Multiple omics
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The plasticity of monocytes enables them to exert multiple roles during an immune response, including promoting immune tolerance. How monocytes alter their functions to convey immune tolerance in the context of lower respiratory tract infections in humans is not well understood.
17p vibransone 28-03-2024 6 1 Download
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Multiple sclerosis is a chronic neuroinfammatory disease with a highly heterogeneous disease course. Preventing lasting disability requires early identification of persons at risk and novel approaches towards patient stratification for personalized treatment decisions. In this comment, we discuss the importance of large datasets of real-world cohorts in order to address this unmet need.
3p viellison 28-03-2024 4 2 Download
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Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in spatial multi-omics technologies, including novel data modalities and computational approaches.
17p vicwell 29-02-2024 5 2 Download
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Association studies using a single type of omics data have been successful in identifying diseaseassociated genetic markers, but the underlying mechanisms are unaddressed. To provide a possible explanation of how these genetic factors affect the disease phenotype, integration of multiple omics data is needed.
5p vihagrid 30-01-2023 5 3 Download
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Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure.
12p vigalileogalilei 27-02-2022 12 1 Download
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The rapid increase of omic data has greatly facilitated the investigation of associations between omic profiles such as DNA methylation (DNAm) and complex traits in large cohorts. Here, we propose a mixed-linear-model-based method called MOMENT that tests for association between a DNAm probe and trait with all other distal probes fitted in multiple random-effect components to account for unobserved confounders.
13p vigalileogalilei 27-02-2022 11 2 Download
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Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of single cell measurements. MATCHER uses manifold alignment to infer single cell multi-omic profiles from transcriptomic and epigenetic measurements performed on different cells of the same type.
19p vialfrednobel 29-01-2022 7 1 Download
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One challenge facing omics association studies is the loss of statistical power when adjusting for confounders and multiple testing. The traditional statistical procedure involves fitting a confounder-adjusted regression model for each omics feature, followed by multiple testing correction.
18p viarchimedes 26-01-2022 11 0 Download
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A growing number of single-cell sequencing platforms enable joint profiling of multiple omics from the same cells. We present Cobolt, a novel method that not only allows for analyzing the data from joint-modality platforms, but provides a coherent framework for the integration of multiple datasets measured on different modalities.
21p viarchimedes 26-01-2022 16 0 Download
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To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method, Primo, for integrative analysis of GWAS summary statistics with multiple sets of omics QTL summary statistics from different cellular conditions or studies.
24p viarchimedes 26-01-2022 11 0 Download
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Emerging single-cell technologies profile multiple types of molecules within individual cells. A fundamental step in the analysis of the produced high-dimensional data is their visualization using dimensionality reduction techniques such as t-SNE and UMAP.
9p viarchimedes 26-01-2022 16 0 Download
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Technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computational strategies to analyze data from complex experimental designs that include multiple data modalities and multiple groups of samples.
17p viarchimedes 26-01-2022 7 0 Download
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Pan-cancer evaluation of gene expression and somatic alteration data for cancer prognosis prediction
Over the past decades, approaches for diagnosing and treating cancer have seen significant improvement. However, the variability of patient and tumor characteristics has limited progress on methods for prognosis prediction. The development of high-throughput omics technologies now provides multiple approaches for characterizing tumors.
11p vimahuateng 26-11-2021 8 1 Download
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Omics profiling is now a routine component of biomedical studies. In the analysis of omics data, clustering is an essential step and serves multiple purposes including for example revealing the unknown functionalities of omics units, assisting dimension reduction in outcome model building, and others. In the most recent omics studies, a prominent trend is to conduct multilayer profiling, which collects multiple types of genetic, genomic, epigenetic and other measurements on the same subjects. In the literature, clustering methods tailored to multilayer omics data are still limited.
13p vibeauty 23-10-2021 3 0 Download
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There exist few, if any, practical guidelines for predictive and falsifiable multi-omic data integration that systematically integrate existing knowledge. Disease modules are popular concepts for interpreting genomewide studies in medicine but have so far not been systematically evaluated and may lead to corroborating multiomic modules.
13p vitzuyu2711 29-09-2021 11 1 Download
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Knowledge Base Commons (KBCommons) v1.1 is a universal and all-inclusive web-based framework providing generic functionalities for storing, sharing, analyzing, exploring, integrating and visualizing multiple organisms’ genomics and integrative omics data.
16p viansan2711 30-07-2021 7 1 Download
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Gene expression is regulated by DNA-binding transcription factors (TFs). Together with their target genes, these factors and their interactions collectively form a gene regulatory network (GRN), which is responsible for producing patterns of transcription, including cyclical processes such as genome replication and cell division.
17p vijeeni2711 24-07-2021 9 0 Download
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Meat quality is a complex trait affected by genotypic and environmental factors. In a previous study, it was found that feedstuffs have various effects on the growth rate and meat quality of lambs. However, the underlying mechanisms are still not entirely clear.
13p vijeeni2711 30-06-2021 6 1 Download
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MultiAlign is a free software tool that aligns multiple liquid chromatography-mass spectrometry datasets to one another by clustering mass and chromatographic elution features across datasets. Applicable to both label-free proteomics and metabolomics comparative analyses, the software can be operated in several modes.
14p viwyoming2711 16-12-2020 23 1 Download
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Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It has been marked by promising methodological developments, improved translation efforts of statistical epistasis to biological epistasis and attempts to integrate different omics information sources into the epistasis screening to enhance power.
10p viwyoming2711 16-12-2020 18 1 Download