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.
224
datasets available to search
ShareScore release 0.9.0
Dataset results
224 results for “Disease Biology”
Data for “Herbivory damage but not plant disease under experimental warming is dependent on weather for three subalpine grass species”, Rocky Mountain Biological Laboratory, Gothic, Colorado, 2015-2017.
Both theory and prior studies predict that climate warming should increase attack rates by herbivores and pathogens on plants. However, past work has often assumed that variation in abiotic conditions other than temperature (e.g., precipitation) do not alter warming responses of plant damage by natural enemies. Studies over short time periods span low variation in weather, and studies over long-time scales often neglect to account for fine-scale weather conditions. Here, we used a 20+ year field warming experiment to investigate if warming affects herbivory and disease are dependent on variation in ambient weather observed over three years. We studied three common grass species in a subalpine meadow in the Colorado Rocky Mountains, USA. We visually estimated herbivory and disease every two-weeks during the growing season and evaluated weather conditions during the previous two- or four-week time interval (two-week average air temperature, two- and four-week cumulative precipitation) as predictors of the probability and amount of damage. Herbivore attack was 13% more likely and amount of damage was 29% greater in warmed plots than controls across the focal species, but warming treatment had little affect on plant disease. Herbivory presence and damage increased the most with experimental warming when preceded by wetter, rather than drier, fine-scale weather, but preceding ambient temperature did not strongly interact with elevated warming to influence herbivory. Disease presence and damage increased, on average, with warmer weather and more precipitation regardless of warming. The effect of warming over reference climate on herbivore damage is dependent on and amplified by fine-scale weather variation, suggesting more boom-and-bust damage dynamics with increasing climate variability. However, the mean effect of regional climate change is likely reduced monsoon rainfall, for which we predict a reduction in insect herbivore damage. Plant disease was generally unrelated
# Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease
<p>Dysregulation of gene expression in Alzheimer’s disease (AD) remains elusive, especially at the cell type level. Gene regulatory network, a key molecular mechanism linking transcription factors (TFs) and regulatory elements to govern target gene expression, can change across cell types in the human brain and thus serve as a model for studying gene dysregulation in AD. However, it is still challenging to understand how cell type networks work abnormally under AD. To address this, we integrated single-cell multi-omics data and predicted the gene regulatory networks in AD and control for four major cell types, excitatory and inhibitory neurons, microglia and oligodendrocytes. Importantly, we applied network biology approaches to analyze the changes of network characteristics across these cell types, and between AD and control. For instance, many hub TFs target different genes between AD and control (rewiring). Also, these networks show strong hierarchical structures in which top TFs (master regulators) are largely common across cell types, whereas different TFs operate at the middle levels in some cell types (e.g., microglia). The regulatory logics of enriched network motifs (e.g., feed-forward loops) further uncover cell type-specific TF-TF cooperativities in gene regulation. The cell type networks are highly modular and several network modules with cell-type-specific expression changes in AD pathology are enriched with AD-risk genes and putative targets of approved and pending AD drugs, suggesting possible cell-type genomic medicine in AD. Finally, using the cell type gene regulatory networks, we developed machine learning models to classify and prioritize additional AD genes. We found that top prioritized genes predict clinical phenotypes (e.g., cognitive impairment) with reasonable accuracy. Overall, this single-cell network biology analysis provides a comprehensive map linking genes, regulatory networks, cell types and drug targets and reveals dysregulated cell type gene dysregulatory mechanisms in AD.</p>
Supplementary data and code to "Known allosteric proteins have central roles in genetic disease" by G. Abrusan, D. Ascher and M. Inouye, PLOS Computational Biology 18(2):e1009806.
