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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: tian l. 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.
RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.
Law CW, Alhamdoosh M, Su S, Dong X, Tian L, Smyth GK, Ritchie ME. Law CW, et al. Among authors: tian l. F1000Res. 2016 Jun 17;5:ISCB Comm J-1408. doi: 10.12688/f1000research.9005.3. eCollection 2016. F1000Res. 2016. PMID: 27441086 Free PMC article.
Easy and efficient ensemble gene set testing with EGSEA.
Alhamdoosh M, Law CW, Tian L, Sheridan JM, Ng M, Ritchie ME. Alhamdoosh M, et al. Among authors: tian l. F1000Res. 2017 Nov 14;6:2010. doi: 10.12688/f1000research.12544.1. eCollection 2017. F1000Res. 2017. PMID: 29333246 Free PMC article.
Interconversion between Tumorigenic and Differentiated States in Acute Myeloid Leukemia.
McKenzie MD, Ghisi M, Oxley EP, Ngo S, Cimmino L, Esnault C, Liu R, Salmon JM, Bell CC, Ahmed N, Erlichster M, Witkowski MT, Liu GJ, Chopin M, Dakic A, Simankowicz E, Pomilio G, Vu T, Krsmanovic P, Su S, Tian L, Baldwin TM, Zalcenstein DA, DiRago L, Wang S, Metcalf D, Johnstone RW, Croker BA, Lancaster GI, Murphy AJ, Naik SH, Nutt SL, Pospisil V, Schroeder T, Wall M, Dawson MA, Wei AH, de Thé H, Ritchie ME, Zuber J, Dickins RA. McKenzie MD, et al. Among authors: tian l. Cell Stem Cell. 2019 Aug 1;25(2):258-272.e9. doi: 10.1016/j.stem.2019.07.001. Cell Stem Cell. 2019. PMID: 31374198 Free article.
A new lymphoid-primed progenitor marked by Dach1 downregulation identified with single cell multi-omics.
Amann-Zalcenstein D, Tian L, Schreuder J, Tomei S, Lin DS, Fairfax KA, Bolden JE, McKenzie MD, Jarratt A, Hilton A, Jackson JT, Di Rago L, McCormack MP, de Graaf CA, Stonehouse O, Taoudi S, Alexander WS, Nutt SL, Ritchie ME, Ng AP, Naik SH. Amann-Zalcenstein D, et al. Among authors: tian l. Nat Immunol. 2020 Dec;21(12):1574-1584. doi: 10.1038/s41590-020-0799-x. Epub 2020 Oct 19. Nat Immunol. 2020. PMID: 33077975
Single-cell analyses reveal the clonal and molecular aetiology of Flt3L-induced emergency dendritic cell development.
Lin DS, Tian L, Tomei S, Amann-Zalcenstein D, Baldwin TM, Weber TS, Schreuder J, Stonehouse OJ, Rautela J, Huntington ND, Taoudi S, Ritchie ME, Hodgkin PD, Ng AP, Nutt SL, Naik SH. Lin DS, et al. Among authors: tian l. Nat Cell Biol. 2021 Mar;23(3):219-231. doi: 10.1038/s41556-021-00636-7. Epub 2021 Mar 1. Nat Cell Biol. 2021. PMID: 33649477
8,031 results