Mark Mimee, Principal Investigator (He/Him)

Mark Mimee is an Assistant Professor in the Department of Microbiology and the Pritzker School of Molecular Engineering. His interest in microbial life began in Montreal, Canada, where he completed his Bachelor of Science in Microbiology & Immunology at McGill University. Inspired by the nascent field of synthetic biology, Mark pursued studies at the Massachusetts Institute of Technology, completing his PhD in Microbiology with Dr. Timothy Lu as an HHMI International Student Fellow and a Qualcomm Innovation Fellow. His research focuses on developing strategies to precisely engineer the activity and composition of the microbiota.  His long-term vision is to implement these technologies to chart new basic and translational studies to exploit the microbiota for human health. Outside of the lab, Mark enjoys baking savoury pies, fermenting food and drink, playing double bass, and trying to stay in shape.


Ella Rotman, Research Specialist

Ella Rotman is a research specialist with a love for bacterial genetics. She did her doctoral work at the University of Illinois at Urbana-Champaign in the lab of Dr. Andrei Kuzminov studying DNA damage avoidance mechanisms in E. coli. She then did a postdoc at Northwestern University studying antigenic variation in Neisseria gonorrhoeae (the causative agent of gonorrhea) in the lab of Dr. Hank Seifert, followed by research in the lab of Dr. Mark Mandel on the colonization of the Hawaiian bobtail squid by bioluminescent Vibrio fischeri bacteria. Her current project involves isolation and manipulation of bacteriophage that infect the gut bacteria Klebsiella. Outside of the lab, Ella enjoys reading and watching science fiction and fantasy.


Jaehyun Lee, Postdoctoral Associate

Jaehyun Lee is a postdoc in the Department of Microbiology. She received her doctoral degree in the lab of Dr. Junsang Doh at Pohang University of Science and Technology (POSTECH), South Korea. During her Ph.D. studies, she investigated T cell dynamics in the complex microenvironment by using microfluidic systems, microfabrication methods, and real-time imaging. Then, she joined the lab of Dr. Esak Lee at Cornell University as a postdoc and expanded her research horizon towards more comprehensive adaptive immunity by dealing with dendritic cell and T cell behavior around the lymphatic systems with both in vitro and in vivo models. Currently, she is interested in engineering Bifidobacterium to modulate the immune system in the body. Outside of the lab, she enjoys playing the guitar and watching the same drama/movie over and over again.


Jack Arnold, PhD Candidate

Jack Arnold is a graduate student in the Pritzker School of Molecular Engineering working jointly with Dr. Mark Mimee and Dr. Cathryn Nagler. His interest in synthetic biology first began when he joined the iGEM Team at Northwestern University where he completed his Bachelor of Science in Chemical Engineering. Currently, his project involves developing genetic tools to engineer Anaerostipes caccae and Anaerostipes hadrus as well as isolating other Lachnospiraceae species to learn more about the role these bacteria play in food allergy. Outside of the lab, he can be found rock climbing, playing board games, or exploring Chicago’s food scene.


Jay Fuerte-Stone, PhD Candidate (They/Them)

Jay Fuerte-Stone is a PhD student in the Committee on Microbiology. After receiving their undergraduate degree from the University of Washington in Bioengineering, they worked for two years at the Infectious Disease Research Institute in Seattle. There, they developed an interest in viruses and viral genome engineering. Currently, they are interested in engineering Bacteroides prophage in order to deliver genetic payloads to targeted strains in the gut. Outside of the lab, they can be found sewing, practicing their mixology skills, hiking, and doting on their three pets.


Sandra McClure, PhD Candidate (She/Her)

Sandra McClure is a PhD student from the Committee on Molecular Metabolism and Nutrition in the Biological Sciences Division. Her interests in metabolic pathways stemmed from her research in electrochemical biomarker detection in the wound environment at Michigan State University where she received her Bachelor of Science in Human Biology and a Bachelor of Arts in Chemistry. She works currently on engineering Bacteroides thetaiotaomicron to investigate its role in short chain fatty acid production in the gut microenvironment for application in metabolic syndrome. Outside of the lab, Sandra enjoys cooking, traveling, crafting, and spending time with friends and family.


Joshua Glazier, PhD Candidate

Josh Glazier is a PhD student in the Pritzker School of Molecular Engineering. After completing his undergraduate degree in Biomedical Engineering from the University of Virginia, he worked for three years at the Gladstone Institutes in San Francisco. There, he worked on novel HIV therapeutics and viral engineering projects, and developed his interest in synthetic biology. Now, Josh is working on designing cell-based biosensors for the gut by harnessing the microbiome’s transcriptional responses to environmental changes. Outside of the lab, Josh loves playing soccer and basketball, snowboarding, backpacking, and reading science fiction and fantasy.


