Related papers: Learning functional groups in complex microbiomes
We investigate the application of mesoscopic response functions (MRFs) to characterize a large set of networks of fungi and slime moulds grown under a wide variety of different experimental treatments, including inter-species competition…
Modularity maximization has been one of the most widely used approaches in the last decade for discovering community structure in networks of practical interest in biology, computing, social science, statistical mechanics, and more.…
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…
Many real-world networks, including nervous systems, exhibit meso-scale structure. This means that their elements can be grouped into meaningful sub-networks. In general, these sub-networks are unknown ahead of time and must be "discovered"…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
We introduce various models for cellulose bio-degradation by micro-organisms. Those models rely on complex chemical mechanisms, involve the structure of the cellulose chains and are allowed to depend on the phenotypical traits of the…
We introduce an effective strategy to generate an annotated synthetic dataset of microbiological images of Petri dishes that can be used to train deep learning models in a fully supervised fashion. The developed generator employs…
Identifying features of molecular regulatory networks is an important problem in systems biology. It has been shown that the combinatorial logic of such networks can be captured in many cases by special functions called nested canalyzing in…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
We consider the problem of finding communities or modules in directed networks. The most common approach to this problem in the previous literature has been simply to ignore edge direction and apply methods developed for community discovery…
It is well known that tumors originating from the same tissue have different prognosis and sensitivity to treatments. Over the last decade, cancer genomics consortia like the Cancer Genome Atlas (TCGA) have been generating thousands of…
The marine microbial food web plays a central role in the global carbon cycle. Our mechanistic understanding of the ocean, however, is biased towards its larger constituents, while rates and biomass fluxes in the microbial food web are…
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…
Biological functions are carried out by groups of interacting molecules, cells or tissues, known as communities. Membership in these communities may overlap when biological components are involved in multiple functions. However, traditional…
Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated…
Many algorithms to detect communities in networks typically work without any information on the cluster structure to be found, as one has no a priori knowledge of it, in general. Not surprisingly, knowing some features of the unknown…
Functional data clustering is to identify heterogeneous morphological patterns in the continuous functions underlying the discrete measurements/observations. Application of functional data clustering has appeared in many publications across…
Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types…
When analyzing communities of microorganisms from their sequenced DNA, an important task is taxonomic profiling: enumerating the presence and relative abundance of all organisms, or merely of all taxa, contained in the sample. This task can…
Numerous networked systems feature a structure of nontrivial communities, which often correspond to their functional modules. Such communities have been detected in real-world biological, social and technological systems, as well as in…