publications | Jack Xiaoyu Chen

2025

bioRxiv

OriGene: A Self-Evolving Virtual Disease Biologist Automating Therapeutic Target Discovery

Z. Zhang, Z. Qiu, Y. Wu, and 9 more authors

bioRxiv, 2025

@article{zhang2025origene,
  title = {OriGene: A Self-Evolving Virtual Disease Biologist Automating Therapeutic Target Discovery},
  author = {Zhang, Z. and Qiu, Z. and Wu, Y. and Li, S. and Wang, D. and Zhou, Z. and An, D. and Chen, Y. and Li, Y. and Wang, Y. and Chen, J.X. and others},
  journal = {bioRxiv},
  year = {2025},
  doi = {10.1101/2025.06.03.657658},
}

arXiv

ODesign: A World Model for Biomolecular Interaction Design

O. Zhang, X. Zhang, H. Lin, and 8 more authors

arXiv preprint arXiv:2510.22304, 2025

Bib

@article{zhang2025odesign,
  title = {ODesign: A World Model for Biomolecular Interaction Design},
  author = {Zhang, O. and Zhang, X. and Lin, H. and Tan, C. and Wang, Q. and Mo, Y. and Feng, Q. and Du, G. and Yu, Y. and Chen, J.X. and others},
  journal = {arXiv preprint arXiv:2510.22304},
  year = {2025},
}

arXiv

Fitness aligned structural modeling enables scalable virtual screening with AuroBind

Z. Zhang, J. Rao, J. Zhong, and 8 more authors

arXiv preprint arXiv:2508.02137, 2025

Bib

@article{zhang2025aurobind,
  title = {Fitness aligned structural modeling enables scalable virtual screening with AuroBind},
  author = {Zhang, Z. and Rao, J. and Zhong, J. and Bai, W. and Wang, D. and Ning, S. and Qiao, L. and Xu, S. and Ma, R. and Chen, J.X. and others},
  journal = {arXiv preprint arXiv:2508.02137},
  year = {2025},
}

Patent

Engineered synthetic IRES with improved and robust translation in circular RNA

J.J. Collins, K. Ilia, K. Zhang, and 2 more authors

2025

Bib

@article{collins2025ires,
  title = {Engineered synthetic IRES with improved and robust translation in circular RNA},
  author = {Collins, J.J. and Ilia, K. and Zhang, K. and Chen, J.X. and Lalwani, M.A.},
  year = {2025},
}

NeurIPS

DynPro: A Large-Scale Dataset of Molecular Dynamics Simulations for Protein Conformational Ensembles and Transitions

J. Yang, J. Chen, S. Zheng, and 1 more author

NeurIPS 2025 AI for Science Workshop, 2025

Bib

@article{yang2025dynpro,
  title = {DynPro: A Large-Scale Dataset of Molecular Dynamics Simulations for Protein Conformational Ensembles and Transitions},
  author = {Yang, J. and Chen, J. and Zheng, S. and He, X.},
  journal = {NeurIPS 2025 AI for Science Workshop},
  year = {2025},
}

2024

Nat. Comput. Sci.

Deep generative design of RNA aptamers using structural predictions

F. Wong, D. He, A. Krishnan, and 8 more authors

Nature Computational Science, 2024

DOI Bib

@article{wong2024rna,
  title = {Deep generative design of RNA aptamers using structural predictions},
  author = {Wong, F. and He, D. and Krishnan, A. and Hong, L. and Wang, A.Z. and Wang, J. and Hu, Z. and Omori, S. and Li, A. and Chen, J.X. and others},
  journal = {Nature Computational Science},
  volume = {4},
  number = {11},
  pages = {829--839},
  year = {2024},
  doi = {10.1038/s43588-024-00720-6},
}

2023

Nat. Commun.

Autocatalytic base editing for RNA-responsive translational control

R.V. Gayet, K. Ilia, S. Razavi, and 5 more authors

Nature Communications, 2023

DOI Bib

@article{gayet2023autocatalytic,
  title = {Autocatalytic base editing for RNA-responsive translational control},
  author = {Gayet, R.V. and Ilia, K. and Razavi, S. and Tippens, N.D. and Lalwani, M.A. and Zhang, K. and Chen, J.X. and others},
  journal = {Nature Communications},
  volume = {14},
  number = {1},
  pages = {1339},
  year = {2023},
  doi = {10.1038/s41467-023-36851-z},
}

2021

ACS Synbio

Rational Design and Characterization of Nitric Oxide Biosensors in E. coli Nissle 1917 and Mini SimCells

X.J. Chen, B. Wang, I.P. Thompson, and 1 more author

ACS Synthetic Biology, 2021

DOI Bib

@article{chen2021nitric,
  title = {Rational Design and Characterization of Nitric Oxide Biosensors in E. coli Nissle 1917 and Mini SimCells},
  author = {Chen, X.J. and Wang, B. and Thompson, I.P. and Huang, W.E.},
  journal = {ACS Synthetic Biology},
  volume = {10},
  number = {10},
  pages = {2566--2578},
  year = {2021},
  doi = {10.1021/acssynbio.0c00556},
}

Microb. Biotechnol.

Redesign of ultrasensitive and robust RecA gene circuit to sense DNA damage

J.X. Chen, B. Lim, H. Steel, and 3 more authors

Microbial Biotechnology, 2021

DOI Bib

@article{chen2021reca,
  title = {Redesign of ultrasensitive and robust RecA gene circuit to sense DNA damage},
  author = {Chen, J.X. and Lim, B. and Steel, H. and Song, Y. and Ji, M. and Huang, W.E.},
  journal = {Microbial Biotechnology},
  volume = {14},
  number = {6},
  pages = {2481--2496},
  year = {2021},
  doi = {10.1111/1751-7915.13778},
}

2019

AEM

Development of Aspirin-Inducible Biosensors in Escherichia coli and SimCells

J.X. Chen, H. Steel, Y.H. Wu, and 5 more authors

Applied and Environmental Microbiology, 2019

DOI Bib

@article{chen2019aspirin,
  title = {Development of Aspirin-Inducible Biosensors in Escherichia coli and SimCells},
  author = {Chen, J.X. and Steel, H. and Wu, Y.H. and Wang, Y. and Xu, J. and Rampley, C.P.N. and Thompson, I.P. and Huang, W.E.},
  journal = {Applied and Environmental Microbiology},
  volume = {85},
  number = {6},
  pages = {e02959-18},
  year = {2019},
  doi = {10.1128/AEM.02959-18},
}

Book Ch.

Application of Bacterial Whole-Cell Biosensors in Health

Y. Song, C.P.N. Rampley, J.X. Chen, and 3 more authors

In Handbook of Cell Biosensors, 2019

DOI Bib

@incollection{song2019biosensors,
  title = {Application of Bacterial Whole-Cell Biosensors in Health},
  author = {Song, Y. and Rampley, C.P.N. and Chen, J.X. and Du, F. and Thompson, I.P. and Huang, W.E.},
  booktitle = {Handbook of Cell Biosensors},
  year = {2019},
  publisher = {Springer},
  doi = {10.1007/978-3-319-47405-2_133-1},
}