Ian J. Majewski

Mbd4 and MutSα protect cells from spontaneous deamination of 5-methylcytosine.

The paper investigates DNA repair pathways that protect against methylation damage, showing that Mbd4 and MutSα cooperate to prevent spontaneous deamination of 5-methylcytosine.

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.

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.

Detecting copy number alterations in RNA-Seq using SuperFreq

This paper introduces SuperFreq, a method to detect copy number alterations from RNA-Seq data, showing high agreement with DNA-based calls in cancer genomes.

Germline loss-of-function variants in the base-excision repair gene MBD4 cause a Mendelian recessive syndrome of adenomatous colorectal polyposis and acute myeloid leukaemia

Life without mismatch repair

The paper quantifies mismatch repair (MMR) activity in human tissues by analyzing mutation rates in individuals with constitutional MMR deficiency, revealing genotype-specific mutational signatures and the role of MMR components in DNA repair.

Finding a suitable library size to call variants in RNA-seq

The paper evaluates the impact of library size on variant detection sensitivity in RNA-seq, finding that 30M-40M fragments are needed to recover 90%-95% of variants in recurrently mutated myeloid genes.

SuperFreq: Integrated mutation detection and clonal tracking in cancer

SuperFreq detects mutations and tracks clones in cancer samples without requiring matched normal samples, achieving high accuracy in identifying clones and mutations.

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.

Germline loss of MBD4 predisposes to leukaemia due to a mutagenic cascade driven by 5mC

This study shows that germline MBD4 loss causes AML with high C>T mutations due to 5mC deamination, and highlights interactions with somatic DNMT3A mutations.

Dynamic changes in clonal architecture during disease progression in follicular lymphoma

This study analyzes DNA and RNA sequencing data from follicular lymphoma patients to identify mutations and transcriptional changes during transformation to diffuse large B cell lymphoma.