Systems Biology at UConn Health
Our Mission
We develop computational and experimental approaches to tackle exciting questions in biology and medicine, bringing a systems biology approach to biomedical research. Quantitative experimental methods aim to measure the dynamic behavior of molecules in cells and tissues. We integrate these experimental data within computational models to produce quantitative, comprehensive, and mechanistic models of cellular and molecular dynamics.
The Center for Cell Analysis and Modeling (CCAM) hosts a confluence of expertise in cell biology, biochemistry, genomics, physics, chemistry, mathematics and computer science. We foster a biomedical research environment that values interdisciplinary collaborations. Our Ph.D. program in Systems Biology (opens in a new tab) provides unique graduate training in systems and computational biology. We also provide research experiences for undergraduates.
CCAM is home to several computational resources including Virtual Cell (opens in a new tab) and COPASI (opens in a new tab) for modeling and simulation of cellular mechanistic models, maintained under the NIH-funded National Resource for Mechanistic Modeling of Cellular Systems, Vivarium for multiscale simulation and whole-cell models, and many other experimental tools for imaging and molecular genetics. The center also hosts state-of-the-art high-performance computing (opens in a new tab) and microscopy (opens in a new tab) facilities.
The center’s values extend beyond rigorous and open science. Our research has benefited greatly from inclusive excellence and the diversity of ideas and backgrounds of all our researchers over the years. CCAM continuously strives to improve the environment in which we perform research and pursue education.
CCAM is committed to fostering an inclusive and tolerant research environment. We support students, faculty, and staff of all races, religions, ethnicities, differing physical abilities, sexual orientations, and gender identities. UConn maintains a number of resources to promote inclusivity and to report complaints:
Office of Institutional Equity
Ombuds Office
Dean of Students Office Bias Reporting
Office for Diversity and Inclusion
School of Medicine Office of Multicultural and Community Affairs
Upcoming Events
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Oct
8
CCAM Seminar Series - Dr. Timothy Duerr 4:00pm
CCAM Seminar Series - Dr. Timothy Duerr
Thursday, October 8th, 2026
04:00 PM
CGSB, 400 Farmington Ave
CCAM Seminar Series
Speaker: Dr. Timothy Duerr Ph.D., Assistant Professor, Department of Orthopaedic Surgery, UConn Health
Title: “Cellular and molecular mechanisms regulating proximodistal positional identity during axolotl limb regeneration”
Abstract: Axolotl salamanders can regenerate their limbs following amputation anywhere along the proximodistal (PD) axis. During this process, resident connective tissue cells, including dermal fibroblasts and periskeletal cells, dedifferentiate and accumulate at the limb stump to form a blastema. Blastema cells retain their genetically encoded PD positional identity, enabling them to redifferentiate and regenerate the appropriate PD limb structures. Retinoic acid (RA) signaling is essential for establishing PD positional identity, as elevated levels of RA instruct blastema cells to adopt a proximal limb identity. We found that RA concentration along the PD axis is regulated by Cyp26b1 expression, which degrades excess RA to generate distal identity during limb regeneration. These differences in RA concentration lead to differential expression of homeobox genes that provide blastema cells with the correct PD positional identity. One such gene identified was Shox, which we show is required for activation of the PTHrP/IHH feedback loop in regenerating chondrocytes of proximally amputated limbs. Once blastema cells genetically adopt positional identity via RA, they express PD-specific cell surface proteins that modify cellular adhesivity. This enables self-sorting with cells of similar positional identities. We have identified several cell surface proteins, including LPHN2, TENM4, and FLRT3 that follow the same spatiotemporal expression patterns as 5’ Hox genes and are both RA responsive and differentially expressed between proximally and distally amputated limbs. Collectively, our results support a model whereby RA directs blastema cells to establish PD identity through transcription factors that regulate the expression of positional identity-specific cell surface proteins.
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News
- Dr. Agmon’s NSF C-CoMP Center funding is renewed through 2031Posted on September 16, 2026
- Dr. Agmon is funded to co-lead NIH MOSAIC projectPosted on September 16, 2026
- Faculty PromotionsPosted on August 28, 2026
- 28th on-site Computational Cell Biology workshopPosted on June 3, 2026
- 27th online Computational Cell Biology workshopPosted on March 20, 2026
















