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491
datasets available to search
ShareScore release 0.9.0
Dataset results
491 results for “population modelling”
Village In a Dish: A Model System for Population-scale hiPSC Studies [scRNA-Seq]
GEO Series GSE225278. Homo sapiens. 19 samples. Type: Expression profiling by high throughput sequencing.
Population dynamics modeling reveals myeloid bias involves both HSC differentiation and progenitor proliferation biases
GEO Series GSE262024. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNA sequencing for vascular cell-enriched cell populations in the liver-specific apoE inducible mouse models
GEO Series GSE206204. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
Sub-population RNAseq characterization of cell types produced over time in an in vitro model of human inhibitory interneuron differentiation.
GEO Series GSE93801. Homo sapiens. 40 samples. Type: Expression profiling by high throughput sequencing.
Village In a Dish: A Model System for Population-scale hiPSC Studies [Affymetrix]
GEO Series GSE224950. Homo sapiens. 20 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations [xenograft]
GEO Series GSE311813. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Uniform Bipartition in Population Protocol Model with Arbitrary Communication Graphs (video)
Full video presentation of the paper: Uniform Bipartition in Population Protocol Model with Arbitrary Communication Graphs.<br><br>Appears in Session 4 of the 24th International Conference on Principles of Distributed Systems OPODIS 2020<br><a href="https://opodis2020.unistra.fr">https://opodis2020.unistra.fr</a>
Data from: Mixture modeling of transcript abundance classes in natural populations
BACKGROUND: Populations diverge in genotype and phenotype under the influence of such evolutionary processes as genetic drift, mutation accumulation, and natural selection. Because genotype maps onto phenotype by way of transcription, it is of interest to evaluate how these evolutionary factors influence the structure of variation at the level of transcription. Here, we explore the distributions of cis-acting and trans-acting factors and their relative contributions to expression of transcripts that exhibit two or more classes of abundance among individuals within populations. RESULTS: Expression profiling using cDNA microarrays was conducted in Drosophila melanogaster adult female heads for 58 nearly isogenic lines from a North Carolina population and 50 from a California population. Using a mixture modeling approach, transcripts were identified that exhibit more than one mode of transcript abundance across the samples. Power studies indicate that sample sizes of 50 individuals will generally be sufficient to detect divergent transcript abundance classes. The distribution of transcript abundance classes is skewed toward low frequency minor classes, which is reminiscent of the typical skew in genotype frequencies. Similar results are observed in reported data on gene expression in human lymphoblast cell lines, in which analysis of association with linked polymorphisms implies that cis-acting single nucleotide polymorphisms make only a modest contribution to bimodal distributions of transcript abundance. CONCLUSION: Population surveys of gene expression may complement genetical genomics as a general approach to quantifying sources of transcriptional variation. Differential expression of transcripts among individuals is due to a complex interplay of cis-acting and trans-acting factors.
Data from: Examining the effects of the histone methyltransferase inhibitor BIX-01294 on histone modifications and gene expression in both a clinical population and mouse models
Schizophrenia has been consistently characterized by abnormal patterns of gene down-regulation, increased restrictive chromatin assemblies, and reduced transcriptional activity. Histone methyltransferase (HMT) mRNA and H3K9me2 levels are elevated in postmortem brain and peripheral blood cells of persons with schizophrenia. Moreover, this epigenomic state likely contributes to the disease, as HMT levels correlate with clinical symptomatology. This manuscript sought to establish the potential therapeutic value of the HMT inhibitor BIX-01294 (BIX). Human peripheral mononuclear cells (PBMC) from 24 individuals with schizophrenia and 24 healthy individuals were cultured in the presence of BIX (5uM or 10uM). Mice were given once daily intraperitoneal injections of BIX (0.5 or 1mg/kg) for one week. Cultured cells, mouse cortex, or striatum was harvested, RNA extracted and RT-PCR conducted for several schizophrenia candidate genes: IL-6, Gad1, Nanog, KLF4, Reln, and Bdnf9a. Total H3K9me2 levels were measured using western blot while H3K9me2 binding to selected genes of interest was conducted using chromatin immunoprecipitation (ChIP). Neuronal subtype-specific BDNF conditional knockdown was conducted using the cre/lox system of mutant animals. Treatment with BIX decreased H3K9me2 and increased selected mRNA levels in cultured PBMCs from both normal controls and participants with schizophrenia. In mice, peripheral administration of BIX decreased cortical H3K9me2 levels and increased schizophrenia candidate gene expression. In BDNF conditional knockdown animals, BIX administration was able to significantly rescue Bdnf9a mRNA levels in ChAT and D1 but not D2 Bdnf conditional knockdown mice. The results presented in this manuscript demonstrate a potential for further research into the clinical effectiveness of histone modifying pharmacology in the treatment of schizophrenia.
