Research Units

The biological nonlinear dynamics data science unit investigates complex systems explicitly taking into account the role of time. We do this by instead of averaging occurrences using their statistics, we treat observations as frames of a movie and if patterns reoccur then we can use their behaviors in the past to predict their future. In most cases the systems that we study are part of complex networks of interactions and cover multiple scales. These include but are not limited to systems neuroscience, gene expression, posttranscriptional regulatory processes, to ecology, but also include societal and economic systems that have complex interdependencies. The processes that we are most interested in are those where the data has a particular geometry known as low dimensional manifolds. These are geometrical objects generated from embeddings of data that allows us to predict their future behaviors, investigate causal relationships, find if a system is becoming unstable, find early warning signs of critical transitions or catastrophes and more. Our computational approaches are based on tools that have their origin in the generalized Takens theorem, and are collectively known as empirical dynamic modeling (EDM). As a lab we are both a wet and dry lab where we design wet lab experiments that maximize the capabilities of our mathematical methods. The results from this data driven science approach then allows us to generate mechanistic hypotheses that can be again tested experimentally for empirical confirmation. This approach merges traditional hypothesis driven science and the more modern Data driven science approaches into a single virtuous cycle of discovery.

The CSE Unit analyzes the dynamics of complex adaptive systems, focusing on behavioral dynamics shaping social systems, eco-evolutionary dynamics shaping ecosystems, and their interactions.

The Computational Neuroethology Unit seeks to uncover the principles governing animal behavior and its neural basis. We are currently focusing on cephalopods: squid, octopus, and cuttlefish.

The ECBS unit studies the effects of symbiotic interactions on the origin and evolution of cellular life.

Research projects of the Evolutionary Neurobiology Unit include (1) anatomical and physiological dissections of the nervous systems of basal metazoans, mainly on diffused and regionally cond...

The Genomics and Regulatory Systems Unit combines computational and experimental methods to study principles of gene regulation during early organismal development, using Oikopleura dioica as a model organism.

Theory-driven research on macroevolution, biodiversity, and evolutionary patterns across space and time, integrating fossils, fishes, biomechanics, phylogenies, and models.

The Marine Biophysics Unit examines how ocean currents affect the marine life of hydrothermal vents and coral reefs around Okinawa.

The Marine Climate Change Unit aims to understand how coral reef fish respond to human society driven environmental changes such as climate change, heatwaves, overfishing, and urbanization.

Most coral reef fishes have an incredible colors but why and how do they appear ? We use clownfish as a model we decipher the origins of the colors and how the fish are using them.

Exploring marine genomic diversity helps understanding organism responses to environmental change in the past and future, both in terms of large-scale evolution and within their ecosystems.

The Marine Physics and Engineering Unit advances the forecast of ocean dynamics and the development of hydrodynamic disaster mitigation alternatives, paving the way for novel ocean technologies.

The Marine Structural Biology Unit uses cryoelectron tomography and single particle cryoelectron microscopy to understand various aspects of coral biology in unprecedented detail.

We work in experimental nonlinear, non-equilibrium and soft matter physics. Our current research focuses on fluids, granular media, fluctuations in renewables and quantitative life sciences.

(Closed since June 2025) The unit studied natural time series data, from NLP to genome sequences to cephalopod camouflage, with dynamical systems and machine learning methods, letting the data lead the way.

The Solar-Terrestrial Environment and Climate Unit conducts research to enhance our understanding of the Sun, its surrounding environment, and their impacts on Earth’s climate and weather.