@article{mao-jia-2026-multimolecular-proofreading,author={Mao, Zhuo and Jia, Yuanqi and Yan, Yuxuan and Wu, Bingze and Xiao, Fangzhou and Chen, Zibo},title={Multimolecular proofreading overcomes the activity-fidelity trade-off},journal={Cell Systems},pages={101658},year={2026},month=jul,publisher={Elsevier},doi={10.1016/j.cels.2026.101658},}
Local stabilizability implies global controllability in catalytically-controlled reaction networks
Yusuke Himeoka , Shuhei A. Horiguchi , Naoto Shiraishi , and 2 more authors
@article{himeoka-horiguchi-2026-global-controllability,author={Himeoka, Yusuke and Horiguchi, Shuhei A. and Shiraishi, Naoto and Xiao, Fangzhou and Kobayashi, Tetsuya J.},title={Local stabilizability implies global controllability in catalytically-controlled reaction networks},journal={Communications Physics},year={2026},month=jul,publisher={Nature Portfolio},doi={10.1038/s42005-026-02727-z},}
Decoupling of global metabolic flux and proteome partitioning in bacteria
Ryan Thiermann , Jin Yang , Aniket Zodage , and 15 more authors
@article{thiermann-yang-2026-metabolic-flux,author={Thiermann, Ryan and Yang, Jin and Zodage, Aniket and She, Fukang and Fung, Danny K. and Rytlewski, Taylor and Abdollah-Nia, Farshad and Xiao, Fangzhou and Sauls, John T. and Cox, Sarah and Ghulam-Jelani, Zulfar and Castillo, Victoria and Paulsen, Quinn A. and Stevenson, David M. and Amador-Noguez, Daniel and Williamson, James R. and Wang, Jue D. and Jun, Suckjoon},title={Decoupling of global metabolic flux and proteome partitioning in bacteria},journal={Science},volume={392},number={6804},pages={eaeb6410},year={2026},month=jun,publisher={American Association for the Advancement of Science},doi={10.1126/science.aeb6410},}
Rate-Cost Tradeoffs in Continuous-Time Control With a Biomolecular Application
Yorie Nakahira , Fangzhou Xiao , Victoria Kostina , and 1 more author
@article{nakahira-xiao-2026-rate-cost,author={Nakahira, Yorie and Xiao, Fangzhou and Kostina, Victoria and Doyle, John C.},title={Rate-Cost Tradeoffs in Continuous-Time Control With a Biomolecular Application},journal={IEEE Transactions on Automatic Control},volume={71},number={4},pages={2614--2621},year={2026},month=apr,publisher={IEEE},doi={10.1109/TAC.2025.3626246},}
Evaluating valid parameter regimes for biocircuits
@article{liu-ren-2026-valid-parameter-regimes,author={Liu, Qinguo and Ren, Xinying and Xiao, Fangzhou},title={Evaluating valid parameter regimes for biocircuits},journal={bioRxiv},pages={2026.01.19.700491},year={2026},month=jan,publisher={Cold Spring Harbor Laboratory},doi={10.64898/2026.01.19.700491},}
2024
With the leisure of time, kinetic proofreading can still perform reliable ligand discrimination
Fangzhou Xiao , and Vahe Galstyan
Proceedings of the National Academy of Sciences, Jan 2024
@article{xiao-galstyan-2024-leisure-of-time,author={Xiao, Fangzhou and Galstyan, Vahe},title={With the leisure of time, kinetic proofreading can still perform reliable ligand discrimination},journal={Proceedings of the National Academy of Sciences},volume={121},number={32},pages={e2320118121},year={2024},doi={10.1073/pnas.2320118121},eprint={https://www.pnas.org/doi/pdf/10.1073/pnas.2320118121},}
2023
Bacterial Replication Initiation as Precision Control by Protein Counting
@article{fu-xiao-2023-replication-initiation,title={Bacterial Replication Initiation as Precision Control by Protein Counting},author={Fu*, Haochen and Xiao*, Fangzhou and Jun, Suckjoon},journal={PRX Life, highlighted with viewpoint},volume={1},issue={1},pages={013011},numpages={21},year={2023},month=aug,publisher={American Physical Society},doi={10.1103/PRXLife.1.013011},highlight={https://physics.aps.org/articles/v16/143}}
Flux exponent control predicts metabolic dynamics from network structure
Fangzhou Xiao , Jing Shuang Li , and John C. Doyle
In 2023 American Control Conference (ACC) , Aug 2023
@inproceedings{xiao2023fec-mpc,author={Xiao, Fangzhou and Shuang Li, Jing and Doyle, John C.},booktitle={2023 American Control Conference (ACC)},title={Flux exponent control predicts metabolic dynamics from network structure},year={2023},volume={},number={},pages={1189-1194},doi={10.23919/ACC55779.2023.10156281},}
2022
Biocontrol of Biomolecular Systems: Polyhedral Constraints on Binding’s Regulation of Catalysis from Biocircuits to Metabolism
@phdthesis{xiao2022thesis,author={Xiao, Fangzhou},title={Biocontrol of Biomolecular Systems: Polyhedral Constraints on Binding's Regulation of Catalysis from Biocircuits to Metabolism},school={California Institute of Technology},year={2022},}
2021
Stability and Control of Biomolecular Circuits through Structure
Fangzhou Xiao , Mustafa Khammash , and John C. Doyle
In 2021 Annual American Control Conference (ACC) , Aug 2021
