The PTEN onco-suppressor gene is likely to play an important role in the onset of brain cancer, namely glioblastoma multiforme. Consequently, the PTEN regulatory network, involving microRNAs and competitive endogenous RNAs, becomes a crucial tool for...
Gene regulatory networks (GRN) govern cellular identity and function through precise control of gene transcription. Single-cell technologies have provided powerful means to dissect regulatory mechanisms within specific cellular states. However, exist...
A model of gene regulatory networks with generalized proportional Caputo fractional derivatives is set up, and stability properties are studied. Initially, some properties of absolute value Lyapunov functions and quadratic Lyapunov functions are disc...
Drought is one of the most serious abiotic stressors in the environment, restricting agricultural production by reducing plant growth, development, and productivity. To investigate such a complex and multifaceted stressor and its effects on plants, a...
Genomic instability has been increasingly recognized over the past decade as a fundamental driver of cancer initiation and progression, largely owing to its association with specific genes and cellular mechanisms that offer therapeutic potential. How...
The debate about what causes the generation of form and structure in embryological development goes back to antiquity. Most recently, it has focused on the divergent views as to whether the generation of patterns and form in development is a largely...
This study explores the genetic regulators of microRNAs (miRNAs) using a set of machine learning models to predict miRNA expression levels from gene expression data. Employing machine learning, we accurately predicted the expression of 353 human miRN...
Gene regulatory networks (GRNs) exhibit the complex regulatory relationships among genes, which are essential for understanding developmental biology and uncovering the fundamental aspects of various biological phenomena. It is an effective and econo...
Selection and adaptation of individuals to their underlying environments are highly dynamical processes, encompassing interactions between the individual and its seasonally changing environment, synergistic or antagonistic interactions between indivi...
The fate of fetal germ cells (FGCs) in primordial follicles is largely determined by how they interact with the surrounding granulosa cells. However, the molecular mechanisms underlying this interactive process remain poorly understood. Here, we deve...
Graph analysis allows exploring transcriptome compartments such as communities and modules for brain mesostructures. In this work, we proposed a bottom-up model of a gene regulatory network to brain-wise connectome workflow. We estimated the gene com...
Gene regulatory networks represent an abstract mapping of gene regulations in living cells. They aim to capture dependencies among molecular entities such as transcription factors, proteins and metabolites. In most applications, the regulatory networ...
Microbial fuel cells (MFC) are an emerging technology for waste, wastewater and polluted soil treatment. In this manuscript, pollutants that can be treated using MFC systems producing energy are presented. Furthermore, the applicability of MFC in env...
Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outco...
Fitness landscapes are a powerful metaphor for understanding the evolution of biological systems. These landscapes describe how genotypes are connected to each other through mutation and related through fitness. Empirical studies of fitness landscape...
Gene regulatory network (GRN) inference can understand the growth and development of animals and plants, and reveal the mystery of biology. Many computational approaches have been proposed to infer GRN. However, these inference approaches have hardly...
A model of gene regulatory networks with generalized Caputo fractional derivatives with respect to another function is set up in this paper. The main characteristic of the model is the presence of a switching rule, which changes at certain times at b...
Different convergent evolutionary strategies adopted by angiosperm fruits lead to diverse functional seed dispersal units. Dry dehiscent fruits are a common type of fruit, characterized by their lack of fleshy pericarp and the release of seeds at mat...
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Epidemiological and experimental studies emphasize the link between environmental chemicals exposure and thyroid cancer. However, this association is strongly debated and the mechanisms of action of environmental thyroid carcinogens still need to be...
Gene regulatory networks (GRN) are one of the etiologies associated with cancer. Their dysregulation can be associated with cancer formation and asymmetric cellular functions in cancer stem cells, leading to disease persistence and resistance to trea...
The reasons for selecting a gene for further study might vary from historical momentum to funding availability, thus leading to unequal attention distribution among all genes. However, certain biological features tend to be overlooked in evaluating a...
The nonparanormal graphical model has emerged as an important tool for modeling dependency structure between variables because it is flexible to non-Gaussian data while maintaining the good interpretability and computational convenience of Gaussian g...
Living beings share several common features at the molecular level, but there are very few large-scale “operating principles” which hold for all (or almost all) organisms. However, biology is subject to a deluge of data, and as such, gene...
The exponential increase in the number of conducted studies combined with the development of sequencing methods have led to an enormous accumulation of partially processed experimental data in the past two decades. Here, we present an approach using...
Inferring the topology of a gene regulatory network (GRN) from gene expression data is a challenging but important undertaking for gaining a better understanding of gene regulation. Key challenges include working with noisy data and dealing with a hi...
