lqad105. eCollection 2023 Dec.
NAR Genom Bioinform. 2023.
PMID: 38046273
Free PMC article.
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: du mrm.
Nat Methods. 2023 Nov;20(11):1810-1821. doi: 10.1038/s41592-023-02026-3. Epub 2023 Oct 2.
Nat Methods. 2023.
PMID: 37783886
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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, Li H, Jerryd Meade M, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Laird Smith M, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Fai Au K, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN.
Pardo-Palacios FJ, et al. Among authors: du mrm.
bioRxiv [Preprint]. 2023 Jul 27:2023.07.25.550582. doi: 10.1101/2023.07.25.550582.
bioRxiv. 2023.
PMID: 37546854
Free PMC article.
Preprint.
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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: du mrm.
Nucleic Acids Res. 2023 Apr 24;51(7):3240-3260. doi: 10.1093/nar/gkad091.
Nucleic Acids Res. 2023.
PMID: 36840716
Free PMC article.
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Corrigendum to 'A transcriptomic dataset evaluating the effect of radiotherapy injury on cells of skin and soft tissue' Data in Brief 41 (2022) 107828.
Shuka L, Lee SA, Du MRM, Karnezis T, Ritchie ME, Shayan R.
Shuka L, et al. Among authors: du mrm.
Data Brief. 2022 Jun 6;43:108358. doi: 10.1016/j.dib.2022.108358. eCollection 2022 Aug.
Data Brief. 2022.
PMID: 35761990
Free PMC article.
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A transcriptomic dataset evaluating the effect of radiotherapy injury on cells of skin and soft tissue.
Shukla L, Lee SA, Du MRM, Karnezis T, Ritchie ME, Shayan R.
Shukla L, et al. Among authors: du mrm.
Data Brief. 2022 Jan 14;41:107828. doi: 10.1016/j.dib.2022.107828. eCollection 2022 Apr.
Data Brief. 2022.
PMID: 35127999
Free PMC article.
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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: du mrm.
Genome Biol. 2021 Nov 11;22(1):310. doi: 10.1186/s13059-021-02525-6.
Genome Biol. 2021.
PMID: 34763716
Free PMC article.
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