Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models
Sign Up to like & getrecommendations! Published in 2020 at "PROTEOMICS"
DOI: 10.1002/pmic.201900282
Abstract: Omic technologies have enabled the complete readout of the molecular state of a cell at different biological scales. In principle, the combination of multiple omic data types can provide an integrated view of the entire… read more here.
Keywords: genome scale; scale models; omic data; biology ... See more keywords
Identification of optimal prediction models using multi-omic data for selecting hybrid rice
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DOI: 10.1038/s41437-019-0210-6
Abstract: Genomic prediction benefits hybrid rice breeding by increasing selection intensity and accelerating breeding cycles. With the rapid advancement of technology, other omic data, such as metabolomic data and transcriptomic data, are readily available for predicting… read more here.
Keywords: rice; support vector; omic data; hybrid rice ... See more keywords
iSOM-GSN: an integrative approach for transforming multi-omic data into gene similarity networks via self-organizing maps
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa500
Abstract: MOTIVATION One of the main challenges in applying graph convolutional neural networks on gene-interaction data is the lack of understanding of the vector space to which they belong, and also the inherent difficulties involved in… read more here.
Keywords: omic data; isom gsn; gene similarity; multi omic ... See more keywords
PyLiger: scalable single-cell multi-omic data integration in Python.
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac190
Abstract: MOTIVATION LIGER (Linked Inference of Genomic Experimental Relationships) is a widely used R package for single-cell multi-omic data integration. However, many users prefer to analyze their single-cell datasets in Python, which offers an attractive syntax… read more here.
Keywords: cell; multi omic; data integration; single cell ... See more keywords
Spectrum: fast density-aware spectral clustering for single and multi-omic data
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DOI: 10.1093/bioinformatics/btz704
Abstract: Abstract Motivation Clustering patient omic data is integral to developing precision medicine because it allows the identification of disease subtypes. A current major challenge is the integration multi-omic data to identify a shared structure and… read more here.
Keywords: spectral clustering; omic data; spectrum; multi omic ... See more keywords
Tensorial blind source separation for improved analysis of multi-omic data
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DOI: 10.1186/s13059-018-1455-8
Abstract: There is an increased need for integrative analyses of multi-omic data. We present and benchmark a novel tensorial independent component analysis (tICA) algorithm against current state-of-the-art methods. We find that tICA outperforms competing methods in… read more here.
Keywords: analysis; source separation; omic data; blind source ... See more keywords
Multilevel omic data clustering reveals variable contribution of methylator phenotype to integrative cancer subtypes.
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DOI: 10.2217/epi-2018-0057
Abstract: AIM We aimed to assess to what extent CpG island methylator phenotype (CIMP) contributes to cancer subtypes obtained by multilevel omic data analysis. MATERIALS & METHODS 16 The Cancer Genome Atlas datasets encompassing three data… read more here.
Keywords: omic data; methylator phenotype; cancer; multilevel omic ... See more keywords
From classical mendelian randomization to causal networks for systematic integration of multi-omics
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2022.990486
Abstract: The number of studies with information at multiple biological levels of granularity, such as genomics, proteomics, and metabolomics, is increasing each year, and a biomedical questaion is how to systematically integrate these data to discover… read more here.
Keywords: mendelian randomization; integration; causal; omic data ... See more keywords