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
Sign Up to like & getrecommendations! Published in 2019 at "Heredity"
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
COMPARATIVE ASSESSMENT OF BIOBANK DATASETS FOR THE STUDY OF INFLAMMATORY BOWEL DISEASE
Sign Up to like & getrecommendations! Published in 2024 at "Gastroenterology"
DOI: 10.1053/j.gastro.2023.11.221
Abstract: Lack of available multiomics datasets has slowed progress in understanding the relationship between genomic variants, gene expression, and disease progress in inflammatory bowel disease (IBD). Biobanks provide an opportunity to produce population-scale datasets to accelerate… read more here.
Keywords: ibd omic; disease; analysis; ovation ibd ... 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
MPAC: a computational framework for inferring pathway activities from multi-omic data
Sign Up to like & getrecommendations! Published in 2025 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaf490
Abstract: Abstract Motivation Fully capturing cellular state requires examining genomic, epigenomic, transcriptomic, proteomic, and other assays for a biological sample and comprehensive computational modeling to reason with the complex and sometimes conflicting measurements. Modeling these so-called… read more here.
Keywords: mpac computational; computational framework; pathway activities; multi omic ... See more keywords
Spectrum: fast density-aware spectral clustering for single and multi-omic data
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
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
Race and “omic” data in glioma: A systematic review of contemporary research to explore the digital divide
Sign Up to like & getrecommendations! Published in 2025 at "Neuro-Oncology Practice"
DOI: 10.1093/nop/npaf016
Abstract: Abstract Background The expanding repertoire of studies generating genome-scale omic datasets from glioma samples provides a generational opportunity to uncover mechanisms driving aggressive biology and develop new treatments. However, ensuring such studies reflect the breadth… read more here.
Keywords: genome scale; biology; omic data; race ethnicity ... See more keywords
Learning Consistency and Specificity of Cells From Single-Cell Multi-Omic Data
Sign Up to like & getrecommendations! Published in 2024 at "IEEE Journal of Biomedical and Health Informatics"
DOI: 10.1109/jbhi.2024.3370868
Abstract: Advancements in single-cell technologies concomitantly develop the epigenomic and transcriptomic profiles at the cell levels, providing opportunities to explore the potential biological mechanisms. Even though significant efforts have been dedicated to them, it remains challenging… read more here.
Keywords: single cell; consistency; cell clustering; multi omic ... See more keywords
Utilizing Omic Data to Understand Integrative Physiology.
Sign Up to like & getrecommendations! Published in 2025 at "Physiology"
DOI: 10.1152/physiol.00045.2024
Abstract: Over the past several decades, physiological research has undergone a progressive shift toward greater-and-greater reductionism, culminating in the rise of 'molecular physiology.' The introduction of Omic techniques, chiefly protein mass spectrometry and next-generation DNA sequencing… read more here.
Keywords: physiology; language; utilizing omic; omic data ... See more keywords
Tensorial blind source separation for improved analysis of multi-omic data
Sign Up to like & getrecommendations! Published in 2018 at "Genome Biology"
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