Dynamical framework gene regulatory networks. Medical search. Frequent questions

This theoretical study would establish a framework for future research on feedback between starch metabolism and circadian clock as well as plant productivity. (frontiersin.org)

The levels are (1) a core gene regulatory network (GRN) architecture from transcription factor (TF) perturbation data, (2) a stochastically controlled chromatin-state gate, and (3) a single-cell proliferation model validated by experimental clonal growth and commitment kinetic assays. (lu.se)
The researchers from MIT Cambridge, USA, and collaborators at the University of Pittsburgh School of Medicine, present DYNAMO - an analytical framework that infers absolute RNA velocity, reconstruct continuous vector fields that predict cell fates, uses differential geometry to obtain underlying regulations, and anticipates optimal reprogramming routes and perturbation results. (cbirt.net)
By functional network, we mean a network such that an experimental perturbation will likely alter the dynamical phenotype of the network. (biomedcentral.com)
Perturbation experiments, in which the expression of a given gene is experimentally altered, are the best approach to learning network structure. (rochester.edu)
By linking genetic perturbation experiments with statistical and computational modeling, we can accelerate the discovery of genetic interactions in cancer-relevant gene networks. (rochester.edu)
In this work, we present a novel sensitivity analysis method, called molecular density function perturbation (MDFP), for the dynamical analysis of cellular heterogeneity. (mdpi.com)

Our structural analysis of mode changes deeply relies on nonstandard analysis, which is a mathematical framework in which infinitesimals and infinities are first class citizens. (merl.com)
This means that I study the interactions of biological networks through the mathematical framework of dynamical systems theory. (wiko-berlin.de)

We have previously developed and applied a novel GRN modeling algorithm, called TopNet, that pinpoints gene interactions that are crucial to the malignant phenotype. (rochester.edu)

Single cell data helps to address the cellular heterogeneity arising from stochastic expression of genes, proteins, and metabolites is a fundamental principle of cell biology. (biomedcentral.com)

Beginning with time-series gene expression data, the Local Edge Machine (LEM) seeks to find functional network models capable of generating the dynamic behavior of the data (Fig. 1 ). (biomedcentral.com)
One interesting feature of our approach is that it provides a coherent framework for modeling both the local motifs (e.g., edges) within the network and the global dynamical behavior of the system. (biomedcentral.com)
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)

The analysis of SDSs uses techniques from combinatorics, abstract algebra, graph theory, dynamical systems and probability theory. (wikipedia.org)
Abstract: For more than fifteen years, our research group has been developing and applying the concept of Targeted Energy Transfer (TET) as an effective strategy for passively managing energy flows in dynamical systems subject to broadband transient loading. (usc.edu)

Investigation of the interactions between genes (and gene products) is necessary to elucidate cellular mechanisms. (rochester.edu)
My research is oriented around measuring and manipulating interactions between genes and their cellular, genomic, environmental, and community contexts giving rise to microbial population behaviours such as antibiotic resistance. (exeter.ac.uk)

Substrate concentration courses resulting from gene expression reflect its oscillatory behaviour utilised in a periodical trigger for subsequent processes. (springer.com)
They are discrete dynamical systems which generalize many aspects of for example classical cellular automata, and they provide a framework for studying asynchronous processes over graphs. (wikipedia.org)
Even with only a few hundred genes retained, this is more than enough in theory to characterize any possible number of cell states or arbitrarily complex dynamical processes. (biorxiv.org)
Mathematical modeling, particularly when combined with dynamical systems theories, is a valuable tool for understanding how gene regulatory networks (GRNs) influence biological processes. (cbirt.net)
Modeling Methods for Medical Systems Biology: Regulatory Dynamics Underlying the Emergence of Disease Processes. (wiko-berlin.de)
These processes are the dynamical and informational opposite of the predictable, information-conservative, convergent, unifying, and hierarchical processes of "development," which work to replicate and maintain that system. (evodevouniverse.com)

Long-term behaviors of biochemical reaction networks (BRNs) are described by steady states in deterministic models and stationary distributions in stochastic models. (sontaglab.org)
We use the probabilistic framework defined in MaBoSS software, based on continuous time Markov chains and stochastic simulations. (researchgate.net)

Graph dynamical system Boolean network Gene regulatory network Dynamic Bayesian network Petri net Henning S. Mortveit, Christian M. Reidys (2008). (wikipedia.org)
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)
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 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)
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)

