• The molecular mechanisms underlying the response to wounding, which is spatially structred into a local and a systemic response, and to other challenges have extensively been studied, and key pathways, mediated by signalling molecules including jasmonic acid, salicylic acid and ethylene, have been identified. (uea.ac.uk)
  • These networks range from those involving gene regulatory and protein-protein interactions underlying intracellular signalling pathways, and single-cell responses, to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune response of an organism ( Subramanian 2015 ). (biorxiv.org)
  • Such as [ 131 ], modified this new TieDIE signaling network diffusion algorithm [ 132 ] so you're able to phosphoproteomics and transcriptomics data discover druggable kinase pathways. (micsem.org)
  • We report the results of integrative systems biology studies of the Hsp90 chaperone and protein kinases with an atomic level analysis of the communication pathways regulating conformational equilibrium of theses protein systems in signaling networks. (utoronto.ca)
  • Based on these findings, we developed a computational synthetic biology framework for design and re-engineering signal transduction networks and pathways that involve cross-talk between molecular chaperones and protein kinase clients. (utoronto.ca)
  • A common approach is to map gene expression on the corresponding genes of given pathways. (saezlab.org)
  • Once their activities have been estimated, transcription factors and signaling pathways signatures can be linked to upstream perturbations (drugs, ligands, mutations, etc.) using network-based approaches such as so-called causal reasoning methods. (saezlab.org)
  • GSEA of two key lncRNAs obtained biological processes and signaling pathways related to RA synovial lesions. (bvsalud.org)
  • The new data support two out of three novel regulatory pathways predicted to mediate expression changes downstream of the yeast transcriptional regulator SWI4 . (biomedcentral.com)
  • These factors operate in signaling pathways that are used extensively in a number of processes in both the embryo and adult. (nih.gov)
  • The nested and interrelated signaling pathways that bring about a specific developmental process are known as developmental cascades. (medscape.com)
  • We provide a temporal and spatial framework for integrating the flowering GRN with cellular changes at the SAM and highlight the role of local regulation of GA. (jic.ac.uk)
  • The allosteric interactions and regulation of molecular chaperones and protein kinases allow for molecular communication and event coupling in signal transduction networks. (utoronto.ca)
  • Biophysical modeling of allosteric regulation in the protein kinases has offered additional insights into organizing principles of kinase activation by molecular chaperones that may be orchestrated by a cross-talk between key regulatory regions. (utoronto.ca)
  • The results of biophysical and computational systems biology analyses combined with proteomics experiments have been integrated into a graph-based network model of allosteric regulation. (utoronto.ca)
  • Integration of computational systems biology and machine learning analysis of the Hsp90 interactions with oncogenic kinase mutants is then used to construct models of allosteric regulation of oncogenic proteins by molecular chaperones in signaling cascades. (utoronto.ca)
  • Network-defined modularity of interacting components and cross-talk in signal transduction networks are quantified through molecular mechanism of allosteric regulation. (utoronto.ca)
  • These relationships may reflect gene co-expression/regulation, protein-protein interactions (PPIs) or information about production or consumption of metabolites [ 14 ]. (biomedcentral.com)
  • The regulation of most aspects of cellular life and functioning is accomplished by complex and sophisticated biochemical (signal transduction,metabolic) and gene regulatory networks. (imperial.ac.uk)
  • PageMan analysis revealed several significantly enriched categories altered by MeJA+NaCl treatment, compared with NaCl treatment alone, including genes involved in secondary metabolism, glutathione-based redox regulation, cell cycle, transcription factors (TFs), and other signal transductions (such as calcium and ROS). (frontiersin.org)
  • As genome-scale measurements lead to increasingly complex models of gene regulation, systematic approaches are needed to validate and refine these models. (biomedcentral.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)
  • The basic motifs used to build more complex networks (that is, simple regulation, reciprocal regulation, feedback loop, feedforward loop, and autoregulation) can be faithfully described and their temporal dynamics can be analyzed. (biomedcentral.com)
  • 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)
  • Environmental signals act in numerous ways to compel transcription factors (TFs) to interact with modular regulatory regions of various genes, to turn them on or off (up- versus down-regulation). (genewhisperer.com)
  • As a result, the types of gene-expression regulation - that can be programmed with synTFs in this manner - represent only a fraction of the capability of natural TFs. (genewhisperer.com)
  • In this study, we present a computational framework to identify miRNA-disease associations, and further construct a bipartite miRNA-disease network for systematically analyzing the global properties of miRNA regulation of disease genes. (biomedcentral.com)
  • MicroRNAs (MiRNAs) are important regulators that can strongly affect cellular functions including proliferation, differentiation, and apoptosis through post-transcriptional negative regulation of target gene expression [ 1 ]. (biomedcentral.com)
  • Non-coding regions are known to regulate gene expression, and the finding indicates that alterations in regulation networks play a larger role in disease risk than protein-coding variants. (jax.org)
