Transformer-based models for T-cell response prediction are evaluated under heterogeneous datasets prone to shortcut learning from peptide source features. A domain-aware evaluation scheme is proposed ...

Genome-wide mapping of factors that bind, package, replicate and transcribe DNA continues to be challenging despite rapid advances in DNA sequencing technologies. For nearly two decades, chromatin ...

We selected a total of 637 trait–annotation pairs, with at least one CTS annotation for 36 of 40 traits (25 of 27 independent traits) (Supplementary Table 9); the 637 CTS annotations contained 2.7% of ...

This study introduces two Bioconductor packages, QTLExperiment and multistateQTL, designed to support the analysis of QTL data across multiple biological contexts such as tissues or environmental ...

MOFA is a factor analysis model that provides a general framework for the integration of multi-omic data sets in a completely unsupervised fashion. Intuitively, MOFA can be viewed as a versatile and ...

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