Luigi Marchionni

Common germline polymorphisms and somatic cancer mutations exhibit non-random positional overlap across the human genome

The paper identifies non-random positional overlap between common germline polymorphisms and somatic cancer mutations, suggesting intrinsically vulnerable genomic loci.

Transcriptome sequencing of Hodgkin lymphoma Hodgkin and Reed-Sternberg cells reveals escape from NK cell recognition and an unfolded protein response

This study identifies unique transcriptional features of Hodgkin lymphoma HRS cells, including immune evasion mechanisms and an unfolded protein response, distinguishing them from other B-cell lymphomas.

Identifying Rare Germline Variants Associated with Metastatic Prostate Cancer Through an Extreme Phenotype Study

This study identifies rare germline variants associated with metastatic prostate cancer using an extreme phenotype cohort and validates their functional impact.

CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species

CALANGO identifies genotype-phenotype associations across species by integrating genomic, evolutionary, and phenotypic data to uncover biologically relevant molecular mechanisms.

Using Biological Constraints to Improve Prediction in Precision Oncology

The paper develops mechanistic classifiers using biological constraints to improve the robustness and interpretability of gene signatures in cancer prediction.

Multi-omics biomarkers aid prostate cancer prognostication

This study identifies multi-omics prognostic signatures for prostate cancer using transcriptomics and metabolomics data, showing their ability to stratify patients into distinct risk groups.

Unleashing alternative polyadenylation analyses with REPAC

The paper introduces REPAC, a framework for analyzing alternative polyadenylation from RNA-sequencing data, showing it identifies APA changes in B cell activation and is faster than existing methods.

Hobotnica: exploring molecular signature quality

Hobotnica estimates molecular signature quality by assessing their ability to stratify data and assign significance scores for comparing different groups.

Efficient Representations of Tumor Diversity with Paired DNA-RNA Aberrations

The paper introduces a method to represent tumor diversity using paired DNA-RNA aberrations, identifies minimal coverings of aberrant gene pairs, and quantifies heterogeneity through entropy measures across cancer types.

An R Package for Divergence Analysis of Omics Data

The paper introduces an R package for divergence analysis of omics data, demonstrating its use with Cancer Genome Atlas data.

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

Recounting the FANTOM Cage Associated Transcriptome

The paper presents FC-R2, an expanded transcriptome atlas of over 109,000 genes, including lncRNAs, and demonstrates its utility in analyzing gene expression across normal and diseased human samples.

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF

The paper introduces PatternMarkers and GWCoGAPS to identify data-driven biomarkers from whole-genome data using NMF, demonstrating their application on GTex data.