  • The team used massively parallel reporter assays (MPRA) to assess the effects of variants on gene expression in cultured MIN6 mouse β cells, which have been found to accurately model the regulation networks found in human islet cells. (jax.org)
  • They also showed that cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity, revealing a new parallel between the myogenic regulatory networks operating in Drosophila and vertebrates. (sdbonline.org)
  • A rapid overview of this morphologic scheme provides the framework for further studying the processes and regulation involved in development. (medscape.com)
  • Special areas of interest include signal transduction and information processing, gene expression and gene regulatory networks, metabolism, proliferation, differentiation and morphogenesis, among others, and the use of multi-scale modeling to connect molecular and cellular systems to the level of organisms and populations. (iospress.com)
  • As a fundamental step, CNA facilitates the construction of network projects which can represent either a mass-flow (stoichiometric, metabolic) or a signal-flow (signal transduction/regulatory) network. (biomedcentral.com)
  • J. Behre, S. Schuster, Modeling signal transduction in enzyme cascades with the concept of elementary flux modes. (springer.com)
  • M.L. Blinov, J.R. Faeder, B. Goldstein, W.S. Hlavacek, BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. (springer.com)
  • We need to simulate the desired behavior of our module, determine the kinetic patterns of the different signal transduction systems, generate libraries of signal transduction components with different kinetic parameters from which we can choose. (igem.org)
  • A qualitative mathematical model of the notion of immunocompetence is developed, based on the formalism of Memory Evolutive Systems (MES), from which, immunocompetence is defined as an emergent structure of a higher order arising from the signal networks that are established between effector cells and molecules of the immune response in the presence of a given antigen. (biorxiv.org)
  • Here, we use the signed, directed interactions in Omnipath as a prior knowledge network and we make use of an integer linear programming (ILP) mathematical formulation to infer regulatory signalling network topology from gene expression data. (saezlab.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)
  • Doug Kellogg's lab is working to elucidate these mechanisms, using biochemistry, genetics, and mathematical modeling to understand signaling networks that are required for control of cell size and cell growth. (ucsc.edu)
  • There have been several attempts to define formal mathematical and computational frameworks for modeling GRNs. (biomedcentral.com)
  • Mathematical modelling of cellular networks is an integral part of Systems Biology and requires appropriate software tools. (biomedcentral.com)
  • Ability to deploy across high performance computing systems sophisticated mathematical modeling frameworks, data analysis pipelines and bioinformatics workflows to address complex biological phenomena. (vliz.be)
  • Finally, a practical method to measure the immunocompetence status is established, using elements of the theory of small random graphs and taking into account the characteristics of the immune networks, established through transcriptional studies, of patients with severe COVID-19 and healthy patients, assuming that both types of patients were vaccinated with an effective biological against SARS-CoV-2. (biorxiv.org)
  • Whenever you are signaling training typically do not work with TFs, chromatin-centered inference out-of TF craft only methods the result off TF binding into the chromatin, which may or may not end up in transcriptional changes of their address genes, while TF hobby inferred away from target gene term can be confounded by indirect outcomes. (micsem.org)
  • Many of these models contain transcriptional interactions for which the regulatory effects (inducer versus repressor) are ambiguous and cannot be determined from publicly available expression profiles. (biomedcentral.com)
  • 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)
  • A major goal of our research program is the identification of the direct transcriptional targets of these factors to unravel the regulatory networks controlling limb development. (nih.gov)
  • In all, they tested 2512 single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) associated with the signals, plus 4124 other SNPs in active transcription locations, for their ability to alter transcriptional activation. (jax.org)
  • MicroRNA-mRNA co-sequencing identifies transcriptional and post-transcriptional regulatory networks underlying muscle wasting in cancer Cachexia. (vliz.be)
  • Stabilizing selection, if ubiquitously spread across the network, could then be a "wall" that makes the formation of novel interactions more difficult and maintains previously established interactions. (wikipedia.org)
  • Immunity is thus not the product of simple signalling events but rather nonlinear behaviours arising from dynamic, feedback-regulated interactions among many components. (biorxiv.org)
  • It works out a great ligand-target gene interaction rating, and you may predicated on this, predicts phone-mobile interactions. (micsem.org)
  • The synergistic roles of the Hsp90-Cdc37 chaperone machinery and protein kinases in biology and disease have stimulated extensive structural and functional studies of regulatory mechanisms underlying the Hsp90-kinase interactions. (utoronto.ca)
  • Allosteric interactions of the Hsp90 with cochaperones and protein kinase clients can determine regulatory mechanisms and cellular functions of many signaling proteins and cascades. (utoronto.ca)
