Disentangling direct from indirect relationships in association networks
Networks are vital tools for understanding and modeling interactions in complex systems in
science and engineering, and direct and indirect interactions are pervasive in all types of …
science and engineering, and direct and indirect interactions are pervasive in all types of …
Network deconvolution as a general method to distinguish direct dependencies in networks
Recognizing direct relationships between variables connected in a network is a pervasive
problem in biological, social and information sciences as correlation-based networks …
problem in biological, social and information sciences as correlation-based networks …
Part mutual information for quantifying direct associations in networks
Quantitatively identifying direct dependencies between variables is an important task in data
analysis, in particular for reconstructing various types of networks and causal relations in …
analysis, in particular for reconstructing various types of networks and causal relations in …
[HTML][HTML] Ecological network inference from long-term presence-absence data
Ecological communities are characterized by complex networks of trophic and nontrophic
interactions, which shape the dy-namics of the community. Machine learning and …
interactions, which shape the dy-namics of the community. Machine learning and …
Network link prediction by global silencing of indirect correlations
B Barzel, AL Barabási - Nature biotechnology, 2013 - nature.com
Predictions of physical and functional links between cellular components are often based on
correlations between experimental measurements, such as gene expression. However …
correlations between experimental measurements, such as gene expression. However …
[HTML][HTML] Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil
High-throughput sequencing technologies have recently made it possible to interrogate the
phylogenetic diversity of soils at considerable depth. This ability has led to the development …
phylogenetic diversity of soils at considerable depth. This ability has led to the development …
iNAP: an integrated network analysis pipeline for microbiome studies
Integrated network analysis pipeline (iNAP) is an online analysis pipeline for generating and
analyzing comprehensive ecological networks in microbiome studies. It is implemented in …
analyzing comprehensive ecological networks in microbiome studies. It is implemented in …
[HTML][HTML] Cautionary notes on the use of co-occurrence networks in soil ecology
M Goberna, M Verdú - Soil Biology and Biochemistry, 2022 - Elsevier
Soil ecology is witnessing exponential growth in the number of studies using co-occurrence
network analysis. Researchers reconstruct networks based on the co-occurrence of taxa or …
network analysis. Researchers reconstruct networks based on the co-occurrence of taxa or …
Structural equation modeling of a winnowed soil microbiome identifies how invasive plants re-structure microbial networks
The development of microbial networks is central to ecosystem functioning and is the
hallmark of complex natural systems. Characterizing network development over time and …
hallmark of complex natural systems. Characterizing network development over time and …
[HTML][HTML] From diversity to complexity: Microbial networks in soils
K Guseva, S Darcy, E Simon, LV Alteio… - Soil Biology and …, 2022 - Elsevier
Network analysis has been used for many years in ecological research to analyze
organismal associations, for example in food webs, plant-plant or plant-animal interactions …
organismal associations, for example in food webs, plant-plant or plant-animal interactions …