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Gene networks
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Ebook "Modeling in systems biology: The petri net approach" aims to meet a challenge that previously has been largely avoided by the Petri net community. The community used to be content with the demonstration that Petri nets were able to simulate quite a large number of partial systems when their homogeneity permitted a rather restricted application of the Petri net methodology. The proof of principle used to say that Petri net models can simulate otherwise established theoretical descriptions.
378p
ladongphongthanh1008
22-04-2024
4
2
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Ebook "Frontiers in computational and systems biology" consists of 19 chapters and covers a wide spectrum of topics. Described applications of an RNA structure sampling algorithm to the rational design of short interfering RNAs for gene silencing by RNA interference and to target identification for microRNAs that play important roles in posttranscriptional gene regulation.
411p
ladongphongthanh1008
22-04-2024
4
2
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Ebook "Epigenetics in cardiac disease" describes important advances in our understanding of how environmental conditions affect cardiac gene expression through epigenetic mechanisms. Further, it discusses the roles of chromatin modifications (in particular DNA methylation and histone modifications) and of chromatin regulators in the context of cardiac diseases. The book provides readers with an overview of our current understanding of epigenetic regulation in the heart, and will stimulate further research in this exciting field.
321p
ladongphongthanh1008
22-04-2024
7
2
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Genome–phenome studies have identified thousands of variants that are statistically associated with disease or traits; however, their functional roles are largely unclear. A comprehensive investigation of regulatory mechanisms and the gene regulatory networks between phenome-wide association study (PheWAS) and genomewide association study (GWAS) is needed to identify novel regulatory variants contributing to risk for human diseases.
15p
vibransone
28-03-2024
3
2
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Cerebral amyloidosis, neuroinflammation, and tauopathy are key features of Alzheimer’s disease (AD), but interactions among these features remain poorly understood. Our previous multiscale molecular network models of AD revealed TYROBP as a key driver of an immune- and microglia-specific network that was robustly associated with AD pathophysiology.
20p
vibransone
28-03-2024
3
2
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Only a small fraction of patients respond to the drug prescribed to treat their disease, which means that most are at risk of unnecessary exposure to side effects through ineffective drugs. This inter-individual variation in drug response is driven by differences in gene interactions caused by each patient’s genetic background, environmental exposures, and the proportions of specific cell types involved in disease.
15p
vibransone
28-03-2024
4
2
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Identification of actionable genomic vulnerabilities is key to precision oncology. Utilizing a large-scale drug screening in patient-derived xenografts, we uncover driver gene alteration connections, derive driver co-occurrence (DCO) networks, and relate these to drug sensitivity.
23p
vibransone
28-03-2024
3
2
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Tight regulatory loops orchestrate commitment to B cell fate within bone marrow. Genetic lesions in this gene regulatory network underlie the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). The initial genetic hits, including the common translocation that fuses ETV6 and RUNX1 genes, lead to arrested cell differentiation.
25p
vibransone
28-03-2024
6
1
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The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative effect on the underlying “personal” gene regulatory network.
13p
vioraclene
31-03-2024
3
2
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The growth factor receptor network (GFRN) plays a significant role in driving key oncogenic processes. However, assessment of global GFRN activity is challenging due to complex crosstalk among GFRN components, or pathways, and the inability to study complex signaling networks in patient tumors.
19p
vioraclene
31-03-2024
3
2
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Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to the disease alone. Therefore, here we set out to identify and characterize intrinsic properties of myocytes, associated independently with T2D or obesity.
12p
vioraclene
31-03-2024
2
1
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Alterations in genetic and epigenetic landscapes are known to contribute to the development of different types of cancer. However, the mechanistic links between transcription factors and the epigenome which coordinate the deregulation of gene networks during cell transformation are largely unknown.
16p
vioraclene
31-03-2024
2
2
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Tumour necrosis factor (TNF) superfamily cytokines and their receptors regulate diverse immune system functions through a common set of signalling pathways. Genetic variants in and expression of individual TNF superfamily cytokines, receptors and signalling proteins have been associated with autoimmune and inflammatory diseases, but their interconnected biology has been largely unexplored.
15p
vioraclene
31-03-2024
2
2
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The bromodomain containing 1 (BRD1) gene has been implicated with transcriptional regulation, brain development, and susceptibility to schizophrenia and bipolar disorder. To advance the understanding of BRD1 and its role in mental disorders, we characterized the protein and chromatin interactions of the BRD1 isoforms, BRD1-S and BRD1-L.
20p
vioraclene
31-03-2024
3
1
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The genetic regulation of metabolic phenotypes (i.e., metabotypes) in type 2 diabetes mellitus occurs through complex organ-specific cellular mechanisms and networks contributing to impaired insulin secretion and insulin resistance. Genome-wide gene expression profiling systems can dissect the genetic contributions to metabolome and transcriptome regulations.
15p
vioraclene
31-03-2024
3
2
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Alzheimer’s disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. However, despite extensive clinical and genomic studies, the molecular basis of AD development and progression remains elusive.
21p
vioraclene
31-03-2024
2
2
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Inter-tissue molecular interactions are critical to the function and behavior of biological systems in multicellular organisms, but systematic studies of interactions between tissues are lacking. Also, existing studies of inter-tissue interactions are based on direct gene expression correlations, which can’t distinguish correlations due to common genetic architectures versus biochemical or molecular signal exchange between tissues.
15p
vioraclene
31-03-2024
7
2
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Basal cell carcinoma (BCC) of the skin is the most common form of human cancer, with more than 90% of tumours presenting with clear genetic activation of the Hedgehog pathway. However, polygenic risk factors affecting mechanisms such as DNA repair and cell cycle checkpoints or which modulate the tumour microenvironment or host immune system play significant roles in determining whether genetic mutations culminate in BCC development.
12p
vibransone
28-03-2024
3
2
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Contemporary deep learning approaches show cutting-edge performance in a variety of complex prediction tasks. Nonetheless, the application of deep learning in healthcare remains limited since deep learning methods are often considered as non-interpretable black-box models.
16p
vibransone
28-03-2024
3
2
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A dynamic single cell-based framework for digital twins to prioritize disease genes and drug targets
Medical digital twins are computational disease models for drug discovery and treatment. Unresolved problems include how to organize and prioritize between disease-associated changes in digital twins, on cellulomeand genome-wide scales. We present a dynamic framework that can be used to model such changes and thereby prioritize upstream regulators (URs) for biomarker- and drug discovery.
21p
viellison
28-03-2024
4
2
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