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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...
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Building High-Confidence Gene Regulatory Networks by Integrating Validated TF–Target Gene Interactions Using ConnecTF
Many methods are now available to identify or predict the target genes of transcription factors (TFs) in plants. These include experimental...
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Constructing gene regulatory networks using epigenetic data
The biological processes that drive cellular function can be represented by a complex network of interactions between regulators (transcription...
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Analysis of co-expression and gene regulatory networks associated with sterile lemma development in rice
BackgroundThe sterile lemma is a unique organ of the rice ( Oryza sativa L.) spikelet. However, the characteristics and origin of the rice sterile...
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Characterization of gene regulatory networks underlying key properties in human hematopoietic stem cell ontogeny
Human hematopoiesis starts at early yolk sac and undergoes site- and stage-specific changes over development. The intrinsic mechanism underlying...
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Transcriptome profiling and network enrichment analyses identify subtype-specific therapeutic gene targets for breast cancer and their microRNA regulatory networks
Previous studies have suggested that breast cancer (BC) from the Middle East and North Africa (MENA) is presented at younger age with advanced tumor...
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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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Predicting Gene Regulatory Interactions Using Natural Genetic Variation
Genome-wide association studies (GWAS) are a powerful tool to elucidate the genotype–phenotype map. Although GWAS are usually used to assess simple...
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Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data
Inferring gene regulatory networks (GRNs) is a fundamental challenge in biology that aims to unravel the complex relationships between genes and...
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Probabilistic Graphical Models for Gene Regulatory Networks
The advancement of technologies has generated high-throughput data of diverse biological entities, such as messenger RNAs (mRNAs), proteins, and...
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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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The art of modeling gene regulatory circuits
The amazing complexity of gene regulatory circuits, and biological systems in general, makes mathematical modeling an essential tool to frame and...
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Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress
BackgroundThe cis-regulatory element became increasingly important for resistance breeding. There were many DNA variations identified by...
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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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Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis
BackgroundHomoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum , is an allohexaploid species with...
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RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique
BackgroundCurrent gene regulatory network (GRN) inference methods are notorious for a great number of indirect interactions hidden in the...
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Gene Networks Inference by Reinforcement Learning
Gene Regulatory Networks inference from gene expression data is an important problem in systems biology field, involving the estimation of gene-gene...
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Inferring circadian gene regulatory relationships from gene expression data with a hybrid framework
BackgroundThe central biological clock governs numerous facets of mammalian physiology, including sleep, metabolism, and immune system regulation....
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Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML
Acute myeloid leukemia (AML) is characterized by uncontrolled proliferation of poorly differentiated myeloid cells, with a heterogenous mutational...
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CVGAE: A Self-Supervised Generative Method for Gene Regulatory Network Inference Using Single-Cell RNA Sequencing Data
Gene regulatory network (GRN) inference based on single-cell RNA sequencing data (scRNAseq) plays a crucial role in understanding the regulatory...
