Deep learning has notably advanced the field of liquid chromatography-mass spectrometry-based proteomics. Accurate prediction of peptide retention times significantly enhances our ability to match LC-MS data with the correct peptides and proteins , especially for DIA data. While numerous models predict peptide LC retention times with high accuracy, few can accurately predict the retention times […]

Mosaic variants, defined as postzygotic mutations occurring during an organism’s development from zygote to adult, play critical roles in developmental biology, aging, and diseases such as cancer and neurological disorders. However, their accurate detection remains challenging due to low abundance in the genome and low variant allelic fractions (VAF). While current mosaic variant callers are […]

Cytokine and chemokine profiling is central to understanding inflammatory processes and the mechanisms driving diverse diseases. We introduce InCytokine, an open source tool for semiquantitative analysis of cytokine and chemokine data generated by protein array technologies. InCytokine features robust and modular image processing workflows, including automated spot detection, template alignment, normalization, quality control measures and […]

Immune systems create antibodies that balance good binding and stability with low toxicity and self-reactivity. Quantifying the nativeness of a candidate sequence – its likelihood of belonging to natural immune repertoires – has thus emerged as a valuable strategy for hit selection from synthetic libraries, optimisation and humanisation, and for guiding de novo design towards […]

Porcine hearts are widely used for preclinical cardiac evaluation. Computational models, by effectively integrating comprehensive experimental data, often reinforce this preclinical assessment. Using extensive multi-modal data, we developed swine ventricular digital twins for healthy and chronic myocardial infarction (MI) conditions to investigate the roles of the cardiac conduction system (CS), spatial repolarization heterogeneities, cardiomyocyte orientation, […]

Despite advances in therapy for inflammatory bowel disease (IBD), current treatments are still associated with poor clinical outcomes and severe systemic side effects. Extracellular vesicles derived from mesenchymal stem cells (MSC-EVs) could have therapeutic applications in IBD due to their regenerative potential and immunomodulatory properties. Previous studies investigating the potential of MSC-EVs in IBD have […]

Accurately predicting gene expression from DNA sequence remains a central challenge in human genetics. Current sequence-based models overlook natural genetic variation across individuals, while population-based models are restricted to variants observed within specific cohorts. Here, we present VariantFormer, a 1.2-billion-parameter transformer that predicts gene-level RNA abundance directly from personalized diploid genomes. Trained on 21,004 genome–transcriptome […]

Genomic functions arise from nucleotide sequences and their overlapping k-mers – subsequences whose contributions depend on their composition, position and associations. Understanding these contributions requires computing a k-mer contribution function that may or may not consider k-mer associations. Neural networks that model associations yield powerful predictors but are notoriously hard to interpret; conversely, models that […]