Boolean network gene regulatory networks. Medical search. Frequent questions

He proposed the Probabilistic Boolean Network (PBN) model for gene regulatory networks. (wikipedia.org)
Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory Networks. (wikipedia.org)
In another paper, Peng Li et al compare probabilistic Boolean Network (PBNs) and Dynamic Bayesian Network (DBNs) approaches to correctly inferring regulatory networks [ 24 ]. (biomedcentral.com)
Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. (auth.gr)
Mappings between probabilistic Boolean networks. (auth.gr)
Steady-state probabilities for attractors in probabilistic Boolean networks. (auth.gr)
Optimal stochastic control based on the transition probability matrix of the underlying Markov chain has been studied extensively for probabilistic Boolean networks. (tamu.edu)
We compare the performance of these three greedy control policies and the MFPT policy using randomly generated probabilistic Boolean networks and give a preliminary example for intervening in a mammalian cell cycle network. (tamu.edu)

We apply the approach to random Boolean networks, and further show that the method can in some cases successfully repair synchronous limit cycles. (biomedcentral.com)
All the nodes of an intercellular network have identical random Boolean networks (RBNs) as intracellular GRNs. (elsevierpure.com)

The number of nodes in the network. (readthedocs.io)
A network , in its most basic form, consists of nodes (denoting system components) and edges between nodes (representing interactions and relationships among components). (biomedcentral.com)
Different visualization features (e.g. pie-nodes, edge-pie matrix, etc.) aid in easy identification of the key nodes/interactions and their significance across the compared networks. (biomedcentral.com)
The tool also allows one to perform network comparisons on the basis of neighbourhood architecture of constituent nodes and community compositions, a feature particularly useful while analyzing biological networks. (biomedcentral.com)
In this paper we study BTNs from the perspective of genotype-phenotype maps, by treating the network{\textquoteright}s set of nodes and connections as its genotype, and dynamic behaviour of the model as its phenotype. (ewha.ac.kr)
Specifically, we will prove that state transition pairs are sufficient and necessary to reconstruct the time delay Boolean network of nodes with high accuracy if the number of input genes to each gene is bounded. (tsinghua.edu.cn)
contains all possible combinations of claims for which nodes of the network can reside, and an is definitely a stable set of claims that other claims evolve towards, manifesting as cellular phenotypes and fates [41,42]. (bioinbrief.com)
The unperturbed network (correct) is normally representative of a trajectory towards a wholesome regular attractor (blue), whereas a network which has obtained mutations in particular nodes (remaining) is definitely representative of a trajectory towards a neoplastic attractor (reddish). (bioinbrief.com)
Building and Analyzing an Connection Network Network building begins with compiling a list of nodes relevant to the biological outcome of interest. (bioinbrief.com)
The type of network is determined relating to how vertices (nodes) and edges are defined. (bioinbrief.com)

The most basic motif, autoregulation, has been associated with bistability (when positive) and with homeostasis and robustness to noise (when negative), but its general importance in network behavior is poorly understood. (ethz.ch)
Here, we used a class of GRN models, Boolean networks, to investigate the relationship between autoregulation and network stability and robustness under various conditions. (ethz.ch)
Kim, H & Sayama, H 2020, ' Robustness and evolvability of multilayer gene regulatory networks ', Paper presented at 2018 Conference on Artificial Life: Beyond AI, ALIFE 2018, Tokyo, Japan, 18/7/23 - 18/7/27 pp. 546-547. (elsevierpure.com)
Elementary Flux Modes (EFMs) provide a rigorous basis to systematically characterize the steady state, cellular phenotypes, as well as metabolic network robustness and fragility. (mdpi.com)

