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View article: Community Detection with the Map Equation and Infomap: Theory and Applications
Community Detection with the Map Equation and Infomap: Theory and Applications Open
Real-world networks have a complex topology comprising many elements often structured into communities. Revealing these communities helps researchers uncover the organizational and functional structure of the system that the network repres…
View article: IsoformMapper: a web application for protein-level comparison of splice variants through structural community analysis
IsoformMapper: a web application for protein-level comparison of splice variants through structural community analysis Open
Alternative splicing (AS) enables cells to produce multiple protein isoforms from single genes, fine-tuning protein function across numerous cellular processes. However, despite its biological importance, researchers lack effective tools t…
View article: IsoformMapper: A Web Application for Protein-Level Comparison of Splice Variants through Structural Community Analysis
IsoformMapper: A Web Application for Protein-Level Comparison of Splice Variants through Structural Community Analysis Open
Alternative splicing (AS) plays a key role in numerous cellular processes by enabling the existence of different protein isoforms with potentially different functions and fine-tuning isoform abundance. However, despite its biological impor…
View article: A Correlation- and Mean-Aware Loss Function and Benchmarking Framework to Improve GAN-based Tabular Data Synthesis
A Correlation- and Mean-Aware Loss Function and Benchmarking Framework to Improve GAN-based Tabular Data Synthesis Open
Advancements in science rely on data sharing. In medicine, where personal data are often involved, synthetic tabular data generated by generative adversarial networks (GANs) offer a promising avenue. However, existing GANs struggle to capt…
View article: Community Detection with the Map Equation and Infomap: Theory and Applications
Community Detection with the Map Equation and Infomap: Theory and Applications Open
Real-world networks have a complex topology comprising many elements often structured into communities. Revealing these communities helps researchers uncover the organizational and functional structure of the system that the network repres…
View article: Infomap Bioregions 2 - Exploring the interplay between biogeography and evolution
Infomap Bioregions 2 - Exploring the interplay between biogeography and evolution Open
Identifying and understanding the large-scale biodiversity patterns in time and space is vital for conservation and addressing fundamental ecological and evolutionary questions. Network-based methods have proven useful for simplifying and …
View article: Spiny but photogenic: amateur sightings complement herbarium specimens to reveal the bioregions of cacti
Spiny but photogenic: amateur sightings complement herbarium specimens to reveal the bioregions of cacti Open
Premise Cacti are characteristic elements of the Neotropical flora and of major interest for biogeographic, evolutionary, and ecological studies. Here we test global biogeographic boundaries for Neotropical Cactaceae using specimen-based o…
View article: Mapping change in higher-order networks with multilevel and overlapping communities
Mapping change in higher-order networks with multilevel and overlapping communities Open
New network models of complex systems use layers, state nodes, or hyperedges to capture higher-order interactions and dynamics. Simplifying how the higher-order networks change over time or depending on the network model would be easy with…
View article: A natural history of networks: Modelling higher-order interactions in geohistorical data
A natural history of networks: Modelling higher-order interactions in geohistorical data Open
Geohistorical records, either stratigraphic sections, boreholes, ice cores, or archaeological sites, are inherently complex. Despite their limitations, the high-dimensional and spatiotemporally resolved data retrieved from individual geohi…
View article: Madagascar's extraordinary biodiversity: a data repository
Madagascar's extraordinary biodiversity: a data repository Open
Data repository for the two sister reviews of Madagascar's biodiversity: Antonelli et al.: "Madagascar's extraordinary biodiversity: Evolution, distribution, and use", Science 378 (6623): eabf0869 – https://doi.org/10.1126/science.abf0869 …
View article: Madagascar's extraordinary biodiversity: a data repository
Madagascar's extraordinary biodiversity: a data repository Open
Data repository for the two sister reviews of Madagascar's biodiversity: Antonelli et al.: "Madagascar's extraordinary biodiversity: Evolution, distribution, and use", Science 378 (6623): eabf0869 – https://doi.org/10.1126/science.abf0869 …
View article: Madagascar’s extraordinary biodiversity: Threats and opportunities
Madagascar’s extraordinary biodiversity: Threats and opportunities Open
Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting da…
View article: Madagascar’s extraordinary biodiversity: Evolution, distribution, and use
Madagascar’s extraordinary biodiversity: Evolution, distribution, and use Open
Madagascar’s biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar’s past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive d…
View article: Madagascar's extraordinary biodiversity: a data repository
Madagascar's extraordinary biodiversity: a data repository Open
Data repository for the double review of Madagascar's biodiversity: Antonelli et al.: "Madagascar's extraordinary biodiversity: Evolution, distribution, and use", https://doi.org/10.1126/science.abf0869 Ralimanana et al.: "Madagascar's ext…
