Lauri A. Aaltonen

OMIDIENT is a multi-omics integration method that uses Dirichlet auto-encoders to improve clustering, classification, and data reconstruction across cancer types.

The paper identifies a phosphorylation switch in PAGE4 as a key mechanism in MED12-mutant fibroid pathogenesis, revealing its role in rewiring the interactome and transcriptional machinery.

This study develops IonStats, a toolkit for profiling DNA adducts using nanopore sequencing, revealing compound-specific effects on sequencing data.

This study identifies interferon signaling in epithelial cells as a factor contributing to incomplete response to chemotherapy in colorectal cancer, suggesting potential therapeutic targets.

The paper identifies tissue-specific transposable element enhancers in colorectal and liver cancers using unbiased reporter assays and shows their association with distinct transcription factors and differentially expressed genes.

The paper introduces MuAt, a deep learning model that learns representations of somatic mutations to predict tumour types and subtypes with high accuracy.

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

This study identifies germline genetic variants influencing somatic mutation patterns in 2,642 cancer genomes across 39 cancer types.

This study characterizes mitochondrial genomes in 2,700 cancer patients across 37 types using whole-genome sequencing and RNA-seq, revealing mutational patterns, truncating mutations, and nuclear transfer of mitochondrial DNA.

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

The paper analyzes POLE exonuclease domain mutants in colorectal cancer, identifying mutation spectra differences and a specific TP53 mutation enrichment.

This study identifies retrotransposon insertions in colorectal tumors, linking them to cancer initiation and poor patient survival.

This study shows that combining oncogenes with lineage reprogramming can transform human cells into tumorigenic liver-like cells.

This study identifies five new genetic loci associated with uterine leiomyoma risk and links them to estrogen receptor alpha and genetic stability.

BasePlayer is a software tool for analyzing large-scale NGS data, enabling variant analysis, visualization, and integration of genomic data.