Related papers: Learning functional groups in complex microbiomes
We have recently introduced an efficient method for the detection and identification of modules in complex networks, based on the de-synchronization properties (dynamical clustering) of phase oscillators. In this paper we apply the…
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…
High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious…
Biological systems operate under simultaneous energetic and informational constraints, yet direct evidence that such constraints shape real metabolic networks is limited. The Network-Weighted Action Principle predicts that networks under…
Bacteria can spontaneously develop collective motions by aligning their motions in dense systems. Here, we show that bacteria can also respond collectively to an alternating electrical field and form dynamic clusters oscillating at the same…
We present an approach to study functional segregation and integration in the living brain based on community structure decomposition determined by maximum modularity. We demonstrate this method with a network derived from functional…
The gut microbiome plays a crucial role in human health, yet the mechanisms underlying host-microbiome interactions remain unclear, limiting its translational potential. Recent microbiome multiomics studies, particularly paired…
The self-organization of microbial ecosystems involves a large variety of mechanisms, ranging from biochemical signaling to population dynamics. Among these, the role of motility regulation has been little studied, despite the importance of…
Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the…
We consider an alternate definition of community structure that is functionally motivated. We define network community structure-based on the function the network system is intended to perform. In particular, as a specific example of this…
High-throughput sequencing techniques such as metagenomic and metatranscriptomic technologies allow cataloging of functional characteristics of microbial community members as well as their taxonomic identity. Such studies have found that a…
We present an automated method of identifying communities of functionally related genes from the biomedical literature. These communities encapsulate human gene and protein interactions and identify groups of genes that are complementary in…
The spread of microbial infections is governed by the self-organization of bacteria on surfaces. Limitations of live imaging techniques make collective behaviors in clinically relevant systems challenging to quantify. Here, novel…
Many real-world systems, from social networks to protein-protein interactions and species distributions, exhibit overlapping flow-based communities that reflect their functional organisation. However, reliably identifying such overlapping…
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…
Microbial communities play a key role in biological wastewater treatment processes. Activated sludge settling characteristics, for example, are affected by microbial community composition, varying by changes in operating conditions and…
Microbiome research has immense potential for unlocking insights into human health and disease. A common goal in human microbiome research is identifying subgroups of individuals with similar microbial composition that may be linked to…
Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for…
In this paper, we propose applying semantic embedding to learn the range of behaviors exhibited by molecular swarms, thereby providing a richer set of features to optimize such systems. Specifically, we consider a standard molecular swarm…
The widespread relevance of increasingly complex networks requires methods to extract meaningful coarse-grained representations of such systems. For undirected graphs, standard community detection methods use criteria largely based on…