Research
The Biomimetic MicroEngineering (BioME) Laboratory advances bioinspired engineering principles to elucidate fundamental mechanisms underlying human health and disease. Central to our work is the human Organ-on-a-Chip, also known as the Microphysiological System (MPS), a next-generation experimental platform that accurately recapitulates host-microbiome ecosystems and predicts human physiological responses with fidelity unattainable by conventional models. We have engineered novel biomimetic architectures that reconstitute the three-dimensional physical microstructure, organ-level physiological functions, and dynamic biomechanical forces of the living human gut.
A defining focus of the laboratory is the emulation of host-microbiome interactions that govern intestinal homeostasis and drive disease pathogenesis. Working in close collaboration with clinical partners, we have developed a breakthrough "Personalized Disease-on-a-Chip" framework that integrates patient-derived organoids, patient-specific microbiomes, and primary immune cells into a single, controllable platform. This technology has enabled mechanistic investigation of microbiome-mediated pathology across a spectrum of gastrointestinal diseases, including inflammatory bowel disease (IBD), encompassing Crohn's disease and ulcerative colitis, colorectal cancer, and enteric infectious diseases.
Our overarching scientific mission is to distinguish causality from consequence in host-microbiome crosstalk across diverse disease contexts, leveraging patient-specific Disease-on-a-Chip models as precision research tools. Looking forward, we are expanding our biomimetic platform to model pathophysiological processes across multiple organ systems, including the oral cavity, nasal airway, vaginal tract, placenta, skin, liver, and gut-brain axis. Ultimately, we are committed to translating this disruptive technology into tangible impact for the scientific, clinical, and pharmaceutical communities, accelerating the resolution of high-priority, high-risk medical challenges.
Biography
Hyun Jung Kim, Ph.D. is an Assistant Staff in the Department of Inflammation and Immunity at the Cleveland Clinic and Principal Investigator of the Biomimetic MicroEngineering (BioME) Laboratory. Where the laboratory builds the platforms, Dr. Kim's research program drives the scientific vision underlying them, advancing bioinspired engineering principles to create next-generation biomedical technologies that bridge mechanistic discovery with clinically actionable innovation.
Dr. Kim is internationally recognized for pioneering miniaturized human Organ-on-a-Chip MPS that faithfully recapitulate the structural architecture, functional physiology, and mechanical dynamics of the human intestine. His laboratory has established foundational biomimetic methodologies for modeling host-microbiome interactions under physiologically relevant flow and mechanical forces, with landmark publications in Advanced Science (2026), PNAS (2016, 2018), Nature Protocols (2022), and Nature Reviews Bioengineering (2024), collectively advancing patient-specific disease modeling and precision interrogation of complex host-microbiome ecosystems. By converging clinical microbiology, microfluidics, and tissue engineering, Dr. Kim's group has uncovered critical mechanistic insights into inflammatory, fibrotic, and oncologic pathologies driven by host-microbiome crosstalk, positioning organ-on-a-chip technology as a rigorous alternative to conventional in vitro and animal models.
His contributions have been recognized by competitive awards, including the NIH NCI IMAT Award (2025, 2018), Kenneth Rainin Foundation Innovator Awards (2024, 2016), VeloSano 10 Pilot Award (2024), Crohn's & Colitis Foundation Senior Research Award (2023), and the Cancer Research Institute Technology Impact Award (2018).
