Article

Using semantic search to find publicly available gene-expression datasets

2025-03-15

Abstract excerpt

Millions of high-throughput, molecular datasets have been shared in public repositories. have been shared in public repositories. Researchers can reuse such data to validate their own findings and explore novel questions. A frequent goal is to find multiple datasets that address similar research topics and to either combine them directly or integrate inferences from them. However, a major challenge is finding rele...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: cbdd16d9-30a3-5b66-a06f-73565221fe61
DOI: 10.1101/2025.03.13.643153

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Using semantic search to find publicly available gene-expression datasetsDOI 10.1101/2025.03.13.643153Read

Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics.Semantic proximity Read

LitGene: a transformer-based model that uses contrastive learning to integrate textual information into gene representationsSemantic proximity Read

Benchmarking gene embeddings from sequence, expression, network, and text models for functional prediction tasksSemantic proximity Read

Domain-specific embeddings uncover latent genetics knowledgeSemantic proximity Read

Enhancing Gene Set Overrepresentation Analysis with Large Language ModelsSemantic proximity Read

Automating scientific annotations for open transcriptomic profiles via multi-stage agentsSemantic proximity Read

Metadata Harmonization from Biological Datasets with Language ModelsSemantic proximity Read

Systematic tissue annotations of –omics samples by modeling unstructured metadataSemantic proximity Read

A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene SetsSemantic proximity Read

The usage of transcriptomics datasets as sources of Real-World Data for clinical triallingSemantic proximity Read

The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression OmnibusSemantic proximity Read

Serial KinderMiner (SKiM) Discovers and Annotates Biomedical Knowledge Using Co-Occurrence and Transformer ModelsSemantic proximity Read