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31 results for “dimensionality reduction”
Intraoperative Three Dimensional Fluoroscopy Compared to Standard Fluoroscopy for the Assessment of Reduction of Ankle Fractures With Syndesmosis Disruption
ClinicalTrials.gov study NCT00556010. IPD Sharing: Not stated. Countries: 1. Publications: 1.
lcUMAPtSNE: Use of non-linear dimensionality reduction techniques with genotype likelihoods
<p>This repository contains genotype likelihood estimations derived from open-access whole-genome re-sequencing datasets of the scimitar-horned oryx (SO). The dataset was downsampled to exhibit varying coverage levels, including 6x, 2x, and 0.5x. Genotype likelihoods were estimated, followed by the calculation of principal components and subsequent application of UMAP and t-SNE with varying parameter settings, as detailed in Uzel et al. (2025). All intermediate and input files generated from these datasets are available here. Genotype likelihood estimations are provided in the formats '.beagle.gz' and '.mafs.gz'. Additionally, the repository contains the input covariance matrix ('.cov') for each dataset and the population information file for each group, which were employed in the non-linear dimensionality reduction steps described in Uzel et al. (2025).</p> <h3>Raw data resources</h3> <p>All raw sequencing data we used in this study were downloaded from public databases, and no new data were generated.</p> <p>The scimitar-horned oryx data were acquired from NCBI BioProject PRJEB37295 (Humble et al. 2023)</p> <h3>Code/Software</h3> <p>All bioinformatic codes used for generating the results and guidelines presented in Çilingir et al. (2024) are available at <strong><a href="https://github.com/fgcilingir/lcUMAPtSNE">https://github.com/fgcilingir/lcUMAPtSNE</a>.</strong></p> <h3>Literature Cited</h3> <p>Humble, E., Stoffel, M. A., Dicks, K., Ball, A. D., Gooley, R. M., Chuven, J., Pusey, R., Remeithi, M. A., Koepfli, K.-P., Pukazhenthi, B., Senn, H., & Ogden, R. (2023). Conservation management strategy impacts inbreeding and mutation load in scimitar-horned oryx. <em>Proceedings of the National Academy of Sciences of the United States of America</em>, <em>120</em>(18), e2210756120.<br><br>Uzel, K., Grossen, C., Çilingir, F.G. (2025) lcUMAPtSNE: Use of non-linear dimensionality reduction techniques with genotype likelihoods. <em>bioRxiv,</em> https://doi.org/10.1101/2024.04.01.587545.</p>
Comparison of dimensional reduction methods in Raman spectral data of mouse uterus and placenta tissues
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Methylation haplotypes of the insulin gene promoter in children and adolescents with type 1 diabetes: could a dimensionality reduction approach predict the disease?
<p>The aim of the present study was to identify insulin gene promoter (IGP) methyl-haplotypes among children and adolescents with T1D and suggest a predictive model for the discrimination of cases and controls according to methyl-haplotypes. Fourty individuals (20 T1D) participated. IGP-region from peripheral whole blood DNA of 40 participants (20 T1D) was sequenced by next generation sequencing, sequences were read using FASTQ files, and methylation status was calculated by python-based pipeline for targeted deep bisulfite sequenced amplicons (ampliMethProfiler). Methylation profile at 10 CpG sites proximal to transcription start site of the IGP was recorded and coded as 0 for unmethylation or 1 for methylation. A single read could result in “1111111111” methyl-haplotype (all methylated), “000000000” methyl-haplotype (all unmethylated) or any other combination.</p>
Data from: Surrogate modelling for the prediction of spatial fields based on simultaneous dimensionality reduction of high-dimensional input/output spaces
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Data from: Dual dimensionality reduction reveals independent encoding of motor features in a muscle synergy for insect flight control
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Data from: Encounter complexes and dimensionality reduction in protein-protein association
An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein–protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles calculated from the docked structures shows that the method captures both specific and non-specific encounter complexes. To explore the energy landscape in the vicinity of the native structure, the nonlinear manifold describing the relative orientation of two solid bodies is projected onto a Euclidean space in which the shape of low energy regions is studied by principal component analysis. Results show that the energy surface is canyon-like, with a smooth funnel within a two dimensional subspace capturing over 75% of the total motion. Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition.
Constructing a histocytometry pipeline suitable for high dimensional reduction analysis of using graphical user interface software
<p>Image, worksheet and reference files for a Current Protocols journal article</p>
External Validation by Machine Learning and Reduction of the Input Dimensions of the D-PSY Scale for Dimensional Psychopathology
ClinicalTrials.gov study NCT05675215. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Encounter complexes and dimensionality reduction in protein-protein association
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Implementing high dimensional reductional analysis on histocytometric data
<p>In the previous protocol article (Munoz-Erazo, Schmidt, Shinko, Eccles, et al., 2022), we demonstrated construction of a histocytometry pipeline that is capable of both segmenting highly-aggregated cell populations and retaining the original intensity data range of the input microscopic images. In the protocol article presented here, using the output from the aforementioned protocol article, we demonstrate how to phenotype the data using the high dimensional reductional analysis technique opt-t-SNE (optimized t-distributed Stochastic Neighbor Embedding) and compare it to traditional manual gating.</p> <p>Additional, we present a support protocol illustrating the advantage of the inclusion of cell junction/membrane marker in accurately segmenting highly-aggregated cell populations in ilastik.</p> <p>In the previous protocol article (Munoz-Erazo, Schmidt, Shinko, Eccles, et al., 2022), we demonstrated construction of a histocytometry pipeline that is capable of both segmenting highly-aggregated cell populations and retaining the original intensity data range of the input microscopic images. In the protocol article presented here, using the output from the aforementioned protocol article, we demonstrate how to phenotype the data using the high dimensional reductional analysis technique opt-t-SNE (optimized t-distributed Stochastic Neighbor Embedding) and compare it to traditional manual gating.</p> <p>Additional, we present a support protocol illustrating the advantage of the inclusion of cell junction/membrane marker in accurately segmenting highly-aggregated cell populations in ilastik.</p>
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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.