Microbiome multi-omics network analysis: statistical considerations, limitations, and opportunities
The advent of large-scale microbiome studies affords newfound analytical opportunities to
understand how these communities of microbes operate and relate to their environment …
understand how these communities of microbes operate and relate to their environment …
Differential network analysis: A statistical perspective
A Shojaie - Wiley Interdisciplinary Reviews: Computational …, 2021 - Wiley Online Library
Networks effectively capture interactions among components of complex systems, and have
thus become a mainstay in many scientific disciplines. Growing evidence, especially from …
thus become a mainstay in many scientific disciplines. Growing evidence, especially from …
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
Transcriptional regulatory networks (TRNs) provide insight into cellular behavior by
describing interactions between transcription factors (TFs) and their gene targets. The assay …
describing interactions between transcription factors (TFs) and their gene targets. The assay …
Integrating gene regulatory pathways into differential network analysis of gene expression data
The advent of next-generation sequencing has introduced new opportunities in analyzing
gene expression data. Research in systems biology has taken advantage of these …
gene expression data. Research in systems biology has taken advantage of these …
Network-based combinatorial CRISPR-Cas9 screens identify synergistic modules in human cells
Y Guo, C Bao, D Ma, Y Cao, Y Li, Z Xie… - ACS synthetic biology, 2019 - ACS Publications
Tumorigenesis is a complex process that is driven by a combination of networks of genes
and environmental factors; however, efficient approaches to identifying functional networks …
and environmental factors; however, efficient approaches to identifying functional networks …
Differential co-expression analyses allow the identification of critical signalling pathways altered during tumour transformation and progression
Biological systems respond to perturbations through the rewiring of molecular interactions,
organised in gene regulatory networks (GRNs). Among these, the increasingly high …
organised in gene regulatory networks (GRNs). Among these, the increasingly high …
Differential network analysis by simultaneously considering changes in gene interactions and gene expression
Motivation Differential network analysis is an important tool to investigate the rewiring of
gene interactions under different conditions. Several computational methods have been …
gene interactions under different conditions. Several computational methods have been …
Incorporating prior information into differential network analysis using non-paranormal graphical models
Motivation Understanding how gene regulatory networks change under different cellular
states is important for revealing insights into network dynamics. Gaussian graphical models …
states is important for revealing insights into network dynamics. Gaussian graphical models …
Identifying gene network rewiring by integrating gene expression and gene network data
Exploring the rewiring pattern of gene regulatory networks between different pathological
states is an important task in bioinformatics. Although a number of computational …
states is an important task in bioinformatics. Although a number of computational …
DiffGRN: differential gene regulatory network analysis
Identification of differential gene regulators with significant changes under disparate
conditions is essential to understand complex biological mechanism in a disease …
conditions is essential to understand complex biological mechanism in a disease …