We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions. (hindawi.com)
ayesian automatic relevance determination algorithms for classifying gene expression data. (auth.gr)
These tools employ different algorithms to compute pair wise similarity between selected networks/paths. (biomedcentral.com)
Broadly speaking, my research has been a mixture of coarse-grained and detailed modeling, often involving gene regulatory networks, and development of algorithms and open source software. (lu.se)
Since the beginning of my research career, I have worked with Boolean gene regulatory network models, the HP model of protein folding, stem cell regulation, circadian clocks in plants, plant-pathogen interactions, evolutionary algorithms, degradation of soil organic matter by fungi and methods for processing spectroscopic imaging data. (lu.se)
Anna Gambin , Piotr Krzyżanowski i Piotr Pokarowski , Aggregation Algorithms for Perturbed Markov Chains with Applications to Networks Modeling , Siam Journal On Scientific Computing 31 (1) 2008, s. 45-73. (edu.pl)

a map is constructed that shows interactions among molecular entities (such as genes, proteins and RNAs), using information from literature and databases. (hindawi.com)
The network combining putative targets of TF and miRNA regulation with experimentally proven molecular interactions was constructed and visualized. (hindawi.com)
We describe a computational methodology allowing to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. (researchgate.net)
In addition, it can be used to predict genetic interactions [3] by comparing the sensitivity value of a double gene mutation from the value predicted from single mutations, and reveal the network intervention [4] by applying the state-flip mutation subject to a single gene. (researchgate.net)
They find that PBNs can reduce the computational complexity, false positive and false negative errors significantly, while DBNs can more accurately derive genetic network interactions, but are more time-consuming. (biomedcentral.com)
Here, we propose a complementary approach wherein interactions are instead modified to alter key regulatory functions and prevent the network damage from triggering a deregulatory cascade. (biomedcentral.com)
A network in an intercellular layer represents interactions between cells, and a network in an intracellular layer indicates interactions between genes. (elsevierpure.com)
Interactions between these genes and with other non-ABC genes are necessary to establish the final pattern of concentric circles of ABC gene expression. (ens-lyon.fr)
To understand this process, the expression and the interactions between these genes in the early stages of development are investigated experimentally. (ens-lyon.fr)
The development of high-throughput technologies provides numerous experimental data such as DNA sequences, protein sequence, and RNA expression profiles makes it possible to study interactions and regulations among genes or other substance in an organism. (tsinghua.edu.cn)
The construction of Boolean regulatory models requires a substantial amount of experimental data on the interactions between the underlying network components. (u-psud.fr)

The typical approach to mitigating network perturbations is to consider the compensatory activation or deactivation of system components. (biomedcentral.com)

For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments. (hindawi.com)
The systems biology approach, combining data-driven modeling and model-driven experiments, provides a systematic and comprehensive perspective on the regulatory roles of miRNAs in gene regulatory networks [ 3 - 5 ]. (hindawi.com)
The application of the systems biology approach to the analysis of a gene regulatory network is demonstrated with a case study of the regulation of p21 by multiple miRNAs [ 4 ]. (hindawi.com)
This novel systems-biology approach to biological network reconstruction investigated urothelial cell response to infection with Enterococcus bacteria. (biomedcentral.com)
Recent emergence of systems biology has brought biological networks into focus. (biomedcentral.com)
With increasing interests in systems biology, tools specialized for analysis of complex metabolic networks (represented in information rich graph formats like SBML) has also been developed [ 15 ]. (biomedcentral.com)
Taking into account the two main systems involved in the regulation of blood pressure, that is, the Renin-Angiotensin system and the Kallikrein-Kinin system, we follow a Bottom-Up systems biology modeling approach in order to built the discrete Boolean model of the gene regulatory network that underlies both the typical hypertensive phenotype and the hypotensive/normotensive phenotype. (easychair.org)
However, it is crucial to make inference of genetic regulatory networks from gene expression profiles and protein interaction data for systems biology. (tsinghua.edu.cn)

Using a binary-coding system to identify unique concordant expression patterns among genes, the model resulted in a digital rendering of single-cell gene expression which enables non-invasive prognosis of prostate cancer patients. (biomedcentral.com)