Biological clocks are cell-autonomous oscillators that can be entrained by periodic environmental cues. This allows organisms to anticipate predictable daily environmental changes and, thereby, to partition physiological processes into appropriate ph...
Maize is one of the most widely grown cereals in the world. However, to address the challenges in maize breeding arising from climatic anomalies, there is a need for developing novel strategies to harness the power of multi-omics technologies. In thi...
Self-expressiveness is a mathematical property that aims at characterizing the relationship between instances in a dataset. This property has been applied widely and successfully in computer-vision tasks, time-series analysis, and to infer underlying...
Improving the bioproduction ability of efficient host microorganisms is a central aim in bioengineering. To control biosynthesis in living cells, the regulatory system of the whole biosynthetic pathway should be clearly understood. In this study, we...
Gene expression profiling is one of the most recognized techniques for inferring gene regulators and their potential targets in gene regulatory networks (GRN). The purpose of this study is to build a regulatory network for the budding yeast Saccharom...
This paper presents the results of research concerning the evaluation of stability of information technology of gene expression profiles processing with the use of gene expression profiles, which contain different levels of noise components. The info...
Gene regulation is crucial for cellular function and homeostasis. It involves diverse mechanisms controlling the production of specific gene products and contributing to tissue-specific variations in gene expression. The dysregulation of genes leads...
Inferring time-varying gene regulatory networks from time-series single-cell RNA sequencing (scRNA-seq) data remains a challenging task. The existing methods have notable limitations as most are either designed for reconstructing time-varying network...
A mathematical justification of some basic structural properties of stochastically perturbed gene regulatory networks, including those with autoregulation and delay, is offered in this paper. By using the theory of stochastic differential equations,...
Whole exome analyses have identified a number of genes associated with autism spectrum disorder (ASD) and ASD-related syndromes. These genes encode key regulators of synaptogenesis, synaptic plasticity, cytoskeleton dynamics, protein synthesis and de...
Gene regulation is orchestrated by a vast number of molecules, including transcription factors and co-factors, chromatin regulators, as well as epigenetic mechanisms, and it has been shown that transcriptional misregulation, e.g., caused by mutations...
In Systems Biology, the complex relationships between different entities in the cells are modeled and analyzed using networks. Towards this aim, a rich variety of gene regulatory network (GRN) inference algorithms has been developed in recent years....
Euphrates poplar (Populus euphratica) is known as a system model to study the genomic mechanisms underlying the salt resistance of woody species. To characterize how dynamic gene regulatory networks (GRNs) drive the defense response of this species t...
In this work, we begin by considering the qualitative modeling of biological regulatory systems using process hitting, from which we define its probabilistic counterpart by considering the chemical master equation within a kinetic theory framework. T...
Control of gene regulatory networks is one of the fundamental topics in systems biology. In the last decade, control theory of Boolean networks (BNs), which is well known as a model of gene regulatory networks, has been widely studied. In this review...
Gene regulatory networks (GRNs) control biological processes like pluripotency, differentiation, and apoptosis. Omics methods can identify a large number of putative network components (on the order of hundreds or thousands) but it is possible that i...
The 3D chromatin architecture establishes a complex network of genes and regulatory elements necessary for transcriptomic regulation in development and disease. This network can be modeled by cis-regulatory hubs (CRH), which underscore the local func...
Time-series experiments are crucial for understanding the transient and dynamic nature of biological phenomena. These experiments, leveraging advanced classification and clustering algorithms, allow for a deep dive into the cellular processes. Howeve...
The “competing endogenous RNA (ceRNA) hypothesis” has recently been proposed for a new type of gene regulatory model in many organisms. Anther development is a crucial biological process in plant reproduction, and its gene regulatory netw...
Bacteria employ regulatory networks to detect environmental signals and respond appropriately, often by adjusting gene expression. Some regulatory networks influence many genes, and many genes are affected by multiple regulatory networks. Here, we in...
Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory machinery. The study of such machinery at the global scale has been challenged by the lack of data integration. Here...
Network medicine relies on different types of networks: from the molecular level of protein–protein interactions to gene regulatory network and correlation studies of gene expression. Among network approaches based on the analysis of the topolo...
This manuscript summarizes information on the diverse range of RNA molecules and their role as competing endogenous RNAs (ceRNAs). Moreover, it provides an overview of ceRNA regulatory networks and their applications in ruminant biology. Knowledge of...
Background: Reconstructing gene regulatory networks (GRNs) from gene expression data remains a major challenge in systems biology due to the inherent complexity of biological systems and the limitations of existing reconstruction methods, which often...
The transcriptomic datasets of the plant model organism Arabidopsis thaliana grown in the International Space Station provided by GeneLab have been mined to isolate the impact of spaceflight microgravity on gene expressions related to root growth. A...
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