Bioinformatics & computational biology
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- Winnow-tax: sensitive and precise taxonomic profiling of low-coverage organisms in shotgun metagenomes
- Point-Process Modelling of Cell-Type Interaction Structure in CosMx Glioma Data for Hypothesis-Driven Tumor Inference from scRNA-seq
- From Sparse Visits to Continuous Molecular Trajectories with Flow Matching
- DECONVersation: Single Cell Foundation Model-Derived Embeddings for Robust Cell Type Deconvolution of Bulk RNA-seq
- Multimodal reasoning for broadly neutralizing antibody discovery from label-free human B cell repertoires across virus families
- Reliable mechanistic operator recovery with biologically-informed neural networks: principles for architecture and optimisation design
- A likelihood-based framework for simultaneously learning both noise and growth dynamics using biologically-informed neural networks
- Parameter uncertainty in dynamical models: a practical identifiability index
- Probing Genomic Foundation Models with Splice-Variant Perturbations
- When Does a Pathway Score Preserve a Mediated Effect? Aggregation Geometry, Minimax Adequacy, and Gap Inference for High-Dimensional Mediation
- A Weighted Estimation Approach to Correct for Imperfect Mutation Detection Due to Intra-tumor Heterogeneity in Tumor Sequencing
- Exploring noise in TCR specificity data through supervised learning
- mzQC: a versatile way to communicate quality information for biological mass spectrometry
- SIMORGH: Ensemble-Aware Geometric Deep Learning for Apo-State and Cryptic Ligand Binding Site Prediction
- STAVelo: deciphering spatiotemporal cellular dynamics via spatial RNA velocity inference from spatial transcriptomics data
- COPD Preferentially Disrupts Constitutive Redox Support Relative to Inducible Antioxidant Defense
- HapSolo2: GPU-accelerated optimization for removing secondary haplotigs from diploid genome assemblies
- Desktop iDMS: A stand-alone application of intelligent differential mobility spectrometry (iDMS), a neural net-work that predicts optimal separation and compensa-tion voltages for field asymmetric differential ion mobil-ity spectrometry
- "Double-dipping" in testing for phenotypic differences with scRNA-Seq
- Toward a Transferable Representation of Protein Dynamics for Functional Prediction and Mechanistic Discovery
- How many cells resolve a perturbation direction? A closed-form, control-aware cell quota for single-cell perturbation screens
- PIE: Generalizing perturbation effects across unseen perturbations, contexts and datasets
- Tracking two decades of global dengue virus lineage dynamics
- A quantitative interactome map reveals affinity tailored hijacking of human cellular functions by resident and pathogenic bacteria
- Physical determinants of reliable RNA–ligand binding prediction revealed by P-RISE