@inproceedings{xiao2021structural-stability,author={Xiao, Fangzhou and Khammash, Mustafa and Doyle, John C.},booktitle={2021 Annual American Control Conference (ACC)},title={Stability and Control of Biomolecular Circuits through Structure},year={2021},volume={},number={},doi={10.23919/ACC50511.2021.9483039}}
Systems Level Model of Dietary Effects on Cognition via the Microbiome-Gut-Brain Axis
Michaëlle N. Mayalu , Anish Sarma , Fangzhou Xiao , and 2 more authors
In 2021 European Control Conference (ECC) , Jun 2021
@inproceedings{mayalu-sarma-2021-microbiome-gut-brain,author={Mayalu, Micha{\"e}lle N. and Sarma, Anish and Xiao, Fangzhou and Doyle, John C. and Murray, Richard M.},title={Systems Level Model of Dietary Effects on Cognition via the Microbiome-Gut-Brain Axis},booktitle={2021 European Control Conference (ECC)},pages={312--318},year={2021},month=jun,publisher={IEEE},doi={10.23919/ECC54610.2021.9655216},}
2020
A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology
John P. Marken , Fangzhou Xiao , and Richard M. Murray
@article{marken2020geometric,author={Marken, John P. and Xiao, Fangzhou and Murray, Richard M.},title={A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology},elocation-id={2020.02.18.953620},year={2020},doi={10.1101/2020.02.18.953620},publisher={Cold Spring Harbor Laboratory},journal={bioRxiv}}
Proofreading through spatial gradients
Vahe Galstyan , Kabir Husain , Fangzhou Xiao , and 2 more authors
@article{galstyan2020proofreading,article_type={journal},title={Proofreading through spatial gradients},author={Galstyan, Vahe and Husain, Kabir and Xiao, Fangzhou and Murugan, Arvind and Phillips, Rob},editor={Yildiz, Ahmet and Walczak, Aleksandra M},volume={9},year={2020},month=dec,pub_date={2020-12-24},pages={e60415},citation={eLife 2020;9:e60415},doi={10.7554/eLife.60415},keywords={error correction, molecular gradients, compartmentalization, energy expenditure, diffusion},journal={eLife},issn={2050-084X},publisher={eLife Sciences Publications, Ltd},}
2019
Architectural Principles for Characterizing the Performance of Antithetic Integral Feedback Networks
@article{olsman2019architecture,title={Architectural Principles for Characterizing the Performance of Antithetic Integral Feedback Networks},journal={iScience,},volume={14},pages={277--291},year={2019},issn={2589-0042},doi={https://doi.org/10.1016/j.isci.2019.04.004},author={Olsman, Noah and Xiao, Fangzhou and Doyle, John C.},keywords={Biological Sciences, Systems Biology, In Silico Biology},}
Coupled Reaction Networks for Noise Suppression
Fangzhou Xiao , Meichen Fang , Jiawei Yan , and 1 more author
In 2019 American Control Conference (ACC) , Dec 2019
@inproceedings{xiao2019coupled-noise,author={Xiao, Fangzhou and Fang, Meichen and Yan, Jiawei and Doyle, John C.},booktitle={2019 American Control Conference (ACC)},title={Coupled Reaction Networks for Noise Suppression},year={2019},volume={},number={},pages={1547-1554},}
Hard Limits and Performance Tradeoffs in a Class of Antithetic Integral Feedback Networks
Noah Olsman , Ania-Ariadna Baetica , Fangzhou Xiao , and 3 more authors
@article{olsman2019seq,title={Hard Limits and Performance Tradeoffs in a Class of Antithetic Integral Feedback Networks},journal={Cell Systems},volume={9},number={1},pages={49-63.e16},year={2019},issn={2405-4712},doi={https://doi.org/10.1016/j.cels.2019.06.001},author={Olsman, Noah and Baetica, Ania-Ariadna and Xiao, Fangzhou and Leong, Yoke Peng and Murray, Richard M. and Doyle, John C.},keywords={Feedback Regulation, Synthetic Biology, Performance Tradeoffs, Antithetic Integral Feedback}}
2018
Robust Perfect Adaptation in Biomolecular Reaction Networks
Fangzhou Xiao , and John Doyle
In 2018 IEEE Conference on Decision and Control (CDC) , Dec 2018
@inproceedings{xiao2018rpa,author={Xiao, Fangzhou and Doyle, John},booktitle={2018 IEEE Conference on Decision and Control (CDC)},title={Robust Perfect Adaptation in Biomolecular Reaction Networks},year={2018},volume={},number={},pages={4345-4352},}
Evaluation of Hansen et.al.: Nuance Is Crucial in Comparisons of Noise
@article{LIU2018428,title={Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing},journal={The Journal of Molecular Diagnostics},volume={20},number={4},pages={428 - 435},year={2018},issn={1525-1578},doi={https://doi.org/10.1016/j.jmoldx.2018.02.006},author={Liu, Chang and Xiao, Fangzhou and Hoisington-Lopez, Jessica and Lang, Kathrin and Quenzel, Philipp and Duffy, Brian and Mitra, Robi D.}}
Fundamental limits and achievable performance in biomolecular control
Yorie Nakahira , Fangzhou Xiao , Victoria Kostina , and 1 more author
In 2018 Annual American Control Conference (ACC) , Dec 2018
@inproceedings{8430933,author={Nakahira, Yorie and Xiao, Fangzhou and Kostina, Victoria and Doyle, John C.},booktitle={2018 Annual American Control Conference (ACC)},title={Fundamental limits and achievable performance in biomolecular control},year={2018},volume={},number={},pages={2707-2714},}
