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Decoding the gene regulatory network of endosperm differentiation in maize
The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm...
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Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona
Tissue-specific gene expression is fundamental in development and evolution, and is mediated by transcription factors and by the cis -regulatory...
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Differential gene expression and miRNA regulatory network in coronary slow flow
Coronary slow flow (CSF) is characterized by slow progression of coronary angiography without epicardial stenosis. The aim of this study was to...
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A novel necroptosis related gene signature and regulatory network for overall survival prediction in lung adenocarcinoma
We downloaded the mRNA expression profiles of patients with LUAD and corresponding clinical data from The Cancer Genome Atlas (TCGA) database and...
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Knowledge of the perturbation design is essential for accurate gene regulatory network inference
The gene regulatory network (GRN) of a cell executes genetic programs in response to environmental and internal cues. Two distinct classes of methods...
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SIGNET: transcriptome-wide causal inference for gene regulatory networks
Gene regulation plays an important role in understanding the mechanisms of human biology and diseases. However, inferring causal relationships...
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Diet-induced rewiring of the Wnt gene regulatory network connects aberrant splicing to fatty liver and liver cancer in DIAMOND mice
Several preclinical models have been recently developed for metabolic associated fatty liver disease (MAFLD) and associated hepatocellular carcinoma...
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Regulatory network analysis based on integrated miRNA-TF reveals key genes in heart failure
The etiology and pathophysiology of heart failure are still unknown. Increasing evidence suggests that abnormal microRNAs (miRNAs) and transcription...
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A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2
A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can...
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Competition and evolutionary selection among core regulatory motifs in gene expression control
Gene products that are beneficial in one environment may become burdensome in another, prompting the emergence of diverse regulatory schemes that...
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Conserved and divergent gene regulatory programs of the mammalian neocortex
Divergence of cis- regulatory elements drives species-specific traits
1 , but how this manifests in the evolution of the neocortex at the molecular and...
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Mechanism-centric regulatory network identifies NME2 and MYC programs as markers of Enzalutamide resistance in CRPC
Heterogeneous response to Enzalutamide, a second-generation androgen receptor signaling inhibitor, is a central problem in castration-resistant...
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Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks
Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the...
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Co-regulatory network analysis of the main secondary metabolite (SM) biosynthesis in Crocus sativus L.
Saffron ( Crocus sativus L.) is being embraced as the most important medicinal plant and the commercial source of saffron spice. Despite the...
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Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor
Streptomyces coelicolor A3(2) is a model microorganism for the study of Streptomycetes, antibiotic production, and secondary metabolism in general....
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The transcription factor OCT6 promotes the dissolution of the naïve pluripotent state by repressing Nanog and activating a formative state gene regulatory network
In the mouse embryo, the transition from the preimplantation to the postimplantation epiblast is governed by changes in the gene regulatory network...
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Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory networks (GRNs) that connect transcription factors and...
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Histone lactylation couples cellular metabolism with developmental gene regulatory networks
Embryonic cells exhibit diverse metabolic states. Recent studies have demonstrated that metabolic reprogramming drives changes in cell identity by...
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A novel approach GRNTSTE to reconstruct gene regulatory interactions applied to a case study for rat pineal rhythm gene
Accurate inference and prediction of gene regulatory network are very important for understanding dynamic cellular processes. The large-scale time...
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Integrated whole transcriptome profiling revealed a convoluted circular RNA-based competing endogenous RNAs regulatory network in colorectal cancer
Recently, it has been identified that circRNAs can act as miRNA sponge to regulate gene expression in various types of cancers, associating them with...