Education & Professional Highlights
ACADEMIC & PROFESSIONAL APPOINTMENT
07/2022 – present Cleveland Clinic, Cleveland Clinic Research, Cleveland, OH, USA
Assistant Staff, Department of Inflammation and Immunity
02/2023 – present Assistant Staff, Department of Biomedical Engineering (Joint Appointment)
04/2023 – present Assistant Professor, Department of Biomedical Engineering, Cleveland Clinic Lerner College of Medicine (CCLCM) of Case Western Reserve University
01/2015 – 06/2022 The University of Texas at Austin, Austin, TX, USA
Assistant Professor, Department of Biomedical Engineering, Cockrell School of Engineering
EDUCATION & TRAINING
Harvard University, Boston, MA, USA
09/2012 – 12/2014 Technology Development Fellow, Wyss Institute for Biologically Inspired Engineering (Advisor: Donald E. Ingber, MD, PhD)
07/2009 – 08/2012 Postdoctoral Fellow, Wyss Institute for Biologically Inspired Engineering (Advisor: Donald E. Ingber, MD, PhD)
The University of Chicago, Chicago, IL, USA
03/2007 – 06/2009 Postdoctoral Scholar, Department of Chemistry (Advisor: Rustem F. Ismagilov, PhD)
Yonsei University, Seoul, Republic of Korea
09/2005 – 02/2007 Research Associate, Institute of Life Science and Biotechnology (Advisor: Chul Soo Shin, PhD)
09/2000 – 08/2005 PhD in Biotechnology (Advisor: Chul Soo Shin, PhD)
03/1998 – 08/2000 MS in Biotechnology (Advisor: Chul Soo Shin, PhD)
03/1994 – 02/1998 BE in Biotechnology
AWARDS & HONORS (Selected)
2025 Appreciation Award, Cleveland Clinic Foundation, USA (Apr and Jun)
2025 Catalyst SPARK Awards, Cleveland Clinic Foundation, USA
2024-2026 Innovator Awards, Kenneth Rainin Foundation, USA
2024 VeloSano 10 Pilot Award, VeloSano and Cleveland Clinic, USA
2024-2026 Ewha Global Fellow (EGF), Ewha Womans University, Seoul, Korea
2023-2026 Senior Research Award, Crohn’s and Colitis Foundation of America, USA
2023 2022 Inventor, Office of Innovations, Cleveland Clinic Foundation, USA
2023 CTSC Core Utilization Pilot Grant Award, Case Western Reserve University, USA
2022 Career Development Program Award, Lerner Research Institute, Cleveland Clinic, USA
2021 2020 Research Excellence in Korean Biomedical Science, Medical Research Information Center, Korea
2018 Technology Impact Award, Cancer Research Institute (CRI), USA
2017 Texas 4000 Seed Grant Award, Dept. of Biomedical Engineering, UT Austin, USA
2016 Innovator Awards, Kenneth Rainin Foundation, USA
2015 Featured Designer for Organs-on-Chips, Museum of Modern Art (MoMA), New York, USA
2013 Abcam Discovery 15 Contest Finalist ($1,000 credit), USA
2013 2013 Invented Here! Honoree. New England’s Breakthrough Inventions and Inventors. Boston, MA, USA
2013 Best Paper Award. ALine, Inc., 2013 ASME (NEMB 2013). Feb 4-6, 2013, Boston, MA, USA
2012 - 2014 Wyss Technology Development Fellowship, Wyss Institute, Harvard University, USA
2012 Best Presentation Award for Postdocs. The Korean Toxicologists Association in America. SOT 2012, San Francisco, CA, USA
2012 Postdoctoral Award (1st place). In Vitro and Alternative Methods Special Section, SOT 2012, San Francisco, CA, USA
2007 - 2008 Leo Kadanoff and Stuart Rice Postdoctoral Fellowship, The University of Chicago, USA
2003 - 2004 Fellowship for Young Scientist, Korea Research Foundation, Korea
2001 Scholarship for Excellent Student, Yonsei University, Seoul, Korea
"CIMER Trained Mentor" indicates the principal investigator has completed mentorship training based on curriculum from the Center for the Improvement of Mentored Experiences in Research, aimed at advancing mentoring relationships and promoting cultural change in research.
Research
Overview
The Biomimetic MicroEngineering (BioME) Laboratory advances bioinspired engineering principles to elucidate fundamental mechanisms underlying human health and disease. Central to our work is the human Organ-on-a-Chip, also known as the Microphysiological System (MPS), a next-generation experimental platform that accurately recapitulates host-microbiome ecosystems and predicts human physiological responses with fidelity unattainable by conventional models. We have engineered novel biomimetic architectures that reconstitute the three-dimensional physical microstructure, organ-level physiological functions, and dynamic biomechanical forces of the living human gut.
A defining focus of the laboratory is the emulation of host-microbiome interactions that govern intestinal homeostasis and drive disease pathogenesis. Working in close collaboration with clinical partners, we have developed a breakthrough "Personalized Disease-on-a-Chip" framework that integrates patient-derived organoids, patient-specific microbiomes, and primary immune cells into a single, controllable platform. This technology has enabled mechanistic investigation of microbiome-mediated pathology across a spectrum of gastrointestinal diseases, including inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, colorectal cancer, and enteric infectious diseases.