A proposal of metrics to automatically populate a user model for intelligent user interfaces in MDD: Experimental material
<p>Material of paper: A proposal of metrics to automatically populate a user model for intelligent user interfaces in MDD</p>
Large-Population based Deep Learning Models in Classifying Primary Bone Tumors and Bone Infections based on Radiographs: a Retrospective and Multi-reader Multi-center Study
<p>This retrospective multicenter study collected patients via consecutive sampling between 2013 and 2022 from two cohorts: training cohort (from the Second Xiangya Hospital of Central South University) and testing cohort (from Xiangya Hospital of Central South University and Hunan Children's Hospital of Central South University). These lesions were identified to have bone involvement through pre-operative radiographs and were histologically diagnosed following biopsy or surgery. <br>(i) For the inclusion criteria, lesions were confirmed and diagnosed as PBTs according to the 2020 World Health Organization (WHO) system for the classification for tumors of bone 1 while bone infections were confirmed and proven by histology and (or) bacterial culture. The other vital inclusion criteria are evident as well as available clinical information and pre-operative radiographs. <br>(ii) The screening criteria: (a) radiographs were from patients diagnosed between 2013 and 2022 (b) in selected three hospitals; (c) radiographs with robust quality for reliable assessments of the bone lesions and (d) all of these radiographs were pre-operative. <br>Clinical characteristics like age, gender, and the location of the lesion of interest and so on were obtained from the patients' electronic medical records after data desensitization and standardization.<br>Radiographs were kept and downloaded as Digital Imaging and Communications in Medicine (DICOM) files from the picture archiving and communication system (PACS) at their original sizes and resolutions. All of these radiograph images have undergone desensitization processing of disengaging patient protected health information from DICOM data to meet the relevant legal criteria and requirements of US (HIPAA) as well as European (GDPR). Delineating the region of interest (ROI) was performed by two proficient radiologists. ROIs were meticulously outlined via Click 2 Crop (version 5.2.2) (https://click-2-crop.en.softonic.com/) to closely segment pertinent entities present in each PBT or bone infection. The smallest rectangular box that can completely cover the ROI was manually annotated as the boundary box by senior seniority radiologist to ensure accuracy. Afterwards, the annotated ROIs were used as ground truth for the model development process.</p>
single-cell RNAseq data (data set 13) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>The present dataset (dataset13) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from pancreas donor11 downloaded from the GEO website (<strong>GSE114297). </strong></p> <p>see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data</p> <p>and github: <a href="https://github.com/sysbiolux/scFASTCORMICS">https://github.com/sysbiolux/scFASTCORMICS</a></p> <p>For more information, version updates of the scFASTCORMICS. </p>
single-cell RNAseq data (data set 10) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>The present dataset (dataset10) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from pancreas donor8 downloaded from the GEO website (<strong>GSE114297). </strong></p> <p>see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data</p> <p>and github: https://github.com/sysbiolux/scFASTCORMICS</p> <p>For more information, version updates of the scFASTCORMICS. </p>
single-cell RNAseq data (data set 6) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>The present dataset (dataset6) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from pancreas donor4 downloaded from the GEO website (<strong>GSE114297). </strong></p> <p>see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data</p> <p>and github: <a href="https://github.com/sysbiolux/scFASTCORMICS">https://github.com/sysbiolux/scFASTCORMICS</a></p> <p>For more information, version updates of the scFASTCORMICS. </p>
single-cell RNAseq data (data set 2) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>The present dataset (dataset2) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from normal mucosa samples downloaded from the GEO website (<strong>GSE81861). </strong></p> <p>see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data</p> <p>and github: https://github.com/sysbiolux/scFASTCORMICS</p> <p>For more information, version updates of the scFASTCORMICS. </p>
Clinical Trial on the Effectiveness of the Model of Centered Care in the Person in the Geriatric Population at Home(Project AICP.Com)
ClinicalTrials.gov study NCT05534737. IPD Sharing: Not stated. Countries: 1. Publications: 0.
External Evaluation of Vancomycin Population Pharmacokinetic Models
ClinicalTrials.gov study NCT05481788. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Precision Drug Use of Immunosuppressants Guided by Population Pharmacokinetics/Pharmacodynamic Models in Kidney Transplant Patients
ClinicalTrials.gov study NCT05872815. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Validation of Population Pharmacokinetic Model Derived From Healthy Volunteer in Kidney Transplant Recipients
ClinicalTrials.gov study NCT02808065. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Population Pharmacokinetic-pharmacodynamic (PK-PD) Modeling of Co-administered Gabapentin in Neuropathic Pain
ClinicalTrials.gov study NCT00967707. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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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.