Bioinformatics & computational biology
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- MintCNA: A Unified Framework for Integrative Copy Number Profiling with Single-Cell Multi-Omics Data
- BOSE: A Bayesian Order Statistics-Based Estimator for Recovering the Sample Mean and Standard Deviation from the Median, Range, and/or Interquartile Range
- PP-MAPS: Dynamic Pharmacophore Signatures of Protein–Peptide Interfaces from Molecular Dynamics Trajectories
- A High-Quality Acetylation Dataset Reveals Modest Data Requirements for Transfer Learning to Identify Little Studied Post-Translational Modifications
- PlantGeneAnn: a high-accuracy ab initio plant gene annotation tool fine-tuned from a genome foundation model
- AI-guided discovery for low-resource peptide engineering using evolutionary scale modeling
- Stability-driven multi-omics integration for reproducible latent structure
- PanRes: A database of latent and acquired antimicrobial resistance allowing 3D-based protein homology search
- Kinetics of template-directed multistate copolymerization
- CNSigs: An R Package for the Identification of Copy Number Mutational Signatures
- A Visually Interpretable Histopathology-Based Immune Model Predicts T-effector Biology and Response to Immune checkpoint inhibition in Clear Cell Renal Cell Carcinoma Clinical Trial and Contemporary Real-World Datasets
- Antibody-Antigen Affinity Prediction with Chain-Aware Protein Language Modeling
- EventHorizon: A Foundation Model for Clinical Flow Cytometry
- fuzzyfold: a high-performance framework for stochastic RNA folding kinetics
- DeepCDS: Ab initio coding sequence prediction in prokaryotic short nucleotide sequences
- Virus-human protein-protein interactions predict viral phenotypes
- Censoring-aware Gaussian process modeling identifies time informative functional dynamics associated with spoilage status of modified atmosphere packaged broiler meat
- RepGene: Auditing Condition-Specific Fusion Biases for Multi-View Gene Representations
- DAQplugin: Interactive Deep Learning-Based Validation of Cryo-EM Protein Models in ChimeraX
- Structured biological evidence enables general-purpose language models to predict bacteriophage-host interactions
- A Graph-based QSAR Modeling Pipeline for Predicting In vitro PubChem Assays and In vivo Human Hepatotoxicity: Mechanistic Analysis of Caspase-3/7 Activation
- [Re] Computational Modelling of Glucose Uptake by SGLT1 and Apical GLUT2 in the Enterocyte
- PhyloZoo: a unified framework for phylogenetic network analysis in Python
- OmniBioTwin: A System-of-Twinned-Systems Framework for Health Digital Twins
- HOMED enables hierarchical and multimodal optimization of DNA methylation deconvolution across tissues