Knut Dagestad Rand

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

KAGE2 improves structural variant genotyping by using pangenomes, offering higher accuracy and speed compared to existing methods.

GKAGE is a GPU-accelerated genotyper that improves the speed of SNP and short indel genotyping by an order of magnitude compared to CPU-based methods like KAGE.

BioNumPy enables efficient array programming on biological data using Python, outperforming vanilla Python and other packages while matching C/C++ speeds for common bioinformatics tasks.

KAGE is a fast and accurate alignment-free genotyper for SNPs and short indels using a pan-genome representation and Bayesian modeling.

immuneML provides an open-source ecosystem for reproducible and interoperable machine learning analysis of adaptive immune receptor repertoires, demonstrating its utility through benchmarking and novel methods.

The paper evaluates two graph-based read mappers against a hybrid baseline approach, showing the baseline improves mapping accuracy to graph-based references.

The paper shows that the choice of metric significantly affects genomic co-occurrence analysis and proposes alternative approaches to guide this choice.

The paper introduces a method for calling ChIP-Seq peaks on graph-based reference genomes and demonstrates its ability to detect more motif-enriched peaks than MACS2.

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

The paper introduces a method to represent genomic intervals on graph-based reference genomes and demonstrates it on the GRCh38 human genome.