Rory J. Bowden

A necroptotic-to-apoptotic signaling axis underlies inflammatory bowel disease

This study identifies dysregulated epithelial cell death signaling in inflammatory bowel disease, showing it persists during remission despite therapy.

Active Learning Enables Efficient Directed Evolution of a Far-Red Fluorescent Protein with Minimal Experimental Data

This paper uses active learning to improve a far-red fluorescent protein with fewer experiments, but performance varies between bacterial and mammalian cells.

Patient cerebral organoids capture Alzheimers disease proteomic biomarkers and drug targets

The paper benchmarks proteomic biomarkers and drug targets in patient-derived cerebral organoids against clinical cohorts, finding they detect most candidates and replicate disease changes in a quarter of reproducible markers.

A highly efficient method to differentiate CGRP-expressing peptidergic nociceptors from human induced pluripotent stem cells

This paper describes a method to efficiently differentiate human iPSC into peptidergic nociceptors expressing CGRP and TRPV1, with functional maturity and drug response.

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

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

alpseq: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing

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

TIRE-seq: an Integrated Sample Extraction and Transcriptomics Workflow for High Throughput Perturbation Studies

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

Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data

Castanet is a pipeline for analyzing multi-pathogen enrichment sequencing data, providing accurate consensus sequences and metrics for pathogen detection and quantification.

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

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.

A Risk-reward Examination of Sample Multiplexing Reagents for Single Cell RNA-Seq

This study evaluates sample multiplexing reagents and protocols for scRNA-Seq, finding that workflow improvements and reagent choice impact data quality and cost-effectiveness.

An optimised protocol for quality control of gene therapy vectors using Nanopore direct RNA sequencing

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.

scPipe: An extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor

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

Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures

The paper benchmarks long-read RNA-sequencing tools using synthetic data to evaluate isoform detection and differential expression analysis performance.

Single-cell sequencing of human iPSC-derived cerebellar organoids shows recapitulation of cerebellar development

The paper develops a method to generate cerebellar organoids from human iPSCs and shows they recapitulate key aspects of cerebellar development through single-cell profiling.

Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma

This study evaluates the ability of long-read sequencing to detect somatic variants in a lymphoma patient, highlighting the need for specialized tools and the advantages of long reads for structural variants.

A human single-cell atlas of the Substantia nigra reveals novel cell-specific pathways associated with the genetic risk of Parkinson's disease and neuropsychiatric disorders.

The paper constructs a single-cell atlas of the Substantia nigra and identifies cell-specific gene expression patterns linked to Parkinson's disease and neuropsychiatric disorders.

Oxford Nanopore MinION sequencing enables rapid whole-genome assembly of Rickettsia typhi in a resource-limited setting

This study evaluates the accuracy of Oxford Nanopore MinION sequencing for whole-genome assembly of Rickettsia typhi in resource-limited settings, finding it insufficient for phylogenetic analysis but useful with error correction.

Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)

This paper describes a method to generate full-length HBV genome data using isothermal amplification and sequencing with Nanopore and Illumina, achieving high consensus accuracy and resolving intra-sample variants.

A comprehensive genomics solution for HIV surveillance and clinical monitoring in a global health setting

This paper introduces veSEQ-HIV, a cost-effective, high-throughput sequencing method for HIV that recovers complete genomes and quantifies viral load, enabling drug resistance monitoring and transmission analysis.

Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi

The paper reports high-quality genomes of six Orientia tsutsugamushi strains using long-read sequencing and identifies a small core genome and phylogenetic relationships.

Interferon lambda 4 impacts broadly on hepatitis C virus diversity.

The paper examines the impact of IFN-lambda4 on HCV diversity using host and viral genetic data from 485 patients, finding that IFN-lambda4 variants influence viral amino acid diversity and load.

Insights into platypus population structure and history from whole-genome sequencing

This study uses whole-genome sequencing of platypuses to reveal strong population structure, recent bottlenecks, and genetic relationships across their range.

A practical solution for preserving single cells for RNA sequencing

This paper describes a method using DSP fixation to preserve single cells for RNA sequencing, showing it maintains RNA complexity and reduces technical variability.

Severe infections emerge from the microbiome by adaptive evolution

Severe S. aureus infections arise from the nasal microbiome through adaptive evolution, with specific mutations enriched in infecting bacteria compared to colonizing ones.