A computational exploration of resilience and evolvability of protein–protein interaction networks

Klein, Brennan; Holmér, Ludvig; Smith, Keith; Johnson, Mackenzie M.; Swain, Anshuman; Stolp, Laura; Teufel, Ashley I.; Kleppe, April Snøfrid

doi:10.1038/s42003-021-02867-8

Cited by 11 publications

(1 citation statement)

References 70 publications

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“…In network parlance, resilience/robustness refers to the area under this plot of secondary removal (Memmott et al, 2004), which in modern ecological texts is referred to as secondary extinctions, representing another measure of how tightly connected a network is. (See Klein et al, 2021;Zitnik et al, 2019 for a broader network context for resilience). Here, we only consider plant removals as they provide the food source and can cause the extirpation of DTs.…”

Section: Resultsmentioning

confidence: 99%

Sampling bias and the robustness of ecological metrics for plant–damage‐type association networks

Swain

Azevedo-Schmidt

Maccracken

et al. 2023

Ecology

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Plants and their insect herbivores have been a dominant component of the terrestrial ecological landscape for the past 410 million years and feature intricate evolutionary patterns and co-dependencies. A complex systems perspective allows for both detailed resolution of these evolutionary relationships as well as comparison and synthesis across systems. Using proxy data of insect herbivore damage (denoted by the damage type or DT) preserved on fossil leaves, functional bipartite network representations provide insights into how plant-insect associations depend on geological time, paleogeographical space, and environmental variables such as temperature and precipitation. However, the metrics measured from such networks are prone to sampling bias. Such sensitivity is of special concern for plant-DT association networks in paleontological settings where sampling effort is often severely limited. Here, we explore the sensitivity of functional bipartite network metrics to sampling intensity and identify sampling thresholds above which metrics appear robust to sampling effort. Across a broad range of sampling efforts, we find network metrics to be less affected by sampling bias and/or sample size than richness metrics, which are routinely used in studies of fossil plant-DT interactions.

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Section: Resultsmentioning

confidence: 99%

Sampling bias and the robustness of ecological metrics for plant–damage‐type association networks

Swain

Azevedo-Schmidt

Maccracken

et al. 2023

Ecology

Self Cite

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The importance of diversity in local food systems: a network analysis of food-related interactions in the Indigenous food system on St. Paul Island, Alaska

Zimmermann,

Dermody,

Davis

et al. 2024

Reg Environ Change

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Arctic Indigenous food systems are typified by diverse social interactions that maintain food security. Given the numerous challenges Arctic Indigenous communities face, it is important to understand diversity in these systems and how they are impacted by change. This study adopts a mixed methods approach that combines participatory methods with network analysis to assess the diversity of food-related interactions between different actor types in the mixed food system on St. Paul Island, Alaska. We conducted 36 interviews with local food system actors to identify current food security challenges and food-related interactions in the local food system. We used network analysis to investigate the diversity of interactions in the food system quantitatively. We simulated the effects of two key food security challenges (out-migration and knowledge loss) on food system diversity and explored interventions to increase diversity. Qualitative data from the same interviews were used to embed our results in the lived realities of the St. Paul Island community. Our approach reveals diverse interactions in the local food system, reflecting both subsistence and market-based elements of the St. Paul Island mixed economy. While both challenges threaten the system's diversity, out-migration presents a more immediate risk to food system diversity than knowledge loss. We advocate for targeting a combination of food system interventions at the community level to enhance food system diversity effectively. Our research contributes to understanding the importance of diversity for Arctic Indigenous food security and emphasizes the need to recognize the complex interactions between food system interventions and their implications for Arctic Indigenous communities.

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A systematic review of graph-based explorations of PPI networks: methods, resources, and best practices

Rout,

Mohapatra,

Kar

2024

Netw Model Anal Health Inform Bioinforma

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A computational exploration of resilience and evolvability of protein–protein interaction networks

Cited by 11 publications

References 70 publications

Sampling bias and the robustness of ecological metrics for plant–damage‐type association networks

Sampling bias and the robustness of ecological metrics for plant–damage‐type association networks

The importance of diversity in local food systems: a network analysis of food-related interactions in the Indigenous food system on St. Paul Island, Alaska

A systematic review of graph-based explorations of PPI networks: methods, resources, and best practices

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