Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
10
datasets available to search
ShareScore release 0.9.0
Dataset results
10 results for “Interactions: coevolution”
NGS data from: Deploying synthetic coevolution and machine learning to engineer protein-protein interactions
<p>Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a synthetic platform for protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes<span class="Apple-converted-space"> </span>drove a systems-level analysis of molecular recognition between Z domain-affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pre-trained protein language models to expand, <em>in silico</em>, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. The integration of these approaches provides a means of generating protein complexes with diverse molecular recognition properties as tools for biotechnology and synthetic biology.</p>
NGS data from: Deploying synthetic coevolution and machine learning to engineer protein-protein interactions
Open the record for dataset details and reuse information.
Siderophore synthetase-receptor gene coevolution reveals habitat and pathogen-specific bacterial iron interaction networks
Open the record for dataset details and reuse information.
Data from: A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species
Evaluating trait correlations across species within a lineage via phylogenetic regression is fundamental to comparative evolutionary biology, but when traits of interest are derived from two sets of lineages that co-evolve with one another, methods for evaluating such patterns in a dual-phylogenetic context remain underdeveloped. Here we extend multivariate permutation-based phylogenetic regression to evaluate trait correlations in two sets of interacting species while accounting for their respective phylogenies. This extension is appropriate for both univariate and multivariate response data, and may utilize one or more independent variables, including environmental covariates. Imperfect correspondence between species in the interacting lineages can also be accommodated, such as when species in one lineage associate with multiple species in the other, or when there are unmatched taxa in one or both lineages. For both univariate and multivariate data, the method displays appropriate type I error, and statistical power increases with the strength of the trait covariation and the number of species in the phylogeny. These properties are retained even when there is not a 1:1 correspondence between lineages. Finally, we demonstrate the approach by evaluating the evolutionary correlation between traits in fig species and traits in their agaonid wasp pollinators. R computer code is provided.
Data for Coevolution and temporal dynamics of species interactions shape species coexistence
<p>This dataset is the one used in our preprint "<a href="https://doi.org/10.1101/2024.08.08.607160">Coevolution and temporal dynamics of species interactions shape species coexistence</a>".</p> <p>R codes to analyse these data can be found here: <a href="https://github.com/f-duchenne/Evolution_pheno_vs_morpho">https://github.com/f-duchenne/Evolution_pheno_vs_morpho</a></p> <p><em>flow_pheno_empirical.csv</em> and <em>poll_pheno_empirical.csv</em> contain the empirical phenological parameters for plant and pollinator species, respectively: the mean activity day (mu) and its standard deviation (sde) representing the duration of the activity period.</p> <p><em>matrices_empirical_networks.RData</em> contains an R object with the 17 networks used. Plants are in rows and pollinators in columns, with each cell representing the average interaction value across sampling rounds, corrected by abundances.</p> <p>You can access it in R via:</p> <div> <pre><code>#load data load("matrices_empirical_networks.RData") #see the structure (a list of 17 networks) str(networks) #access the first network networks[[1]]</code></pre> <pre> </pre> </div>
The effects of sex allocation coevolution on the coexistence of two closely related plant species interacting via interspecific pollen transfer
Open the record for dataset details and reuse information.
Data from: A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species
Open the record for dataset details and reuse information.
Data from: Coevolution between positive reciprocity, punishment, and partner switching in repeated interactions
Open the record for dataset details and reuse information.
Data from: Coevolution-based inference of amino acid interactions underlying protein function
Protein function arises from a poorly understood pattern of energetic interactions between amino acid residues. Sequence-based strategies for deducing this pattern have been proposed, but lack of benchmark data has limited experimental verification. Here, we extend deep-mutation technologies to enable measurement of many thousands of pairwise amino acid couplings in several homologs of a protein family – a deep coupling scan (DCS). The data show that cooperative interactions between residues are loaded in a sparse, evolutionarily conserved, spatially contiguous network of amino acids. The pattern of amino acid coupling is quantitatively captured in the coevolution of amino acid positions, especially as indicated by the statistical coupling analysis (SCA), providing experimental confirmation of the key tenets of this method. This work exposes the collective nature of physical constraints on protein function and clarifies its link with sequence analysis, enabling a general practical approach for understanding the structural basis for protein function.
Data from: Coevolution-based inference of amino acid interactions underlying protein function
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.