Bioinformatics & computational biology
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- Fine-Grained and Reliable Cell Classification from Pathology Images
- pyreml: a general-purpose, GPU-accelerated mixed model solver in Python
- Two opposite failure modes in alignment-based conservation scores, one inflating and one concealing constraint, are computable before the score is used
- Language models annotate mass cytometry clusters within the range where human experts disagree
- The GA4GH Workflow Execution Service: A Standard API for Workflow Execution and Management in Genomics
- Multi-scale microenvironment covariance for unsupervised spatial domain identification
- A physics-informed neural network framework for inferring infinitesimal phase response curves from finite-pulse circadian recordings
- CAI-Vax: Computational Design of Personalized mRNA Cancer Vaccine Constructs After Antigen Selection
- Denoising single-cell ATAC-seq data with Shannon entropy
- Averaging in gene perturbation benchmarks hides perturbation-strength variation: Consequences for model evaluation
- UnibindMD: An Integrated AI and Molecular Dynamics Platform for De Novo Peptide Binder Design
- PROTFIG: one-command, publication-quality biomolecular figures
- LiverHomo: An Integrated and Interactive Human Liver Single-Cell Atlas with Protein Interaction and Cell-Cell Communication Networks
- T2G: fast and accurate transcriptome to genome BAM liftover for short and long read RNA sequencing
- Locally deployed AI agents for CRISPR guide discovery from outbreak reports
- Helix Design Studio: designing antimicrobial peptide candidates for membrane environments
- PhyloScore: Improved covariation score for RNA alignments using phylogeny
- Evaluation of object detection neural networks to find topologically associated domains in bulk Hi-C data
- RiboTxAlign maps and quantifies ribosome footprints using sample-specific transcript references
- When do hybrid models help? Combining mechanistic modelling and machine learning to predict gene regulatory network dynamics
- ct-validation: an open framework for benchmarking target-indication evidence against clinical trial outcomes
- ALHENA, an H&E encoder distilled from transcriptomic foundation models for multi-scale slide analysis
- QProtFuse: Query-Guided Layer Fusion for Retrieval-Augmented Protein Function Prediction
- EMBER: Predicting TCR--pMHC Binding Without a Docked Complex
- Cross-disorder Learning of Imaging-derived Joint Mophometric Markers in Alzheimer's and Parkinson's Diseases