AIMC Journal:
bioRxiv

Showing 631 to 640 of 4938 articles

Perturbation response decomposition enables biologically aligned generalization to unseen perturbations and cellular contexts

bioRxiv Jul 27, 2026
Predicting single-cell responses to genetic perturbations could reveal the vast combinatorial space of perturbations and cellular contexts that is infeasible to measure experimentally, yet current deep learning models generalize poorly and often fail...
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Interpretable gene networks from single-cell foundation models reveal conserved neurogenic dysfunction in Parkinson's disease

bioRxiv Jul 27, 2026
Interpreting large-scale singlecell transcriptomic data remains a major challenge for understanding disease mechanisms. Recent single-cell foundation models learn rich representations of gene relationships across millions of cells, yet methods for tr...
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Spaceland: Histology-Guided Reconstruction of High-Resolution Whole-Organ 3D Molecular Atlases from Sparse Spatial Transcriptomics

bioRxiv Jul 27, 2026
Reconstructing whole organs in three-dimensional molecular detail is a key step toward building virtual organs for modeling tissue organization, disease progression and drug perturbation responses. However, high-resolution whole-organ spatial transcr...
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A generalizable speech neuroprosthesis

bioRxiv Jul 27, 2026
Intracortical brain-computer interfaces (BCIs) can restore communication to people with vocal tract paralysis by decoding cortical activity during attempted speech into text. State-of-the-art systems pairing neural-to-phoneme decoders with phoneme-to...
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Explainable Artificial Intelligence for Cross-Dataset Generalizable Biomarker Discovery in Cardiovascular diseases (CVDs)

bioRxiv Jul 27, 2026
CVDs are heterogeneous, multifactorial disorders that remain the leading cause of global mor- tality from infancy to old age. It requires an early identification and treatment of risk factors to accelerate disease prevention and morbidity improvement...
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B-SMART-Former: An Explainable Transformer-Based Deep Learning Model for Predicting Drug-Drug Interactions Between Biotech and Small-Molecule Drugs

bioRxiv Jul 27, 2026
Drug-drug interactions between biotech and small-molecule drugs play a critical role in medication safety and therapeutic efficacy. However, most existing computational DDI prediction methods focus primarily on interactions between small-molecule dru...
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Chromatin state shapes site-specific A-to-I RNA editing

bioRxiv Jul 27, 2026
Adenosine-to-inosine (A-to-I) RNA editing is a widespread post-transcriptional mechanism that diversifies the transcriptome. While ADAR enzymes catalyze this reaction, the upstream mechanisms that determine why individual adenosines are edited at mar...
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Ontology-guided harmonization enables unified discovery of public metabolomics studies within and across repositories

bioRxiv Jul 27, 2026
Public metabolomics repositories contain thousands of studies, but differences in metadata structure, vocabulary, and repository-specific terms still limit reliable search, comparison, and reuse within and across databases. Here we present HARMONY, a...
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Deep learning enables cross-species annotation and attribution of ageing states in haematopoietic stem and immune cells

bioRxiv Jul 26, 2026
Cross-species transfer is a central bottleneck in single-cell ageing research: mouse studies provide experimentally tractable age labels, whereas human datasets are scarcer and strongly shaped by species-specific transcriptomic and chromatin programs...
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A Reproducible MFASS Benchmark of Splice-Disruption Predictors Reveals a Shared Exon-Interior Blind Spot

bioRxiv Jul 26, 2026
We benchmark four published splicing variant-effect predictors against a multiplexed experi- mental splicing assay. On 27,733 single-nucleotide variants in and around human exons from MFASS with measured exon-inclusion outcomes, Pangolin is the stron...
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