  • Identification of the potential regulatory interactions in rheumatoid arthritis through a comprehensive analysis of lncRNA-related ceRNA networks. (bvsalud.org)
  • 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)
  • We recently reported a procedure for inferring gene-regulatory network models by integrating gene-expression profiles with high-throughput measurements of protein interactions [ 18 ]. (biomedcentral.com)
  • We consider approaches for representing the role of protein complexes in the cell cycle, displaying modules of metabolism in a hierarchical format, integrating experimental interaction data with structured vocabularies such as Gene Ontology categories and representing conserved interactions among orthologous groups of genes. (nature.com)
  • Developmental processes such as axis formation and organogenesis employ regulatory components and interactions that are often also used in normal tissue renewal/homeostasis in the adult organism, as well as contributing to the pathogenesis of disease when aberrantly reactivated. (nih.gov)
  • Mouse genetics have spotlighted many mutations affecting this process, and a wealth of embryologic information from experimental manipulations in chick has uncovered a network of inductive tissue interactions, providing a rich conceptual framework for molecular analysis. (nih.gov)
  • Gene regulatory networks are widely used by biologists to describe the interactions among genes, proteins and other components at the intra-cellular level. (biomedcentral.com)
  • We use Statecharts for modeling small and recurring patterns of interactions in gene regulatory networks, called motifs . (biomedcentral.com)
  • Their behavior is often represented by using gene regulatory networks (GRNs), which describe the interactions among genes, proteins and other components at the intra-cellular level. (biomedcentral.com)
  • However, building dynamic models with high predictive power requires an amount of reliable quantitative data which is often not available in large-scale networks with hundreds of players and interactions. (biomedcentral.com)
  • When a synTF is designed to have one-to-one binding to its cognate DNA target (the promoter region of a particular gene), the dose-response of gene expression is largely a gradient (until one reaches saturation), typically fitted by a Michaelis-Menten saturation curve (i.e. similar to enzyme-substrate, transporter-substrate, or receptor-ligand interactions). (genewhisperer.com)
  • In eukaryotic gene networks, cooperative assembly occurs when core initiation machinery is recruited to basal promoter regions through multivalent, mutually reinforcing interactions between TFs and associated cofactors. (genewhisperer.com)
  • They established theoretical contexts and designed frameworks in yeast - for programming cooperative TF assembly on the basis of the configuration, and strength, of intra-complex interactions, and they constructed synthetic gene circuits composed of interconnected regulatory assemblies. (genewhisperer.com)
  • 6 ] assessed potential miRNA-disease interactions through a miRNA-miRNA functional similarity network that was constructed based on the similarity of miRNA-associated diseases. (biomedcentral.com)
  • A developmental systems perspective on epistasis: computational exploration of mutational interactions in model developmental regulatory networks. (vliz.be)
  • In addition, we will have regular interactions with the permanent staff at Physical Chemistry and will get to meet students in their fi nal studies thereby enlarging our network and creating possibilities for future recruitment. (lu.se)
  • These data have spawned a variety of methods to infer the structure of gene-regulatory networks or to study their high-level properties, as recently reviewed [ 5 ]. (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)
  • Each other signaling and TF-theme oriented inference from TF interest has its blind locations. (micsem.org)
  • We demonstrate the applicability of the learned features for targeted omics inference tasks: transcription factor (TF)-target prediction, integrated omics network (ION) inference, and module identification. (biomedcentral.com)
  • We have ongoing interests in the systems level analysis and reconstruction of regulatory networks, inference of enhancer-promoter contacts, predictive models of gene expression and integration of three-dimensional chromatin structure with one-dimensional epigenetic measurements in the context of cancer, malaria, asthma and several autoimmune diseases. (ucsd.edu)
  • This project will focus on developing regulatory network inference methods for the joint analysis of gene expression and histone modification data from several different types of tumor infiltrating lymphocytes, which are gathered from a cohort of patients with solid tumors. (ucsd.edu)
  • Here, making use of coupled data: single-cell gene expression and dynamic molecular measurements, we develop new methods for parameter inference. (biorxiv.org)
  • In application to the Ca 2+ signaling pathway, we show that cell predecessor-informed priors accelerate inference of the Ca 2+ model parameters in single cells. (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)
  • Gupta R, Stincone A, Antczak P, Durant S, Bicknell R, Bikfalvi A, Falciani F. (2011) A Computational framework for gene regulatory network inference that combines multiple methods and datasets. (u-bordeaux.fr)
  • We are analyzing the normal developmental function of early transcription factors that regulate digit patterning (Gli3, 5'Hoxd), with the long-term aim of linking regulatory cascades and patterned gene expression to the morphogenesis of specific structures. (nih.gov)
  • Identifying the direct target promoters of developmental gene-regulators will be critical to understand how these regulators function and to link regulatory cascades in developmental genetic programs to the basic cellular processes that drive morphogenesis of anatomic structures. (nih.gov)