We show that the method can stabilize any single state (e.g., fixed point attractors or time-averaged representations of multi-state attractors) to be an attractor of the repaired network. (biomedcentral.com)
These phenotypes correspond to the dynamic attractors of the regulatory network modeled on the basis of publicly available experimental information. (easychair.org)
Considering network state space, the ball would correspond to a preliminary set of claims, and valleys would correspond to basins of appeal that result in attractors. (bioinbrief.com)

Because Banjo implements both Bayesian and dynamic Bayesian networks, it can infer gene networks from steady-state gene expression data or from time-series gene expression data. (biomedcentral.com)
In this paper, we present a new dynamic Bayesian network (DBN) framework embedded with structural expectation maximization (SEM) to model gene relationship. (sciweavers.org)
It is well-suited for analyzing the time-series data and can deal with cyclical structures that can not be tackled by static Bayesian network. (sciweavers.org)

We use the proposed method to gain insight into the nature of asynchronous vs. synchronous updating in Boolean models and successfully simulate a 41 species apoptosis model on a standard desktop workstation. (biorxiv.org)
Mechanistic models are commonly used to acquire insights about the biochemical reaction networks that govern cellular processes inside a cell. (biorxiv.org)
However, especially for Boolean models (for details see below) this essentially assumes that a large number of species is either on or off with probability 1, a very unrealistic assumption. (biorxiv.org)
We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. (researchgate.net)
Boolean threshold networks (BTNs) are a class of mathematical models used to describe complex dynamics on networks. (ewha.ac.kr)
This talk will focus on discrete models of gene regulatory networks and the challenges they present, in particular data selection and model stability. (gatech.edu)
Integrating Metabolic, Transcriptional Regulatory, and Signal Transduction Models in Escherichia Coli. (simtk.org)
In general, the existing models for network inference can be grouped into three categories: logical models, continuous models and single-molecule level models [ 1 ]. (biomedcentral.com)
Logical models such as Boolean networks and Petri nets could represent the network structure but are unable to describe dynamic processes. (biomedcentral.com)
Single-molecule level models are not suitable for large scale regulatory network reconstruction. (biomedcentral.com)
There may be other models which could integrate prior knowledge to improve the performance, but we only considered the ab initio network inference approaches here as prior knowledge is able to be integrated into most de novo network reconstruction methods easily. (biomedcentral.com)
One of these probes unifies aspects of two well studied dynamic models -- cellular automata and Boolean networks -- for arbitrary architectures. (tu-darmstadt.de)
Furthermore to providing a starting point prior to quantitative modeling, Boolean network models can also be utilized to discover novel therapeutic focuses on and combinatorial treatment strategies. (bioinbrief.com)
With this review, we discuss the process of developing Boolean network models and the various analyses that can be performed to identify novel drug focuses on and combinatorial methods. (bioinbrief.com)
Determined SCA12 examples of Boolean Phloridzin ic50 network models of human being (patho-)physiological systems will also be reviewed in brief. (bioinbrief.com)
Network Development With this section, methods involved in the development of Boolean network models are covered, which consists of constructing an connection network, adding Boolean logic, determining initial conditions, and network validation. (bioinbrief.com)
In a study published in PNAS Nexus , an IPS2 researcher ( Team REGARN ) and a team at IMSc, Chennai (India), compile 2687 logic rules from 88 reconstructed discrete models reported in the Boolean modeling literature. (u-psud.fr)

An example for each of these analyses is definitely provided using a previously developed Boolean network of signaling pathways in multiple myeloma. (bioinbrief.com)
Quantifying the regularity at which preliminary state governments reach an attractor recognizes the relative need for each attractor and its own associated natural phenotype, underscoring the tool of executing Phloridzin ic50 attractor analyses on Boolean systems. (bioinbrief.com)
With this review, we spotlight the applications of Boolean network modeling in systems pharmacology as well as provide examples of numerous analyses using a previously published Boolean network of signaling pathways in multiple myeloma [23]. (bioinbrief.com)
Types of Boolean network analyses useful in drug finding and development are covered, such as dynamic simulations, attractor analysis, and minimal treatment analysis. (bioinbrief.com)

