Pathway-based meta-analysis for partially paired transcriptomics analysis.
Sign Up to like & getrecommendations! Published in 2019 at "Research synthesis methods"
DOI: 10.1002/jrsm.1381
Abstract: Pathway-based differential expression analysis allows the incorporation of biological domain knowledge into transcriptomics analysis to enhance our understanding of disease mechanisms. To integrate information among multiple studies at the pathway level, pathway-based meta-analysis can be… read more here.
Keywords: pathway based; analysis; based meta; partially paired ... See more keywords
Recommendations toward a human pathway-based approach to disease research.
Sign Up to like & getrecommendations! Published in 2018 at "Drug discovery today"
DOI: 10.1016/j.drudis.2018.05.038
Abstract: Failures in the current paradigm for drug development have resulted in soaring research and development costs and reduced numbers of new drug approvals. Over 90% of new drug programs fail, the majority terminated at the… read more here.
Keywords: research; toward human; pathway based; drug ... See more keywords
Pathway-based biomarker identification with crosstalk analysis for robust prognosis prediction in hepatocellular carcinoma
Sign Up to like & getrecommendations! Published in 2019 at "EBioMedicine"
DOI: 10.1016/j.ebiom.2019.05.010
Abstract: BACKGROUND Although many prognostic single-gene (SG) lists have been identified in cancer research, application of these features is hampered due to poor robustness and performance on independent datasets. Pathway-based approaches have thus emerged which embed… read more here.
Keywords: hepatocellular carcinoma; prognosis; pathway based; crosstalk ... See more keywords
Characteristic analysis of the pathway-based weighted network of hypertension-related genes
Sign Up to like & getrecommendations! Published in 2019 at "Physica A: Statistical Mechanics and its Applications"
DOI: 10.1016/j.physa.2019.122069
Abstract: Abstract Complex network is an effective approach for analyzing the complex interactions in diseases. Hypertension is a complex multifactorial disease involving multiple biological pathways and interactions between genetic and environmental factors. By combining network approach… read more here.
Keywords: based weighted; hypertension; weighted network; hypertension related ... See more keywords
A cognitive pathway to punishment insensitivity
Sign Up to like & getrecommendations! Published in 2023 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2221634120
Abstract: Significance Insensitivity to the adverse consequences of our actions drives problematic behaviors such as those observed in substance use disorders, conduct disorder, and antisocial personality disorder. Two pathways have been proposed for this insensitivity: a… read more here.
Keywords: pathway based; pathway punishment; insensitivity; pathway ... See more keywords
Kernel-based hierarchical structural component models for pathway analysis.
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac276
Abstract: MOTIVATION Pathway analyses have led to more insight into the underlying biological functions related to the phenotype of interest in various types of omics data. Pathway-based statistical approaches have been actively developed, but most of… read more here.
Keywords: hiscom kernel; hierarchical structural; pathway based; structural component ... See more keywords
Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data
Sign Up to like & getrecommendations! Published in 2018 at "GigaScience"
DOI: 10.1093/gigascience/giy136
Abstract: Abstract Lilikoi (the Hawaiian word for passion fruit) is a new and comprehensive R package for personalized pathway-based classification modeling using metabolomics data. Four basic modules are presented as the backbone of the package: feature… read more here.
Keywords: classification; package personalized; classification modeling; pathway based ... See more keywords
Pathway-Based Single-Cell RNA-Seq Classification, Clustering, and Construction of Gene-Gene Interactions Networks Using Random Forests
Sign Up to like & getrecommendations! Published in 2020 at "IEEE Journal of Biomedical and Health Informatics"
DOI: 10.1109/jbhi.2019.2944865
Abstract: Single-cell RNA-Sequencing (scRNA-Seq), an advanced sequencing technique, enables biomedical researchers to characterize cell-specific gene expression profiles. Although studies have adapted machine learning algorithms to cluster different cell populations for scRNA-Seq data, few existing methods have… read more here.
Keywords: cell rna; cell populations; gene; cell ... See more keywords
PRSet: Pathway-based polygenic risk score analyses and software
Sign Up to like & getrecommendations! Published in 2023 at "PLOS Genetics"
DOI: 10.1371/journal.pgen.1010624
Abstract: Polygenic risk scores (PRSs) have been among the leading advances in biomedicine in recent years. As a proxy of genetic liability, PRSs are utilised across multiple fields and applications. While numerous statistical and machine learning… read more here.
Keywords: pathway based; pathway prss; disease; risk ... See more keywords
A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants
Sign Up to like & getrecommendations! Published in 2017 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2017.00174
Abstract: Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP) data analysis, such as genome-wide association study data, because… read more here.
Keywords: analysis tools; pathway based; analysis; pathway analysis ... See more keywords
Identification of Pathway-Based Biomarkers with Crosstalk Analysis for Overall Survival Risk Prediction in Breast Cancer
Sign Up to like & getrecommendations! Published in 2021 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2021.689715
Abstract: Recently, many studies have investigated the role of gene-signature on the prognostic assessment of breast cancer (BC), however, the tumor heterogeneity and sequencing noise have limited the clinical usage of these models. Pathway-based approaches are… read more here.
Keywords: crosstalk analysis; pathway based; analysis; breast cancer ... See more keywords