View article: Madagascar's extraordinary biodiversity: a data repository
Madagascar's extraordinary biodiversity: a data repository Open
Data repository for the double review on Madagascar's biodiversity [ADD FULL CITATIONS + DOI WHEN ACCEPTED] REVIEW I: EVOLUTION, DISTRIBUTION AND USE CatalogueOfVascularPlantsOfMadagascar.csv -- Comma-separated table with comprehensive tax…
View article: Variable Markov dynamics as a multi-focal lens to map multi-scale complex networks
Variable Markov dynamics as a multi-focal lens to map multi-scale complex networks Open
From traffic flows on road networks to electrical signals in brain networks, many real-world networks contain modular structures of different sizes and densities. In the networks where modular structures emerge due to coupling between node…
View article: A natural history of networks: Modeling higher-order interactions in geohistorical data
A natural history of networks: Modeling higher-order interactions in geohistorical data Open
Paleobiologists are increasingly employing network-based methods to analyze the complex data retrieved from geohistorical records, including stratigraphic sections, sediments, and fossil collections. However, the lack of a common framework…
View article: Anomalous buoyancy of quantum bubbles in immiscible Bose mixtures
Anomalous buoyancy of quantum bubbles in immiscible Bose mixtures Open
Buoyancy is a well-known effect in immiscible binary Bose-Einstein condensates. Depending on the differential confinement experienced by the two components, a bubble of one component sitting at the center of the other eventually floats to …
View article: Madagascar's extraordinary biodiversity: a data repository
Madagascar's extraordinary biodiversity: a data repository Open
Data repository for the double review on Madagascar's biodiversity [ADD FULL CITATIONS + DOI WHEN ACCEPTED] REVIEW I: EVOLUTION, DISTRIBUTION AND USE CatalogueOfVascularPlantsOfMadagascar.csv -- Comma-separated table with comprehensive tax…
View article: Mapping flows on weighted and directed networks with incomplete observations
Mapping flows on weighted and directed networks with incomplete observations Open
Detecting significant community structure in networks with incomplete observations is challenging because the evidence for specific solutions fades away with missing data. For example, recent research shows that flow-based community detect…
View article: B<scp>io</scp>‐D<scp>em</scp>, a tool to explore the relationship between biodiversity data availability and socio‐political conditions in time and space
B<span>io</span>‐D<span>em</span>, a tool to explore the relationship between biodiversity data availability and socio‐political conditions in time and space Open
Aim Geo‐referenced species occurrence records are a prime example of biodiversity data and a cornerstone of biodiversity research. Yet, their availability depends on non‐biological factors, including the political framework in the region o…
View article: Data and Analysis scripts for "BIO-DEM, a tool to explore the relationship between biodiversity data availability and socio-political conditions in time and space"
Data and Analysis scripts for "BIO-DEM, a tool to explore the relationship between biodiversity data availability and socio-political conditions in time and space" Open
This folder contains the data and analysis scripts necessary to reproduce the example analysis presented in Zizka et al (2021) Bio-Dem, a tool to explore the relationship between biodiversity data availability and socio-political condition…
View article: Data for: Madagascar's rapidly declining biodiversity: Patterns, trends, and opportunities for terrestrial conservation and restoration
Data for: Madagascar's rapidly declining biodiversity: Patterns, trends, and opportunities for terrestrial conservation and restoration Open
CatalogueOfPlantsOfMadagascar.csv -- Comma-separated table with comprehensive taxonomic database of plants of Madagascar, from the “Catalogue of the Plants of Madagascar” project. Contact: Peter Phillipson - [email protected] and …
View article: Data for: Madagascar's rapidly declining biodiversity: Patterns, trends, and opportunities for terrestrial conservation and restoration
Data for: Madagascar's rapidly declining biodiversity: Patterns, trends, and opportunities for terrestrial conservation and restoration Open
CatalogueOfPlantsOfMadagascar.csv -- Comma-separated table with comprehensive taxonomic database of plants of Madagascar, from the “Catalogue of the Plants of Madagascar” project. Contact: Peter Phillipson - [email protected] and …
View article: Ecological-Complexity-Lab/infomap_ecology_package: Release along with submission to CRAN
Ecological-Complexity-Lab/infomap_ecology_package: Release along with submission to CRAN Open
Package with functions to handle network data and run Infomap, inspired by ecological networks
View article: Identifying flow modules in ecological networks using Infomap
Identifying flow modules in ecological networks using Infomap Open
Analysing how species interact in modules is a fundamental problem in network ecology. Theory shows that a modular network structure can reveal underlying dynamic ecological and evolutionary processes, influence dynamics that operate on th…
View article: Mapping flows on hypergraphs
Mapping flows on hypergraphs Open
Hypergraphs offer an explicit formalism to describe multibody interactions in complex systems. To connect dynamics and function in systems with these higher-order interactions, network scientists have generalised random walk models to hype…