Matthew E. Ritchie

seqsizzle is a tool for visualizing and troubleshooting long-read sequencing data, enabling primer sequence identification and quality control through fuzzy matching and k-mer analysis.

This study identifies γδ T cell infiltration in SCLC and shows their anti-tumor activity, suggesting they could be therapeutic targets.

The paper develops a CRISPR library for TPD-compatible screens to better identify genetic interactions downstream of protein degradation by reducing UPS resistance dominance.

SpatialBench evaluates spatial transcriptomics platforms using a mouse spleen model, finding consistent biological signals but varying resolution across technologies.

alpseq is an open-source pipeline for processing NGS data from nanobody libraries, enabling efficient analysis and identification of enriched sequences.

matchbox provides a flexible and scalable read processor for handling diverse sequencing tasks, demonstrating versatility in demultiplexing, restranding, CRISPR efficiency assessment, and haplotyping.

This study develops J-DTR mice to deplete antibody-secreting cells with diphtheria toxin and analyze their differentiation kinetics.

FLAMESv2 is a flexible R/Bioconductor package for analyzing long-read single-cell RNA-seq data, demonstrating field-leading performance in isoform analysis and cell-type identification.

This paper develops a ratio-based framework using Quartet reference materials to integrate long- and short-read RNA-seq data, showing hybrid-seq achieves the highest quantification accuracy.

LongBench benchmarks long-read RNA-sequencing technologies using a cross-platform dataset of cancer cell lines, showing high gene-level concordance but reduced transcript-level consistency across platforms.

This study compares single-nucleus and single-cell RNA sequencing in human bone marrow mononuclear cells, identifying method-specific biases and trade-offs.

This paper develops D4Z4End2End, a workflow using long-read sequencing to characterize D4Z4 macrosatellite genetics and methylation in FSHD, BAMS, and reference cohorts, revealing new variants and methylation patterns.

stPipe provides a flexible R/Bioconductor pipeline for preprocessing spatial transcriptomics data from multiple platforms, enabling standardized analysis and benchmarking.

This study evaluates long-read de novo transcriptome assembly tools for differential expression analysis without a reference genome, finding RNA-Bloom2 with Corset as the most accurate and efficient.

TIRE-seq streamlines RNA-seq workflows by integrating mRNA purification into library preparation, improving efficiency and data quality in perturbation studies.

This study uses adaptive nanopore sequencing to measure X inactivation skew in carrier females with X-linked retinal diseases, showing a strong correlation between skew and disease presentation.

This study shows that CLL cells rapidly adapt to venetoclax by upregulating pro-survival proteins and cytokines, suggesting combination therapies targeting these pathways could improve treatment outcomes.

The paper identifies a lipid signature associated with BAK-driven apoptotic pore formation and shows cholesterol inhibits pore formation by preventing BAK clustering.

This study compares six sequencing-based spatial transcriptomic methods using reference tissues, highlighting molecular diffusion as a key variable affecting resolution and identifying unique attributes of spatial transcriptomic data.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

The paper benchmarks spatial transcriptomics technologies using a multi-sample dataset from mouse spleen tissue, finding improved data quality with probe-based capture methods and CytAssist.

Flexiplex is a versatile sequence searching and demultiplexing tool for omics data that balances accuracy and efficiency, demonstrated on single cell RNA-seq and genotyping tasks.

The paper introduces scRaCH-seq, a method for single-cell long-read sequencing that improves detection of isoform usage and mutations in targeted genes, demonstrating its application in CLL samples.

This paper compares long-read sequencing technologies to identify RNA quality issues in lentiviral vectors, finding Nanopore direct RNA sequencing most effective for detecting incomplete RNA.

This paper shows that dividing out quantification uncertainty from transcript counts improves differential expression analysis using edgeR.

scPipe provides a preprocessing pipeline for single-cell ATAC-Seq and multi-modal data in R/Bioconductor, enabling quality control and downstream analysis.

This study identifies a mutation in SMCHD1 that enhances gene silencing and disrupts developmental processes, revealing distinct roles of SMCHD1 in chromatin structure and gene regulation.

The paper introduces two methods to handle group heteroscedasticity in pseudo-bulk single-cell RNA-seq data, showing improved error control and power compared to existing methods.

Restrander improves the orientation and quality control of long-read cDNA data by accurately inferring strandedness and detecting artefacts.

The paper shows that MEK1/2 signaling is essential for male fetal germline development in mice, while FGF signaling has a limited role.