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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 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: herwig r. 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.
ARH-seq: identification of differential splicing in RNA-seq data.
Rasche A, Lienhard M, Yaspo ML, Lehrach H, Herwig R. Rasche A, et al. Among authors: herwig r. Nucleic Acids Res. 2014 Aug;42(14):e110. doi: 10.1093/nar/gku495. Epub 2014 Jun 11. Nucleic Acids Res. 2014. PMID: 24920826 Free PMC article.
Cancer drug sensitivity estimation using modular deep Graph Neural Networks.
Campana PA, Prasse P, Lienhard M, Thedinga K, Herwig R, Scheffer T. Campana PA, et al. Among authors: herwig r. NAR Genom Bioinform. 2024 Apr 27;6(2):lqae043. doi: 10.1093/nargab/lqae043. eCollection 2024 Jun. NAR Genom Bioinform. 2024. PMID: 38680251 Free PMC article.
The 1000 Genomes Project: data management and community access.
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium. Clarke L, et al. Nat Methods. 2012 Apr 27;9(5):459-62. doi: 10.1038/nmeth.1974. Nat Methods. 2012. PMID: 22543379 Free PMC article.
DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer.
Grimm C, Chavez L, Vilardell M, Farrall AL, Tierling S, Böhm JW, Grote P, Lienhard M, Dietrich J, Timmermann B, Walter J, Schweiger MR, Lehrach H, Herwig R, Herrmann BG, Morkel M. Grimm C, et al. Among authors: herwig r. PLoS Genet. 2013;9(2):e1003250. doi: 10.1371/journal.pgen.1003250. Epub 2013 Feb 7. PLoS Genet. 2013. PMID: 23408899 Free PMC article.
232 results