Oct 2022: Workshop on modeling and analysis tools at IWBDA 2022 and at iGEM Grand Jamboree on "Learning Parameters from Experimental Data using Bayesian Inference and Model Reduction". Computational notebook on model reduction with AutoReduce is available here and the computational notebook on parameter inference with Biosrape is available here.
Oct 2022: Co-organizing a special issue on bio-design automation for ACS Synthetic Biology. More details here.
Oct 2022: Served as the publication chair at the IWBDA 2022!
Aug 2022: Two papers (one on contract-based design for synthetic biology and the other on a modeling and analysis pipeline) accepted at the 14th International Workshop on Bio-Design Automation (IWBDA) 2022. To be organized in Paris, France together with iGEM Grand Jamboree, 2022. Both papers were accepted as talks.
April 2022: Last lecture at Harvey Mudd! It was a pleasure teaching the class on Introduction to Biological System Design at the Harvey Mudd College. Here's a snapshot of the class review lecture at the end:
April 2022: New preprint! We posted a new bioRxiv preprint on our recent work: "From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology". PDF on bioRxiv. You can use the implementation of our paper on Google Colab to convert your own biological system specification into simple mathematical models!
March 2022: Presented a poster at the 8th Build-A-Cell workshop on "Full-Stack Modeling of Biological Circuits: From Specifications to Implementation using Python. PDF.
February 2022: Our paper on "BioCRNpyler: Compiling Chemical Reaction Networks from Biomolecular Parts in Diverse Contexts" was accepted (in February) and published (in April) in PLoS Computational Biology.
January 2022: Our paper on "Robustness guarantees for structured model reduction of dynamical systems with applications to biomolecular models" was accepted and published in the Special Issue on Life Sciences of the International Journal of Robust and Nonlinear Control. URL.
December 2021: Appointed as Adjunct Professor at Harvey Mudd College for the Spring 2021-22 semester.
November 2021: Released a summary video of my research on model reduction. You can watch the video here:
September 2021: We organized a workshop at International Workshop on Bio-Design Automation (IWBDA) 2021 on "Chemical Reaction Network Compilation to Bayesian Parameter Inference". You can check out the workshop poster and the recording on Youtube. All content of the workshop was interactive using Google Colaboratory notebook, which is available here.
September 2021: Helped write a research grant proposal on forward design of synthetic biological circuits. Details soon.
August 2021: Served as a reviewer for the Journal of Open Source Software (JOSS) to review the paper on OSTIR: open source translation initiation rate prediction. Check out the software on Github and the paper here.
August 2021: Co-mentored three Caltech undergraduate students in their summer internship projects in our lab. Details on the Teaching and Mentoring page.
July 2021: Our theory paper on robustness of model reduction for linear dynamical systems accepted at Conference on Decision and Control (CDC) 2021. You can read the paper PDF here. I am also a student host volunteer for the conference - to be organized virtually in December 2021.
May 2021: Joined the Biology and Biological Engineering (BBE) division Diversity, Equity, and Inclusion (DEI) committee as a representative from my lab.
January 2021: Enrolled in the Physical Biology of the Cell course at Caltech taught by Rob Phillips. Great course material, all available online here: BE/APh 161
December 2020: Uploaded a bioRxiv preprint on our latest work: "A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression". I wrote a short thread on Twitter and presented this paper at the 1st International Bio-Design Research Confernece (virtually). My poster for the conference is here.
September 2020: I am now a beginner in Spanish! Enrolled in Spanish language learning course at Caltech.
October 2020: Organized a Chemical Reaction Network (CRN) modeling tutorial for Build-A-Cell members. The tutorial series is available on YouTube here.
June - August 2020: Mentored five different undergraduate students in their summer internship projects at Caltech (under the SURF program). More details on the mentoring and teaching page under Summer 2020.
August 2020: Invited lightning talk at the 7th Build-A-Cell workshop organized by National Institute of Standards and Instruments (NIST) on BioCRNpyler.
August 2020: Our poster won the Best Poster Award at IWBDA 2020.
August 2020: New bioRxiv preprint on "BioCRNpyler: Compiling Chemical Reaction Networks from Biomolecular Parts in Diverse Contexts".
July 2020: Extended abstract on BioCRNpyler accepted at the 12th International Workshop on Bio-Design Automation (IWBDA 2020).
July 2020: Invited lightning talk at ACC 2020 on a new approach to derive converse Lyapunov theorems. Paper available on IEEE Xplore here.
May 2020: Passed my candidacy exam for PhD in Control and Dynamical Systems!
April 2020: Teaching assistant for the Open Source Tools for Modeling and Analysis of Synthetic Biology Circuits course at Caltech (BE240). Gave a total of 5 lectures on different software tools including: bioscrape, biocrnpyler, subsbml, parameter inference and further hands-on demo for ~20 graduate students.
Feb 2020: Gave a talk at winter q-Bio 2020 at the Big Island, Hawaii on 21st February on model reduction tools for synthetic biology. The slides used for the talk are available here.
Feb 2020: New bioRxiv preprint out. Our recent progress on model reduction tools for synthetic biology is available here. The accompanying software package Auto-Reduce is available here. It has various common model reduction examples obtained in an automated fashion.
Jan 2020: Participated in the 6th Build-A-Cell workshop at NASA, Ames at Mountain View, California. Our progress with the work in the Interlab study is available here.
ACC 2020: Paper accepted! Our paper on a converse Lyapunov theorem for nonlinear dynamical systems was accepted for presentation at the American Control Conference, 2020.
October 2019: Teaching assistant of the graduate level linear systems course (CDS131).
September 2019: Poster presentation at the international workshop on control engineering and synthetic biology at Oxford University (SynBioControl2019). Poster PDF.
September 2019: Visiting researcher at Imperial College London kick-starting the work on NSF cell-free project.
August 2019: Attended the 5th Build-A-Cell workshop at MIT, Boston. Worked on the interlab study group that aims to build a synthetic circuit out of parts assembled across labs. Details here.
July 2019: IWBDA 2019 conference talk at University of Cambridge. Slides here.
June 2019: Extended abstract submitted to International Workshop on Bio-Design Automation (IWBDA) accepted.
May 2019: New bioRxiv submission on an automated tool for model reduction to simplify the analysis of synthetic biological circuit models. Available here.
May 2019: New bioRxiv submission on the design of a population and composition control of a two-member bacterial population. Available here.
February 2019: Attended the Build-A-Cell and the NIST cell-free workshop at JCVI, La Jolla, CA. Worked on the modeling sub-groups to identify the challenges in modeling synthetic biological circuits. Details here.
October 2018: Attended the COMBINE 2018 conference at Boston, MA to give a talk on Sub-SBML. Slides here.
August 2018: Attended the Build-A-Cell workshop at University of Minnesota, Minneapolis, MN. Worked on the in-silico cells and essential genes sub-groups to identify the challenges in modeling synthetic cells. Details here.
