William Stephenson

Direct RNA Sequencing reveals epitranscriptomic regulation of brain cells and Alzheimer's Disease pathology

This study uses direct RNA sequencing to analyze epitranscriptomic changes in brain cells, revealing m6A modification patterns linked to Alzheimer's disease progression.

Benchmarking long-read RNA-seq across modalities, methods, and sequencing depth in iNeurons

This study benchmarks long-read RNA-seq across bulk and single-cell platforms, technologies, and sequencing depths, identifying optimal methods for transcript discovery and quantification.

Fibroblastic FLT3L supports lymph node dendritic cells in the interfollicular niche

The paper identifies Grem1-expressing fibroblastic reticular cells as a source of FLT3L that supports dendritic cell homeostasis and function in lymph nodes.

Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer

This study introduces scTaILoR-seq, a long-read targeted RNA sequencing method, to enhance single-cell transcriptome analysis and identify isoform variation and SNV associations in ovarian cancer.

Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles

Isosceles improves isoform detection and quantification accuracy in single-cell and bulk RNA-seq data using nanopore long-reads.

Transcriptional dysregulation and impaired neuronal activity in FMR1 knock-out and Fragile X patients iPSC-derived models.

This study compares FMR1 knock-out and Fragile X patient iPSC-derived neuronal models, finding shared transcriptional and functional impairments in neuronal activity and differentiation.

Direct detection of RNA modifications and structure using single molecule nanopore sequencing

This paper demonstrates direct detection of RNA modifications and structure using single molecule nanopore sequencing, showing it can identify endogenous and exogenous modifications in rRNA from E. coli and S. cerevisiae.

isoformant: A visual toolkit for reference-free long-read isoform analysis at single-read resolution

isoformant analyzes long-read RNA sequencing data to identify isoform consensus sequences without a reference genome, enabling differential isoform usage comparisons across samples.

PySeq2500: An open source toolkit for repurposing HiSeq 2500 sequencing systems as versatile fluidics and imaging platforms.

PySeq2500 converts the HiSeq 2500 into an open platform for programmable fluidics and imaging, enabling automated multi-day workflows for multiplexed imaging of biological samples.

Single-Cell RNA-Seq Of Rheumatoid Arthritis Synovial Tissue Using Low Cost Microfluidic Instrumentation

The paper develops a low-cost microfluidic instrument for scRNA-seq and applies it to profile synovial tissue from a rheumatoid arthritis patient, identifying 16 transcriptomic clusters and fibroblast subpopulations.

Large-scale simultaneous measurement of epitopes and transcriptomes in single cells.

The paper introduces a method to simultaneously measure epitopes and transcriptomes in single cells using oligonucleotide-labeled antibodies.