Bioinformatics & computational biology
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- Documenting Trofinetide Treatment Phenotypes in Rett Syndrome with a Dual-LLM Consensus Pipeline
- Poisoning the corpora of protein design systems during pre-training and retrieval
- OmicsBench: a long-horizon multi-turn benchmark of AI agents on research-study-scale bioinformatics
- RetroTAC: Learning Route-Derived Synthetic Accessibility for PROTACs
- MorphoBranch: A Fine-Structure-Preserving Workbench for Morphometric Analysis of Branched Cellular Structures
- Sequence-only prediction of VHH nanobody epitopes and paratopes on HER2 with a frozen protein language model ( ESM2) and a structure-derived residue prior
- LKOM: Longitudinal Knockoff with Masked Likelihood Ratio for FDR-Controlled Association Discovery
- Robust Identification of Drug Mechanism of Action Associated Genes Across Heterogeneous Drug Treated Datasets
- CPMsi: a data-driven Computational Pipeline for fast, large-scale Mass Spectrometry Imaging analysis
- Differential sensitivity of k-mer based identification tools using closely related database sequences affects relative abundance estimation
- GENOAR: Global Engine for Navigating the Omnicell space via Agent-based Research
- CnidoSite: A Multi-Omics Database for Cnidarians
- A computable probability landscape for T cell receptor repertoire sampling and comparison
- Going beyond labels: Semi-supervised learning for enzyme kinetic parameter prediction
- DEEP: Extracting Latent Energetic Landscapes from Protein Structure Predictors
- The Role of Environmental Information and the Limitations of Predictability with Transformer-based Time-Series Models for complex Astrocyte Trajectories
- LoCoFlow: Local-Context Flow Matching for Single-Cell Dynamics and Fate Inference
- GEO-BERT: A Retrieval augmented LLM Framework for Intelligent Dataset Retrieval from the Gene Expression Omnibus
- Combining RNA-seq and proteomics boosts sensitivity to detect differentially expressed genes by rpMeta
- BiNVaST: niche boundary-preserving and synthetic data-guided variational autoencoders for concordant inference across high-resolution spatial transcriptomic platforms
- Optimal transport reveals unresolved cells in single cell multi-omics
- In Other Words: Learning When to Trust Generated Protein Function Descriptions
- Single-nucleus chromatin accessibility time course of excisional wound repair in rat skin
- RiboBridge couples RNA backbone generation to sequence design through a learned interaction topology
- Scalable Enzyme Reaction Retrieval Enables Metagenomic Biocatalyst Discovery