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List of works by Matthew E Ritchie

A comparison of background correction methods for two-colour microarrays

scientific article

A guide to creating design matrices for gene expression experiments

publication published on 10 December 2020

A new lymphoid-primed progenitor marked by Dach1 downregulation identified with single cell multi-omics

scientific article published on 19 October 2020

A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1.

scientific article

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data

scientific article

A transcriptomic dataset evaluating the effect of radiotherapy injury on cells of skin and soft tissue

publication published on 14 January 2022

Allele-specific expression analysis methods for high-density SNP microarray data.

scientific article

Apoptotic caspases suppress mtDNA-induced STING-mediated type I IFN production

scientific article published in December 2014

Author Correction: The neuropeptide VIP confers anticipatory mucosal immunity by regulating ILC3 activity

scientific article published on 01 March 2020

BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation

scientific article published on 29 March 2022

BASH: a tool for managing BeadArray spatial artefacts

scientific article published on 25 October 2008

BeadArray expression analysis using bioconductor.

scientific article published on December 2011

Benchmarking UMI-based single-cell RNA-seq preprocessing workflows

scientific article published on 14 December 2021

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

scientific article published on 27 May 2019

BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem.

scientific article

Cisplatin Increases Sensitivity to FGFR Inhibition in Patient-Derived Xenograft Models of Lung Squamous Cell Carcinoma.

scientific article published on 13 June 2017

Combining multiple tools outperforms individual methods in gene set enrichment analyses

scientific article

Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips

scientific article published on 8 March 2011

Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

scientific article published on 11 November 2021

Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms.

scientific article published on 19 January 2009

Covering all your bases: incorporating intron signal from RNA-seq data

scientific article published on 22 September 2020

Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with <i>Glimma</i> 2.0.

scientific article published on 22 December 2021

Data analysis issues for allele-specific expression using Illumina's GoldenGate assay

scientific article

Deciphering the Innate Lymphoid Cell Transcriptional Program

scientific article published in October 2016

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

scientific article published on 13 September 2019

Easy and efficient ensemble gene set testing with EGSEA.

scientific article published on 14 November 2017

Empirical array quality weights in the analysis of microarray data

scientific article

Epigenetic modulators of B cell fate identified through coupled phenotype-transcriptome analysis

scientific article published in 2022

Functional and metabolic remodelling in GLUT4-deficient hearts confers hyper-responsiveness to substrate intervention

scientific article

Gene expression changes during step-wise differentiation of embryonic stem cells along the inner ear hair cell pathway

scientific article published in December 2006

Gene network disruptions and neurogenesis defects in the adult Ts1Cje mouse model of Down syndrome

scientific article

Genome-wide binding and mechanistic analyses of Smchd1-mediated epigenetic regulation

scientific article published on 19 June 2015

Germline heterozygous mutations in Nxf1 perturb RNA metabolism and trigger thrombocytopenia and lymphopenia in mice

scientific article published on 01 April 2020

Glimma: interactive graphics for gene expression analysis

scientific article published on 15 February 2017

Global changes in the mammary epigenome are induced by hormonal cues and coordinated by Ezh2.

scientific article

High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS).

scientific article

High-LET Radiation Increases Tumor Progression in a K-Ras-Driven Model of Lung Adenocarcinoma.

scientific article

High-resolution transcription atlas of the mitotic cell cycle in budding yeast

scientific article (publication date: 2010)

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.

scientific article

Identification of quiescent and spatially restricted mammary stem cells that are hormone responsive.

scientific article

Illumina WG-6 BeadChip strips should be normalized separately

scientific article

Integrative analysis of RUNX1 downstream pathways and target genes

scientific article

Interferon-gamma released from omental adipose tissue of insulin-resistant humans alters adipocyte phenotype and impairs response to insulin and adiponectin release

scientific article published on 3 August 2017

KRLMM: an adaptive genotype calling method for common and low frequency variants

scientific article

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

scientific article published on 7 December 2013

Loss of PUMA (BBC3) does not prevent thrombocytopenia caused by the loss of BCL-XL (BCL2L1).

scientific article

Microarray background correction: maximum likelihood estimation for the normal-exponential convolution

scientific article published on 08 December 2008

Modifier effects between regulatory and protein-coding variation

scientific article

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

scientific article published on 7 April 2014

Myocardial Gene Expression Associated with Genetic Cardiac Hypertrophy in the Absence of Hypertension

article

NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data

scientific article published on 25 October 2021

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

scientific article published on 5 May 2010

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.

scientific article published on 06 August 2009

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

scientific article published in 2016

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.

scientific article published on 17 June 2016

RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods

scientific article

Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung

scientific article

Sensitization of BCL-2-expressing breast tumors to chemotherapy by the BH3 mimetic ABT-737

scientific article published on 18 July 2011

Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing

scientific article published on 18 May 2016

Spike-in validation of an Illumina-specific variance-stabilizing transformation

scientific article

Statistical issues in the analysis of Illumina data

scientific article

Swift: primary data analysis for the Illumina Solexa sequencing platform.

scientific article

Targeting BCL-2 with the BH3 mimetic ABT-199 in estrogen receptor-positive breast cancer

scientific article

Targeting BCL-2–expressing basal-like breast cancer with BH3-mimetics.

scientific article

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

scientific article published on 27 April 2020

The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools

scientific article published on 26 April 2021

The neuropeptide VIP confers anticipatory mucosal immunity by regulating ILC3 activity

scientific article published on 23 December 2019

Thymospheres Are Formed by Mesenchymal Cells with the Potential to Generate Adipocytes, but Not Epithelial Cells.

scientific article published in October 2017

Transcriptional Profiling of Individual Airway Projecting Vagal Sensory Neurons

scientific article published on 19 October 2019

Transcriptional profiling of the epigenetic regulator Smchd1.

scientific article published on 31 December 2015

Transcriptome and H3K27 tri-methylation profiling of Ezh2-deficient lung epithelium

scientific article

Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal

scientific article published on 15 May 2020

Using the R Package crlmm for Genotyping and Copy Number Estimation.

scientific article published on May 2011

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

scientific article

beadarray: R classes and methods for Illumina bead-based data.

scientific article

edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens

scientific article

illuminaio: An open source IDAT parsing tool for Illumina microarrays

scientific article published on 04 December 2013

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

scientific article (publication date: 20 April 2015)

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data

scholarly article by Luyi Tian published in August 2018

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