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The Li group studies how cells use temporal and mechanical dynamics to sense and shape tissue geometry during development.
An embryo begins as a collection of identical cells with no distinguishing features and ends as an organism with an intricate three-dimensional structure. Building this shape requires cells to know not only their identity but also their geometric context: when to divide, curve, or stop growing. We study this problem using tools from non-equilibrium statistical physics, treating developing tissues as active systems whose macroscopic behavior emerges from local, time-dependent rules. Our research spans three connected directions: the physics of biological oscillations, the geometry of organoid morphogenesis, and the active mechanics of the cytoskeleton. Together, these ask how cells sense, generate, and respond to shape.
Biological oscillations, such as segmentation clocks, calcium waves, and cell cycles, are a distinctive and deeply underexplored class of non-equilibrium phenomena: unlike physical waves, they carry no energy of their own but are continuously driven by local energy input. We ask what determines their collective behavior at the tissue scale: do biological oscillators share universal dynamical properties that transcend the microscopic details of individual biological systems? And how do geometry and cell-to-cell variations reshape them? For example, do phase waves in the segmentation clock during somitogenesis increase the robustness of somite segmentation? Do variations in mechanical properties of the heart tissue make arrhythmia more likely? We address this in two ways: firstly, via generic, minimal theoretical models that explore the universal features of coupled oscillatory systems beyond microscopic details, and secondly, via micro-inspired, system-specific models that bridge the gap between theory and experiments.
We use intestinal organoids as a model system to ask how a tissue collectively builds its own three-dimensional shape. We are developing computational methods, based on spherical-harmonic decomposition and heat-kernel curvature, to quantify organoid geometry systematically across large multiplexed datasets and to correlate shape with cell identity over time. This unbiased, data-driven analysis has already uncovered surprising results: there is not a single deterministic trajectory for crypt formation but rather multiple complementary pathways. We will combine this approach with mechanistic modelling of signaling dynamics and cell-fate decisions on curved, growing surfaces, aiming to understand how a tissue senses its local geometry, and how this geometric information feeds back to steer cell-fate decisions.
Tissues are shaped by the forces that cells generate through their cytoskeleton, a network of filaments and motors that is itself a striking example of active matter, operating far from thermal equilibrium. We use mesoscopic active matter theories to understand how cytoskeletal self-organization produces coherent mechanical behavior, from the actin flows that facilitate division of large embryonic cells, to the emergent elasticity of assemblies of active filaments and colloids.
Nikhil Mishra, Yuting I. Li, Edouard Hannezo, Carl-Philipp Heisenberg
Download|2026
Xin Tong*, Yuting I. Li*, […], Edouard Hannezo, Carl-Philipp Heisenberg
Download|2024
preprint
Toshiyuki Sato, Yuting I. Li, […], Benjamin D. Simons, Shosei Yoshida
Quentin Martinet*, Yuting I. Li*, […] Edouard Hannezo, Jérémie Palacci
Marek J. van Oostrom, Yuting I. Li, […], Benjamin D. Simons, Katharina F. Sonnen
Download|2025
Yuting I. Li, […], Michael E. Cates, R. Adhikari, Robert L. Jack
Download|2021
Yuting I. Li, Michael E Cates
2021
Yuting I. Li, Michael E. Cates
2020
Yuting Irene Li (who goes by Irene) is a group leader at the Hubrecht Institute, starting September 2026. Trained as a theoretical physicist, she works on developing non-equilibrium statistical theories to understand developmental processes. During her PhD, she studied the thermodynamics of active matter, focusing on phase-separating systems such as biomolecular condensates. In her postdocs, she worked on problems spanning active assemblies, zebrafish embryogenesis, somitogenesis, and intestinal organoids.
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One PhD position and one postdoc position are available for people enthusiastic about theoretical biophysics in close collaboration with experiments. We also support applications to national and international programs. If you are interested in joining our group, please get in touch with me. All inquiries in English.