Here, making use of coupled data: single-cell gene expression and dynamic molecular measurements, we develop new methods for parameter inference. (biorxiv.org)
Though use of cell chains informed by single-cell gene expression does not improve sampling relative to random chain assignment, we show that the posteriors produced via gene expression-informed cell chains capture distinct properties of the dynamic Ca 2+ response. (biorxiv.org)
Through the analysis of large populations of posterior distributions we are able to quantify the relationships between single-cell transcriptional states and dynamic cellular responses, paving the way for more detailed mappings between gene expression states and dynamic cell fates. (biorxiv.org)
Take single-cell gene expression as an example: even if the overwhelming majority of the genes measured in a given experiment contain very little information about the phenotypes under investigation (say 90-95%, for sake of argument) that still leaves hundreds or thousands of genes that do contain relevant information. (biorxiv.org)
This leads us to the central question underlying this work: can the integration of singlecell gene expression data into a framework for dynamic modeling and inference improve our understanding of the cellular phenotypes of interest? (biorxiv.org)
We address this question below using novel computational methods for single-cell data-informed parameter inference of Ca 2+ dynamics coupled with an innovative dataset jointly measuring dynamics and gene expression in the same single cells [ 7 ]. (biorxiv.org)
MicroRNAs (miRNAs) are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. (hindawi.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)
Effects of noise gene expression on background and cooperator-defector fitness. (nimbios.org)
We know little about their prevalence in the gene expression phenotypes of regulatory circuits, important sources of evolutionary innovations. (biomedcentral.com)
Here, we study a space of more than sixteen million three-gene model regulatory circuits, where each circuit is represented by a genotype, and has one or more functions embodied in one or more gene expression phenotypes. (biomedcentral.com)
Both circuits and gene expression phenotypes that are robust to genetic change are associated with a greater number of latent phenotypes. (biomedcentral.com)
Experimental [ 21 ] and theoretical [ 22 ] studies hint that gene regulatory circuits harbor latent phenotypes because their gene expression patterns often vary when a circuit is exposed to distinct external stimuli. (biomedcentral.com)
We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. (biomedcentral.com)
Temporally dynamic gene expression programs have been observed in a wide variety of organisms. (biomedcentral.com)
Indeed, the network inference problem persists in systems biology, despite an abundance of regulatory evidence in the form of TF binding experiments, genetic screens for candidate nodes, and mutant expression profiling experiments. (biomedcentral.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)
Alternative approaches based on observational data suffer from the large number of unmeasured technical and biological sources of variation that plague gene expression studies. (rochester.edu)
We applied the new method to learning the regulatory network and the metabolic pathway from Saccharomyces Cerevisiae cell cycle gene expression data. (sciweavers.org)
However, the cis-regulatory sequence controlling this posterior expression pattern has not been precisely identified. (sdbonline.org)
Individual oscillating cells are synchronized with their neighbors, forming a coherent wave pattern of gene expression. (ens-lyon.fr)
At the core of his interest are multi-drug efflux pumps and gene expression programmes that mediate bacterial survival and adaptation to antibiotic exposure. (exeter.ac.uk)
We are testing the hypothesis that specific transcription factors form regulatory networks to execute gene expression programs important for SSC fate decisions (self-renewal and differentiation), and ultimately, spermatogenesis. (utsa.edu)
Those with schizophrenia and bipolar depression express different isoforms, or end products of gene expression, which markedly changes what proteins are made 15 . (autismsciencefoundation.org)

Structural characteristics of downstream effector gene cassettes and their control functions. (nature.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)
1) What are the shared structural properties of the regulatory networks that maintain homeostasis in biological systems operating at different scales? (wiko-berlin.de)

My research interests include the mathematics and applications of nonlinear dynamical systems, especially synchronization problems, bifurcations, computational modelling, spatially extended systems and nonautonomous systems. (exeter.ac.uk)

To generalize and quantify these promising results, a broader collection of 19 well-defined CRMs from 9 Drosophila genes known to be required for proper embryonic development was compiled. (sdbonline.org)

a map is constructed that shows interactions among molecular entities (such as genes, proteins and RNAs), using information from literature and databases. (hindawi.com)

To explain these features in light of reported cis -acting chromatin effects and experimental kinetic data, we develop a three-level dynamic model of commitment based upon regulation of the commitment-linked gene Bcl11b . (lu.se)
Due to the discrete manner of molecular assembly in cell signalling and gene regulation, we define a framework of membrane systems equipped with discretised forms of reaction kinetics in concert with variable intramolecular structures. (springer.com)
In this context, our third study cytometrically quantifies the dynamical behaviour of a bistable toggle switch resulting from mutual gene regulation. (springer.com)
Although microRNAs (miRNAs) are physically small, they have been shown to play an important role in gene regulation [ 1 ]. (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)
The network combining putative targets of TF and miRNA regulation with experimentally proven molecular interactions was constructed and visualized. (hindawi.com)
Our observations suggest that latent phenotypes are pervasive in regulatory circuits, and may thus be an important source of evolutionary adaptations and innovations involving gene regulation. (biomedcentral.com)
We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. (versila.com)