In addition to comparison of graph properties/metrics in form of tables or charts, identifying and comprehending the patterns of variations across different networks becomes several folds easier if provisions exist for visual comparisons, such as creation of graph layouts, overlaying of multiple networks, and interactive analysis of graph components. (biomedcentral.com)
We explore here the systems-based regulatory mechanisms that determine human blood pressure patterns. (easychair.org)
Gene regulatory networks capture interaction patterns and mechanics of how gene expression is regulated based on signals and components that are internal or external to the organism. (sdsu.edu)
Salazar-Ciudad, I., Newman, S. A. and Sole, R. V. Phenotypic and dynamical transitions in model genetic networks I. Emergence of patterns and genotype-phenotype relationships . (panmental.de)
states'' or gene expression patterns. (lu.se)

The result of this investigation is the distributed control of transcriptional gene regulation: depending on the genotypic conditions, regulation is mediated either by dedicated transcription factors (digital) of by the change of DNA conformation (analog), that is, DNA supercoiling. (tu-darmstadt.de)
In terminally differentiated cell fate is coupled to appropriate regulation of the alternative cells, transcriptional networks must be stable and irreversible, pathways. (lu.se)

For example, the effects of genetic mutations can cascade through within-cell signaling and regulatory networks and alter the behavior of cells, possibly leading to a wide variety of diseases. (biomedcentral.com)
We implement this approach in a Boolean dynamic framework, which has been shown to effectively model the behavior of biological regulatory and signaling networks. (biomedcentral.com)
For instance, cellular signaling networks may be damaged via mutations or changes in the activation levels of constituent components, which may lead to abnormal cell behavior [ 6 ]. (biomedcentral.com)
Signaling networks are one class of complex systems: i.e., collections of interacting components that, on a holistic level, display behavior that cannot be predicted from analysis of the system's components in isolation. (biomedcentral.com)
Boolean network versions have already been proven to explain effectively, within a qualitative way, the complicated behavior of indication transduction Phloridzin ic50 and gene/proteins regulatory processes. (bioinbrief.com)
Intervention in gene regulatory networks via greedy control policies based on long-run behavior. (tamu.edu)
RESULTS: In this paper, we propose three new greedy stationary control policies by directly investigating the effects on the network long-run behavior. (tamu.edu)

Dougherty is a specialist in nonlinear image processing, small-sample classification problems, and modeling gene regulatory networks. (wikipedia.org)
Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. (hindawi.com)
Their modeling can be tackled via Boolean networks, a mathematical framework where directed edges represent dependences and where a logic rule specifies how a gene's state is determined by the values of its regulatory inputs. (u-psud.fr)

Restrictions in the flexibility of the digital component through adaption and, consequently, mutations can be buffered by the regulatory impact of DNA structural proteins, the analog component of regulation. (tu-darmstadt.de)

Environmental versatility promotes modularity in genome-scale metabolic networks. (uni-trier.de)
Hence, graph theoretical methods can be applied to systems of various scales: from the description of interacting gene regulatory mechanisms over the architecture of metabolic networks to the spread of contagious diseases. (tu-darmstadt.de)
For real metabolic networks it is shown that the global structure of the metabolic reactions enhances the regularization of complex dynamics, independent of the specific network representation and dynamics applied. (tu-darmstadt.de)
Together with metabolic networks and signal networks, they provide a functional description of cell processes. (sdsu.edu)

Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model. (researchgate.net)
Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. (researchgate.net)
There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. (researchgate.net)
To demonstrate the utility of CompNet, we have compared a (time-series) human gene-expression dataset, post-infection by two strains of Mycobacterium tuberculosis , overlaid on the human protein-protein interaction network. (biomedcentral.com)
Interaction networks are a convenient way of representing the complex nature of multi-component systems. (biomedcentral.com)
The process of Boolean network development is definitely described, which includes construction of an interaction network, conversion of an connection network into a Boolean platform, determination of initial conditions, network validation, and reduction. (bioinbrief.com)

