A foreword
This page is a list of our publications. The name of the journal has been omitted. If you want to get a sense of whether our research is sound, read it. Some of the entries on this page are un-reviewed preprints; if it appears here, we stand behind it.
Remember that when publishers turn the labor of researchers into profit, or re-direct public research funding to their shareholders through mandatory open access, they bring great value to humankind. If you are tempted to use a website like sci-hub to get access to our research for free (instead of paying a publisher for it), ask yourself: what would Aaron Swartz do?
List of publications
114
What Constrains Food Webs? a Maximum Entropy Framework for Predicting Their Structure With Minimal Biases
2023 — 10.1371/journal.pcbi.1011458
113
Spatially Explicit Predictions of Food Web Structure From Regional Level Data
2023
112
The Future of Ecological Research Will Not Be (Fully) Automated
2023 — 10.22541/au.169384322.27179185/v1
111
A Global Biodiversity Observing System to Unite Monitoring and Guide Action
2023 — 10.1038/s41559-023-02171-0
110
Network Embedding Unveils the Hidden Interactions in the Mammalian Virome
2023 — 10.1016/j.patter.2023.100738
108
Shortcomings of Reusing Species Interaction Networks Created by Different Sets of Researchers
2023 — 10.1371/journal.pbio.3002068
107
Species Distribution Models: The Delicate Balance Between Signal and Noise
2023 — 10.24072/pci.ecology.100523
105
Graph Embedding and Transfer Learning Can Help Predict Potential Species Interaction Networks Despite Data Limitations
2022
104
Optimising Predictive Models to Prioritise Viral Discovery in Zoonotic Reservoirs
2022 — 10.1016/S2666-5247(21)00245-7
103
Guidelines for the Validation of Machine Learning Predictions of Species Interactions
2022 — 10.32942/osf.io/aty7n
102
Dissimilarity of Species Interaction Networks: Quantifying the Effect of Turnover and Rewiring
2022 — 10.24072/pcjournal.105
99
Evaluating Ecological Uniqueness Over Broad Spatial Extents Using Species Distribution Modelling
2022 — 10.1111/oik.09063
98
The Global Virome in One Network (VIRION): An Atlas of Vertebrate-Virus Associations
2022 — 10.1128/mbio.02985-21
97
Food Web Reconstruction Through Phylogenetic Transfer of Low‐rank Network Representation
2022 — 10.1111/2041-210X.13835
96
Increasing the Uptake of Ecological Model Results in Policy Decisions to Improve Biodiversity Outcomes
2022 — 10.1016/j.envsoft.2022.105318
95
[Re] the Evolution of Virulence in Pathogens With Vertical and Horizontal Transmission
2021 — 10.5281/ZENODO.5722853
94
A Roadmap Towards Predicting Species Interaction Networks (Across Space and Time)
2021 — 10.1098/rstb.2021.0063
93
SimpleSDMLayers.jl and GBIF.jl: A Framework for Species Distribution Modeling in Julia
2021 — 10.21105/joss.02872
92
Environment–host–microbial Interactions Shape the Sarracenia Purpurea Microbiome at the Continental Scale
2021 — https://doi.org/10.1002/ecy.3308
91
Sampling and Asymptotic Network Properties of Spatial Multi-Trophic Networks
2021 — 10.1111/oik.08650
87
Mangal.jl and EcologicalNetworks.jl: Two Complementary Packages for Analyzing Ecological Networks in Julia
2021 — 10.21105/joss.02721
86
Imputing the Mammalian Virome With Linear Filtering and Singular Value Decomposition
2021
84
Beta and Phylogenetic Diversities Tell Complementary Stories About Ecological Networks Biogeography
2021 — 10.32942/osf.io/zsnj4
81
Omnidirectional and Omnifunctional Connectivity Analyses With a Diverse Species Pool
2020 — 10.1101/2020.02.03.932095
80
Testing Predictability of Disease Outbreaks With a Simple Model of Pathogen Biogeography
2020 — 10.1098/rsos.190883
79
Novel Application of Convolutional Neural Networks for the Meta-Modeling of Large-Scale Spatial Data
2020
77
76
Food Web Structure Alters Ecological Communities Top-Heaviness With Little Effect on the Biodiversity-Functioning Relationship.