Gene regulatory networks (GRNs) provide system level explanations of developmental and physiological functions in the terms of the genomic regulatory code. (nature.com)
Stathopoulos, A. & Levine, M. Genomic regulatory networks and animal development. (nature.com)
As he has pioneered for many years, the University of Chicago geneticist reports with new veracity, backed by over 200 references, upon a whole scale reconception of genomic phenomena in complementary terms of its dynamic, network, and communicative propensities. (naturalgenesis.net)

The core gene regulatory network controlling these transitions consists of a system made up of coupled SNAIL/miRNA-34 and ZEB1/miRNA-200 subsystems. (sontaglab.org)

The Regulatory Genome. (nature.com)
They exist in biological systems as different as promiscuous enzymes and genome-scale metabolic reaction networks, and can give rise to evolutionary adaptations and innovations. (biomedcentral.com)
A major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. (sdbonline.org)
The first step in this process is the identification of regions of the genome that contain regulatory information. (sdbonline.org)
PWMs are a useful way to represent binding specificities and provide a statistical framework for searching for novel instances of the motif in genome sequences (Berman, 2002). (sdbonline.org)
In a contribution to the total rethinking of the nature of gene and genome, the old Mendelian version is supplanted by malleable information processing systems capable of nonrandom change guided by dynamic cellular networks. (naturalgenesis.net)
At the beginning of the 21st century, molecular cell biology has revealed a dense structure of information-processing networks that use the genome as an interactive read-write memory system rather than an organism blueprint. (naturalgenesis.net)
Genome sequencing has documented the importance of mobile DNA activities and major genome restructuring events at key junctures in evolution: exon shuffling, changes in cis-regulatory sites, horizontal transfer, cell fusions and whole genome doublings. (naturalgenesis.net)

Accurate models of gene regulatory networks (GRNs) present in healthy cells and how these GRNs are altered in disease have the potential to inform both prognosis and treatment. (rochester.edu)
The overall goal of the research is to develop and apply novel methodology to estimate GRNs based on thousands of gene perturbations at single cell resolution. (rochester.edu)

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)
Exploring gene regulatory network is a key topic in molecular biology. (sciweavers.org)
The authors provided convincing evidence for the heterogeneity of postnatal enthesis growth and the molecular dynamics and signaling networks during enthesis formation. (elifesciences.org)
The applications to living systems I am interested in include biophysical modelling (active transport and organelle dynamics in cell biology), cognition (perceptual rivalry, computational aspects of networks), molecular networks, functional dynamics in neural and biomedical systems and tipping points in nonautonomous systems. (exeter.ac.uk)
Molecular cell biology has uncovered sophisticated networks in all organisms. (naturalgenesis.net)

Positive stability analysis and bio-circuit design for nonlinear biochemical networks. (zbmath.org)
Summary: This paper is concerned with positive stability analysis and bio-circuits design for nonlinear biochemical networks. (zbmath.org)
A fuzzy interpolation approach is employed to approximate nonlinear biochemical networks. (zbmath.org)
Based on the Lyapunov stability theory, sufficient conditions are developed to guarantee the equilibrium points of nonlinear biochemical networks to be positive and asymptotically stable. (zbmath.org)
Finally, a real biochemical network model is provided to illustrate the effectiveness and validity of the obtained results. (zbmath.org)
Synopsis： COPASI is a widely used software tool for creating, simulating and analysing models of biochemical reaction networks. (aeplan.co.jp)

In my research, I tackle this question from a dynamical systems biology perspective. (wiko-berlin.de)
These information-processing networks are central to the systems biology perspective of the new century. (naturalgenesis.net)

Most recently, several studies have developed inference methods based on nonlinear ordinary differential equations (ODEs) for the chemical kinetics and a Bayesian formalism on the network structure [ 24 - 27 ]. (biomedcentral.com)

Currently, an increasing number of studies are being carried out to deepen our understanding of miRNA regulatory mechanisms and functions. (hindawi.com)
Various types of mathematical models and systems analyses of biological networks have further been used to gain a better understanding of the sources and regulatory mechanisms of such variability. (mdpi.com)

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)
These systems tools incorporate and analyse the complex biological networks involved. (biomedcentral.com)