Network motifs have been identified as building blocks of regulatory networks, including gene regulatory networks (GRNs). (ethz.ch)
We present multilayer gene regulatory networks (GRNs) consisting of an intercellular layer and an intracellular layer. (elsevierpure.com)

Finally, a brief overview is definitely offered of previously developed Boolean networks of human being intracellular physiology/pathophysiology and their numerous applications. (bioinbrief.com)

Estimation of genewise variance arises from two important applications in microarray data analysis: selecting significantly differentially expressed genes and validation tests for normalization of microarray data. (tsinghua.edu.cn)

Owing to computational complexity, it is difficult to apply optimal control for large networks. (tamu.edu)
and they can be used to predict the best control gene with reduced computational complexity, even when one is employing dynamic programming to derive the final control policy. (tamu.edu)

explosion further, consider that a fictitious small genome with 2002) More recently and more dramatically, the potential for 260 genes would host the same number of combinations as cell state conversions is exemplified by the reprogramming of the number of atoms in the visible universe! (lu.se)

Optimization is based on minimization of a cost function and a key goal of control is to reduce the steady-state probability mass of undesirable network states. (tamu.edu)

BACKGROUND: A salient purpose for studying gene regulatory networks is to derive intervention strategies, the goals being to identify potential drug targets and design gene-based therapeutic intervention. (tamu.edu)
CONCLUSION: The newly proposed control policies have better performance in general than the MFPT policy and, as indicated by the results on the mammalian cell cycle network, they can potentially serve as future gene therapeutic intervention strategies. (tamu.edu)

This study will develop a new approach to reconstruct time delay Boolean networks as a tool for exploring biological pathways. (tsinghua.edu.cn)

Currently, an increasing number of studies are being carried out to deepen our understanding of miRNA regulatory mechanisms and functions. (hindawi.com)
Understanding gene expression and regulation is essential for understanding biological mechanisms. (biomedcentral.com)

Binary analysis and optimization-based normalization of gene expression data. (auth.gr)

On the one hand, dynamic probes are developed and applied in order to characterize network topologies. (tu-darmstadt.de)

Though the structure of such networks has been studied quite extensively, a comprehensive characterization of the logic rules has not been carried out so far. (u-psud.fr)

To investigate a gene regulatory network, an iterative process of four steps is needed. (hindawi.com)

With roughly 30,000 genes in mammalian genomes, fection with a vector encoding MyoD (Tapscott et al. (lu.se)

While collaborating with L.L. Cavalli-Sforza, he introduced a quantitative theory of cultural evolution, which led to further research into the cultural transmission and gene-culture coevolution. (academicinfluence.com)
We therefore measured cytokine values in bronchoalveolar lavage (BAL) samples of the lower respiratory tract obtained from 83 asthma patients, and used bipartite network visualizations with associated quantitative measures to conduct an exploratory analysis of the co-occurrence of cytokines across patients. (cdc.gov)

In the inference strategy, we will compare all pairs of input genes in those basic relationships by their corresponding -scores for every output gene. (tsinghua.edu.cn)

In Banjo, heuristic approaches are used to search the network space to find the network graph G, which requires large datasets in which the number of genes is much smaller than the number of experiments. (biomedcentral.com)

Construct a network from weights and thresholds. (readthedocs.io)
Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapeutics effective in one cancer type to others with a matching genomic profile, and to construct personalized networks for use in developing combinatorial therapy. (biomedcentral.com)

Then, we will combine those consistent relationships to reveal the most probable relationship and reconstruct the genetic network. (tsinghua.edu.cn)