<p>Scripts and data to reproduce the figures and supplementary figures of "G. Abrusan, D. Ascher and M. Inouye (2022) Known allosteric proteins have central roles in genetic disease." PLOS Computational Biology 18(2):e1009806. https://doi.org/10.1371/journal.pcbi.1009806.</p>
A Study of the Efficacy and Safety of Upadacitinib (ABT-494) in Participants With Moderately to Severely Active Crohn's Disease Who Have Inadequately Responded to or Are Intolerant to Biologic Therapy
ClinicalTrials.gov study NCT03345836. IPD Sharing: YES. Countries: 48. Publications: 7.
A Study to Assess the Efficacy and Safety of Risankizumab in Participants With Moderately to Severely Active Crohn's Disease Who Failed Prior Biologic Treatment
ClinicalTrials.gov study NCT03104413. IPD Sharing: YES. Countries: 43. Publications: 5.
A Study to Observe Vedolizumab and Anti-tumour Necrosis Factors (Anti-TNFs) Outcomes in Real-world Biologic Ulcerative Colitis (UC) and Crohn's Disease (CD) Participants
ClinicalTrials.gov study NCT03710486. IPD Sharing: YES. Countries: 2. Publications: 1.
Pathformer: a biological pathway informed Transformer for disease diagnosis and prognosis using multi-omics data
<p>Integrating multi-omics data offers a more comprehensive view of gene regulation, which would be helpful in achieving accurate diagnosis of diseases like cancer. To improve the accuracy of disease diagnosis and prognosis, we developed Pathformer, a multi-omics integration method for both tissue and liquid biopsy data. We implemented Pathformer's network architecture using the “PyTorch” package in Python v3.6.9, and our codes can be found in the GitHub repository (https://github.com/lulab/Pathformer). This repository contains preprocessed TCGA dataset data, preprocessedliquid biopsy dataset data, result of Pathformer and comparison_methods, mentioned in GitHub project and article.</p>
Bridging the Chromosome-Centric and Biology and Disease Human Proteome Projects: Accessible and automated tools for interpreting biological and pathological impact of protein sequence variants detected via proteogenomics
<p>Bridging the Chromosome-Centric and Biology and Disease Human Proteome Projects: Accessible and automated tools for interpreting biological and pathological impact of protein sequence variants detected via proteogenomics</p>
Supplementary tables for the paper: "Comprehensive Mapping of the AOP-Wiki Database: Identifying Biological and Disease Gaps"
<p><strong>Supplementary tables for the paper: "Comprehensive Mapping of the AOP-Wiki Database: Identifying Biological and Disease Gaps"</strong></p> <p><em>Original Research Article</em><br><strong>Frontiers in Toxicology</strong>, March 8, 2024<br>Section: Regulatory Toxicology<br><strong>Volume 6 - 2024</strong> | <a href="https://doi.org/10.3389/ftox.2024.1285768" target="_new" rel="noopener">https://doi.org/10.3389/ftox.2024.1285768</a></p> <p><strong>Authors</strong>:<br>Thomas Jaylet, Thibaut Coustillet, Nicola M. Smith, Barbara Viviani, Birgitte Lindeman, Lucia Vergauwen, Oddvar Myhre, Nurettin Yarar, Johanna M. Gostner, Pablo Monfort-Lanzas, Florence Jornod, Henrik Holbech, Xavier Coumoul, Dimosthenis A. Sarigiannis, Philipp Antczak, Anna Bal-Price, Ellen Fritsche, Eliska Kuchovska, Antonios K. Stratidakis, Robert Barouki, Min Ji Kim, Olivier Taboureau, Marcin W. Wojewodzic, Dries Knapen, Karine Audouze</p>
Network analysis reveals rare disease signatures across multiple levels of biological organization - Co-expression dataset
<p>The GTEx-derived co-expression data in 38 tissues generated in Buphamalai et.al., Network analysis reveals rare disease signatures across multiple levels of biological organization, Nature Communications 2021. Please see the publication's Methods section for details.</p>
Protein network analysis links the NSL complex to Parkinson's disease via mitochondrial & nuclear biology