  • Developmental systems also afford an excellent avenue to study complex regulatory circuits designed to ensure the robust functioning of a normal process. (nih.gov)
  • The application of systems biology principles to developmental biology promises to reveal the quantitative interrelationships between signaling and regulatory systems necessary to support robust physiological processes, and thereby provide a framework for the interpretation of the pathology (especially cancer) resulting from gross or subtle disturbances in these interrelationships. (nih.gov)
  • Sonic hedgehog (Shh) signaling plays key roles in stem cell maintenance, developmental morphogenesis, and cancer pathogenesis. (nih.gov)
  • Using the limb as a model for vertebrate organogenesis, we deleted Shh at different developmental times in genetically engineered mice with a conditional, floxed-Shh gene and inducible Cre to determine the temporal requirements for Shh during limb development. (nih.gov)
  • Such frameworks allow analysis of the genome-scale expression data to understand changes in the overall metabolisms of an organism (or organs, tissues, and cells) in response to various extrinsic (e.g. developmental and differentiation) and/or extrinsic signals (e.g. pathogens and abiotic stresses) from the surrounding environment. (oregonstate.edu)
  • He has delivered over 14 Keynote speeches at international conferences on morphogenetic robotics and morphogenetic self-organizing systems, developmental neural computation, modeling and analysis of gene regulatory networks, evolutionary optimization in dynamic and uncertain environments and multi-objective machine learning. (soft-computing.de)
  • Imposed upon this gross morphological description is the modern understanding of gene expression and protein elucidation, which bring about these developmental processes. (medscape.com)
  • Modularity refers to the ability of a system to organize discrete, individual units that can overall increase the efficiency of network activity and, in a biological sense, facilitates selective forces upon the network. (wikipedia.org)
  • Regulatory gene networks are generally a central biological mechanism of decoding genetic information that confers adaptive capabilities into phenotypic responses and other traits. (uea.ac.uk)
  • To this end, networks are widely used to represent individual bio-molecules (nodes) and their biological relationships (edges). (biomedcentral.com)
  • Representation and analysis of complex biological and engineered systems as directed networks is useful for understanding their global structure/function organization. (nih.gov)
  • In this study we used a supercomputer to analyze cyclic motifs made of 3-20 nodes for 6 biological and 3 technological networks. (nih.gov)
  • We strive to provide computational frameworks for understanding how observable biological properties arise from complex systems. (iospress.com)
  • Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. (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 present a Statecharts-based approach for the modeling of gene regulatory network motifs in biological systems. (biomedcentral.com)
  • A largely studied class of biological systems is constituted by systems which regulate the expression of genes in an organism. (biomedcentral.com)
  • Systems biology aims at a holistic analysis of biological networks. (biomedcentral.com)
  • Using a novel iterative framework developed in a companion manuscript, we have analyzed single-cell RNA-seq data obtained from mouse embryonic stem cells taken at various time points during early germ layer differentiation to identify cell types as well as the lineage relationships between these individual cell types. (harvard.edu)
  • This allowed us to essentially map out a lineage tree in gene expression space that describes the continuous gene expression dynamics of early germ layer differentiation. (harvard.edu)
  • The overarching goal of understanding molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many tumor-inducing signaling proteins. (utoronto.ca)
  • We develop methods that are based in statistics, machine learning, optimization and graph theory to understand how changes in the 3D genome affect cellular outcome such as development, differentiation and gene expression. (ucsd.edu)
  • Recently, we have focused on the role of Shh/Gli3 and 5'Hoxd genes in regulating several aspects of limb development, including early digit patterning, as well as condensation and differentiation of cartilage precursors during final morphogenesis of the limb skeleton. (nih.gov)
  • Further, premature blood cell differentiation when PSC specification or signaling was impaired, led to assigning the PSC a role equivalent to the vertebrate hematopoietic niche. (sdbonline.org)
  • The mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host protection against pathogens. (biorxiv.org)
  • These regulatory mechanisms have strong connections with cellular metabolism. (biomedcentral.com)
  • These regulatory processes are affected by specific bio-molecules potentially in separate cellular compartments with interconnected steps [ 1 ]. (biomedcentral.com)
  • This gene product is a bZIP protein, which was also identified as a cellular transcription factor that binds to an enhancer in the promoter of the T cell leukemia virus type 1 promoter. (cancerindex.org)
  • Understanding the functioning of and information processing through such networks at both the intracellular level as well as the intercellular level (accounting for cellular communication and interaction) is of importance from both basic and applied perspectives. (imperial.ac.uk)
  • Ca 2+ signaling is a highly conserved pathway that regulates a host of cellular responses in epithelial cells: from death and division to migration and molecule secretion, as well as collective behaviors from organogenesis to wound healing [ 8 ]. (biorxiv.org)