Joyce Ghali, PhD Student

Joyce is a PhD student in the Committee on Molecular Metabolism & Nutrition working jointly with Drs. Mark Mimee and Sam Light. Prior to arriving at UChicago, Joyce received her B.S. in Biochemistry from the University of Cincinnati where she worked on developing an atomic mass spectrometry method to investigate insulin independent glucose uptake in skeletal muscle. Joyce is currently interested in investigating the effect of microbial metabolites on human health as well as developing novel microbiome therapeutics. Outside of the lab, Joyce enjoys hiking, listening to podcasts, and spending time with friends and family.


Madhu Prakash, PhD Student

Madhu Prakash is a Ph.D. student at the Pritzker School of Molecular Engineering working jointly with Dr. Mark Mimee and Dr. Savas Tay. She completed her B.S. in Biological Engineering at Purdue University where she worked on developing recombinant elastin-like polypeptides for imaging probes and nanoparticles targeting bladder cancer. In addition, she worked on developing a microfluidic COVID-19 diagnostic device as president of her university’s iGEM team. Her current research focuses on using droplet microfluidics to conduct high-throughput bacteriophage susceptibility screens. Outside of the lab, she enjoys watching anime, painting, and traveling.


Sadiksha Shakya, PhD Student

Sadiksha Shakya, a PhD student at the Pritzker School of Molecular Engineering pursuing immune engineering. Her academic journey commenced with an undergraduate degree in Biotechnology from Kathmandu University, Nepal, followed by a master’s degree in Molecular Mechanisms of Disease from Radboud University in the Netherlands. During her master’s program, Sadiksha focused her efforts on characterizing Kidney organoids derived from Human-induced Pluripotent Stem Cells (HiPSCs) under the guidance of Dr. Joost Hoenderop in the Department of Physiology at Radboud Institute of Molecular Life Sciences. Subsequently, as a non-degree visiting student under Dr. Mark Mimee, she found herself captivated by the field of synthetic biology, which prompted her interest in generating integrative vectors for engineering commensal bacteria. Beyond her academic pursuits, she enjoys cooking, watching anime, sitcoms, movies etc. and spending time with her loved ones.


Rory McGann, Undergraduate Researcher

Rory McGann is a rising second-year undergraduate student in the College majoring in Molecular Engineering, on the Bioengineering track. His research project involves isolating and tuning bacteriophage to better infect Klebsiella in the gut. Outside of the lab, Rory enjoys singing, writing fiction, and rock climbing.


Tracy Chen, Undergraduate Researcher

Tracy is a rising fourth-year undergraduate student majoring in molecular engineering and minoring in computer science. She is working with Jack to develop and characterize promoters in Lachnospiraceae to enhance our understanding of their roles in disease prevention and remediation, as well as to produce gene products of interest. When she’s not doing experiments, she enjoys working out, cooking, and binge-watching animal videos.




Support Staff


Kala was born in Oklahoma and joined the Mimee Lab in October 2019 at three months of age. As a hound mix, she enjoys the pursuit of small animal research and will self-appoint new projects when she completes her work. Kala’s favourite pasttime is people-watching, tilting her head side-to-side to get new vantage points when she encounters new specimens, and playing double ball. Kala works remotely for now, but can be seen making guest appearances in the office from time to time.




Korra is Josh’s dog.







Annie was adopted by Jay’s family in 2010. Since then, she has lived in Washington and Idaho before being adopted by Jay and their partner, Dan, in 2018. She loves to spend the day snoozing on her couch, watching squirrels, barking at noises, and trying to make Jun love her. She has been unsuccessful in the latter thus far.





Junipurr (Jun) was adopted by Jay in 2017. A very nervous cat, she took several years to become comfortable in her environment but is now running the house. She loves napping on her cat tree, attention, pets, cuddling, yowling at 3am, and ignoring Annie.





Sage was adopted by Jay and their partner in late 2022. He is rambunctious and curious. His favorite past times are annoying his two sister (Jun and Annie), napping as close to a human face as he can, and sticking his face in any open cup he can find.





Sabrina and Cicely

These two young littermates belong to Ella and Brian. They come from Hyde Park Cats, a local rescue network of foster homes, and are very friendly and snuggly. Sabrina (eyepatch) is curious and playful, while Cicely (forehead blaze) is more reserved. Of the two cats, Cicely is a keen huntress, catching bugs and toys alike. Sabrina, on the other hand, likes to chase her own tail.
To see photos of Ella and Brian’s handsome cats, follow @misha_cici_sabi on Instagram.


Lab Alumni


p style=”font-size: 15px;”>Recep Erdem Ahan, Visiting Graduate Student – Current Position: Graduate Student at Bilkent University
Ameera Abu-Khalil, Undergraduate Researcher
Ali Erani, Undergraduate Researcher – Current Position: Research Specialist at the University of Chicago
Sergio Escobar, Post-Baccalaurate Student – Current Position: Graduate Student at Vanderbilt University
Jonathan Foldi, Undergraduate Researcher – Current Position: Tessera Therapeutics


This handsome cat was Misha, who lived with Ella and her husband Brian until 2020. Misha’s favorite activities included sleeping, napping, lounging, and snoozing. He also enjoyed catnip and fishy food with shrimp (the smellier the better). You can read about Misha here or follow his siblings on Instagram @misha_cici_sabi for more photos.