CoNet - Co-occurrence Network inference

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CoNet - Who used it

Below you find references to a number of publications that include networks inferred with CoNet. If your publication with CoNet is not in this list, please contact me.

Articles co-authored by CoNet developer are marked by a star.

Zheng et al. "Improving the Inference of Co-occurrence Networks in the Bovine Rumen Microbiome"
IEEE Transactions on Computational Biology and Bioinformatics 2018

Mandakovic et al. "Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience"
Scientific Reports 2018

Jackson et al. "Detection of stable community structures within gut microbiota co-occurrence networks from different human populations"
PeerJ 2018

Wasimuddin et al. "Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats"
The ISME Journal 2018

Bush et al. "Oxic-anoxic regime shifts mediated by feedbacks between biogeochemical processes and microbial community dynamics"
Nature communications 2017

Aschenbrenner et al. "Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens"
Molecular Ecology 2017

Mondav et al. "Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient"
Environmental Microbiology 2017

Mackenzie et al. "Bacterial community collapse: a meta-analysis of the sinonasal microbiota in chronic rhinosinusitis"
Environmental Microbiology 2017

Zaura et al. "On the ecosystemic network of saliva in healthy young adults"
The ISME Journal 2017

Hosen et al. "Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition"
Fronties in Microbiology 2017

Wang et al. "Fishmeal Application Induces Antibiotic Resistance Gene Propagation in Mariculture Sediment."
Environmental Science & Technology 2017

Peng et al. "Temporal variation and co-occurrence patterns of bacterial communities in eutrophic Lake Taihu, China."
Geomicrobiology Journal 2017

Meuric et al. "Signature of microbial dysbiosis in periodontitis."
Appl. Environ. Microbiol. 2017

Marques et al. "High-Fiber Diet and Acetate Supplementation Change the Gut Microbiota and Prevent the Development of Hypertension and Heart Failure in Hypertensive Mice"
Thorax 2017

Zakharkina et al. "The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia"
Frontiers in Microbiology 2017

Bhute et al. "Gut Microbial Diversity Assessment of Indian Type-2-Diabetics Reveals Alterations in Eubacteria, Archaea, and Eukaryotes"
Frontiers in Microbiology 2017

Wang et al. "Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil"
Soil Biology and Biochemistry 2017 *

Muyzer "Marine Microbial Systems Ecology: Microbial Networks in the Sea"
The Marine Microbiome 335-344 2016

Pérez-Valera et al. "Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks"
Environmental Microbiology 2016 *

Günther et al. "Species-sorting and mass-transfer paradigms control managed natural metacommunities"
Environmental Microbiology 2016 *

Parente et al. "FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis"
International Journal of Food Microbiology 2016

Yadav et al. "Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups"
Gut Pathogens 2016

Weiss et al. "Correlation detection strategies in microbial data sets vary widely in sensitivity and precision"
The ISME Journal 2016 *
See a comment here.

Wang et al. "Lung microbiome dynamics in COPD exacerbations"
Eur. Respir. Journal 2016

Welsh et al. "Bacterial predation in a marine host-associated microbiome"
The ISME Journal 2015

Faust et al. "Cross-biome comparison of microbial association networks"
Frontiers in Microbiology 2015 *
See supplementary data here

Lima-Mendez et al. "Determinants of community structure in the global plankton interactome"
Science 2015 *

Navarrete et al. "Soil microbiome responses to the short-term effects of Amazonian deforestation"
Molecular Ecology 2015 *

İnceoğlu et al. "Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu"
Microbial Ecology 2015

Misic et al. "The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites"
Microbiome 2015

Roggenbuck et al. "The microbiome of New World vultures"
Nature Communications 2014

Meyer et al. "Community Shifts in the Surface Microbiomes of the Coral Porites astreoides with Unusual Lesions"
PLoS one 2014

Nielsen et al. "Comparative analysis of the microbial communities in agricultural soil amended with enhanced biochars or traditional fertilisers"
Agriculture, Ecosystems and Environment 2014

Soffer et al. "Phage-bacteria network analysis and its implication for the understanding of coral disease"
Environmental Microbiology 2014

Xu et al. "Bioinformatic Approaches Reveal Metagenomic Characterization of Soil Microbial Community"
PLoS ONE 2014

Lozupone et al. "Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts."
Genome Research 2012 *

Huttenhower et al. "Structure, function and diversity of the healthy human microbiome"
Nature 2012 *

Faust et al. "Microbial Co-occurrence Relationships in the Human Microbiome"
PLoS Computational Biology 2012 *


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