Matthew E. Ritchie

The E3-ome gene-centric compendium reveals the human E3 ligase landscape

<i>Alpseq</i>: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing.

Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End.

<i>SpatialBench</i> : Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue

Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset.

Benchmarking long-read RNA-sequencing technologies with <i>LongBench:</i> a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches

γδ T cells modulate anti-tumor immunity in small cell lung cancer

D4Z4End2End: complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS and reference cohorts

Igniting full-length isoform analysis in single-cell and spatial RNA-seq data with FLAMESv2

stPipe: a flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data.

<i>alpseq</i> : an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing

Comparative Analysis of Single-Nucleus and Single-Cell RNA Sequencing in Human Bone Marrow Mononuclear Cells: Methodological Insights and Trade-offs

<i>stPipe:</i> A flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data

Powerful read processing with <i>matchbox</i>

Towards accurate, reference-free differential expression: A comprehensive evaluation of long-read <i>de novo</i> transcriptome assembly

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

Systematic comparison of sequencing-based spatial transcriptomic methods.

An immunohistochemical atlas of necroptotic pathway expression

Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR.

Establishment of single-cell transcriptional states during seed germination.

Flexiplex: a versatile demultiplexer and search tool for omics data

Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing.

Spotlight on 10x Visium: a multi-sample protocol comparison of spatial technologies

Venetoclax dose escalation rapidly activates a BAFF/BCL-2 survival axis in chronic lymphocytic leukemia.

An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing.

A dataset examining technical factors on fixed white blood cell single-cell RNA-seq.

A streamlined workflow for long-read DNA methylation analysis with NanoMethViz and Bioconductor.

A lipid signature of BAK-driven apoptotic pore formation

Measuring X inactivation skew for retinal diseases with adaptive nanopore sequencing