About me

I am a Postdoc in Marnix Lab from Wageningen University & Research. My research interests include the evolution and ecology of secondary metabolism, especially non-ribosmal peptide synthetase (NRPS), in individual, population and community level. And I am also interested in resource allocation (trade-off bewteen benefit and cost) in the microbe such as primary metabolism and secondary metabolism, cross-feeding in microbial community, and energetics in th microbe.

Education

- Bachelor of science in Biology, 2020

ShanghaiTech University

- Docter of integrated life science (Physics), 2025

Peking University

Completed Projects

1. Peptaibol recommbination events analysis in Trichoderma genus
2. NRPS standardization by conserved motifs
3. Digitized siderophore information database construction

Skills

Bioinformatics analysis by MATLAB and Python
Genome-scaling model construction from genome

Resources

NRPS Motif Finder: a tool for standardization by conserved motifs and prediction of all 18 Condensation domains.

SIDERITE - Siderophore Information Database: a digitized integrated siderophore information database. It covers all 649 known siderophores as of May 2023.

Publications

He R, Gu S, Xu J, et al. SIDERITE: Unveiling hidden siderophore diversity in the chemical space through digital exploration[J]. Imeta, 2024, 3(2): e192.

He R, Zhang J, Shao Y, et al. Knowledge-guided data mining on the standardized architecture of NRPS: Subtypes, novel motifs, and sequence entanglements[J]. PLOS Computational Biology, 2023, 19(5): e1011100.

Li Z, Ióca L P, He R, et al. Natural diversifying evolution of nonribosomal peptide synthetases in a defensive symbiont reveals nonmodular functional constraints[J]. PNAS nexus, 2024, 3(9): pgae384.

Fan J, Ren J, He R, et al. Biosynthetic diversification of peptaibol mediates fungus-mycohost interactions[J]. bioRxiv, 2022: 2022.06. 05.494846.