| Opportunities and challenges in long-read sequencing data analysis SL Amarasinghe, S Su, X Dong, L Zappia, ME Ritchie, Q Gouil Genome biology 21 (1), 30, 2020 | 1443 | 2020 |
| RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR CW Law, M Alhamdoosh, S Su, X Dong, L Tian, GK Smyth, ME Ritchie F1000Research 5, ISCB Comm J-1408, 2018 | 807 | 2018 |
| Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments L Tian, X Dong, S Freytag, KA Lê Cao, S Su, A JalalAbadi, ... Nature methods, 1, 2019 | 306 | 2019 |
| Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing L Tian, JS Jabbari, R Thijssen, Q Gouil, SL Amarasinghe, O Voogd, ... Genome biology 22, 1-24, 2021 | 147 | 2021 |
| scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data L Tian, S Su, X Dong, D Amann-Zalcenstein, C Biben, A Seidi, DJ Hilton, ... PLoS computational biology 14 (8), e1006361, 2018 | 116 | 2018 |
| Distinct initiating events underpin the immune and metabolic heterogeneity of KRAS-mutant lung adenocarcinoma SA Best, S Ding, A Kersbergen, X Dong, JY Song, Y Xie, B Reljic, K Li, ... Nature communications 10 (1), 1-14, 2019 | 88 | 2019 |
| Harnessing natural killer immunity in metastatic SCLC SA Best, JB Hess, F Souza-Fonseca-Guimaraes, J Cursons, ... Journal of Thoracic Oncology 15 (9), 1507-1521, 2020 | 75 | 2020 |
| Benchmarking UMI-based single-cell RNA-seq preprocessing workflows Y You, L Tian, S Su, X Dong, JS Jabbari, PF Hickey, ME Ritchie Genome Biology 22 (1), 339, 2021 | 53 | 2021 |
| A guide to creating design matrices for gene expression experiments CW Law, K Zeglinski, X Dong, M Alhamdoosh, GK Smyth, ME Ritchie F1000Research 9, 2020 | 52 | 2020 |
| Evaluation of Fowler–Stephens orchiopexy for high-level intra-abdominal cryptorchidism: a systematic review and meta-analysis C Yu, C Long, Y Wei, X Tang, B Liu, L Shen, X Dong, T Lin, D He, S Wu, ... International Journal of Surgery 60, 74-87, 2018 | 43 | 2018 |
| The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools X Dong, L Tian, Q Gouil, H Kariyawasam, S Su, R De Paoli-Iseppi, ... NAR genomics and bioinformatics 3 (2), lqab028, 2021 | 41 | 2021 |
| Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures X Dong, MRM Du, Q Gouil, L Tian, JS Jabbari, R Bowden, PL Baldoni, ... Nature Methods 20 (11), 1810-1821, 2023 | 38 | 2023 |
| CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods S Su, L Tian, X Dong, PF Hickey, S Freytag, ME Ritchie Bioinformatics 36 (7), 2288-2290, 2020 | 19 | 2020 |
| Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data Y You, X Dong, YK Wee, MJ Maxwell, M Alhamdoosh, GK Smyth, ... Genome biology 24 (1), 107, 2023 | 11 | 2023 |
| Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR PL Baldoni, Y Chen, S Hediyeh-Zadeh, Y Liao, X Dong, ME Ritchie, W Shi, ... Nucleic Acids Research 52 (3), e13-e13, 2024 | 10 | 2024 |
| Epigenetic modulators of B cell fate identified through coupled phenotype-transcriptome analysis IY Kong, S Trezise, A Light, I Todorovski, GM Arnau, S Gadipally, ... Cell Death & Differentiation, 1-12, 2022 | 6 | 2022 |
| RNA-seq analysis is easy as 1–2-3 with limma Glimma and edgeR [version 3; peer review: 3 approved] CW Law, M Alhamdoosh, S Su, X Dong, L Tian, GK Smyth, ME Ritchie F1000Res, 0 | 1 | |
| Evaluating long-read RNA-sequencing analysis tools with in silico mixtures X Dong, ME Ritchie NATURE METHODS 20 (11), 1643-1644, 2023 | | 2023 |
Matthew E RitchieThe Walter and Eliza Hall Institute of Medical ResearchVerified email at wehi.edu.au
