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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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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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Inferring Gene Regulatory Networks and Predicting the Effect of Gene Perturbations via IQCELL
IQCELL is a platform that infers Boolean gene regulatory networks from single-cell RNA sequencing data. Boolean networks can be simulated under...
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Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks
BackgroundResearch on gene duplication is abundant and comes from a wide range of approaches, from high-throughput analyses and experimental...
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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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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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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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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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AGENT for Exploring and Analyzing Gene Regulatory Networks from Arabidopsis
Gene regulatory networks (GRNs) are important for determining how an organism develops and how it responds to external stimuli. In the case of...
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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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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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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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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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NetREX-CF integrates incomplete transcription factor data with gene expression to reconstruct gene regulatory networks
The inference of Gene Regulatory Networks (GRNs) is one of the key challenges in systems biology. Leading algorithms utilize, in addition to gene...
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Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data
Existing methods for gene regulatory network (GRN) inference rely on gene expression data alone or on lower resolution bulk data. Despite the recent...
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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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Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types
A major question in plant biology is to understand how plant growth, development, and environmental responses are controlled and coordinated by the...
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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...
