Bioinformatics & computational biology
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- Benchmarking of cell type deconvolution techniques for microarray data
- mFrag: Integrating External DNA Methylation References Improves Lung Cancer Early Detection by Fragmentomics
- Cellular composition and the interpretation of candidate RNA readouts of trogocytosis in colorectal cancer
- scSTEC: Annotating Chromatin Subcompartments from Individual Single-Cell Hi-C Data via Direct Two-Dimensional Embedding and Chromosome-wise Consensus
- AI-based structural modelling and pathogenic variant mapping across the human protein interactome
- ARCADE disentangles cell abundance from continuous transcriptional state in spatial transcriptomics
- Protein Pocket Coengagement Prioritizes Drug-Drug Interactions
- LabWeaver: reliable agentic data analysis grounded in laboratory knowled
- Follow-up availability and the robustness of immune transcriptomic recovery after myocardial infarction
- ssGSEA3.0: Feature-Level Bootstrap Resampling for Robust Assessment of Statistical Significance
- FastaGuard: FASTA preflight QC for modern bioinformatics pipelines
- DEEPNET-LLM: Highly accurate structure prediction of unknown metabolites from mass spectra via their molecular neighborhoods
- A comparison of two culture and three sequencing methods for detection of the urobiome
- BioResearchBench: 50 Long Horizon Biological Research Tasks
- CNVision: a computational framework for functional interpretation of intragenic copy number variants
- Ark-ADMET: endpoint-specific selection of molecular representations and hyperparameters for gradient-boosted ADMET models under the Therapeutics Data Commons benchmark protocol
- Phylogeny-Guided Global-Local Shrinkage for Microbiome Feature Selection
- LOTUS: lineage-aware optimal transport reconstructs continuous clonal fate dynamics
- GraphExperiment: infrastructure for high-dimensional quantitative data and associated networks in R/Bioconductor
- Refining RNA-Seq Transcriptome Profiles with Transcript-Specific Minimal-Shared Regions
- A single-cell multimodal foundation model enables cross modality analysis between transcriptome and chromatin
- Automatic Construction of Strong Simple Baselines
- The Findings Workflow: An agentic, collaborative, provenance-tracked framework for scientific data analysis with Claude Code
- Improving Molecular Docking Pose Recovery through Targeted Side-Chain Monte Carlo Sampling of an Apo Structure
- LIMBER: A Hybrid RNA Foundation Model for Predicting and Understanding RNA Structure and Function