2020 — 10.1101/2020.06.10.144949
68
Data-Based, Synthesis-Driven: Setting the Agenda for Computational Ecology
2019 — 10.24908/iee.2019.12.2.e
63
Homogenization of Species Composition and Species Association Networks Are Decoupled
2018 — 10.1111/geb.12825
61
Bringing Elton and Grinnell Together: A Quantitative Framework to Represent the Biogeography of Ecological Interaction Networks
2018 — 10.1111/ecog.04006
59
Identifying a Common Backbone of Interactions Underlying Food Webs From Different Ecosystems
2018 — 10.1038/s41467-018-05056-0
57
Management, Archiving, and Sharing for Biologists and the Role of Research Institutions in the Technology-Oriented Age
2018 — 10.1093/biosci/biy038
56
Network Structure and Local Adaptation in Coevolving Bacteria-Phage Interactions
2017 — 10.1111/mec.14008
52
Using Peer Review to Support Development of Community Resources for Research Data Management
2017 — 10.7191/jeslib.2017.1114
50
Hosts, Parasites and Their Interactions Respond to Different Climatic Variables
2017 — 10.1111/geb.12602
47
Compositional Turnover in Host and Parasite Communities Does Not Change Network Structure
2017 — 10.1111/ecog.03514
45
BiMAT: A MATLAB Package to Facilitate the Analysis and Visualization of Bipartite Networks
2016 — 10.1111/2041-210X.12458
41
Synthetic Datasets and Community Tools for the Rapid Testing of Ecological Hypotheses
2016 — 10.1111/ecog.01941
39
Describe, Understand and Predict: Why Do We Need Networks in Ecology?
2016 — 10.1111/1365-2435.12799
38
Temperature and Trophic Structure Are Driving Microbial Productivity Along a Biogeographical Gradient
2015 — 10.1111/ecog.01748
37
The Spread of a Novel Behavior in Wild Chimpanzees: New Insights Into the Ape Cultural Mind
2015 — 10.1080/19420889.2015.1017164
36
Connecting People and Ideas From Around the World: Global Innovation Platforms for Next-Generation Ecology and Beyond
2015 — 10.1890/ES14-00198.1
35
Bacteriophage Richness Reduces Bacterial Niche Overlap in Experimental Microcosms
2015 — 10.7287/peerj.preprints.1100v1
34
A Continuum of Specialists and Generalists in Empirical Communities
2015 — 10.1371/journal.pone.0114674
33
Beyond Species: Why Ecological Interaction Networks Vary Through Space and Time
2015 — 10.1111/oik.01719
32
When Is Co-Phylogeny Evidence of Coevolution?
2015
31
Evolutionary Ecology of Specialisation
2015
30
The Next Generation of Action Ecology: Novel Approaches Towards Global Ecological Research
2015 — 10.1890/es14-00485.1
29
Best Publishing Practices to Improve User Confidence in Scientific Software
2015 — 10.4033/iee.2015.8.8.f
28
When Is an Ecological Network Complex? Connectance Drives Degree Distribution and Emerging Network Properties
2014 — 10.7717/peerj.251
27
Lack of Quantitative Training Among Early-Career Ecologists: A Survey of the Problem and Potential Solutions
2014 — 10.7717/peerj.285
26
Using Neutral Theory to Reveal the Contribution of Meta-Community Processes to Assembly in Complex Landscapes
2014 — 10.4081/jlimnol.2014.807
24
Dispersal and Spatial Heterogeneity Allow Coexistence Between Enemies and Protective Mutualists
2014 — 10.1002/ece3.1151
23
Social Network Analysis Shows Direct Evidence for Social Transmission of Tool Use in Wild Chimpanzees
2014 — 10.1371/journal.pbio.1001960
22
Inferring Food Web Structure From Predator-Prey Body Size Relationships
2013 — 10.1111/2041-210X.12103
20
Moving Toward a Sustainable Ecological Science: Don't Let Data Go to Waste!
2013 — 10.4033/iee.2013.6b.14.f
18
Trophic Complementarity Drives the Biodiversity-Ecosystem Functioning Relationship in Food Webs
2013 — 10.1111/ele.12118
16
Facultative and Obligate Parasite Communities Exhibit Different Network Properties
2013 — 10.1017/S0031182013000851
13
A Simple Model to Study Phylogeographies and Speciation Patterns in Space
2012
12
10
Terminal Investment Induced by a Bacteriophage in a Rhizosphere Bacterium
2012 — 10.12688/f1000research.1-21.v2
9
A Global Network of Next Generation Ecologists
2011
8
A Conceptual Framework for the Evolution of Ecological Specialisation
2011 — 10.1111/j.1461-0248.2011.01645.x
7
The Digitize Package: Extracting Numerical Data From Scatterplots
2011
6
Morphological and Molecular Evolution Are Not Linked in Lamellodiscus (Plathyhelminthes, Monogenea)
2011 — 10.1371/journal.pone.0026252
5
Trophic Network Structure Emerges Through Antagonistic Coevolution in Temporally Varying Environments
2011 — 10.1098/rspb.2011.0826
4
Putative Speciation Events in Lamellodiscus (Monogenea: Diplectanidae) Assessed by a Morphometric Approach
2010 — 10.1111/j.1095-8312.2009.01381.x
3
Resource Availability Affects the Structure of a Natural Bacteria--Bacteriophage Community
2010 — 10.1098/rsbl.2010.0774
2
Putative Effects of Recreational Fishing of Paracentrotus Lividus on Populations of Sea Urchins in Mediterranean Shallow Water
2010
1
Interactions Between Immunocompetence, Somatic Condition and Parasitism in the Chub Leuciscus Cephalus in Early Spring
2009 — 10.1111/j.1095-8649.2009.02400.x