  • Thus, understanding how normal transcription programs are regulated during development may also help to decipher abnormal gene expression patterns in tumors and devise new strategies to intercept cellular targets driving tumor cell behavior. (nih.gov)
  • An important class of methods in Systems Biology deals with structural or topological (parameter-free) analysis of cellular networks. (biomedcentral.com)
  • CellNetAnalyzer provides a single suite to perform structural and qualitative analysis of both mass-flow- and signal-flow-based cellular networks in a user-friendly environment. (biomedcentral.com)
  • CellNetAnalyzer (CNA) is a graphical user interface for MATLAB providing a comprehensive toolbox for structural and functional analysis of different types of cellular networks. (biomedcentral.com)
  • The species-specific plant Pathway Genome Databases (PGDBs) based on the BioCyc platform provide a conceptual model of the cellular metabolic network of an organism. (oregonstate.edu)
  • The maintenance of stem or progenitor cell fate relies on intrinsic factors as well as local cues from the cellular microenvironment and systemic signaling. (sdbonline.org)
  • Initial analysis of Collier/Early B Cell Factor function in the lymph gland revealed the role of the Posterior Signaling Center (PSC) in mounting a dedicated cellular immune response to wasp parasitism. (sdbonline.org)
  • A modified pathway analysis algorithm determines steady states for the given Boolean network. (sdsu.edu)
  • Furthermore, we have developed a genome-wide epistasis analysis framework that efficiently reveals the organization of these genes within signaling and regulatory networks such as the Rcs phosphorelay pathway and the cyclic-di-GMP second-messenger system. (columbia.edu)
  • transcription factors differentially activated (brown), and pathway activities as determined by their footprints on gene expression (pink). (saezlab.org)
  • IRE1α-XBP1 were essential for expansion of activated mouse and human NK cells and are situated downstream of the mammalian target of rapamycin signaling pathway. (cancerindex.org)
  • CellNetAnalyzer extends its predecessor FluxAnalyzer (originally developed for metabolic network and pathway analysis) by a new modelling framework for examining signal-flow networks. (biomedcentral.com)
  • This topology provides more dynamic stability in large networks. (nih.gov)
  • Propagation of kinetic uncertainties through a canonical topology of the TLR4 signaling network in different regions of biochemical reaction space. (vliz.be)
  • My lab previously identified several transcription factors (homeobox genes and T-box genes) involved in formation and patterning of both the primary embryonic axis and the limb axis in vertebrates. (nih.gov)
  • This gene encodes a transcription factor that regulates MHC class II genes by binding to a promoter element referred to as an X box. (cancerindex.org)
  • Gene Ontology analysis revealed a strong enrichment in proteins with DNA binding and/or transcription-regulatory properties. (sdbonline.org)
  • The MDP will use transsys, a computational framework for RGN modelling. (uea.ac.uk)
  • We have developed a powerful computational framework for revealing the genetic basis of bacterial traits by correlating the inheritance patterns of genes and phenotypes across all the sequenced bacterial genomes (Jim et al. (columbia.edu)
  • We developed a computational framework to identify miRNA-disease associations by performing random walk analysis, and focused on the functional link between miRNA targets and disease genes in protein-protein interaction (PPI) networks. (biomedcentral.com)
  • 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)
  • We evaluate our framework using multi-omics data of Saccharomyces cerevisiae , a well-studied yeast model organism. (biomedcentral.com)
  • The ability of genes or alleles to affect the representation of the host organism in a biome is an operational definition for the "function" of the gene (in that context). (genomicglossaries.com)
  • Our framework learns features for differentially expressed bio-molecules showing heat stress response. (biomedcentral.com)
  • Conducted to discern both differentially expressed lncRNAs (DELncRNAs) and differentially expressed genes (DEGs). (bvsalud.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)
  • The isoform encoded by the unspliced mRNA, XBP1(U), is constitutively expressed, and thought to function as a negative feedback regulator of XBP1(S), which shuts off transcription of target genes during the recovery phase of ER stress. (cancerindex.org)
  • In vivo Col binding peaks were associated to 415 potential direct target genes. (sdbonline.org)
  • Figure 7: Illustration of steps to determine a network in Homo sapiens using the metagraph concept, where each metanode represents a set of orthologous eukaryotic genes from the COG database 53 . (nature.com)
  • Another useful module would be a bacterial system that senses a eukaryotic protein and transduces the sensed signal into a certain behavior. (igem.org)
  • Thus, common evolutionary rates could be forcing the genes for certain proteins to evolve together while preventing other genes from being co-opted unless there is a shift in evolutionary rate. (wikipedia.org)
  • By showcasing a family of cyclin-dependent (CDK) kinases that display a broad repertoire of chaperone dependencies, we discovered that unique functional dynamics signatures and chaperone addiction of CDK4 and CDK7 client proteins can explain divergences in their regulatory mechanisms that require a confluence of events, including formation of the inhibitory ternary complex, substrate recruitment and activation loop phosphorylation. (utoronto.ca)
