You Y, Fu Y, Li L, Zhang Z, Jia S, Lu S, Ren W, Liu Y, Xu Y, Liu X, Jiang F, Peng G, Sampath Kumar A, Ritchie ME, Liu X, Tian L. Systematic comparison of sequencing-based spatial transcriptomic methods. Nature Methods. 2024;:10.1038/s41592-024-02325-3
Chiou S, Al-Ani AH, Pan Y, Patel KM, Kong IY, Whitehead LW, Light A, Young SN, Barrios M, Sargeant C, Rajasekhar P, Zhu L, Hempel A, Lin A, Rickard JA, Hall C, Gangatirkar P, Yip RK, Cawthorne W, Jacobsen AV, Horne CR, Martin KR, Ioannidis LJ, Hansen DS, Day J, Wicks IP, Law C, Ritchie ME, Bowden R, Hildebrand JM, O’Reilly LA, Silke J, Giulino-Roth L, Tsui E, Rogers KL, Hawkins ED, Christensen B, Murphy JM, Samson AL. An immunohistochemical atlas of necroptotic pathway expression. EMBO Molecular Medicine. 2024;16(7):10.1038/s44321-024-00074-6
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 J-L, 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 M-M, 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. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature Methods. 2024;21(7):10.1038/s41592-024-02298-3
Cheng O, Ling MH, Wang C, Wu S, Ritchie ME, Göke J, Amin N, Davidson NM. Flexiplex: a versatile demultiplexer and search tool for omics data. Bioinformatics. 2024;40(3):10.1093/bioinformatics/btae102
Baldoni PL, Chen Y, Hediyeh-zadeh S, Liao Y, Dong X, Ritchie ME, Shi W, Smyth GK. Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR. Nucleic Acids Research. 2024;52(3):10.1093/nar/gkad1167
Blücher RO, Lim RS, Jarred EG, Ritchie ME, Western PS. FGF-independent MEK1/2 signalling in the developing foetal testis is essential for male germline differentiation in mice. BMC Biology. 2023;21(1):10.1186/s12915-023-01777-x
Ferguson AA, Inclan-Rico JM, Lu D, Bobardt SD, Hung L, Gouil Q, Baker L, Ritchie ME, Jex AR, Schwarz EM, Rossi HL, Nair MG, Dillman AR, Herbert DR. Hookworms dynamically respond to loss of Type 2 immune pressure. PLOS Pathogens. 2023;19(12):10.1371/journal.ppat.1011797
Dong X, Du MRM, Gouil Q, Tian L, Jabbari JS, Bowden R, Baldoni PL, Chen Y, Smyth GK, Amarasinghe SL, Law CW, Ritchie ME. Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures. Nature Methods. 2023;20(11):10.1038/s41592-023-02026-3
Amarasinghe SL, Yang P, Voogd O, Yang H, Du MRM, Su S, Brown DV, Jabbari JS, Bowden R, Ritchie ME. scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor. NAR Genomics and Bioinformatics. 2023;5(4):10.1093/nargab/lqad105
Schuster J, Ritchie ME, Gouil Q. Restrander: rapid orientation and artefact removal for long-read cDNA data. NAR Genomics and Bioinformatics. 2023;5(4):10.1093/nargab/lqad108
