ÉPICBiodiversity
Machine Learning Enables Viral Genome-Agnostic Classification of RNA Virus Infections from Host Transcriptomes
,
, et al.
(2025)
bioRxiv
Genomics
Infectious diseases
Site selection algorithms for optimal ecological monitoring design
&
(2025)
Ecological Indicators
Biodiversity monitoring
NCBITaxonomy.jl: rapid biological names finding and reconciliation
,
, et al.
(2025)
BMC Ecology and Evolution
Software
The LISTEN principles for genetic sequence data governance and database engineering
,
, et al.
(2025)
Nature Genetics
Access and Benefits Sharing
Genomics
Open science
Pandemics
Moving functional network ecology forward (without traits)
(2025)
Peer Community in Ecology
Editorial
Overcoming the disconnect between species interaction networks and biodiversity conservation
,
, et al.
(2025)
Trends in Ecology & Evolution
Conservation
Ecological networks
Biodiversity science and biosurveillance are fellow travelers
,
, et al.
(2025)
Bioscience
Biodiversity monitoring
Infectious diseases
One Health
A minimum data standard for wildlife disease research and surveillance
,
, et al.
(2025)
Scientific Data
Data management
Infectious diseases
The archaeology of climate change: a blueprint for integrating environmental and cultural systems
,
, et al.
(2025)
Nature communications
Climate change
Species distributions
Vaccination and immigration rates influence raccoon rabies elimination and recolonization in simulated urban-suburban landscapes
&
(2025)
Infectious diseases
Spatial ecology
Assessing the species habitats in Colombia’s tropical dry forest over a 20 years period
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, et al.
(2025)
EcoEvoRxiv
Biodiversity monitoring
Conservation
Species distributions
Bridging one health and sustainability: The anatomy of a socioethical issue
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, et al.
(2025)
Bioscience
One Health
Deciphering the dynamics of Cyanobacteria-Phage in a natural lake: Insights from a decade-long investigation
,
, et al.
(2025)
bioRxiv
Spatial landscape structure influences cross-species transmission in a rabies-like virus model
,
, et al.
(2025)
Microorganisms
Infectious diseases
Spatial ecology
Ten quick tips to build a model life cycle
,
, et al.
(2025)
PLoS Computational Biology
Data management
Pathogens and planetary change
,
, et al.
(2025)
Nature Reviews Biodiversity
Climate change
Infectious diseases
Review
A Julia toolkit for species distribution data
,
, et al.
(2025)
Peer Community Journal
Software
Species distributions
Publication‐driven consistency in food web structures: Implications for comparative ecology
,
, et al.
(2024)
Ecology
Ecological networks
Conformal prediction quantifies the uncertainty of species distribution models
(2024)
EcoEvoRxiv
Explainable ML
Species distributions
BON in a Box: An open and collaborative platform for biodiversity monitoring, indicator calculation, and reporting
,
, et al.
(2024)
EcoEvoRxiv
Biodiversity monitoring
Software
Best practices for ecological analysis are required to act on concrete challenges
(2024)
Peer Community in Ecology
Editorial
Spatially explicit predictions of food web structure from regional-level data
,
&
(2024)
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Ecological networks
Species distributions
Pooled samples hold information about the prevalence of wildlife pathogens
(2024)
Peer Community in Ecology
Editorial
Introduction to Environmental Data Science: Jerry D. Davis, Boca Raton, FL: Chapman & Hall/CRC Press, 2023
(2024)
Journal of the American Statistical Association
Book review
Multilayer biological networks to upscale marine research to global change-smart management and sustainable resource use
,
, et al.
(2024)
The Science of the total environment
Conservation
Save lives in the next pandemic: ensure vaccine equity now
,
, et al.
(2024)
Nature
Access and Benefits Sharing
Pandemics
The coevolutionary mosaic of bat betacoronavirus emergence risk
,
, et al.
(2024)
Virus Evolution
Infectious diseases
Spatial ecology
Disease ecology and pathogeography: Changing the focus to better interpret and anticipate complex environment–host–pathogen interactions
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, et al.
