Armin Scheben

Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data

This paper introduces BEAM, a Bayesian framework for inferring tissue migration histories in metastatic cancer from lineage tracing data, showing improved performance over existing methods.

A patient-derived ovarian cancer organoid platform to study susceptibility to natural killer cells

The paper develops a live cell imaging assay using patient-derived ovarian cancer organoids to study natural killer cell-mediated apoptosis and identifies resistant organoid populations.

Extensive modulation of a conserved cis-regulatory code across 589 grass species

The paper identifies a conserved cis-regulatory code across 589 grass species and finds that motif conservation declines rapidly but remains significant over evolutionary time, with adaptive changes linked to ecological transitions.

Extreme mobility creates contrasting patterns of panmixia, isolation-by-distance and hybridization in four flying-fox species (Pteropus)

This study examines population genetics in four flying-fox species, finding isolation-by-distance, hybridization, and recent secondary contact shaping their evolution.

Extensive genome evolution distinguishes maize within a stable tribe of grasses

The paper examines genome evolution in maize and related grasses, revealing variable outcomes of polyploidy across species.

Differences in activity and stability drive transposable element variation in tropical and temperate maize.

The paper develops a pan-TE annotation tool to analyze TE variation in maize, finding that tropical maize has more TE sequences due to active and less methylated LTR retrotransposons.

Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model

The paper introduces PlantCaduceus, a DNA language model for plants, showing high transferability across species and improved performance in mutation prediction and variant identification.

Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification

This study evaluates AlphaMissense's ability to classify ASNS variants in ASNSD, finding it accurately identifies most known pathogenic variants and provides a useful tool for variant classification.

Long-read sequencing reveals rapid evolution of immunity- and cancer-related genes in bats

This study uses long-read sequencing to analyze immune and cancer-related gene evolution in bats, finding gene contractions, expansions, and positive selection linked to their unique traits.

Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution

The paper constructs a duck pan-genome and identifies transposon-derived structural variations linked to bodyweight and white plumage traits in ducks.

Two independent approaches converge to the cloning of a new Leptosphaeria maculans avirulence effector gene, AvrLmS-Lep2

The paper clones a new avirulence gene, AvrLmS-Lep2, using two independent methods and confirms its role in inducing resistance in Brassica napus.

A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants

The paper develops a multiple genome alignment workflow for plants, showing that k-mer masking and parameter tuning improve alignment of functional regions.