Lingchong You

James L. Meriam Distinguished Professor of Biomedical Engineering

Director, Center for Quantitative Biodesign

you@duke.edu
Duke BME
Google Scholar

Ph.D. University of Wisconsin at Madison, 2002
M.S. University of Science and Technology of China (China), 1997
B.S.E. Chengdu University of Science and Technology (China), 1994

Postdoctoral Fellows

Emrah Simsek emrah.simsek@duke.edu

Ph.D. Physics, Emory University (2019)

My research revolves around ecology and evolution of microbial communities with specific emphases on antibiotic resistance, spatial dynamics, and pattern formation. I generally employ a combination of mathematical modeling, experimental microbiology, and synthetic biology

Dongheon Lee dongheon.lee@duke.edu

Ph.D. Chemical Engineering, Texas A&M University (2020)

Currently I’m working on a hybrid mechanistic-data-driven approach to model complex biological processes.

Zhenjiao Du zhenjiao.du@duke.edu

Ph.D. in Grain Science, Kansas State University, 2024

I am interested in AI4Science research and its applications in scientific  discovery. Currently, my work focuses on leveraging foundation models for horizontal gene transfer, with a particular emphasis on predicting plasmid traits.

Xiaoli Chen xiaoli.chen@duke.edu

Ph.D. Energy and Resources Engineering, Peking University (2024)

I am broadly interested in the assembly and evolution of microbial communities, mainly focusing on how microbial interactions impact the evolutionary and ecological dynamics of microbial communities.

Jia Lu
jia.lu@duke.edu

Ph.D. Biomedical Engineering, Duke University (2024)

I’m interested in understanding and designing self-organized pattern formation in living bacteria.

Jing-Mei Qian jingmei.qian@duke.edu

Ph.D., Genetics, University of the Chinese Academy of Sciences, 2025

My current research focuses on curing plasmids in bacteria to prevent the spread of antibiotic resistance. My broader research interests lie in synthetic biology, particularly in engineering microbial communities.

PhD Students

Katherine Duncker
katherine.duncker@duke.edu

B.S. Biomedical Engineering, Northwestern University (2019)

I'm working on encapsulating engineered bacteria to control bacterial population dynamics and create a multi-sensing and actuating system for applications in medicine and environmental remediation.

Zhengqing Zhou (personal website) zhengqing.zhou@duke.edu

B.S. Physics, Peking University (2021)

I am broadly interested in the ecology of microbial communities and plasmids. I combine mechanistic modelling, machine learning and quantitative experiments to elucidate the principles of bacteria interactions.

César Villalobos cesar.villalobos@duke.edu

B.S. Biotechnology Engineering, Monterrey Institute of Technology and Higher Education (2021)

I am interested in feedback systems within bacterial communities. I want to understand how they can be modeled and engineered for industrial and pharmaceutical settings.

Ashwini Shende

ashwini.shende@duke.edu

B.S.E. Chemical and Biological Engineering, Princeton University (2023)

I am interested in investigating the environmental factors that influence horizontal gene transfer and plasmid persistence in bacterial communities.

Irida Shyti

irida.shyti@duke.edu

BA Mathematics And Computer Science, American University in Bulgaria (2020)

I am interested in the intersection of artificial intelligence and complex microbial communities, focusing on how computational tools can enhance our understanding and manipulation of microbial behaviors.

Yuanchi Ha
yuanchi.ha@duke.edu

B.S. Computer Science and Mathematics, University of California San Diego (2018)

I am using mathematical analysis, modeling, and machine learning to predict relationships in complex microbial communities to understand the information encoded by complex biological features.

Zachary Holmes
zachary.a.holmes@duke.edu

B.S. Chemical Engineering, Purdue University (2013)

I am using gene circuits to develop population dependent behavior to manufacture molecules of interest. Within my research, I use division of labor (DOL) and encapsulation with the intention of developing an effective biomanufacturing platform. 

Grayson Hamrick grayson.hamrick@duke.edu

B.S. Chemistry, B.S. Mathematics, Haverford College (2021)

My current research is focused on combining metabolic division of labor and horizontal gene transfer for the design of microbial communities with robust function.

Kinshuk Sahu kinshuk.sahu@duke.edu

B. Tech. and M. Tech. Biochemical Engineering, IIT (BHU) Varanasi, India (2019) M.S. Bioengineering, University of California San Diego (2022)

I am interested in using synthetic and systems biology tools to understand the dynamics of pattern formation in microbial systems.

Kristen Lok

kristen.lok@duke.edu

B.S. Bioengineering, UC Berkeley (2023)

I am interested in using directed evolution, division of labor, and horizontal gene transfer to engineer microbial consortia.

Ryan Su

ryan.su@duke.edu

Biomedical Engineering and Computer Science (2026)

I'm currently working with Dongheon on studying population density-dependent antibiotic resistance in bacterial populations, with the goal of finding a universal mechanism responsible for resistance to many antibiotics.