(2024)
Ecography
Infectious diseases
One Health
Gradient Boosted Trees can deliver more than accurate ecological predictions
(2023)
Peer Community in Ecology
Editorial
Postdoctoral scientists are mentors, and it is time to recognize their work
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, et al.
(2023)
PLoS Biology
Equity
What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases
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&
(Sep.)
PLOS Computational Biology
The future of ecological research will not be (fully) automated
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, et al.
(2023)
Authorea
Editorial
Generative AI
A global biodiversity observing system to unite monitoring and guide action
,
, et al.
(2023)
Nature Ecology & Evolution
Biodiversity monitoring
Network embedding unveils the hidden interactions in the mammalian virome
,
, et al.
(2023)
Patterns
Infectious diseases
Interaction prediction
Plant resistance to pathogens: just you wait?
(2023)
Peer Community in Evolutionary Biology
Editorial
SpatialBoundaries.jl: edge detection using spatial wombling
&
(2023)
Ecography
Software
Spatial ecology
Species Distribution Models: the delicate balance between signal and noise
(2023)
Peer Community in Ecology
Editorial
Shortcomings of reusing species interaction networks created by different sets of researchers
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, et al.
(Apr )
PLOS Biology
Mismatch between IUCN range maps and species interactions data illustrated using the Serengeti food web
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, et al.
(2023)
PeerJ
Species distributions
The missing link: discerning true from false negatives when sampling species interaction networks
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, et al.
(2023)
EcoEvoRxiv
A social–ecological geography of southern Canadian lakes
,
, et al.
(2023)
Facets (Ottawa)
Guidelines for the prediction of species interactions through binary classification
(05/2)
Methods in Ecology and Evolution
Interaction prediction
Graph embedding and transfer learning can help predict potential species interaction networks despite data limitations
,
, et al.
(2023)
Methods in Ecology and Evolution
Ecological networks
Interaction prediction
Optimising predictive models to prioritise viral discovery in zoonotic reservoirs
,
, et al.
(2022)
The Lancet Microbe
Food web reconstruction through phylogenetic transfer of low‐rank network representation
,
, et al.
(2022)
Methods in Ecology and Evolution
The Global Virome in One Network (VIRION): an Atlas of Vertebrate-Virus Associations
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, et al.
(2022)
mBio
Evaluating ecological uniqueness over broad spatial extents using species distribution modelling
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&
(05/2)
Oikos
Dissimilarity of species interaction networks: quantifying the effect of turnover and rewiring
(2022)
Peer Community Journal
The science of the host–virus network
,
, et al.
(2021)
Nature Microbiology
[Re] The Evolution of Virulence in Pathogens with Vertical and Horizontal Transmission
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, et al.
(2021)
[Re]Science
A roadmap towards predicting species interaction networks (across space and time)
,
, et al.
(Nove)
Philosophical Transactions of the Royal Society B: Biological Sciences
Refocusing multiple stressor research around the targets and scales of ecological impacts
,
, et al.
(2021)
Nature ecology & evolution
Data Proliferation, Reconciliation, and Synthesis in Viral Ecology
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, et al.
(Augu)
BioScience
Computers Can Help us Find Raccoons and Other Living Creatures
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, et al.
(2021)
Frontiers for Young Minds
Beta and phylogenetic diversities tell complementary stories about ecological networks biogeography
&
(2021)
Parasitology
Mangal.jl and EcologicalNetworks.jl: Two complementary packages for analyzing ecological networks in Julia
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&
(2021)
Journal of Open Source Software
Environment-host-microbial interactions shape the Sarracenia purpurea microbiome at the continental scale
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, et al.
(2021)
Ecology
Optimal transportation theory for species interaction networks
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&
(2021)
Ecology and Evolution
Global knowledge gaps in species interaction networks data
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, et al.
(2021)
Journal of Biogeography
SimpleSDMLayers.jl and GBIF.jl: A Framework for Species Distribution Modeling in Julia
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(2021)
Journal of Open Source Software
SVD Entropy Reveals the High Complexity of Ecological Networks
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&
(2021)
Frontiers in Ecology and Evolution
Sampling and asymptotic network properties of spatial multi-trophic networks
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, et al.