  • Additionally, it is possible to use gene expression data to estimate the activity status of transcription factor (TF) proteins by looking at the mRNA levels of its direct targets (TF footprint). (saezlab.org)
  • It has been found that upon accumulation of unfolded proteins in the endoplasmic reticulum (ER), the mRNA of this gene is processed to an active form by an unconventional splicing mechanism that is mediated by the endonuclease inositol-requiring enzyme 1 (IRE1). (cancerindex.org)
  • Studies published in In Silico Biology generally use theoretical models and computational analysis to gain quantitative insights into regulatory processes and networks, cell physiology and morphology, tissue dynamics and organ systems. (iospress.com)
  • 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)
  • Together with metabolic networks and signal networks, they provide a functional description of cell processes. (sdsu.edu)
  • Here, we can combine phosphoproteomic, transcriptomic and metabolomics data to find causal paths linking signaling, gene-regulatory, and metabolic processes. (saezlab.org)
  • Our goal is to efficiently integrate multi-omics data to study different regulatory aspects of multilayered processes that occur in organisms. (biomedcentral.com)
  • This is because information processing through these networks is the key ingredient which allows us to understand how cells regulate different processes, respond to their environment, interact with one another and affords ways of controlling or manipulating them through synthetic and other means. (imperial.ac.uk)
  • 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)
  • Substrate concentration courses resulting from gene expression reflect its oscillatory behaviour utilised in a periodical trigger for subsequent processes. (springer.com)
  • Among our primary findings is the emerging evidence that a small number of functional motifs may be utilized by the chaperone and protein kinases to act collectively as central regulators of the intermolecular communications, ATP hydrolysis, and protein client binding in signaling networks. (utoronto.ca)
  • In the case of gene expression, a number of functional features can be extracted. (saezlab.org)
  • Examples include 3D point clouds and 3D shapes in computer graphics, functional MRI signals on the brain structural connectivity network, the DNA of the gene regulatory network in genomics, drugs design in quantum chemistry, neutrino detection in high energy physics, and knowledge graph for common sense understanding of visual scenes. (ucla.edu)
  • Finally, gene set enrichment analysis (GSEA) was executed on the identified key lncRNAs to elucidate their functional implications in RA. (bvsalud.org)
  • The particular strengths of CellNetAnalyzer are methods for functional network analysis, i.e. for characterising functional states, for detecting functional dependencies, for identifying intervention strategies, or for giving qualitative predictions on the effects of perturbations. (biomedcentral.com)
  • It provides a large toolbox with various, partially unique, functions and algorithms for functional network analysis. (biomedcentral.com)
  • The hypergeometric distribution method considers the number of overlapping genes while neglecting the functional link between them, and the scoring system used in their study only considered the direct neighbour information of each miRNA in the miRNA functional network. (biomedcentral.com)
  • Functional connections between miRNA targets and disease genes could be obtained via PPI network. (biomedcentral.com)
  • Perturbation-response genes reveal signaling footprints in cancer gene expression. (saezlab.org)
  • Sites associated with insulin transcription and secretion were prominent among those with decreased activity, and the findings reveal the specific regulatory elements that respond to ER stress conditions. (jax.org)
  • The increasingly growing fraction of cancer driver mutations emerging from sequencing studies of protein kinase genes appeared to be inactivating or kinase-dead leading to the loss of function. (utoronto.ca)
  • There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. (researchgate.net)
  • 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)
  • Her lab focuses on mutations that cause changes in gene expression by affecting a process called alternative splicing of RNA. (ucsc.edu)
  • One in eight women in the United States will develop breast cancer in her lifetime, yet only about 15 percent of these cancers have been linked to inherited gene mutations. (ucsc.edu)
  • We propose a principled approach that uses the probabilistic soft logic (PSL) framework to encode well-studied constraints to recover long-range patterns and consistent predictions, while cheaply acquired extractions provide a proxy for unseen observations. (dsridhar.com)
  • Elucidating multi-input processing 3-node gene regulatory network topologies capable of generating striped gene expression patterns. (vliz.be)
  • Using tools from statistical physics, we developed a theoretical framework for characterizing the ensemble of cyclic motifs in real networks. (nih.gov)
  • Our study offers a systems-based perspective on drug design and re-engineering of signaling networks by unravelling relationships between protein kinase networks with molecular chaperones and binding specificity of targeted kinase drugs. (utoronto.ca)
  • Omics technologies give access to these regulatory mechanisms and are thus able to provide large amounts of data at each molecular level. (biomedcentral.com)
  • The detailed structure of molecular networks, including their dependence on conditions and time, are now routinely assayed by various experimental techniques. (nature.com)
  • Intrathymic development of committed progenitor (pro)-T cells from multipotent hematopoietic precursors offers an opportunity to dissect the molecular circuitry establishing cell identity in response to environmental signals. (lu.se)
