Yair D. J. Prawer

GenomeProt: User friendly proteogenomics for canonical and non-canonical proteoform characterisation

GenomeProt integrates genomics, transcriptomics, and proteomics to characterise proteoforms, discovering novel proteins and variant-containing peptides in human brain and melanoma samples.

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 reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain

The paper uses long-read sequencing to identify novel RNA isoforms in neuropsychiatric risk genes, revealing previously undetected exons and isoforms that may contribute to disease mechanisms.

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.

Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE

BLAZE identifies 10x cell barcodes from long-read nanopore scRNA-seq data without requiring matched short-read data, outperforming existing tools in accuracy and reducing false positives.

Discovery of NRG1-VII: a novel myeloid-derived class of NRG1 isoforms

The paper identifies a new class of NRG1 isoforms, NRG1-VII, expressed in myeloid cells and suggests it may be the most common NRG1 class in adult tissues outside the brain.

Proliferation drives quorum sensing of microbial products in human macrophage populations

This study compares proliferation and tolerance in tissue-resident and recruited macrophages using single-cell RNA sequencing, finding that proliferative capacity differs between cell types.

Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing

The paper develops FLT-seq and FLAMES to characterize full-length isoforms in single cells of human and mouse, identifying thousands of unannotated isoforms and linking them to functional modules and drug resistance mutations.

Nanopore direct RNA sequencing detects differential expression between human cell populations

This study uses nanopore direct RNA sequencing to accurately detect differential gene and isoform expression between human cell populations during differentiation.

The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read tools

This study analyzes nanopore long-read RNA-seq data using short-read tools to assess differential gene and isoform expression in synthetic and mouse datasets.