Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Coordination-Driven Metal-Phenolic Network Complexes for Programmable Colorimetric Signal Transduction and Defined Nano-Bio Interfaces.

Small (Weinheim an der Bergstrasse, Germany)·2026

Same author

MRDsteer: quality-aware AI-driven closed-loop optimization enhances ctDNA-based minimal residual disease detection.

Briefings in bioinformatics·2026

Same author

Modulating interfacial adsorption and lipid stability in myofibrillar protein-soy protein isolate emulsion gels: Insights from structurally representative polyphenols.

Food chemistry·2026

Same author

STGBench: sequencing-level spatial DNA-RNA simulation for multimodal and virtual cell-oriented benchmarking of genomic alterations.

Briefings in bioinformatics·2026

Same author

Universal Two-Excitation Scattering in Two-Dimensional Subwavelength Atomic Arrays.

Physical review letters·2026

Same author

Disrupted erythrocyte S1P-eNOS axis promotes hypoxia, hypertension and fibrosis in obstructive sleep apnoea-hypopnoea syndrome.

European heart journal·2026

Search research articles

Related Experiment Video

Updated: Jan 11, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

BioWorkflow: Retrieving comprehensive bioinformatics workflows from publications.

Yidan Wang^1,2, Jiayin Wang^1,2,3

¹School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China.

Briefings in Bioinformatics

|November 8, 2025

Summary

BioWorkflow, a new framework using large language models (LLMs), automates bioinformatics workflow reconstruction from scientific papers. This enhances reproducibility and accuracy, significantly reducing manual curation time.

Keywords:

bioinformatics large language models multimodal retrieval-augmented generation workflow extraction

More Related Videos

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

Related Experiment Videos

Last Updated: Jan 11, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

Area of Science:

Bioinformatics
Computational Biology
Scientific Literature Mining

Background:

Reconstructing bioinformatics workflows from publications is crucial for scientific analysis but is hindered by dispersed information across various document formats.
Manual reconstruction is time-consuming and prone to errors, while existing systems lack the full-text, multimodal capabilities for complete workflow extraction.

Purpose of the Study:

To introduce BioWorkflow, a novel large language model (LLM)-based framework designed for automated, end-to-end reconstruction of bioinformatics workflows from scientific literature.
To improve the accuracy, completeness, and reproducibility of bioinformatics pipeline extraction and reuse.

Main Methods:

BioWorkflow employs a retrieval-augmented framework that parses PDFs to create a unified index of text, tables, and figures.
It uses hierarchical query decomposition with dynamic reformulation and iterative, context-aware retrieval to assemble directed workflows.
The framework links predicted elements to cited evidence and performs automated consistency checks to ensure traceability and minimize hallucinations.

Main Results:

BioWorkflow recovers approximately 80% of workflow steps, a significant improvement over existing tools (~20%).
It demonstrates a >20% improvement in reproducibility, completeness, and accuracy compared to strong LLM baselines.
Curation time is reduced to 3-5 minutes per paper, enabling faster reuse of published pipelines.

Conclusions:

BioWorkflow effectively automates the extraction of detailed bioinformatics workflows from scientific publications.
The framework enhances the reliability and efficiency of reusing published computational pipelines, fostering scientific reproducibility.