Article

Integrating natural language processing and genome analysis enables accurate bacterial phenotype prediction

2024-12-11

Abstract excerpt

Understanding microbial phenotypes from genomic data is crucial in areas of research including co-evolution, ecology and pathology. This study proposes a new approach to integrate literature-derived information with genomic data to study microbial traits, combining natural language processing (NLP) with functional genome analysis. We applied this methodology to publicly available data to overcome current limitatio...

Topics

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

Identifiers and source

Literature Corpus work: 158cb2f6-f522-507e-95d7-1aa6695a5172
DOI: 10.1101/2024.12.07.627346

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Integrating natural language processing and genome analysis enables accurate bacterial phenotype predictionDOI 10.1101/2024.12.07.627346Read

Comparative assessment of large language models for microbial phenotype assignment.Semantic proximity Read

Large Language Model-assisted text mining reveals bacterial pathogen diversitySemantic proximity Read

SAP: Synteny-aware gene function prediction for bacteria using protein embeddingsSemantic proximity Read

Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models, with PathogenFinder2Semantic proximity Read

Genomic Language Models (gLMs) decode bacterial genomes for improved gene prediction and translation initiation site identificationSemantic proximity Read

LAMBDA: A Prophage Detection Benchmark for Genomic Language ModelsSemantic proximity Read

Gene-language models are whole genome representation learnersSemantic proximity Read

Ultra-Accurate Classification and Discovery of Functional Protein-Coding Genes from Microbiomes Using FunGeneTyper: An Expandable Deep Learning-Based FrameworkSemantic proximity Read

The landscape of microbial phenotypic traits and associated genes.Semantic proximity Read

Systematic association of genes to phenotypes by genome and literature mining.Semantic proximity Read

MicroGenomer: A Foundation Model for Transferable Microbial Genome Representations Enabling Multi-scale Genomic Understanding and Ecophysiological Trait PredictionSemantic proximity Read

PathoLM: Identifying pathogenicity from the DNA sequence through the Genome Foundation ModelSemantic proximity Read