Group Members

Tripti Midha

B.S. Mathematics (Hons), University of Delhi, Miranda House, India, 2012
M.S. Mathematics, University of Delhi, Miranda House, India, 2014
Ph.D. Applied Mathematics, Indian Institute of Technology Ropar, India, 2020

My present research focuses on analyzing the interplay of speed and accuracy of fundamental biological processes such as DNA replication, RNAP transcription elongation, and protein synthesis translation. I aim at developing stochastic models to investigate the various mechanisms of proofreading using theoretical and computational methods.

Cristina Palma

B.S., Biomedical Engineering Sciences, NOVA University of Lisbon, Portugal, 2015
M.S., Biomedical Engineering, NOVA University of Lisbon, Portugal, 2017
Ph.D., Thesis "Repression Mechanisms in Bacterial Transcription", Faculty of Medicine and Health Technology, Tampere University, Finland, 2022

During my doctoral studies at the Laboratory of Biosystem Dynamics of Tampere University, I focused on the dynamics of natural repression mechanisms of gene expression in E. coli and their outcome on the single-cell statistics of RNA and/or protein numbers. Specifically, I studied the effects of transcription factors, positive supercoiling accumulation, and distance between promoters. I joined the Cellular Systems Dynamics Lab and the Tabor Lab in 2023 to investigate the mechanisms that control bacteria, specifically B. subtilis, adaptation to stress conditions using optogenetics, microscopy, transcriptomics, and stochastic modeling. I am grateful to the Jenny and Antti Wihuri Foundation for funding this work. On my time off, I enjoy skiing, swimming, and sewing.

B.Sc., Mathematical Sciences, KAIST, 2017
Ph.D., Mathematical Sciences, KAIST, 2024

My research focuses on analyzing spatially heterogeneous systems using mathematical models. Specifically, I am interested in understanding protein dynamics within cells and their effects on various processes, including enzyme catalysis and circadian clocks. I have also collaborated with experimental biologists and medical professionals to optimize immunotherapy and accurately predict PTSD risk. Recently, my work has involved exploring the role of molecular glues and PK-PD models to enhance the design of therapeutics for various diseases.

Andrew Hecht

B.S., Microbiology, University of Kansas, 2018

B.S., Biological Science, Peking University, 2018

My primary research interest centers on applying multi-disciplinary models into biological research. I am taking advantage of deep learning to transfer phase-contrast images of Myxococcus xanthus into fluorescent images, which can be easily interpreted to cell density maps. I am also working on extracting Myxo cell aggregation features, which will be helpful to cluster mutant strains into different genetic pathways.

Zheng Diao

B.S., Biochemistry, University of Minnesota, Twin Cities, 2018

My research focuses on understanding eukaryotic transcriptional regulation through computational and experimental approach. The goal of the project includes developing mechanistic modeling framework to investigate the role of non-equilibrium epigenetic processes on information integration in eukaryotic gene regulation. I am interested in examining how various processes impact the shape of the gene regulatory function, i.e., the dose-response between TF concentration and gene expression.

Shuyuan Yang

B.S., Chemistry, University of Chinese Academy of Sciences, 2019

B.S., Biomedical Engineering, Minor, Electrical Engineering and Chemistry, Boston University, 2021

Yujia graduated from Boston University with a Bachelor Degree of Biomedical Engineering and two minors (Chemistry and Electrical engineering). She is a computational biologist studying prokaryotic gene regulation, specifically promoter switching behaviors, at Dr. Igoshin's Lab. She would like to develop an interesting story explaining when and why Bacillus subtillis goes through sporulation, and one day continue the story by engineering bacteria cells for therapeutic purposes. She is also a classical musician and enjoys playing with Shepherd School of Music friends.

Jon DeBonis

B.S., Chemical Engineering, Minor, Biotechnology and Biochemical Engineering, Northwestern University, 2022

My research focuses on modeling pharmacokinetics and pharmacodynamics of cancer therapeutics to allow for optimal treatment design. In collaboration with the Segatori and Veiseh Labs at Rice, I am working to develop models of cytokine treatment to accurately predict human response to treatment from in vivo data. Additionally, I am working on a model of interleukin-12 pharmacokinetics and pharmacodynamics capable of capturing IL-12 desensitization for better prediction of long-term therapy.

Yiduo Wang

B.S., Biochemistry and Computer Science, University of Wisconsin-Madison, 2022

I am working on using various methods to model gene regulatory component. Co-advised by Dr. Bashor, I use a high throughput method to build large libraries to measure the effect of promoters and ribosome binding sites to expression level. I then use both biophysical models and neural networks to study their relationship.

Alumni