A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data
Gene regulatory network is a complicated set of interactions between genetic materials,
which dictates how cells develop in living organisms and react to their surrounding …
which dictates how cells develop in living organisms and react to their surrounding …
A comprehensive survey of the approaches for pathway analysis using multi-omics data integration
Pathway analysis has been widely used to detect pathways and functions associated with
complex disease phenotypes. The proliferation of this approach is due to better …
complex disease phenotypes. The proliferation of this approach is due to better …
Plasma proteome of Long-COVID patients indicates HIF-mediated vasculo-proliferative disease with impact on brain and heart function
C Iosef, MJ Knauer, M Nicholson… - Journal of Translational …, 2023 - Springer
Aims Long-COVID occurs after SARS-CoV-2 infection and results in diverse, prolonged
symptoms. The present study aimed to unveil potential mechanisms, and to inform prognosis …
symptoms. The present study aimed to unveil potential mechanisms, and to inform prognosis …
RCPA: An Open‐Source R Package for Data Processing, Differential Analysis, Consensus Pathway Analysis, and Visualization
Identifying impacted pathways is important because it provides insights into the biology
underlying conditions beyond the detection of differentially expressed genes. Because of the …
underlying conditions beyond the detection of differentially expressed genes. Because of the …
Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer
Motivation To better understand the molecular features of cancers, a comprehensive
analysis using multi-omics data has been conducted. In addition, a pathway activity …
analysis using multi-omics data has been conducted. In addition, a pathway activity …
Dwen: A novel method for accurate estimation of cell type compositions from bulk data samples
Advances in single-cell RNA sequencing (scRNAseq) technologies have allowed us to
study the heterogeneity of cell populations. The cell compositions of tissues from different …
study the heterogeneity of cell populations. The cell compositions of tissues from different …
Disease subtyping using community detection from consensus networks
Cancer is a complex disease including a range of disorders that are activated
simultaneously by multiple biological processes on multiple levels. Various genome-wide …
simultaneously by multiple biological processes on multiple levels. Various genome-wide …
Single-cell RNA sequencing data imputation using deep neural network
Recent research in biology has shifted the focus toward single-cell data analysis. The new
single-cell technologies have allowed us to monitor and characterize cells in early …
single-cell technologies have allowed us to monitor and characterize cells in early …
Advances in Network-Based Drug Repositioning
M Pellegrini - From Computational Logic to Computational Biology …, 2024 - Springer
Network-based drug repositioning is a fast-growing approach to computational drug
repositioning that has had a powerful impulse at the onset of the COVID-19 pandemic. In this …
repositioning that has had a powerful impulse at the onset of the COVID-19 pandemic. In this …
[PDF][PDF] BLMA: A package for bi-level meta-analysis
T Nguyen, S Draghici - R package version, 2017 - andersvercelli.com
This package provides a bi-level meta-analysis (BLMA) framework that can be applied in a
wide range of applications: functional analysis, pathway analysis, differential expression …
wide range of applications: functional analysis, pathway analysis, differential expression …