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Regulatory Networks
This chapter elaborates on the overview presented in Chapter 3. Gene regulatory networks are complex systems that control the expression of genes in...
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Plant Gene Regulatory Networks Methods and Protocols
This second edition details protocols that analyze and explore gene regulatory networks (GRNs). Chapters guide readers through experimental...
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Inference of Gene Regulatory Networks Based on Multi-view Hierarchical Hypergraphs
Since gene regulation is a complex process in which multiple genes act simultaneously, accurately inferring gene regulatory networks (GRNs) is a...
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RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations
Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships....
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Transcription Factor Regulatory Networks
This book covers various state-of-the-art techniques regarding the associations between transcription factors (TFs) and genes, with a focus on...
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Flexible modeling of regulatory networks improves transcription factor activity estimation
Transcriptional regulation plays a crucial role in determining cell fate and disease, yet inferring the key regulators from gene expression data...
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Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation
BackgroundCommon diseases manifest differentially between patients, but the genetic origin of this variation remains unclear. To explore possible...
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Feedback circuits are numerous in embryonic gene regulatory networks and offer a stabilizing influence on evolution of those networks
The developmental gene regulatory networks (dGRNs) of two sea urchin species, Lytechinus variegatus (Lv) and Strongylocentrotus purpuratus (Sp), have...
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Architecture and topologies of gene regulatory networks associated with breast cancer, adjacent normal, and normal tissues
Most cancer studies employ adjacent normal tissues to tumors (ANTs) as controls, which are not completely normal and represent a pre-cancerous state....
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Reconstructing gene regulatory networks of biological function using differential equations of multilayer perceptrons
BackgroundBuilding biological networks with a certain function is a challenge in systems biology. For the functionality of small (less than ten...
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NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity
A major question in systems biology is how to identify the core gene regulatory circuit that governs the decision-making of a biological process....
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Genetic Regulatory Networks Guiding Islet Development
The pancreatic islet is a mini-organ that consists of several hormone-secreting endocrine cell types in adults. Islets execute a vital physiological...
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Exploring Plant Transcription Factor Databases and Regulatory Networks
This chapter provides an analysis of the involvement of transcription factors (TFs) in plant genomes. To enhance the knowledge of the regulatory...
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Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
BackgroundGenetic variation influences both chromatin accessibility, assessed in chromatin accessibility quantitative trait loci (caQTL) studies, and...
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Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
BackgroundEnhancer RNAs (eRNAs) play a crucial role in transcriptional regulation. While significant progress has been made in understanding...
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Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based on their location within the liver lobule. However, it is...
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Distinct regulatory networks control toxin gene expression in elapid and viperid snakes
BackgroundVenom systems are ideal models to study genetic regulatory mechanisms that underpin evolutionary novelty. Snake venom glands are thought to...
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SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene...
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Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins
BackgroundMetazoans inherited genes from unicellular ancestors that perform essential biological processes such as cell division, metabolism, and...
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The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo...
