Michael B. Clark

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.

Alternative promoters used during myeloid differentiation and upon activation change the gene products available for innate immune programs.

The paper identifies new gene products and transcript isoforms in macrophage differentiation and activation, revealing how alternative promoters influence innate immune functions.

Powerful read processing with matchbox

matchbox provides a flexible and scalable read processor for handling diverse sequencing tasks, demonstrating versatility in demultiplexing, restranding, CRISPR efficiency assessment, and haplotyping.

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.

Isoform-level profiling of m6A epitranscriptomic signatures in human brain

The paper uses Oxford Nanopore DRS to profile m6A modifications at the isoform level in human brain regions, identifying thousands of m6A sites and region-specific patterns.

Fear extinction is regulated by long noncoding RNA activity at the synapse

The paper identifies a lncRNA, Gas5, involved in fear extinction by regulating RNA granule trafficking and clustering at synapses in mice.

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.

NanoSplicer: Accurate identification of splice junctions using Oxford Nanopore sequencing

NanoSplicer identifies splice junctions from Oxford Nanopore sequencing data without relying on short-read data or annotations, improving accuracy in high-error regions.

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.

RNA sequencing identifies a cryptic exon caused by a deep intronic variant in NDUFB10 resulting in isolated Complex I deficiency.

The paper identifies a deep intronic variant in NDUFB10 causing a cryptic exon and isolated Complex I deficiency through RNA sequencing in two affected siblings.

Long-read sequencing reveals the splicing profile of the calcium channel gene CACNA1C in human brain

The paper uses long-read sequencing to uncover the complex splicing profile of the CACNA1C gene in human brain, identifying numerous novel exons and transcripts with potential functional implications.

Universal Alternative Splicing Of Noncoding Exons

The paper identifies that nearly all noncoding exons undergo alternative splicing, generating a vast repertoire of regulatory RNAs and highlighting conserved splicing patterns across species.