Ritchie, Matthew E.

limma powers differential expression analyses for RNA-sequencing and microarray studies

Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 40,458

Opportunities and challenges in long-read sequencing data analysis

Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020) · Genome Biology

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 2,530

Apoptotic Caspases Suppress mtDNA-Induced STING-Mediated Type I IFN Production

White, M. J., McArthur, K., Metcalf, D., Lane, R. M., Cambier, J. C., Herold, M. J., van Delft, M. F., Bedoui, S., Lessene, G., Ritchie, M. E., et al. (2014) · Cell

interferon and immune responsesCell death mechanisms and regulation

Cited by 983

A comparison of background correction methods for two-colour microarrays

Ritchie, M. E., Silver, J., Oshlack, A., Holmes, M., Diyagama, D., Holloway, A., & Smyth, G. K. (2007) · Bioinformatics

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 907

Empirical array quality weights in the analysis of microarray data

Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic, A., Holloway, A., & Smyth, G. K. (2006) · BMC Bioinformatics

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 312

Systematic comparison of sequencing-based spatial transcriptomic methods

You, Y., Fu, Y., Li, L., Zhang, Z., Jia, S., Lu, S., Ren, W., Liu, Y., Xu, Y., Liu, X., et al. (2024) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 220

Synergy between the KEAP1/NRF2 and PI3K Pathways Drives Non-Small-Cell Lung Cancer with an Altered Immune Microenvironment

Best, S. A., De Souza, D. P., Kersbergen, A., Policheni, A. N., Dayalan, S., Tull, D., Rathi, V., Gray, D. H., Ritchie, M. E., McConville, M. J., et al. (2018) · Cell Metabolism

Genomics, phytochemicals, and oxidative stressFerroptosis and cancer prognosis

Cited by 217

Multidisciplinary diabetes care with and without bariatric surgery in overweight people: a randomised controlled trial

Wentworth, J. M., Playfair, J., Laurie, C., Ritchie, M. E., Brown, W. A., Burton, P., Shaw, J. E., & O'Brien, P. E. (2014) · The Lancet Diabetes & Endocrinology

Bariatric Surgery and OutcomesDiabetes, Cardiovascular Risks, and Lipoproteins

Cited by 144

Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells

Majewski, I. J., Ritchie, M. E., Phipson, B., Corbin, J., Pakusch, M., Ebert, A., Busslinger, M., Koseki, H., Hu, Y., Smyth, G. K., et al. (2010) · Blood

Hematopoietic Stem Cell TransplantationEpigenetics and DNA Methylation

Cited by 135

Distinct initiating events underpin the immune and metabolic heterogeneity of KRAS-mutant lung adenocarcinoma

Best, S. A., Ding, S., Kersbergen, A., Dong, X., Song, J.-Y., Xie, Y., Reljic, B., Li, K., Vince, J. E., Rathi, V., et al. (2019) · Nature Communications

Lung Cancer Treatments and MutationsProtein Kinase Regulation and GTPase Signaling

Cited by 108

A guide to creating design matrices for gene expression experiments

Law, C. W., Zeglinski, K., Dong, X., Alhamdoosh, M., Smyth, G. K., & Ritchie, M. E. (2020) · F1000Research

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 69

Using the R Package crlmm for Genotyping and Copy Number Estimation

Scharpf, R. B., Irizarry, R. A., Ritchie, M. E., Carvalho, B., & Ruczinski, I. (2011) · Journal of Statistical Software

Genomic variations and chromosomal abnormalitiesGene expression and cancer classification

Cited by 52

Targeting triple-negative breast cancers with the Smac-mimetic birinapant

Lalaoui, N., Merino, D., Giner, G., Vaillant, F., Chau, D., Liu, L., Kratina, T., Pal, B., Whittle, J. R., Etemadi, N., et al. (2020) · Cell Death & Differentiation

Cell death mechanisms and regulationHistone Deacetylase Inhibitors Research

Cited by 51

Laparoscopic adjustable gastric banding and progression from impaired fasting glucose to diabetes

Wentworth, J. M., Hensman, T., Playfair, J., Laurie, C., Ritchie, M. E., Brown, W. A., Skinner, S., Shaw, J. E., & O’Brien, P. E. (2014) · Diabetologia

Bariatric Surgery and OutcomesDiabetes, Cardiovascular Risks, and Lipoproteins

Cited by 16

SIS-seq, a molecular ‘time machine’, connects single cell fate with gene programs

Tian, L., Schreuder, J., Zalcenstein, D., Tran, J., Kocovski, N., Su, S., Diakumis, P., Bahlo, M., Sargeant, T., Hodgkin, P. D., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory)

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 10