Related papers: Friend or Foe
Concurrent with advancements in molecular communication (MC), bacterial communication is emerging as a key area of interest. Given the frequent use of bacteria in various MC models, it is essential to have a thorough grasp of their…
Learning causal relationships from time series data is an important but challenging problem. Existing synthetic datasets often contain hidden artifacts that can be exploited by causal discovery methods, reducing their usefulness for…
Microbiome `omics approaches can reveal intriguing relationships between the human microbiome and certain disease states. Along with the identification of specific bacteria taxa associated with diseases, recent scientific advancements…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
Universities are microcosms of urban ecosystems, with concentrated consumption patterns in food, transport, energy, and product usage. These environments not only contribute substantially to sustainability pressures but also provide a…
Plants rarely occur in isolated systems. Bacteria can inhabit either the endosphere, the region inside the plant root, or the rhizosphere, the soil region just outside the plant root. Our goal is to understand if using genomic data and…
Microbial communities play a significant role in bioremediation,plant growth,human and animal digestion,global elemental cycles including the carbon-cycle,and water treatment.They are also posed to be the engines of renewable energy via…
The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…
Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this…
The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional data-driven methods face challenges in capturing inherently…
We explore how physical scale and population size shape the emergence of complex behaviors in open-ended ecological environments. In our setting, agents are unsupervised and have no explicit rewards or learning objectives but instead evolve…
This paper demonstrates that simple yet important characteristics of coevolution can occur in evolutionary algorithms when only a few conditions are met. We find that interaction-based fitness measurements such as fitness (linear) ranking…
Due to their high predictive performance and flexibility, machine learning models are an appropriate and efficient tool for ecologists. However, implementing a machine learning model is not yet a trivial task and may seem intimidating to…
Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
Antimicrobial protocols - using substances such as antibiotics or disinfectants - remain the preferred option for preventing the spread of pathogenic bacteria. However, bacteria can develop mechanisms to reduce their antimicrobial…
Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses…
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…