(2021)
Oikos
Revisiting the links-species scaling relationship in food webs
,
&
(2020)
Patterns
Food web structure alters ecological communities top-heaviness with little effect on the biodiversity-functioning relationship.
,
&
(2020)
bioRxiv
The theory of ecological specialization
(2020)
The theory of evolution, University of Chicago Press
Omnidirectional and omnifunctional connectivity analyses with a diverse species pool
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&
(2020)
bioRxiv
Novel application of Convolutional Neural Networks for the meta-modeling of large-scale spatial data
&
(2020)
AI for Earth Sciences Workshop at Advances in Neural Information Processing Systems (NeurIPS)
Testing predictability of disease outbreaks with a simple model of pathogen biogeography
,
&
(2020)
Royal Society Open Science
EcologicalNetworks.jl: analysing ecological networks of species interactions
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, et al.
(2019)
Ecography
Artificial intelligence for ecological and evolutionary synthesis
,
&
(2019)
Frontiers in Ecology and Evolution
Revealing biases in the sampling of ecological interaction networks
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, et al.
(2019)
PeerJ
Ecogeographical rules and the macroecology of food webs
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, et al.
(2019)
Global Ecology and Biogeography
The marine fish food web is globally connected
,
, et al.
(Augu)
Nature Ecology & Evolution
Data-based, synthesis-driven: Setting the agenda for computational ecology
,
, et al.
(2019)
Ideas in Ecology and Evolution
Ecological data should not be so hard to find and reuse
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, et al.
(2019)
Trends in Ecology & Evolution
[Re] Insect natural enemies as regulating factors
,
, et al.
(Marc)
[Re]Science
Bringing Elton and Grinnell together: a quantitative framework to represent the biogeography of ecological interaction networks
,
, et al.
(2019)
Ecography
Inferring predator–prey interactions in food webs
,
, et al.
(2019)
Methods in Ecology and Evolution
Analysing ecological networks of species interactions
,
, et al.
(2019)
Biological Reviews
Ecological networks
Review
Open Science Isn't Always Open to All Scientists
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, et al.
(2019)
American Scientist
Open science
Key questions for next-generation biomonitoring
,
, et al.
(2019)
Frontiers in Environmental Science
Compositional turnover in host and parasite communities does not change network structure
&
(2018)
Ecography
Identifying a common backbone of interactions underlying food webs from different ecosystems
,
, et al.
(2018)
Nature Communications
Management, archiving, and sharing for biologists and the role of research institutions in the technology-oriented age
,
, et al.
(2018)
Bioscience
Interactions retain the co-phylogenetic matching that communities lost
&
(2018)
Oikos
Homogenization of species composition and species association networks are decoupled
,
, et al.
(2018)
Global Ecology and Biogeography
Sustainable computational science: the ReScience initiative
,
, et al.
(2017)
PeerJ Computer Science
Using Peer Review to Support Development of Community Resources for Research Data Management
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, et al.
(2017)
Journal of eScience Librarianship
paco: implementing Procrustean Approach to Cophylogeny in R
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, et al.
(Augu)
Methods in Ecology and Evolution
Simulations of biomass dynamics in community food webs
,
, et al.
(2017)
Methods in Ecology and Evolution
Linear filtering reveals false negatives in species interaction data
,
, et al.
(2017)
Scientific reports
Network structure and local adaptation in co-evolving bacteria-phage interactions
,
, et al.
(2017)
Molecular Ecology
Hosts, parasites and their interactions respond to different climatic variables
,
, et al.
(08/2)
Global Ecology and Biogeography
Wind drives microbial eukaryote communities in a temperate closed lagoon
,
, et al.
(2017)
Aquatic Microbial Ecology
Describe, understand and predict: why do we need networks in ecology?
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&
(Dece)
Functional Ecology
Ten simple rules for digital data storage
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, et al.
(2016)
PLoS Computational Biology
Temperature and trophic structure are driving microbial productivity along a biogeographical gradient
,
, et al.
(2016)
Ecography
Synthetic datasets and community tools for the rapid testing of ecological hypotheses
,
, et al.
(Apri)
Ecography
The structure of probabilistic networks
,
, et al.
