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Although networks provide a powerful approach to study a large variety of ecological systems, their formulation does not typically account for multiple interaction types, interactions that vary in space and time, and interconnected systems…
Software sustainability is a key multifaceted non-functional requirement that encompasses environmental, social, and economic concerns, yet its integration into the development of Machine Learning (ML)-enabled systems remains an open…
Resilience is a feature that is gaining more and more attention in computer science and computer engineering. However, the definition of resilience for the cyber landscape, especially embedded systems, is not yet clear. This paper discusses…
There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can…
Species-rich communities, such as the microbiota or microbial ecosystems, provide key functions for human health and climatic resilience. Increasing effort is being dedicated to design experimental protocols for selecting community-level…
The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide the first deep investigation of the predictive potential of machine…
A central feature of complex systems is the relevance and entanglement of different levels of description. For instance, the dynamics of ecosystems can be alternatively described in terms of large ecological processes and classes of…
Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Biofilm infections on medical implants are difficult to eradicate because insufficient nutrient availability promotes antibiotic-tolerant persister cells that survive treatment and reseed growth. Existing mathematical models usually omit…
Interactions in natural communities can be highly heterogeneous, with any given species interacting appreciably with only some of the others, a situation commonly represented by sparse interaction networks. We study the consequences of…
Antibiotic resistance is a major threat to global health. It emerges in multispecies microbial communities under antibiotic exposure. This makes antibiotic spectrum -- a drug's distribution of effects across species -- a potential key…
In a living system composed of interacting components such as molecules, cells, and tissues, each component often adaptively changes its internal states in response to interactions with its surrounding components. For example, individual…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
Smart agriculture applications, integrating technologies like the Internet of Things and machine learning/artificial intelligence (ML/AI) into agriculture, hold promise to address modern challenges of rising food demand, environmental…
In the last years, a remarkable theoretical effort has been made in order to understand stability and complexity in ecological communities. The non-random structures of real ecological interaction networks has been recognized as one key…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Interest in the study of in-host microbial communities has increased in recent years due to our improved understanding of the communities' significant role in host health. As a result, the ability to model these communities using…
The advent of high-throughput sequencing technologies has made data from DNA material readily available, leading to a surge of microbiome-related research establishing links between markers of microbiome health and specific outcomes.…
In order to understand the phenomenon of longevity in biological world, the relationship between the potential of longevity and the structural complexity of an organism is analyzed. I. The potential of longevity is the maximum lifespan of…