Bioinformatics & computational biology
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- Ontologizer 3: a cross-platform desktop application for frequentist and Bayesian GO enrichment analysis
- Rp-Bp and the Ribotools box for translatome profiling
- A validation approach for RNA structures based on deep-learning 3D-structure predictions
- Aging reshapes cardiac extravascular leukocyte transcription through bidirectional remodeling during LPS-induced endotoxemia
- Continuous Topological Accessibility (RFA) as a 3D-Aware GRN Filter: Anticorrelation with eQTL and No Prediction of ΔRNA
- Res ipSAE adhuc loquuntur: What the directionality of predicted aligned error in cofolding models can tell us about scoring diverse molecular complexes
- From FAIR to AI-FAIR Metadata-First Infrastructure for AI-Enabled Science
- Coupling cellular trajectories and RNA kinetics on continuous expression manifolds with ManifoldVelo
- HistoTx: Early fusion of H&E images and spatial transcriptomics at varying spatial transcriptomics resolution with self-supervised learning
- A Scientific Claim Stability Framework for Evaluating MRI Morphometry Pipelines
- Attribution-based diagnostics for single-cell foundation models
- The DynaCell Evaluation Suite for Dynamic 3D Virtual Staining of Live Cells
- When perfect is a warning: explanations expose shortcuts that accuracy hides in cancer gene-expression classifiers
- Knockdown of a regulatory barcode shifts macrophage polarization destination from M1 to M2 and increases pathogen burden upon S. aureus infection
- Quantifying microbial fitness in high-throughput experiments
- Comparative transcriptomic responses of tomato to Xanthomonas strains isolated from different hosts
- Development and cross-cohort evaluation of a multimodal deep-learning model for ER, PR and HER2 status classification in breast cancer
- irAEGIS: Pathway-guided interpretable prediction of immune-related adverse events
- Comparative Strategies for Handling Imbalanced QSAR Regression: A Case Study on hERG Activity Prediction
- Stand-In Effects and Pooling Amplification: Design-Based Tests of Whether Biological World Models Use Actions
- Cell lines that share a well are not independent observations in the Tahoe-100M drug screen
- Accurate automated photo-identification of Near Eastern and European fire salamanders
- From Tool State to Scientific Action: Auditing Decision Provenance in Biomedical Research Agents
- FACET: Feasibility-Automaton Complete Enumeration and Truncation-Free Scoring of Molecular Formulas from MS/MS
- Can agents reliably design therapeutic antibodies?