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Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells
Epigenetic features such as DNA accessibility dictate transcriptional regulation in a cell type- and cell state- specific manner, and map** this in...
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Construction of ceRNA regulatory networks for active pulmonary tuberculosis
Delayed diagnosis in patients with pulmonary tuberculosis (PTB) often leads to serious public health problems. High throughput sequencing was used to...
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Weighted gene co-expression network analysis reveals genes related to growth performance in Hu sheep
Hu sheep are a unique breed in our country with great reproductive potential, the extent of whose breeding has been steadily rising in recent years....
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Genome-wide epistasis analysis reveals gene–gene interaction network on an intermediate endophenotype P-tau/Aβ42 ratio in ADNI cohort
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia in the elderly worldwide. The exact...
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Identification of Hedyotis diffusa Willd-specific mRNA–miRNA–lncRNA network in rheumatoid arthritis based on network pharmacology, bioinformatics analysis, and experimental verification
Hedyotis diffusa Willd (HDW) possesses heat-clearing, detoxification, anti-cancer, and anti-inflammatory properties. However, its effects on...
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Dynamic changes in gene-to-gene regulatory networks in response to SARS-CoV-2 infection
The current pandemic of SARS-CoV-2 has caused extensive damage to society. The characterization of SARS-CoV-2 profiles has been addressed by...
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Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo
Linkage logic theory provides a mathematical criterion to control network dynamics by manipulating activities of a subset of network nodes, which are...
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Integrated transcriptomic and regulatory network analyses uncovers the role of let-7b-5p, SPIB, and HLA-DPB1 in sepsis
Sepsis has affected millions of populations of all age groups, locations, and sexes worldwide. Immune systems, either innate or adaptive are...
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Connectome and regulatory hubs of CAGE highly active enhancers
Evidence indicates that enhancers are transcriptionally active. Herein, we investigated transcriptionally active enhancers by using cap analysis of...
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An order independent algorithm for inferring gene regulatory network using quantile value for conditional independence tests
In recent years, due to the difficulty and inefficiency of experimental methods, numerous computational methods have been introduced for inferring...
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Gene regulatory network inference from sparsely sampled noisy data
The complexity of biological systems is encoded in gene regulatory networks. Unravelling this intricate web is a fundamental step in understanding...
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Integrated gene expression profiles reveal a transcriptomic network underlying the thermogenic response in adipose tissue
Obesity and type 2 diabetes are two closely related diseases representing a serious threat worldwide. An increase in metabolic rate through...
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Exploring shared molecular signatures and regulatory mechanisms in nonalcoholic steatohepatitis and inflammatory bowel disease using integrative bioinformatics analysis
The co-existence of inflammatory bowel disease (IBD) and non-alcoholic steatohepatitis (NASH) has raised interest in identifying shared molecular...
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Modeling regulatory network topology improves genome-wide analyses of complex human traits
Genome-wide association studies (GWAS) have cataloged many significant associations between genetic variants and complex traits. However, most of...
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Epigenetic profiling reveals key genes and cis-regulatory networks specific to human parathyroids
In all terrestrial vertebrates, the parathyroid glands are critical regulators of calcium homeostasis and the sole source of parathyroid hormone...
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Reprogramming of cis-regulatory networks during skeletal muscle atrophy in male mice
A comprehensive atlas of cis-regulatory elements and their dynamic activity is necessary to understand the transcriptional basis of cellular...
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Gene regulation of adult skeletogenesis in starfish and modifications during gene network co-option
The larval skeleton of the echinoderm is believed to have been acquired through co-option of a pre-existing gene regulatory network (GRN); that is,...
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An atlas of gene regulatory elements in adult mouse cerebrum
The mammalian cerebrum performs high-level sensory perception, motor control and cognitive functions through highly specialized cortical and...
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Plasma metabolomics and gene regulatory networks analysis reveal the role of nonstructural SARS-CoV-2 viral proteins in metabolic dysregulation in COVID-19 patients
Metabolomic analysis of blood plasma samples from COVID-19 patients is a promising approach allowing for the evaluation of disease progression. We...
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Rapid response of fly populations to gene dosage across development and generations
Although the effects of genetic and environmental perturbations on multicellular organisms are rarely restricted to single phenotypic layers, our...