Our overarching scientific mission is to distinguish causality from consequence in host-microbiome crosstalk across diverse disease contexts, leveraging patient-specific Disease-on-a-Chip models as precision research tools. Looking forward, we are expanding our biomimetic platform to model pathophysiological processes across multiple organ systems, including the oral cavity, nasal airway, vaginal tract, placenta, skin, liver, and gut-brain axis. Ultimately, we are committed to translating this disruptive technology into tangible impact for the scientific, clinical, and pharmaceutical communities, accelerating the resolution of high-priority, high-risk medical challenges.
Our Team
Selected Publications
View publications for Hyun Jung Kim, PhD
(Disclaimer: This search is powered by PubMed, a service of the U.S. National Library of Medicine. PubMed is a third-party website with no affiliation with Cleveland Clinic.)
Selected Publications
- Soyoun Min, Nam Than, Yong Cheol Shin, Elif G. Ertugral, Chandrasekhar R. Kothapalli, Olumuyiwa Awoniyi, and Hyun Jung Kim. Mechanostimulatory cues determine intestinal fibroblast fate and profibrotic remodeling in a physiodynamic gut-on-a-chip. Adv. Sci. 2026. (Published online on Apr 10, 2026).
- Yong Cheol Shin*, Nam Than*, Soyoun Min, Woojung Shin+, and Hyun Jung Kim+. Modelling Host-Microbiome Interactions in Organs-on-chip Platforms. Nat. Rev. Bioeng., 2023. (*Equally contributed; +Co-correspondence; Published online on Nov 17, 2023)
- Soyoun Min*, Nam Than*, Yong Cheol Shin, Grace Hu, Woojung Shin, Yoko M. Ambrosini, and Hyun Jung Kim. Live probiotic bacteria administered in a pathomimetic Leaky Gut Chip ameliorate impaired epithelial barrier and mucosal inflammation. Sci. Rep., 2022, 12, 22641. (*Equally contributed; Published online on Dec 31, 2022)
- Woojung Shin*, Zhe Su*, Song Yi+, and Hyun Jung Kim+. Single-cell transcriptomic mapping of intestinal epithelium that undergoes mechanodynamic stimulation and 3D morphogenesis in a gut-on-a-chip. iScience, 2022, 25, 105521 (*Equally contributed; +Co-correspondence; Published online on Nov 7, 2022)
- Woojung Shin and Hyun Jung Kim. 3D In Vitro Morphogenesis of Human Intestinal Organoids or Caco-2 Cells in a Gut-on-a-chip or a Hybrid Chip with a Cell Culture Insert. Nat. Protoc. 2022, 17, 910-939. (Published online on Feb 2, 2022)
- Woojung Shin, Alexander Wu, Soyoun Min, Yong Cheol Shin, R. Y. Declan Fleming, S. Gail Eckhardt, and Hyun Jung Kim. Spatiotemporal gradient and instability of Wnt induce heterogeneous growth and differentiation of human intestinal organoids. iScience 2020, 23, 101372. (Published online: Aug 21, 2020)
- Woojung Shin*, Yoko M. Ambrosini*, Yong Cheol Shin*, Alexander Wu, Soyoun Min, Domin Koh, Sowon Park, Seung Kim, Hong Koh, and Hyun Jung Kim. Robust Formation of an Epithelial Layer of Human Intestinal Organoids in a Polydimethylsiloxane-based Gut-on-a-chip Microdevice. Front. Med. Technol. 2020, 2, 2. (*Equally contributed; Published online: Aug 7, 2020)
- Yong Cheol Shin*, Woojung Shin*, Yoko M. Ambrosini, Domin Koh, Alexander Wu, Soyoun Min, S. Gail Eckhardt, R. Y. Declan Fleming, Seung Kim, Sowon Park, Hong Koh, Tae Kyung Yoo, and Hyun Jung Kim. Three-dimensional regeneration of patient-derived intestinal organoid epithelium in a physiodynamic mucosal interface-on-a-chip. Micromachines 2020, 11, 663. (*Equally contributed; Published online: Jul 7, 2020)
- Woojung Shin, Christopher D. Hinojosa, Donald E. Ingber, and Hyun Jung Kim, Human intestinal morphogenesis controlled by transepithelial morphogen gradient and flow-dependent physical cues in a microengineered gut-on-a-chip. iScience 2019, 15, 391-406. (Published online: May 31, 2019)
- Woojung Shin*, Alexander Wu*, Miles Massidda*, Charlie Foster, Newin Thomas, Dong-Woo Lee, Hong Koh, Youngwon Ju, Joohoon Kim, and Hyun Jung Kim. A robust longitudinal co-culture of obligate anaerobic gut microbiome with human intestinal epithelium in an anoxic-oxic interface-on-a-chip. Front. Bioeng. Biotechnol. 2019, 7, 13. (*Equally contributed; Published online: Feb 7, 2019)
