Bioinformatics & computational biology
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- Evidence of active whole-genome doubling (WGD) subclones in non-WGD tumors
- Characterization of immunoglobulin loci in Pongo abelii and Pongo pygmaeus : Insights from multi-genome annotation and IMGT-based curation
- THiRST: Computer Vision Empowered Three-dimensional High-Resolution Spatial Transcriptomics Analytics
- MELD: Mutation Effect Learning through Differential embeddings
- AOPTK: Open-Source Software for AI-Assisted Toxicological Literature Analysis
- Unveiling immune targets via TriStageHLA: high-throughput screening of peptide presentation, peptide-HLA binding, and immunogenicity
- PEEK: integrated primer design for silent-mutation and restriction-site engineering, validated in silico and by whole-plasmid sequencing
- RoDPAA: A Robust Dissimilarity-Based Principal Angle Analysis Framework for Multi-View Microbiome Data Integration
- Differential Gene Expression and Functional Enrichment Analysis of Breast Tumor and Normal Tissue RNA-seq Data: A Reanalysis of GEO Dataset GSE210787
- NeuroWeave-3D: Uncertainty-Aware Evidence Completion for Brain Tumor Segmentation with Missing MRI Modalities
- TileScope quantifies spatial gene expression relationships beyond colocalization
- DoAggregate: a pipeline for aggregation testing for rare-variant on a gene and pathway level
- Integrated transcriptomic and epigenomic profiling of human cartilage reveals coordinated changes in fibronectin expression, splicing, and receptor signaling during osteoarthritis progression
- Unsupervised prioritization of gene-regulatory variants with isolation forests
- PhenoMe: An interactive AI framework for interpretable, microscopy-driven phenotyping
- Bridging Bibliometrics and Biology: A Framework for the Relevance Scoring and Biological Stratification of Scalable MeSH Co-occurrence Networks
- PHATE-Derived Ancestry Coordinates Capture Continuous Population Structure in Human Genomic Data
- A multidimensional benchmark of confounder-aware differential abundance strategies for single- and multi-cohort microbiome studies
- Temporal and spatial couplings in the dynamics of human walking and running
- GraphTFactor: A graph-based approach for proteins transcription factor prediction
- Differentiable Spin-Center Diffusion Model Enables DEER-Guided Generative Pipeline of Weighted Protein Ensembles
- ScanFold3: a robust and rapid approach for identifying structured RNA targets in genomes and transcriptomes
- Small molecule structure elucidation from NMR spectra with generative and reasoning models
- A comprehensive map of the sequence basis of transcription initiation in humans
- Agentic cryo-EM structure determination with CryoPilot