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ShareScore release 0.7.1
Dataset results
107 results for “mechanistic model”
Mechanistic models position ceritinib as a nuclear integrity disrupting therapy in pediatric liver tumors
GEO Series GSE306477. Homo sapiens. 21 samples. Type: Expression profiling by high throughput sequencing.
LASSIM -a network inference toolbox for genome-wide mechanistic modeling
GEO Series GSE60683. Homo sapiens. 70 samples. Type: Expression profiling by array.
Dual inhibition of histone deacetylases and the mechanistic target of rapamycin promotes apoptosis in cell line models of uveal melanoma
GEO Series GSE155452. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Identification of mechanistic chronic kidney disease biomarkers by comprehensive bulk RNA-seq transcriptomics and SWATH proteomics of the rat sub-total nephrectomy model of kidney fibrosis [RNA-Seq_2]
GEO Series GSE253008. Rattus norvegicus. 6 samples. Type: Expression profiling by high throughput sequencing.
Mechanistic Exploration and Kinetic Modeling through In-Silico Data Generation and Probabilistic Machine Learning Analysis
<p>This zip file includes the dataset 'two_reactions_022624.csv,' which is used for training and testing ML/DL models in the paper 'Mechanistic Exploration and Kinetic Modeling through In-Silico Data Generation and Probabilistic Machine Learning Analysis,' as well as trained models and some files used for training the model. When running the model downloaded from GitHub, copy and paste the files downloaded from here into the subfolder with the same name and path as the one downloaded from GitHub.</p>
Data from: Predicting local and non-local effects of resources on animal space use using a mechanistic step-selection model
Open the record for dataset details and reuse information.
Mechanistic impacts of bacterial diet on dopaminergic neurodegeneration in a Caenorhabditis elegans α-synuclein model of Parkinson's disease
GEO Series GSE210005. Caenorhabditis elegans. 12 samples. Type: Expression profiling by high throughput sequencing.
Mechanistic dissection of dominant AIRE mutations in mouse models reveals evidence for AIRE auto-regulation [RNA-seq]
GEO Series GSE151012. Mus musculus. 74 samples. Type: Expression profiling by high throughput sequencing.
Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer
GEO Series GSE78286. Homo sapiens. 17 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer [ChIP-Seq]
GEO Series GSE78284. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Growth retardation in a mouse model of Kabuki syndrome 2 bears mechanistic similarities to Kabuki syndrome 1.
GEO Series GSE262539. Mus musculus. 32 samples. Type: Expression profiling by high throughput sequencing.
Mechanistic dissection of dominant AIRE mutations in mouse models reveals AIRE auto-regulation [ChIP-Seq]
GEO Series GSE165550. Mus musculus. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Can we implement mechanistic niche models without measuring traits?
<p>Despite increasing demand for more mechanistic models of species' distributions, they remain difficult to implement due to their intense data requirements. Here, we suggest that three existing tools might help researchers estimate missing trait data that can fill necessary requirements: phylogenetic imputation (incorporating evolutionary relationships into the imputation process), allometry, and biophysics. These tools can bridge the gap between species for which we have fairly little data and ecological models of their distributions. We focus on ecophysiological traits of salamanders; a simple theoretical model of water loss showed that changing body mass results in a decrease in mass-specific water loss, driven by both increasing total size and increasing the thickness of the epidermis. Yet this has two costs – mass-specific oxygen absorption decreases with the surface area-to-volume ratio, and a thicker epidermis slows the rate of respiration. Using a mechanistic distribution model, we modeled the ranges of six species of lungless, terrestrial salamanders. The model performed well for two species of <i>Plethodon</i> and one species of <i>Desmognathus</i>, but poorly for three other species; this discrepancy likely reflects biases in the data available to build the imputation model and biological assumptions on which the mechanistic distribution model is based. Though overall model performance was mediocre, the parameter estimates used in this study may be useful when fewer total parameters are missing. We provide relevant R functions for the mechanistic niche model in the package 'ManderGander'.</p>
Fig. 4 Model 2 in Modelling sympatric speciation by means of biologically plausible mechanistic processes as exemplified by threespine stickleback species pairs
Fig. 4 Model 2. Typical distribution of T, the phenotypic values, at generation 100. Nm = Nf =100; σ =0.5; Τ= 0.5; μ = 1%; n =256 alleles. Only 10 out of 200 (5%) individuals are hybrids. Similar results were obtained in 10 out of 20 replicate simulations with Τ =0.5, and in ten out of ten replicate simulations with Τ =0.25
Fig. 7 Model 5 in Modelling sympatric speciation by means of biologically plausible mechanistic processes as exemplified by threespine stickleback species pairs
Fig. 7 Model 5: Reinforcement of divergent mating preferences. Columns: 1 Typical distribution of morphology alleles, 2 typical distribution of preference alleles, 3 typical distribution of morphology phenotypes T. Rows: 1 Generation 0, 2 generation 100, 3 generation 200. At generation 100, 92% of individuals have either all benthic alleles at both loci, or all limnetic alleles at both loci. At generation
Fig. 2 in Modelling sympatric speciation by means of biologically plausible mechanistic processes as exemplified by threespine stickleback species pairs
Fig. 2 Relative fitness is a function of morphology T. Here fitness ¼ sinð 2p»TÞ 2 þ 1 (relative fitness varies between 1 and 2, i.e. two-fold). In model 3, we used a flat fitness function: fitness=1. In model 5, we used the above fitness function, well fitness ¼ sinð 2p»TÞ 2 þ 0: 5 as as: (relative fitness varies between 0.5 and 1.5, i.e. a threefold selection differential), and fitness ¼ sinð 2p»TÞ 2 þ 0: 25 (relative fitness varies between 0.25 and 1.25, i.e. a five-fold selection differential)
AIM4 AI and Mechanistic Modeling in Molecular Medicine
ClinicalTrials.gov study NCT06535828. IPD Sharing: NO. Countries: 0. Publications: 0.
Can we implement mechanistic niche models without measuring traits?
Open the record for dataset details and reuse information.
Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer [RNA-Seq]
GEO Series GSE78285. Homo sapiens. 11 samples. Type: Expression profiling by high throughput sequencing.
A first truly systems level mechanistic model unravelling the gene regulation of Th2 differentiation [IRF4]
GEO Series GSE56434. Homo sapiens. 10 samples. Type: Expression profiling by array.
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.