- Woojung Shin and Hyun Jung Kim. Intestinal barrier dysfunction orchestrates the onset of inflammatory host-microbiome cross-talk in a human gut inflammation-on-a-chip. Proc. Natl. Acad. Sci. U.S.A. 2018, 115, E10539-E10547. (Published online: Oct 22, 2018)
- Hyun Jung Kim, Hu Li, James J. Collins,and Donald E. Ingber. Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip. Proc. Natl. Acad. Sci. U.S.A. 2016, 113, E7-E15. (Published online: Dec 14, 2015)
- Hyun Jung Kim and Donald E. Ingber. Gut-on-a-Chip microenvironment induces human intestinal cells to undergo villus differentiation. Integr. Biol. 2013, 5, 1130-1140. (Published online: Jun 26 2013)
- Hyun Jung Kim, Dongeun Huh, Geraldine Hamilton, and Donald E. Ingber. Human Gut-on-a-Chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow. Lab Chip 2012, 12, 2165-2174. (Published online: Mar 8, 2012)
- Hyun Jung Kim*, James Q. Boedicker*, Jang Wook Choi, and Rustem F. Ismagilov. Defined spatial structure stabilizes a synthetic multispecies bacterial community. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 18188-18193. (*Equally contributed; Published online: Nov 14, 2008)
Careers
Apr 1, 2026
Biomimetic Microengineering (BioME) Lab (PI: Hyun Jung Kim, PhD) at the Cleveland Clinic has developed an advanced human Organ-on-a-Chip microphysiological system to model the host-microbiome ecosystem with unprecedented pathophysiological fidelity. By integrating patient-derived cells and microbiome, we create a personalized Disease-on-a-Chip platform to discover disease mechanisms and identify novel therapeutic strategies. We are seeking motivated candidates at various levels to join our interdisciplinary team and advance innovations in translational science, engineering, and medicine.
POSITION 1: Microbiome-Associated Disease Modeling in Organ-on-a-Chip Platforms. We are seeking talented candidates to join collaborative projects investigating how the gut microbiome orchestrates human gastrointestinal (GI) diseases, including inflammatory bowel disease (IBD) such as Crohn’s disease (CD) and ulcerative colitis (UC), colorectal cancer (CRC), gut-brain and gut-liver axis disorders, and infectious diseases. Our transdisciplinary initiatives, in collaboration with physician-scientists, immuno-oncologists, and pharmaceutical partners, aim to elucidate microbiome-driven mechanisms of disease development, advancing precision therapeutics and translational medicine.
POSITION 2: Advanced Engineering for Multiscale Organ-on-a-Chip Platforms. We are hiring dedicated candidates to advance our multiscale Organ-on-a-Chip platform, enabling scalable operations through multiple experimentation, configurable modules, and a cost-effective, reproducible design that supports strong reproducibility and replicability. The ideal candidate will have expertise in i) mechanical engineering, including precision electromechanical design for compact, multi-unit laboratory systems with embedded automation, ii) 3D printing, prototyping, and precision manufacturing processes for multiscale hardware development, and iii) microfluidics, microfabrication, or microengineering to integrate an engineered system with microscale biological models and implement automated system control.
Skills Required: Candidates must possess rigorous scientific training in research design and analysis, with a strong track record of research achievements. Ideal candidates will demonstrate expertise in one or more of the following areas: i) GI mucosal biology and immunology; ii) stem cell engineering and regenerative medicine; iii) cancer biology or cancer immunology; iv) pharmacology, ADME/toxicology, PK/PD, and drug metabolism; v) clinical microbiology or host-microbiome interactions; vi) spatial multi-omics, bioinformatics, and high-content imaging; or vii) microtechnology, 3D printing, or manufacturing.
Applicants are required to send i) CV and ii) Cover Letter to [email protected]. In the cover letter, please highlight the qualifications pertinent to the project outlined in the job description and a list of 3 references.
Research News
In inflammatory bowel disease, colon cells lining the intestine are more susceptible to physical damage and scarring.