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Bio-digital systems that merge microbial life with technology promise new modes of computation, combining biological adaptability with digital precision. Yet realizing this potential symbiotically -- where biological and digital agents…
Smart phone apps that enable users to easily track their diets have become widespread in the last decade. This has created an opportunity to discover new insights into obesity and weight loss by analyzing the eating habits of the users of…
Bacteria populations rely on mechanisms such as quorum sensing to coordinate complex tasks that cannot be achieved by a single bacterium. Quorum sensing is used to measure the local bacteria population density, and it controls cooperation…
The human gastrointestinal tract is an environment that hosts an ecosystem of microorganisms essential to human health. Vital biological processes emerge from fundamental inter- and intra-species molecular interactions that influence the…
In this paper, models of the blood glucose (BG) dynamics in people with Type 1 diabetes (T1D) in response to moderate intensity aerobic activity are derived from physiology-based first principles and system identification experiments. We…
Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in major model uncertainties. To facilitate the consideration of…
The majority of real-world networks are dynamic and extremely large (e.g., Internet Traffic, Twitter, Facebook, ...). To understand the structural behavior of nodes in these large dynamic networks, it may be necessary to model the dynamics…
Food is very essential for human life and it is fundamental to the human experience. Food-related study may support multifarious applications and services, such as guiding the human behavior, improving the human health and understanding the…
Microorganisms employ sophisticated mechanisms for intercellular communication and environmental sensing, with quorum sensing serving as a fundamental regulatory process. Dysregulation of quorum sensing has been implicated in various…
Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large…
With the acceleration of urbanization and living standards, microorganisms play increasingly important roles in industrial production, bio-technique, and food safety testing. Microorganism biovolume measurements are one of the essential…
Food journaling is an effective method to help people identify their eating patterns and encourage healthy eating habits as it requires self-reflection on eating behaviors. Current tools have predominately focused on tracking food intake,…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed environments of a test tube or a chemostat. Since spatial organization can…
Advances in IoT technologies combined with new algorithms have enabled the collection and processing of high-rate multi-source data streams that quantify human behavior in a fine-grained level and can lead to deeper insights on individual…
Mixed microbial communities, usually composed of various bacterial and fungal species, are fundamental in a plethora of environments, from soil to human gut and skin. Their evolution is a paradigmatic example of intertwined dynamics, where…
Food and nutrition occupy an increasingly prevalent space on the web, and dishes and recipes shared online provide an invaluable mirror into culinary cultures and attitudes around the world. More specifically, ingredients, flavors, and…
Online controlled experimentation is widely adopted for evaluating new features in the rapid development cycle for web products and mobile applications. Measurement of the overall experiment sample is a common practice to quantify the…
Soil is a complex, dynamic material, with physical properties that depend on its biological content. We propose a cellular automaton model for self-organizing soil structure, where soil aggregates and serves as food for microbial species.…
A primary motivation for research in Digital Ecosystems is the desire to exploit the self-organising properties of natural ecosystems. Ecosystems arc thought to be robust, scalable architectures that can automatically solve complex, dynamic…