Sigve Nakken

The paper maps the tumor microenvironment in DLBCL using imaging mass cytometry and finds that immune-cell depleted tumors have reduced MHC-I expression and worse survival.

The paper introduces CANCAN, a computational framework for analyzing copy number and mutation heterogeneity in DNA sequencing data, showing high concordance with existing methods and improved performance on targeted sequencing data.

This study uses deep learning and time-resolved imaging to map the genetic network controlling autophagy dynamics, revealing a hierarchical control mechanism and new regulatory aspects.

This study identifies cooperative and suppressive interclonal interactions during early Ras-driven tumourigenesis using a Drosophila model, revealing key modifiers like SWI/SNF and cell competition regulators.

This study uses information theory to analyze CRISPR screens and quantifies gene function through geometric measures of selection dynamics and environmental perturbations.

This study identifies SYTL5 as a RAB27A effector that regulates mitophagy and mitochondrial metabolism, with reduced expression linked to poor survival in adrenocortical carcinoma.

StarSignDNA is an algorithm for mutational signature analysis in cancer sequencing data, improving accuracy and biological validity by addressing overfitting and underfitting.

CPSR generates structured reports of germline variants in cancer predisposition genes using ACMG criteria, with customizable gene panels and actionable findings.

The paper shows that sample-index misassignment in tumor exome sequencing can create false somatic variant calls and recommends dual indexing to prevent this.

The paper introduces a tool for interpreting cancer genomes by generating prioritized variant reports for clinical use.

GSuite HyperBrowser provides a platform for integrative analysis of genome and epigenome datasets with customizable statistical methods and a Galaxy-based interface.

This study benchmarks somatic mutation calling in cancer genomes, identifying inconsistencies and proposing solutions to improve accuracy.