Related papers: Friend or Foe
Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we…
We study distributed agreement in microbial distributed systems under stochastic population dynamics and competitive interactions. Motivated by recent applications in synthetic biology, we examine how the presence and absence of direct…
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
The Web today has millions of datasets, and the number of datasets continues to grow at a rapid pace. These datasets are not standalone entities; rather, they are intricately connected through complex relationships. Semantic relationships…
The analysis of environmental mixtures is of growing importance in environmental epidemiology, and one of the key goals in such analyses is to identify exposures and their interactions that are associated with adverse health outcomes.…
The spread of an infection on a real-world social network is determined by the interplay of two processes: the dynamics of the network, whose structure changes over time according to the encounters between individuals, and the dynamics on…
Bacteriophage-bacteria interactions are central to microbial ecology, influencing evolution, biogeochemical cycles, and pathogen behavior. Most theoretical models assume static environments and passive bacterial hosts, neglecting the joint…
Recent multi-omic microbiome studies enable integrative analysis of microbes and metabolites, uncovering their associations with various host conditions. Such analyses require multivariate models capable of accounting for the complex…
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…
How large ecosystems can create and maintain the remarkable biodiversity we see in nature is probably one of the biggest open questions in science, attracting attention from different fields, from Theoretical Ecology to Mathematics and…
Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule…
Human cognition is profoundly shaped by the environments in which it unfolds. Yet, it remains an open question whether learning and decision making can be explained as a principled adaptation to the statistical structure of real-world…
Detecting feature interactions is imperative for accurately predicting performance of highly-configurable systems. State-of-the-art performance prediction techniques rely on supervised machine learning for detecting feature interactions,…
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…
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…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
Why, contrary to theoretical predictions, do marine microbe communities harbor tremendous phenotypic heterogeneity? How can so many marine microbe species competing in the same niche coexist? We discovered a unifying explanation for both…
Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance…
Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex natural products, and commodity chemicals at scale. However, the adoption of biocatalysis is limited by our ability to select enzymes that will catalyze…
Environmental microorganism (EM) offers a high-efficient, harmless, and low-cost solution to environmental pollution. They are used in sanitation, monitoring, and decomposition of environmental pollutants. However, this depends on the…