Sven Nahnsen

Genomic correlates of metastatic competence and progression in human melanoma

This study identifies genomic features, particularly copy-number alterations, that predict metastatic progression in melanoma and defines a six-gene signature associated with relapse.

From Abandoned Scripts to FAIR Community Pipelines: Rescuing Orphan Bioinformatics Workflows with nf-core - Lessons from Light-Sheet Fluorescence Microscopy

The paper re-engineers an abandoned MATLAB-based image analysis toolkit into a sustainable, FAIR-compliant Nextflow workflow for light-sheet microscopy.

Deep learning enables direct HLA typing from immunopeptidomics data

This paper introduces Immunotype, a deep learning model that directly types HLA alleles from immunopeptidomics data with 87.2% accuracy.

Resistance Training Reshapes the Gut Microbiome for Better Health

This study shows resistance training causes time-dependent gut microbiome changes, especially in those with greater strength gains, enriching health-associated taxa like Faecalibacterium and Roseburia hominis.

t2pmhc: A Structure-Informed Graph Neural Network to predict TCR-pMHC Binding

The paper introduces t2pmhc, a structure-informed graph neural network for predicting TCR-pMHC binding, showing improved generalization to unseen peptides compared to existing methods.

Empowering bioinformatics communities with Nextflow and nf-core

This paper discusses the adoption of Nextflow and nf-core frameworks to standardize bioinformatics pipelines, improving collaboration and interoperability across research communities.

nf-core/detaxizer: A Benchmarking Study for Decontamination from Human Sequences

The paper benchmarks decontamination tools for removing human sequences from metagenomic data, showing significant variation in effectiveness among tools.

Building pangenome graphs

This paper introduces PGGB, a pipeline for building pangenome graphs that includes all variation without bias, enabling variation detection, conservation measurement, recombination event detection, and phylogenetic inference.

Cluster efficient pangenome graph construction with nf-core/pangenome

The paper introduces nf-core/pangenome, a scalable and reference-unbiased pipeline for constructing pangenome graphs, achieving faster performance than PGGB on large datasets.

nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework

The paper introduces nf-core/airrflow, a Nextflow-based workflow for processing AIRR-seq data, validated on simulated and real datasets to analyze immune receptor repertoires.

Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery

The paper presents an optimized variant calling pipeline that reduces storage and runtime costs for DNA sequencing analysis.

How tool combinations in different pipeline versions affect the outcome in RNA-seq analysis

The paper compares RNA-seq pipeline versions and tool combinations to assess their impact on differential expression and gene classification consistency across species.

nf-root: a best-practice pipeline for deep learning-based analysis of apoplastic pH in microscopy images of developmental zones in plantroot tissue

nf-root automates apoplastic pH analysis in plant root images using deep learning, achieving near-human performance and reducing analysis time.

Pangenome graph layout by Path-Guided Stochastic Gradient Descent

This paper introduces a graph layout algorithm for pangenome graphs, enabling efficient visualization of large-scale genomic data.

ODGI: understanding pangenome graphs

ODGI is a tool suite for analyzing pangenome graphs, enabling efficient exploration and manipulation of large-scale genomic data.

nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning

The paper introduces a pipeline for metagenome assembly and binning using Nextflow, enabling the reconstruction of MAGs from shotgun metagenomic data.

Efficient data management infrastructure for the integration of imaging and omics data in life science research

The paper proposes a FAIR-compliant data management system integrating imaging and omics data using Service Oriented Architecture principles, demonstrating its use in plant biology and hepatocellular carcinoma studies.

nf-core: Community curated bioinformatics pipelines

A peer-reviewed, community-run framework for Nextflow analysis pipelines, plus helper tooling, meant to make workflows portable and reproducible across institutions rather than tied to one cluster.