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Page 1
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. Update in: Nat Methods. 2024 Jul;21(7):1349-1363. doi: 10.1038/s41592-024-02298-3 PMID: 37546854 Free PMC article. Updated. Preprint.
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.
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
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 Martinez JM, Hunt T, Lagarde J, Liang CE, Li H, Meade MJ, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Çelik MH, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Li JL, Lienhard M, Mikheenko A, Mulligan D, Nip KM, Pertea M, Ritchie ME, Sim AD, Tang AD, Wan YK, Wang C, Wong BY, Yang C, Barnes I, Berry AE, Capella-Gutierrez S, Cousineau A, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Götz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Ren X, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Smith ML, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Maehr R, Shen Y, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Au KF, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Pardo-Palacios FJ, et al. Among authors: du mrm. Nat Methods. 2024 Jul;21(7):1349-1363. doi: 10.1038/s41592-024-02298-3. Epub 2024 Jun 7. Nat Methods. 2024. PMID: 38849569 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: 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.