  • Such synTFs have been successfully used to program activation, or repression, of a gene of interest - a functionality that has proven essential for many studies in molecular biology as well as applications in biotechnology. (genewhisperer.com)
  • Soulet F, Kilarski WW, Antczak P, Herbert J, Bicknell R, Falciani F, Bikfalvi A. (2010) Gene signatures in wound tissue as evidenced by molecular profiling in the chick embryo model. (u-bordeaux.fr)
  • For over a decade, researchers examined the dynamics of selection on network modularity. (wikipedia.org)
  • 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)
  • We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. (researchgate.net)
  • Toward a proteome-scale map of the human protein-protein interaction network. (nature.com)
  • Limb development is a particularly attractive model for unraveling the function and interaction of such regulatory components, because it is very accessible to study and is extremely well conserved between genetic (mouse) and embryologic (chick) model organisms and humans. (nih.gov)
  • Two of the novel methods implemented in CellNetAnalyzer are discussed in more detail regarding algorithmic issues and applications: the computation and analysis (i) of shortest positive and shortest negative paths and circuits in interaction graphs and (ii) of minimal intervention sets in logical networks. (biomedcentral.com)
  • In addition we will address important areas of modern epidemiology such as the influence of early life factors on adult health and disease, but also the importance of the gene-diet-microbiota interaction for body function and health. (lu.se)
  • The recent expansion of repeated HERV sequences has offered a framework for genetic and epigenetic innovation. (mdpi.com)
  • By applying this framework to mild resistance, we have identified a large number of loci whose genetic perturbations significantly affect antibiotic sensitivity. (columbia.edu)
  • We propose the Non-cooperative stochastic game (NCSG) model for control of the genetic regulatory networks and formulate the intervention problem into solving the Nash equilibrium (NE). (uic.edu)
  • Towards this goal, we describe an automated procedure for prioritizing genetic perturbations in order to discriminate optimally between alternative models of a gene-regulatory network. (biomedcentral.com)
  • DeRisi, J.L., Iyer, V.R. & Brown, P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. (nature.com)
  • Yeast microarrays for genome wide parallel genetic and gene expression analysis. (nature.com)
  • Altered islet cell CRE activity has been implicated in T2D genetic risk, but previous investigations have found altered gene expression levels or transcription accessibility at only about a quarter of the T2D-associated locations under steady-state conditions. (jax.org)
  • Daniel Kim's lab studies the role of long noncoding RNA molecules (lncRNAs) in gene expression and cancer. (ucsc.edu)
  • Importantly, our results show that cell types occupy discrete locations in gene expression space and correspondingly, cells exhibit abrupt changes in gene expression profile as they transition from one cell type to another. (harvard.edu)
  • Both cell number and size increased during doming, and these changes were partially controlled by the gene regulatory network (GRN) that triggers flowering. (jic.ac.uk)
  • Finally, and as a result of defining the underlying immune pattern as a small random graph, it is possible to estimate the probability that an individual is immunocompetent to a given antigen, using information from the immune cell networks involved in the response to SARS-CoV-2 in patients with severe COVID-19 and healthy patients. (biorxiv.org)
  • The goal of this project is to model the natural variation in gene expression across many immune cell types using an already established database at LJI ( https://dice-database.org ) and to identify cell type-specific epigenetic regulators of important immune genes. (ucsd.edu)
  • 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)
  • A central challenge is to move beyond the display of a static network to visualizations of networks as a function of time, space and cell state, which capture the adaptability of the cell. (nature.com)
  • This transition encompasses programmed shutoff of stem/progenitor genes, upregulation of T cell specification genes, proliferation, and ultimately commitment. (lu.se)
  • 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)
  • However, continued activity is required to produce the correct number of 5 digits, and if signaling is prematurely interrupted, fewer, but morphologically normal digits are formed due to reduced cell survival and proliferation. (nih.gov)
  • To directly test this model of Shh function, we have restored cell survival in Shh mutant embryos after transient Shh expression by concomitant removal of the pro-apoptotic genes Bak/Bax to intercept cell death, in order to rescue the proposed late Shh role. (nih.gov)
  • Besides comparing gene- and cell-level quality control summaries in both one- and two-dimensional settings, we further quantified these at the batch- and cluster-level. (biomedcentral.com)
  • Blood cell production in the Drosophila hematopoietic organ, the lymph gland , is controlled by intrinsic factors and extrinsic signals. (sdbonline.org)
  • Taking advantage of the finding that certain locations in gene expression space are more "stable" (i.e., far more cells are found in these locations than expected by chance) than others, we used a novel framework to build a probabilistic model of the underlying gene regulatory network. (harvard.edu)
  • We use the probabilistic framework defined in MaBoSS software, based on continuous time Markov chains and stochastic simulations. (researchgate.net)