This project includes several MATLAB scripts that simulate E. coli central metabolism and the effects of single gene deletions on metabolism using 3 approaches -- iFBA, rFBA, and ODE. (simtk.org)
Provides MATLAB scripts that simulate E. coli central metabolism and the effects of single gene deletions on metabolism using 3 approaches -- iFBA, rFBA, and ODE. (simtk.org)
Thus, information-theoretic approaches can deal with steady-state gene expression data or with time-series data given that the sampling interval is long enough to assume that each point is independent of the previous points. (biomedcentral.com)

Kandel, E. R. The Molecular Biology of Memory Storage: A Dialogue Between Genes and Synapses. (panmental.de)
Exploring gene regulatory network is a key topic in molecular biology. (sciweavers.org)

Joachimczak, M. and Wrobel, B. Evo-devo in silico: a model of a gene network regulating multicellular development in 3D space with artificial physics. (panmental.de)
Francois, P. and Hakim, V. Design of genetic networks with specified functions by evolution in silico. (panmental.de)

Although microRNAs (miRNAs) are physically small, they have been shown to play an important role in gene regulation [ 1 ]. (hindawi.com)
They have been used to study gene regulation, but also to model the brain, and are similar to artificial neural networks used in machine learning applications. (ewha.ac.kr)

One great challenge of genomic research is to efficiently and accurately identify complex gene regulatory networks. (tsinghua.edu.cn)

"Identifying All of Cancer's Manifestations through Integrated Pan Cancer Analysis" Dr. Josh Stuart presented the recent work of The Pan-Cancer Initiative of The Cancer Genome Atlas (TCGA) Research Network, including the analysis of thousands of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels in order to uncover data-driven tumor subtypes. (biomedcentral.com)

A complex response was mapped out involving cytoskeletal rearrangement, immune response, modulation of growth and cellular metabolism, and Wnt signaling, as well as responses heretofore unrecognized because they involve poorly annotated genes. (biomedcentral.com)

MicroRNAs (miRNAs) are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. (hindawi.com)

Genotype networks in metabolic reaction spaces. (uni-trier.de)

However, there are no proper tools to examine the network sensitivity against many different types of mutations, including user-defined ones. (researchgate.net)
To address this issue, we developed RMut, which is an R package to analyze the Boolean network-based sensitivity by efficiently employing not only many well-known node-based and edgetic mutations but also novel user-defined mutations. (researchgate.net)
In the first case study, we observed that the real biological networks were most sensitive to overexpression/state-flip and edge-addition/-reverse mutations among node-based and edgetic mutations, respectively. (researchgate.net)

We applied the new method to learning the regulatory network and the metabolic pathway from Saccharomyces Cerevisiae cell cycle gene expression data. (sciweavers.org)

Although low-rank approximations have been used in the past - particularly in the quantum physics literature - our approach departs from traditional applications by exploiting the underlying structure of the network rather than reducing the equations to single species basis functions (orbitals in the language of quantum dynamics). (biorxiv.org)

Anatomy10

Organisms13

Diseases1

Chemicals and Drugs14

Analytical, Diagnostic and Therapeutic Techniques and Equipment18

Psychiatry and Psychology2

Phenomena and Processes45

Disciplines and Occupations5

Anthropology, Education, Sociology and Social Phenomena1

Humanities1

Information Science19

Health Care9

Probabilistic8

Random Boolean networks2

Nodes10

Robustness4

Algorithms6

Interactions11

Perturbations1

Systems biology8

Among genes1

Attractors3

Bayesian3

Models17

Analyses4

Patterns5

Transcriptional2

Behavior7

Modeling3

Proteins1

Metabolic networks4

Interaction6

GRNs2

Intracellular1

Microarray1

Computational complexity2

20021

Steady-state probability1

Intervention2

Pathways1

Mechanisms2

Optimization1

Characterize1

Extensively1

Investigate1

Mammalian1

Quantitative2

Inference1

Graph1

Construct2

Genetic network1

Approaches3

Molecular Biology2

Silico2

Regulation2

Genomic1

Protein1

Poorly1

Aberrant1

Genotype1

Mutations3

Cell cycle1

Dynamics1