Related papers: Microbial community pattern detection in human bod…
Recent work suggests that cross-feeding -- the secretion and consumption of metabolic biproducts by microbes -- is essential for understanding microbial ecology. Yet how cross-feeding and competition combine to give rise to ecosystem-level…
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the…
The tremendous boost in the next generation sequencing and in the omics technologies makes it possible to characterize human gut microbiome (the collective genomes of the microbial community that reside in our gastrointestinal tract). While…
The problem of finding overlapping communities in networks has gained much attention recently. Optimization-based approaches use non-negative matrix factorization (NMF) or variants, but the global optimum cannot be provably attained in…
Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development, cancerous cells during tumor…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Analyzing microscopy images to extract biological object properties (e.g., their morphological organization, temporal dynamics, and population density) is fundamental to various biomedical research. Yet conducting this manually is costly…
Semi-supervised clustering seeks to augment traditional clustering methods by incorporating side information provided via human expertise in order to increase the semantic meaningfulness of the resulting clusters. However, most current…
Microbial networks, representing microbes as nodes and their interactions as edges, are crucial for understanding community dynamics in various environments. Analyzing microbiome networks is crucial for identifying keystone taxa that play…
Many approaches have been proposed to discover clusters within networks. Community finding field encompasses approaches which try to discover clusters where nodes are tightly related within them but loosely related with nodes of other…
Research data sets are growing to unprecedented sizes and network modeling is commonly used to extract complex relationships in diverse domains, such as genetic interactions involved in disease, logistics, and social communities. As the…
This paper aims at a newly raising task in visual surveillance: re-identifying people at a distance by matching body information, given several reference examples. Most of existing works solve this task by matching a reference template with…
Especially in lattice structured populations, homogeneous mixing represents an inadequate assumption. Various improvements upon the ordinary pair approximation based on a number of assumptions concerning the higher-order correlations have…
It is well known that dietary habits have a significant influence on health. While many studies have been conducted to understand this relationship, little is known about the relationship between eating environments and health. Yet…
Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities encoded in patterns of association among microbial gene…
Networks (or graphs) appear as dominant structures in diverse domains, including sociology, biology, neuroscience and computer science. In most of the aforementioned cases graphs are directed - in the sense that there is directionality on…
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…
Objective: In recent years, the functional connectivity of the human brain has been studied with graph theoretical tools. One such approach is community detection which is fundamental for uncovering the localized networks. Existing methods…
Clustering and community structure is crucial for many network systems and the related dynamic processes. It has been shown that communities are usually overlapping and hierarchical. However, previous methods investigate these two…
Spatial structure and species interactions jointly shape the dynamics and biodiversity of ecological systems, yet most theoretical models either neglect spatial heterogeneity or sacrifice analytical tractability. Here, we provide a unified…