N. Davidson

Nailpolish: Reference-free UMI deduplication and consensus read generation

Nailpolish reduces error rates and improves deduplication of UMI-tagged long reads across multiple sequencing technologies and protocols.

seqsizzle: decoding complex barcode and adapter architectures in long-read sequencing data

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.

MNT loss in MYC-driven B lymphoma cells enhances apoptosis, inhibits proliferation and increases sensitivity to cancer drugs.

This study shows that losing MNT in MYC-driven lymphoma cells increases apoptosis, reduces proliferation, and makes them more sensitive to cancer drugs.

IdentifiHR: predicting homologous recombination deficiency in high-grade serous ovarian carcinoma using gene expression

IdentifiHR predicts homologous recombination deficiency in high-grade serous ovarian carcinoma using gene expression, achieving 85% accuracy in TCGA and 91% in an independent cohort.

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

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.

Long-read sequencing-based atlas of tissue-specific expression of Drp1 transcript variants

The paper uses long-read sequencing to map Drp1 transcript variants in human and mouse tissues, revealing tissue-specific expression and isoform-dependent mitochondrial fission activity.

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

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.

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

This study benchmarks Nanopore long read RNA sequencing in human cell lines, showing improved isoform resolution compared to short reads.

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

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.

Flexiplex: A versatile demultiplexer and search tool for omics data

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.

Single-cell Rapid Capture Hybridization sequencing (scRaCH-seq) to reliably detect isoform usage and coding mutations in targeted genes at a single-cell level

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.

Extraction and quantification of lineage-tracing barcodes with NextClone and CloneDetective

The paper introduces NextClone and CloneDetective for extracting and quantifying lineage-tracing barcodes from scRNA-seq and DNA sequencing data.

JAFFAL: Detecting fusion genes with long read transcriptome sequencing

JAFFAL detects fusion genes from long-read transcriptome sequencing with high accuracy, outperforming existing methods and enabling single-cell resolution.

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

MINTIE identifies novel structural and splice variants in transcriptomes using RNA-seq data, outperforming existing methods in detecting a wide range of variants.

ALLSorts: a RNA-Seq classifier for B-Cell Acute Lymphoblastic Leukemia.

ALLSorts classifies B-ALL samples into 18 subtypes and five meta-subtypes using RNA-Seq data with high accuracy.

Fast and accurate differential transcript usage by testing equivalence class counts

The paper introduces a method for differential transcript usage analysis using equivalence class counts, showing comparable sensitivity and speed to exon-level counts.

Clinker: visualising fusion genes detected in RNA-seq data

Clinker visualizes fusion genes detected in RNA-seq data, enabling interpretable analysis of fusion transcripts and breakpoints in B-ALL.

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis

Necklace combines reference and assembled transcriptomes to create a comprehensive superTranscriptome for RNA-Seq analysis, enabling more accurate differential expression testing.