We study how synthetic gene networks and genetic context can be used to enact feedback control.
We experiment with biological nonlinearities in living cells to realize novel computation.
We build models to represent computation, adaptation, and memory in living cells.
May 2023: Charles Johnson presented an invited talk titled “Subspace Invariance Properties of Mixed Dictionary Functions for Approximating Koopman Operators” at the SIAM Data Sciences Conference. Well done, Charles!
Link to Slides Below:
May 2023: Jamiree was accepted to the 2023 SIAM Mathematical Modeling Camp. Congratulations, Jamiree!
May 2023: Aqib Hasnain successfully defended his PhD dissertation, titled “Modeling transcriptional regulation for analysis and design of synthetic biological systems”. Congratulations, Aqib!
Aqib has accepted a postdoctoral scholar position at Lawrence Berkeley National Laboratory working with Dr. Dawn Chiniquy! Congratulations, Aqib!
May 2023: Enoch Yeung won an NSF 2023 CAREER Award titled “A Novel Framework for Measuring and Engineering Twisting and Writhing in DNA”. Many thanks to Cannon Mallory, Dennis Joshy, Alec Taylor, and Amanda Hart for all their supporting work in the preparation process!
March 2023: Charles Johnson submitted a paper to the IEEE Conference on Decision and Control, studying how control shapes identification in data-driven control problems.
March 2023: Harris Clark and Alec Taylor submitted their first scholarly publication to the IEEE Conference on Decision and Control, studying the use of CRISPRi to functionalize supercoiling for transcriptional bursting. Congratulations Harris and Alec !
March 2023: Shara Balakrishnan successfully defended his dissertation. Congratulations Dr. Balakrishnan!
March 2023: We hosted Dr. Victoria Hsiao from from the biotech company Amyris for a visit at UCSB; she gave a seminar titled “Synthetic biology for sustainable manufacturing”!
Right: Lunch with Dr. Hsiao, Enoch, Shara, Alec, and Sarah Seagrave (O’ Malley lab, BioE PhD student)
March 2023: Jamiree Harrison presented a talk titled “Analysis and Validation of Parameter-Varying Genetic Toggle Switches Using Koopman Operators” at the SIAM CSE 2023 conference in Amsterdam.
Congratulations Jamiree on a great conference talk!
March 2023: Aqib Hasnain’s bioRxiv manuscript titled “Learning Perturbation-Inducible Cell States of Novel Compounds from Observability Analysis of Transcriptome Dynamics” was accepted to Nature Communications!
Feb. 2023: Enoch gave an invited talk titled “Koopman Operator Methods for Modeling Complex Biological Networks from Data” at Kyoto University, hosted by Professor Yoshihiko Susuki!
Jan. 2023: Enoch gave an invited talk titled “Modeling Supercoiling Dynamics of Multi-Gene Circuits to Inform Design of a Transcriptional In Vivo Supercoiling Sensor” at the 2023 International Conference on Biomolecular Engineering!
December 2022: Charles Johnson posted a new two-part paper to arXiv on using heterogeneous mixtures of new and old classes of dictionary functions to approximate Koopman operators.
September 2022: Our paper with Dr. Sai Pushpak Nandanoori and Dr. Subhrajit Sinha on data-driven methods for learning phase spaces of nonlinear systems has been accepted in the Journal of Nonlinear Science! Congratulations Sai and Subhrajit!
PDF of Preprint.
July 2022: Prof. Yeung gave an invited tutorial at the SIAM Life Sciences meeting in Pittsburgh.
June 2022: Aqib Hasnain posted a new paper on discovering biosensors for novel compounds in Pseudomonas fluorescens using data-driven methods to bioRxiv.
January 2022: Our collaborative paper on modeling whole-cell transcriptional response is out in Bioinformatics with Dr. Mohammed Eslami of Netrias!
[Link to article]
December 2021: Jamiree published a paper in Mathematics to analyze stability of time-varying nonlinear systems with the method of Koopman
September 2021: Prof. Yeung published a paper in the Royal Society Interface showcasing dynamical structure functions for debugging and verifying functionality of genetic circuits.