Prompt-based bioinformatics: a new interface for multi-omics analysis

Abstract

Prompt-based bioinformatics redefines how scientists interact with biological data, enabling natural language queries across multi-omics layers. By removing coding barriers and streamlining integration, this paradigm facilitates accessible, hypothesis-driven discovery. We call for community standards, educational adoption and collaborative development to realize its full potential in research and clinical settings. Prompt-based methods, which involve the careful design of inputs to guide large language model (LLM) outputs, are beginning to reshape bioinformatic analytical workflows. The authors compare prompt-driven approaches to conventional bioinformatics pipelines, outline their potential for multi-omics analysis and explore how these models may shape the future of computational biology.