Haopeng Yu

Postdoctoral Scientist · HFSP Fellow · John Innes Centre, UK

I am a computational biologist working to decipher the code of life. My research harnesses artificial intelligence to uncover the fundamental rules of nature encoded in DNA, RNA, and beyond. I build biological foundation models such as PlantRNA-FM, develop autonomous AI agents like PlantScience.ai, and combine advanced AI, bioinformatics, and statistical methods to accelerate scientific discovery. Drawing on expertise spanning high-throughput sequencing analysis, ML/DL/LLM modeling, and full-stack web development, my work aims to turn biology into an AI-native science, and ultimately, to decode the language of life.

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Haopeng Yu

// research & software

Research & Software

Publications Google Scholar ↗

Molecular Plant2026

PlantScience.ai: An LLM-Powered Virtual Scientist for Plant Science.

*Yu H., Zhou S., Huang M., et al.

co-first author

10.1016/j.molp.2026.03.010

RNA Biology2026

AI foundation models for RNA biology.

#Yu H., Ding Y.

co-corresponding author

10.1080/15476286.2026.2650517

Cryo-EM structure of human telomerase dimer reveals H/ACA RNP-mediated dimerization.

Balch S., Sekne Z., ..., Yu H., et al.

10.1126/science.adr5817

Nature Mach. Intell.2024

An interpretable RNA foundation model for exploring functional RNA motifs in plants.

*Yu H., Yang H., Sun W., et al.

co-first author

10.1038/s42256-024-00946-z

Nature Comms.2024

Unveiling RNA Structure-mediated Regulations of RNA Stability in Wheat.

Wu H., *Yu H., Zhang Y., et al.

co-first author

10.1038/s41467-024-54172-7

Nucleic Acids Res.2024

iM-Seeker: A Webserver for DNA i-Motifs Prediction and Scoring via Automated Machine Learning.

#Yu H., Li F., Yang B., et al.

co-corresponding & co-first author

10.1093/nar/gkae315

Nucleic Acids Res.2024

Prediction of DNA i-motifs via machine learning.

Yang B., Guneri D., #Yu H., et al.

co-corresponding & co-first author

10.1093/nar/gkae092

Nature Comms.2024

A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics.

Zhang Y., Dong Q., Wang Z., Liu Q., Yu H., Sun W., et al.

10.1038/s41467-024-47678-7

Nature Catalysis2023

Structure and engineering of miniature Acidibacillus sulfuroxidans Cas12f1.

Wu Z., Liu D., Pan D., Yu H., et al.

10.1038/s41929-023-00995-4

Nucleic Acids Res.2023

G4Atlas: A comprehensive transcriptome-wide G-quadruplex database.

#Yu H., Qi Y., Yang B., Yang X., & Ding Y.

co-corresponding author

10.1093/nar/gkac896

Front. Mol. Biosci.2022

Deep Learning in RNA Structure Studies.

#Yu H., Qi Y., & Ding Y.

co-corresponding author

10.3389/fmolb.2022.869601

Cell Reports2022

Guide RNA engineering enables efficient CRISPR editing with a miniature Syntrophomonas palmitatica Cas12f1 nuclease.

Wang Y., Wang Y., Pan D., Yu H., et al.

10.1016/j.celrep.2022.111418

New Phytologist2022

A cytosolic pentatricopeptide repeat protein is essential for tapetal plastid development by regulating OsGLK1 transcript levels in rice.

Zheng S., Dong J., Lu J., ..., Yu H., et al.

10.1111/nph.18105

Nature Comms.2022

RNA G-quadruplex structure contributes to cold adaptation in plants.

Yang X., *Yu H., Duncan S., et al.

co-first author

10.1038/s41467-022-34040-y

Genome Biology2021

Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry.

Yang X., *Yu H., Sun W., et al.

co-first author

10.1186/s13059-021-02549-y

Nature Chem. Biol.2021

Programmed genome editing by a miniature CRISPR-Cas12f nuclease.

Wu Z., Zhang Y., Yu H., Pan D., et al.

10.1038/s41589-021-00868-6

CRISPR-CBEI: A Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation.

Yu H., Wu Z., Chen X., Ji Q., & Tao S.

Briefings in Bioinformatics2020

RSVdb: A comprehensive database of transcriptome RNA structure.

Yu H., Zhang Y., Sun Q., Gao H., & Tao S.

10.1093/bib/bbaa071

RNA Biology2019

Deciphering the rules of mRNA structure differentiation in Saccharomyces cerevisiae in vivo and in vitro with deep neural networks.

Yu H., Meng W., Mao Y., Zhang Y., Sun Q., & Tao S.

10.1080/15476286.2019.1612692

Websites

PlantScience.ai

plantscience.ai

An LLM-powered virtual scientist for plant science. AI agents that reason across literature, data, and experimental knowledge.

LLM AgentsPlant ScienceAI

A comprehensive transcriptome-wide G-quadruplex database. Published in Nucleic Acids Research 2023.

G-quadruplexDatabase

Webserver for DNA i-Motif prediction and scoring via automated machine learning. Published in Nucleic Acids Research 2024.

atlasbioinfo.github.io/CRISPR-CBEI

Toolkit for cytosine base editor-mediated gene inactivation. Published in mSystems 2020.

CRISPRBase Editing

AtlasBioinfo Tools

tools.atlasbioinfo.com

20+ bioinformatics tools running entirely in your browser. No data upload, no server, fully private.

Vue3WebAssemblyPrivacy-first

AI-powered RNA analysis platform. Decoding the language of RNA structure and function with deep learning models.

RNA BiologyAI Models

Exploring the RNA world hypothesis through AI. Computational analysis of RNA structure and evolution.

RNA EvolutionComputational

blog.atlasbioinfo.com

Notes on bioinformatics, AI in biology, tool development, and computational methods.

BioinformaticsTutorials