Ashley Byrne

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.

Coordinated wound responses in a regenerative animal-algal photosymbiotic metaorganism

This study shows that injury in the acoel Convolutriloba longifissura triggers coordinated responses between the host and its symbiotic algae, mediated by the runt transcription factor.

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.

Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion

Mandalorion v4 improves isoform identification and quantification from full-length transcriptome sequencing data, showing high precision and recall even without genome annotation.

Concordance of MERFISH Spatial Transcriptomics with Bulk and Single-cell RNA Sequencing

The paper compares MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing in mouse liver and kidney, finding MERFISH provides comparable results and robust cell type identification without needing integration with scRNA-seq atlases.

Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing

The paper uses full-length cDNA sequencing to accurately characterize the human immune cell transcriptome, enabling HLA allele typing and adaptive immune receptor repertoire analysis.

Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

The paper depletes hemoglobin transcripts using Long-DASH to improve transcriptome annotation in polar bears, discovering 6,000 high-confidence isoforms and novel genes.

Mountain lion genomes provide insights into genetic rescue of inbred populations

The paper analyzes mountain lion genomes to study genetic rescue effects in inbred populations, finding that translocated individuals quickly lose genetic diversity due to local inbreeding.

R2C2: Improving nanopore read accuracy enables the sequencing of highly-multiplexed full-length single-cell cDNA

R2C2 improves nanopore read accuracy for full-length single-cell cDNA sequencing, enabling more accurate isoform-level transcriptome analysis.

Tn5Prime, a Tn5 based 5’ Capture Method for Single Cell RNA-seq

Tn5Prime is a 5' capture method for RNA-seq that enables accurate transcription start site identification and transcriptome quantification in single cells and bulk samples.

Nanopore Long-Read RNAseq Reveals Widespread Transcriptional Variation Among the Surface Receptors of Individual B cells

The paper uses long-read RNAseq to identify and quantify complex isoforms in individual B cells, revealing widespread transcriptional variation in surface receptors and the antibody heavy chain locus.