(2016)
Methods in ecology and evolution
BiMat: a MATLAB package to facilitate the analysis of bipartite networks
,
, et al.
(2016)
Methods in Ecology and Evolution
Ecological networks
Software
Best publishing practices to improve user confidence in scientific software
(2015)
Ideas in Ecology and Evolution
Connecting people and ideas from around the world: global innovation platforms for next‐generation ecology and beyond
,
, et al.
(2015)
Ecosphere
When is co-phylogeny evidence of coevolution?
(2015)
Parasite diversity and diversification, Cambridge University Press
The spread of a novel behavior in wild chimpanzees: New insights into the ape cultural mind
,
, et al.
(2015)
Communicative & integrative biology
The next generation of action ecology: novel approaches towards global ecological research
,
, et al.
(2015)
Ecosphere
Beyond species: why ecological interaction networks vary through space and time
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&
(2015)
Oikos
Bacteriophage richness reduces bacterial niche overlap in experimental microcosms
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, et al.
(2015)
PeerJ PrePrints
A continuum of specialists and generalists in empirical communities
,
, et al.
(2015)
PloS One
Dispersal and spatial heterogeneity allow coexistence between enemies and protective mutualists
,
, et al.
(Oct )
Ecology and Evolution
Social network analysis shows direct evidence for social transmission of tool use in wild chimpanzees
,
, et al.
(Sep )
PLoS biology
Using neutral theory to reveal the contribution of meta-community processes to assembly in complex landscapes
,
&
(2014)
Journal of Limnology
When is an ecological network complex? Connectance drives degree distribution and emerging network properties
&
(Febr)
PeerJ
Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions
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, et al.
(2014)
PeerJ
Inferring food web structure from predator–prey body size relationships
,
, et al.
(2013)
Methods in Ecology and Evolution
Facultative and obligate parasite communities exhibit different network properties
,
, et al.
(2013)
Parasitology
An a posteriori measure of network modularity
(2013)
F1000Research
Ecological networks
Terminal investment induced by a bacteriophage in a rhizosphere bacterium
,
, et al.
(2013)
F1000Research
High-throughput sequencing: a roadmap toward community ecology
,
&
(2013)
Ecology and Evolution
The structure of natural microbial enemy-victim networks
,
&
(2013)
Ecological Processes
Moving toward a sustainable ecological science: don't let data go to waste!
,
&
(2013)
Ideas in Ecology and Evolution
Phage–bacteria infection networks
,
, et al.
(2013)
Trends in Microbiology
Trophic complementarity drives the biodiversity-ecosystem functioning relationship in food webs
,
&
(2013)
Ecology Letters
A simple model to study phylogeographies and speciation patterns in space
,
, et al.
(2012)
arXiv [q-bio.PE]
The dissimilarity of species interaction networks
,
, et al.
(2012)
Ecology Letters
A comparative study of ecological specialization estimators
,
, et al.
(2012)
Methods in Ecology and Evolution
Morphological and molecular evolution are not linked in Lamellodiscus (Plathyhelminthes, Monogenea)
,
&
(2011)
PloS one
Resource availability affects the structure of a natural bacteria-bacteriophage community
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, et al.
(2011)
Biology Letters
The digitize package: Extracting numerical data from scatterplots
(2011)
The R journal
Trophic network structure emerges through antagonistic coevolution in temporally varying environments
,
&
(2011)
Proceedings of the Royal Society of London B: Biological Sciences
A conceptual framework for the evolution of ecological specialisation
,
, et al.
(2011)
Ecology Letters
Effects of recreational fishing of Paracentrotus lividus on populations of sea urchins in Mediterranean
,
, et al.
(2010)
Vie et Milieu
Putative effects of recreational fishing of Paracentrotus lividus on populations of sea urchins in Mediterranean shallow water
,
, et al.
(2010)
Vie et milieu
Putative speciation events in Lamellodiscus (Monogenea: Diplectanidae) assessed by a morphometric approach
&
(2010)
Biological Journal of the Linnean Society
Interactions between immunocompetence, somatic condition and parasitism in the chub Leuciscus cephalus in early spring
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, et al.
(2009)
Journal of Fish Biology