Matthew Ritchie-Publications

Matthew Ritchie-Publications

Researcher: 

Selected publications

  1. Tian L, Su S, Dong X, Amann-Zalcenstein D, Biben C, Seidi A, Hilton DJ, Naik SH, Ritchie ME. scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data. PLoS Comput Biol, 2018,14(8):e1006361. PMID: 30096152
  2. Su S, Law CW, Ah-Cann C, Asselin-Labat ML, Blewitt ME, Ritchie ME. Glimma: interactive graphics for gene expression analysis. Bioinformatics. 2017, 33(13):2050-52. PMID: 28203714
  3. Alhamdoosh M, Ng M, Wilson NJ, Sheridan JM, Huynh H, Wilson MJ, Ritchie ME. Combining multiple tools outperforms individual methods in gene set enrichment analyses. Bioinformatics. 2017, 33(3):414-24. PMID: 27694195
  4. Holik A.Z., Law, C.W., Liu, R., Wang, Z., Wang, W., Ahn, J., Asselin-Labat, M.L., Smyth, G.K., Ritchie, M.E. RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods. Nucleic Acids Res. 2017, 45(5):e30. PMID: 27899618
  5. Fu N, Rios AC, Pal B, Law CW, Liu R, Vaillant F, Jackling F, Liu HK, Smyth GK, Lindeman GJ, Ritchie ME, Visvader JE. Identification of a dormant and spatially-restricted mammary stem cell subset that remains highly responsive to hormones. Nat Cell Biol. 2017, 19:164–76. PMID: 28192422
  6. Law CW, Alhamdoosh M, Su S, Smyth GK, Ritchie ME. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR, F1000Research, 2016, 5:1408. PMID: 27441086
  7. Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME, Asselin-Labat ML, Smyth GK, Ritchie ME. Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Res. 2015;43(15):e97. PMID: 25925576
  8. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. PMID: 25605792
  9. Chen K, Hu J, Moore DL, Liu R, Kessans SA, Breslin K, Lucet IS, Keniry A, Leong HS, Parish CL, Hilton DJ, Lemmers RJLF, van der Maarel SM, Czabotar PE, Dobson RC, Ritchie ME, Kay GF, Murphy JM, Blewitt ME. Genome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation, Proc Natl Acad Sci U S A, 2015, 112(27):E3535-44. PMID: 26091879
  10. White MJ, McArthur K, Metcalf D, Lane RM, Cambier JC, Herold MJ, van Delft MF, Bedoui S, Lessene G, Ritchie ME, Huang DC, Kile BT. Apoptotic caspases suppress mtDNA-induced STING-mediated type I IFN production. Cell. 2014;159(7):1549-62. PMID: 25525874

Further publications