<p>This online depository corresponds to manuscript : <em>Protein network analysis links the NSL complex to Parkinson’s disease via mitochondrial & nuclear biology.</em></p> <p><strong>Authors: </strong><em>Katie Kelly, Patrick A. Lewis, Helene Plun-Favreau, Claudia Manzoni</em></p> <p>Whilst the majority (~90-95%) of PD cases are sporadic, much of our understanding of the pathophysiological basis of disease can be traced back to the study of rare, monogenic forms of disease. However, in the past decade, the availability of Genome-Wide Association Studies (GWAS) has facilitated a shift in focus, toward identifying common risk variants conferring an increased risk of developing PD across the population. </p> <p>A recently developed mitophagy screening assay of GWAS candidates, has functionally implicated the non-specific lethal (NSL) complex, a chromatin remodeler, in the regulation of PINK1-mitophagy. Here, a bioinformatics approach has been taken to investigate the interactome of the NSL complex, to unpick its relevance to PD progression. The mitochondrial interactome of the NSL complex has been built, mining 3 separate repositories: PINOT, HIPPIE and MIST, for curated, literature-derived protein-protein interaction (PPI) data. A multi-layered approach has been taken to; i) build the ‘mitochondrial’ NSL interactome, applying PD gene-set enrichment analysis to explore the relevance of the NSL mitochondrial interactome to PD and, ii) build the PD-oriented NSL interactome, using functional enrichment, to uncover biological pathways underpinning the NSL /PD association.</p>
Study to Assess the Safety and Biological Activity of AMX0035 for the Treatment of Alzheimer's Disease
ClinicalTrials.gov study NCT03533257. IPD Sharing: NO. Countries: 1. Publications: 2.
A Study of the Efficacy and Safety of Upadacitinib in Participants With Moderately to Severely Active Crohn's Disease Who Have Inadequately Responded to or Are Intolerant to Conventional and/or Biolog
ClinicalTrials.gov study NCT03345849. IPD Sharing: YES. Countries: 49. Publications: 7.
Trial Comparing Infliximab and Infliximab and Azathioprine in the Treatment of Patients With Crohn's Disease na�ve to Both Immunomodulators and Biologic Therapy (Study of Biologic and Immunomodulator
ClinicalTrials.gov study NCT00094458. IPD Sharing: Not stated. Countries: 15. Publications: 7.
Efficacy of GSK Biologicals' Candidate Malaria Vaccine 257049 Against Malaria Disease in Infants and Children in Africa
ClinicalTrials.gov study NCT00866619. IPD Sharing: YES. Countries: 7. Publications: 22.
Mediterranean Diet and Disease Activity in Axial Spondyloarthritis Receiving Biologic Therapy
ClinicalTrials.gov study NCT07170384. IPD Sharing: NO. Countries: 1. Publications: 1.
Study of Abatacept (BMS-188667) in Subjects With Active Rheumatoid Arthritis on Background Non-biologic DMARDS (Disease Modifying Antirheumatic Drugs) Who Have an Inadequate Response to Anti-TNF Thera
ClinicalTrials.gov study NCT00124982. IPD Sharing: Not stated. Countries: 10. Publications: 5.
Efficacy and Safety of GSK3196165 (Otilimab) Versus Placebo and Sarilumab in Participants With Moderately to Severely Active Rheumatoid Arthritis Who Have an Inadequate Response to Biological Disease-
ClinicalTrials.gov study NCT04134728. IPD Sharing: YES. Countries: 15. Publications: 1.
A Study Comparing Upadacitinib (ABT-494) to Placebo and to Adalimumab in Participants With Psoriatic Arthritis Who Have an Inadequate Response to at Least One Non-Biologic Disease Modifying Anti-Rheum
ClinicalTrials.gov study NCT03104400. IPD Sharing: YES. Countries: 46. Publications: 14.
Evaluation of Effectiveness of GSK Biologicals' Pneumococcal Conjugate Vaccine 1024850A Against Invasive Disease
ClinicalTrials.gov study NCT00861380. IPD Sharing: YES. Countries: 1. Publications: 9.
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.