Under the framework of Bayesian parameter inference and model selection, the available data is used along with prior knowledge to infer a posterior parameter distribution for the model [ 5 ]. (biorxiv.org)
Furthermore, LEM operates in a Bayesian framework, which accounts for uncertainty, prior information, and robustness in the parameter space. (biomedcentral.com)
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)

the extent to which they do can be used as the basis for the computational identification of cis-regulatory modules. (sdbonline.org)

Previous methods for network inference from dynamics data may be broadly classified according to the tools involved. (biomedcentral.com)

Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. (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)

Shoot branching is regulated by an environmentally sensitive network of systemically moving hormone signals, providing a rich source of information that can be locally interpreted to determine branching behaviour. (ens-lyon.fr)

Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. (researchgate.net)

Using RNA fluorescence in situ hybridization (FISH) measurements of genes encoding key TFs and measured bulk population dynamics, this single-cell model predicts state-switching kinetics validated by measured clonal proliferation and commitment times. (lu.se)
The resulting multi-scale model provides a mechanistic framework for dissecting commitment dynamics. (lu.se)
In previous work, we have developed an approach to understanding the long-term dynamics of classes of chemical reaction networks, based on rate-dependent Lyapunov functions. (sontaglab.org)
This paper deals with the analysis of the dynamics of chemical reaction networks, developing a theoretical framework based only on graphical knowledge and applying regardless of the particular form of kinetics. (sontaglab.org)
We are particularly interested in the functional components of networks (rather than the most expansive or inclusive network), where the function of the network is manifested by the dynamics of the network. (biomedcentral.com)
Since its 3.3 release, Modelica offers the possibility to specify models of dynamical systems with multiple modes having different DAE-based dynamics. (merl.com)

Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. (hindawi.com)
Next, the network was translated into a detailed mechanistic model, which was characterized and validated with experimental data. (hindawi.com)
The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. (versila.com)

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

It provides a useful theoretical framework useful to help assess what policies related to growth and financial depth are likely to affect sustainability (Working Paper no. 23-05). (financialresearch.gov)

2006. Communication logic design and analysis for networked control systems . (ucsb.edu)
Park H, Imoto S , Miyano S. Comprehensive information-based differential gene regulatory networks analysis (CIdrgn): Application to gastric cancer and chemotherapy-responsive gene network identification. (google.com)
To investigate the conformational change of c-Src tyrosine kinase, we applied network analysis to time series of correlation among residues. (intechopen.com)

This allows us to derive the stationary distributions of a large class of BRNs, including autophosphorylation networks of EGFR, PAK1, and Aurora B kinase and a genetic toggle switch. (sontaglab.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)

This transition encompasses programmed shutoff of stem/progenitor genes, upregulation of T cell specification genes, proliferation, and ultimately commitment. (lu.se)
Enthesis development has historically been studied with lineage tracing of individual genes selected a priori, which does not allow for the determination of single-cell landscapes yielding mature cell types and tissues. (elifesciences.org)

28. I. Tokuda, Z. Levnajić, K. Ishimura, A practical method for estimating coupling functions in complex dynamical systems, Philosophical Transactions of the Royal Society A 377, 20190015, 2019. (unm.si)
Finally, we use an atlas of transcription data in a mammalian circadian system to illustrate how the method can be used for discovery in the context of large complex networks. (biomedcentral.com)
It uses a local approximation to the system of differential equations that relies on sparse priors, which localizes uncertainty and renders the algorithm scalable to complex networks. (biomedcentral.com)
rather they act together in complex networks that govern cellular function. (rochester.edu)
The object of study is called a framework, that is, mapping vertices of a graph into the real or complex plane satisfying some given set of constraints. (fau.edu)
Network science has developed as an effective framework with which to study complex systems. (biomedcentral.com)

Alon, U. Network motifs: theory and experimental approaches. (nature.com)
Synopsis： Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. (aeplan.co.jp)

21. M. Grau Leguia, R. G. Andrzejak, Z. Levnajić, Evolutionary optimization of network reconstruction from derivative-variable correlations, Journal of Physics A: Mathematical and Theoretical 50, 334001, 2017. (unm.si)
An important source of evolutionary adaptations are gene regulatory circuits. (biomedcentral.com)
Such a cognitive component is absent from conventional evolutionary theory because 19th and 20th century evolutionists were not sufficiently knowledgeable about cellular response and control networks. (naturalgenesis.net)

Developmental gene regulatory networks in the zebrafish embryo. (nature.com)

