Marco A. Marra

This study evaluates Parent-of-Origin-Aware genomic analysis (POAga) to improve cascade testing in pancreatic cancer families by clarifying familial risk.

The paper identifies epigenetic differences between HPV-human hybrid and human-only ecDNAs in cervical cancer, showing allele-specific regulation and enhancer activity in hybrid ecDNAs.

GIRAFI improves sparse single-cell proteomics by imputing missing values and revealing cell states using graph-informed statistical learning, outperforming existing methods and recovering biological structure.

The paper introduces a cost-effective single-cell proteomics workflow and a data evaluation framework to improve data quality and biological interpretability.

This study identifies that 3q-gain aneuploidy in squamous cell carcinomas creates a vulnerability to SREBP-pathway inhibition, offering a target for lipid-targeted therapies.

The paper identifies gene expression signatures related to neutrophil extracellular traps (NETs) in pancreatic ductal adenocarcinoma (PDAC) and shows they correlate with patient survival and metastasis, with potential therapeutic targets.

The paper uses long-read sequencing to analyze HPV integration sites in cervical cancer genomes, identifying structural and epigenetic impacts of integration.

This paper presents a long-read sequencing dataset of cancer samples, showing its ability to resolve structural variants, haplotypes, and methylation patterns in precision medicine.

IMPALA detects allele-specific expression in cancer samples and identifies potential regulatory mechanisms influencing ASE.

GRETA is an R package that enables in silico genetic interaction and essentiality network analyses using public data, with documentation and tutorials provided.

The paper uses nanopore sequencing to detect imprinted differentially methylated regions in human B-lymphocyte cell lines, identifying known and novel DMRs and showing conservation across species.

PORI is an open-source platform for interpreting somatic variants in cancer, demonstrating that 88.2% of TCGA tumors have at least one potentially targetable alteration.

The paper optimizes a magnetic bead-based nucleic acid extraction protocol for SARS-CoV-2 testing to reduce cross-well contamination while maintaining sensitivity.

This study identifies genetic drivers of mantle cell lymphoma through exome and genome sequencing, revealing novel mutations in genes involved in RNA splicing and regulation.

This study identifies somatic coding and regulatory variants in DLBCL, revealing novel mechanisms of oncogene deregulation and potential therapeutic targets.

This study characterizes genomic, transcriptomic, and epigenomic artifacts in FFPE tissues and provides best practices to mitigate their impact on molecular analysis.