  • 100.000 cCREs in total), dispersed within the genome and present in cis-regulatory regions of ~81% of human genes, as calculated following gene enrichment analysis. (mdpi.com)
  • Festival [ 126 ], specifically, clearly rates TF- and path-products [ 128, thirteen ] on the gene expression investigation playing with earlier in the day studies, and therefore enhances the abilities of the approach as compared to almost every other causal reason steps. (micsem.org)
  • A variety of one another causal need and you can head usage of entry to info is found in strategies like CellOracle [ 129 ] and you can Inferelator3.0 [ 130 ] that use chromatin accessibility data so you can describe the fresh new cellphone-type certain earlier in the day regulating circle that is following simple by knowledge an excellent regularized linear regression model towards the gene phrase data. (micsem.org)
  • We apply our method gene regulatory networks and show the promise of exploiting KB signals in causal discovery, suggesting a critical, new area of research. (dsridhar.com)
  • Using this procedure, we evaluate 38 candidate regulatory networks in yeast and perform four high-priority gene knockout experiments. (biomedcentral.com)
  • First, we use the previously described modeling procedure to generate a library of models corresponding to different gene-regulatory systems in yeast. (biomedcentral.com)
  • 1997. The hardwiring of development: organization and function of genomic regulatory systems. (wikipedia.org)
  • We have identified a generic property of real complex networks, antiferromagnetic organization, which is characterized by minimal directional coherence of edges along cyclic subgraphs, such that consecutive links tend to have opposing direction. (nih.gov)
  • Comparing these synthetic profiles to empirically measured gene expression data gives some indication how well a computational RGN model corresponds to the real RGN. (uea.ac.uk)
  • In this project we will develop and use a statistsical approach to discriminate alternative RGN models based on the consistence of their synthetic profiles with a data set of empirical gene expression measurements. (uea.ac.uk)
  • The experimental part of the project will produce a data set of gene expression measurements from various Arabidopsis mutants with altered wounding responses. (uea.ac.uk)
  • Data are available at the Gene Expression Omnibus under accession number GSE156478 . (nature.com)
  • I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. (mdpi.com)
  • However, if we are to accurately model large gene networks in complex organisms, including fly, worm, mouse, and human, automated procedures will be essential for analyzing the network, choosing the best new experiments to test the model, conducting the experiments, and integrating the resulting data. (biomedcentral.com)
  • 2006. Communication logic design and analysis for networked control systems . (ucsb.edu)
  • 2004. Communication logics for networked control systems . (ucsb.edu)
  • He is a past Associate Editor of the IEEE Transactions on Neural Networks and Learning Systems , the IEEE Transactions on Systems, man and Cybernetics, Part C: Applications and Reviews , and the IEEE Transactions on Control Systems Technology . (soft-computing.de)
  • Subsequent transcriptomic analysis identified genes differentially regulated by MeJA+NaCl treatment and NaCl alone. (frontiersin.org)
  • The refined networks support previously unknown regulatory mechanisms downstream of SOK2 and SWI4 . (biomedcentral.com)
  • We also observed that most diseases in the same co-regulated module tended to belong to the same disease category, indicating that these diseases might share similar miRNA regulatory mechanisms. (biomedcentral.com)
  • Despite the promise of wastewater sur- gen concentrations represent input from the human veillance, for these measurements to translate into use- population served by the network of pipes within the ful public health tools, bridging the communication and sewershed. (cdc.gov)
  • Genomic Signal Processing (GSP) is a discipline to study the processing of genomic signal. (uic.edu)
  • GSP studies a large collection of genomic sequence instead of individual gene. (uic.edu)
  • In GSP, one would find a proper representation of the genomic information and employ various signal processing methodologies such as detection, prediction, classification, control, etc. (uic.edu)
  • CNA extends its predecessor FluxAnalyzer , originally developed for metabolic network analysis [ 7 ], by new methods for signalling and regulatory networks, i.e. for networks where signal flows are dominating (in contrast to mass flows in metabolic networks). (biomedcentral.com)
  • A ceRNA network was obtained through key lncRNAs, key miRNAs , and key genes . (bvsalud.org)
  • The 2 key lncRNAs, 7 key miRNAs and 6 key genes related to the pathogenesis of RA were obtained, as well as 2 key lncRNA - miRNA - mRNA axes (KRTAP5-AS1-hsa-miR-30b-5p-PNN, XIST-hsa-miR-511-3p/hsa-miR-1277-5p-F2RL1). (bvsalud.org)
  • created a series of models that compared the efficiency of various evolved network topologies in an environment where performance, their only metric for selection, was taken into account, and another treatment where performance as well as the connectivity cost were factored together. (wikipedia.org)
  • This suggests a potential model for module evolution whereby modules form from a system's tendency to resist maximizing connections to create more efficient and compartmentalized network topologies. (wikipedia.org)
  • Genes generally provide the information (in the form of RNA that is transcribed from the DNA) that ultimately leads to translation of the mRNA into protein, the gene product. (genewhisperer.com)
  • For both types of networks, the abstract network model can be set-up and edited via a Network Composer and input masks (see Figure 2 ) or, alternatively, via ASCII (text) files. (biomedcentral.com)