publications

2023

1. Bacterial Replication Initiation as Precision Control by Protein Counting

   Haochen Fu* ,  Fangzhou Xiao* ,  and  Suckjoon Jun

   PRX Life, highlighted with viewpoint, Aug 2023

   highlight Bib HTML PDF

   @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}
   }

2. 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

   Bib HTML PDF Slides

   @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

1. Biocontrol of Biomolecular Systems: Polyhedral Constraints on Binding’s Regulation of Catalysis from Biocircuits to Metabolism

   Fangzhou Xiao

   California Institute of Technology , Aug 2022

   Bib HTML PDF

   @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

1. 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

   Bib HTML PDF Video

   @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}
   }

2020

1. 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

   bioRxiv, Aug 2020

   Bib HTML PDF

   @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}
   }

2. Proofreading through spatial gradients

   Vahe Galstyan ,  Kabir Husain ,  Fangzhou Xiao , and 2 more authors

   eLife, Dec 2020

   Bib HTML PDF

   @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

1. Architectural Principles for Characterizing the Performance of Antithetic Integral Feedback Networks

   Noah Olsman ,  Fangzhou Xiao ,  and  John C. Doyle

   iScience,, Dec 2019

   Bib HTML PDF

   @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},
   }

2. Coupled Reaction Networks for Noise Suppression

   Fangzhou Xiao ,  Meichen Fang ,  Jiawei Yan , and 1 more author

   In 2019 American Control Conference (ACC) , Dec 2019

   Bib HTML PDF Slides

   @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},
   }

3. Hard Limits and Performance Tradeoffs in a Class of Antithetic Integral Feedback Networks

   Noah Olsman ,  Ania-Ariadna Baetica ,  Fangzhou Xiao , and 3 more authors

   Cell Systems, Dec 2019

   Bib HTML

   @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

1. Robust Perfect Adaptation in Biomolecular Reaction Networks

   Fangzhou Xiao ,  and  John Doyle

   In 2018 IEEE Conference on Decision and Control (CDC) , Dec 2018

   Bib HTML PDF Slides

   @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},
   }

2. Evaluation of Hansen et.al.: Nuance Is Crucial in Comparisons of Noise

   Noah Olsman ,  Fangzhou Xiao ,  and  John Doyle

   Cell Systems, Dec 2018

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3. Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing

   Chang Liu ,  Fangzhou Xiao ,  Jessica Hoisington-Lopez , and 4 more authors

   The Journal of Molecular Diagnostics, Dec 2018

   Bib HTML

   @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.}
   }

4. 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

   Bib HTML

   @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},
   }