Koide, T., Hayata, T. & Cho, K. W. Y. Xenopus as a model system to study transcriptional regulatory networks. (nature.com)
For the reduced system, monotone dynamical systems theory can be used to prove generic convergence to the set of equilibria for all bounded trajectories. (sontaglab.org)
Indeed, using the locally inferred network structure and parameters, LEM produces a complete system of ODEs capable of generating dynamic predictions. (biomedcentral.com)
In this project, we aim to break the boundaries between different components in an end-to-end visual processing system and propose to model an end-to-end co-design framework that combines imagers, processors, and algorithms vertically across the system stack. (rochester.edu)
At the heart of this network is the auxin transport system. (ens-lyon.fr)
The shoot auxin transport system involves diverse transporters and mounting evidence suggests that different transporters are differentially sensitive to shoot branching regulatory signals, including auxin flux, cytokinin and strigolactone. (ens-lyon.fr)
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)
In contrast, systems biology choses to represent the whole system by investigating the networks, which are the large scale interactions of many molecules in a systematic and simultaneously way. (biomedcentral.com)
Turning to analyses of gene function across these overlapping genes, these three disorders also showed similar impact of synaptic genes and those affecting the central nervous immune system 13 . (autismsciencefoundation.org)

Sequential dynamical systems (SDSs) are a class of graph dynamical systems. (wikipedia.org)
These chromatic graphs are derived from the angle graph of a given constrained framework. (fau.edu)

M.L. Blinov, J.R. Faeder, B. Goldstein, W.S. Hlavacek, A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. (springer.com)
Organ formation during flower development in Arabidopsis is regulated by only few genes, what can be summarized by the so-called 'ABC' model. (ens-lyon.fr)
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)
Network theory has elucidated the emergent properties of technological systems, including the World Wide Web and Internet, and is used to model power grids and roads [ 17 ]. (biomedcentral.com)

I will demonstrate how we can equip neural networks with inductive biases that enables them to learn 3D geometry, appearance, and even semantic information, self-supervised only from posed images. (merl.com)

These two genes are expressed very early and are in mutual repression with TERMINAL FLOWER 1 ( TFL1 ), a gene that maintains the inflorescence meristem's identity. (ens-lyon.fr)

Modellen är anpassad till experimentell data och förutsäger en tillståndsbytande kinematik som valideras med klondata. (lu.se)

Mangan, S. & Alon, U. Structure and function of the feed-forward loop network motif. (nature.com)
Maduro, M. F. Structure and evolution of the C. elegans embryonic endomesoderm network. (nature.com)

A common feature of these cis-regulatory modules is the presence of multiple binding sites for multiple transcription factors. (sdbonline.org)

Peter, I. S. & Davidson, E. H. Modularity and design principles in the sea urchin embryo gene regulatory network. (nature.com)
Davidson, E. H. Network design principles from the sea urchin embryo. (nature.com)

Disease progression produces drastic changes in genetic networks critical to normal cellular function. (rochester.edu)

A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation. (nature.com)

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)
Mutation and in vitro DNA binding studies completed on a subset of the CRMs provide evidence for a direct regulatory relationship. (sdbonline.org)

By clustering posterior parameters we can identify markers genes that correspond with variable Ca 2+ responses. (biorxiv.org)

We start by developing a detailed reaction network with 24 state variables. (sontaglab.org)
This paper introduces a class of networks that are "structurally (mono) attractive", by which we mean that they are incapable of exhibiting multiple steady states, oscillation, or chaos by the virtue of their reaction graphs. (sontaglab.org)

Anatomy12

Organisms15

Chemicals and Drugs17

Analytical, Diagnostic and Therapeutic Techniques and Equipment27

Psychiatry and Psychology2

Phenomena and Processes59

Disciplines and Occupations5

Information Science20

Health Care11

Circadian Clock1

Perturbation6

Mathematical framework2

Phenotype1

Cellular heterogeneity1

Behavior6

Abstract2

Interactions between genes2

Processes6

Stochastic2

Boolean5

Expression25

Structural3

Synchronization1

Drosophila1

Proteins1

Regulation8

Genomic3

Core gene regulat1

Genome8

GRNs2

Molecular5

Biochemical6

Systems biology perspective2

Nonlinear1

Mechanisms2

Biological networks2

Bayesian3

Computational1

Inference1

Modeling2

Behaviour1

Experimentally1

Dynamics6

Mechanistic3

Perturbations1

Theoretical framework1

Analysis3

Derive2

Cell2

Complex6

Experimental2

Evolutionary3

Developmental1

System9

Graph2

Model4

Neural networks1

Mutual1

Data1

Structure2

Transcription1

Embryo2

Genetic networks1

Roles1

Mutation2

Posterior1

Reaction2