Human genesRegulationMulti-omicsProtein-codinGeneticInteractionsBayesianGRNsMutationsTranscriptionalPatternsPathwaysAnalytical frameworkQuantitativeTheoreticalCharacterizeProteinsMathematicalInteractionProcessesEffectorAllelesCorrelationsDynamicsDifferentialPhenotypeFunctionalMetabolicDevelopmentalPromotersConceptualEnrichmentFunctionallyAnalysisReconstructionHeterogeneousRegulateCoherentAnalysesMolecularNeuralAssayGenomeBiological systemsChromatinComputationalSystemsTherapiesTemporalIntegrate2022PathwayMorphogenesisTranscription factorsInnovationAssaysCharacterizationModelsDYNAMORegulationsCoherenceNCDsTarget geneLegal frameworkMutation
Human genes2
- 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)
- Controversy also marked the approval of GM animals for food, the patenting of human genes, the screening of embryos through preimplantation genetic diagnosis and direct-to-consumer genetic testing. (ethz.ch)
Regulation8
- Understanding gene expression and regulation is essential for understanding biological mechanisms. (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)
- The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. (biomedcentral.com)
- This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach. (biomedcentral.com)
- 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)
- In the third mode, reguland regulation, the regulated entity is the target of a regulatory shift, which is often irreversible or requires action of another regulator to return to original state. (researchsquare.com)
- Alongside, the commission intends to allocate approximately €50 million via the Horizon 2020 Framework Program for Research and Innovation for around 10 basic and applied-research projects to better understand endocrine disruption and develop tools for their assessment and regulation. (medscape.com)
Multi-omics3
- Multi-omics factor analysis-a framework for unsupervised integration of multi-omics data sets. (nature.com)
- Ma, T. & Zhang, A. Integrate multi-omics data with biological interaction networks using multi-view factorization autoencoder (MAE). (nature.com)
- SALMON: survival analysis learning with multi-omics neural networks on breast cancer. (nature.com)
Protein-codin1
- ncRNAs with more than 200 nucleotides are considered as lncRNAs, which originate from intronic and exonic regions of protein-coding genes in both sense and antisense strands, as well as from the intergenic regions [ 21 ]. (biomedcentral.com)
Genetic12
- The recent expansion of repeated HERV sequences has offered a framework for genetic and epigenetic innovation. (mdpi.com)
- Olariu V, Manesso E, commitment and Peterson C. 2017 A deterministic method for estimating free energy genetic network reprogramming paths landscapes with applications to cell commitment and reprogramming paths. (lu.se)
- 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)
- 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)
- 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)
- Genetic variants in the iron regulatory systems influence the likelihood of iron deficiency. (europa.eu)
- 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)
- 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)
- We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. (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)
- In this study, the researchers give a mechanistic understanding of how the mutations in two different molecules interact, explains Mato Lagator: "Most excitingly, we show that - in this gene regulatory system - most of the epistasis arises from the genetic structure of the system. (ist.ac.at)
Interactions12
- 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)
- The construction of Boolean regulatory models requires a substantial amount of experimental data on the interactions between the underlying network components. (u-psud.fr)
- 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)
- We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. (biomedcentral.com)
- Spateo delivers novel methods for digitizing spatial layers/columns to identify spatially-polar genes, and develops a comprehensive framework of cell-cell interaction to reveal spatial effects of niche factors and cell type-specific ligand-receptor interactions. (amillionpieces.com)
- They cautioned that the additive effects model used in the current study "did not incorporate the effects of epistatic interactions," but noted that "our current framework can be extended by using more complex models that capture both additive and epistatic variance. (genomeweb.com)
- T]he FunSeq tool assigns a molecular functional impact score to a mutation based on various features," the authors explained, such as "inter-species conservation, gain or break of transcription factor motifs, disruption of known enhancer-gene interactions, and centrality in the gene regulatory or protein-interaction network. (genomeweb.com)
- They also explored potential passenger mutation interactions with transcription factor binding sites and other regulatory features in the genome and looked at the relationship between proposed passenger mutations and tumor features overall - from the apparent mutational processes at play to the mutation patterns in tumor sub-clones. (genomeweb.com)
- 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)
Bayesian4
- 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)
- 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)
- Furthermore, LEM operates in a Bayesian framework, which accounts for uncertainty, prior information, and robustness in the parameter space. (biomedcentral.com)
- We trained a Bayesian machine learning neural network model to generate a neuroimaging phenotype and AD score representing the probability of AD using structural MRI data in the Alzheimer's Disease Neuroimaging Initiative (ADNI) Cohort (cut-off 0.5, AUC 0.92, PPV 0.90, NPV 0.93). (cdc.gov)
GRNs2
- 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)
- There have been several attempts to define formal mathematical and computational frameworks for modeling GRNs. (biomedcentral.com)
Mutations7
- Along with strong driver mutations and passenger mutations predicted to have neutral effects, the team's analysis pointed to a set of passenger mutations suspected of having intermediate effects on genes from immune, metabolic, and other pathways. (genomeweb.com)
- Muscle function requires unique structural and metabolic adaptations that can render muscle cells selectively vulnerable, with mutations in some ubiquitously expressed genes causing myopathies but sparing other tissues. (bvsalud.org)
- 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)
- 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)
- Genetically speaking, one point mutation changes the transcription factor so that the phenotype of our gene regulatory system changes by X, and the other point mutation changes the binding site so that the phenotype changes by Y. Now, when both mutations occur together, the phenotype is not simply X+Y, it is different. (ist.ac.at)
Transcriptional4
- However, the inherent complexity of transcriptional signatures, with thousands of differentially expressed genes, makes them hard to interpret, thus giving poor mechanistic insights and hampering translation to clinics. (biomedcentral.com)
- 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)
- 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)
- Collectively, these results indicate the potential for therapeutic alteration of cell fate decisions and pathological gene regulatory networks by GATA4-targeted compounds modulating chamber-specific transcriptional programs in multipotent cardiac progenitor cells and cardiomyocytes. (biomedcentral.com)
Patterns5
- Her lab has recently worked with gene expression patterns during sexual reproduction and regeneration of syllids. (uni-goettingen.de)
- My research focuses on the study of macroevolutionary patterns of taxononomic diversity, morphological disparity and biogeographic distribution in a phylogenetic framework. (uni-goettingen.de)
- 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)
- Lastly, Spateo introduces the concept of 'morphometric vector field' of cell migrations, and integrates spatial differential geometry to unveil regulatory programs underlying various organogenesis patterns of Drosophila. (amillionpieces.com)
- 2017. Regulatory network structure determines patterns of intermolecular epistasis. (ist.ac.at)
Pathways1
- Most network biology capitalizes on the observation that genes whose function is altered in a particular phenotype tend to be co-expressed in common pathways and, therefore, co-localized in specific network regions [ 19 ]. (biomedcentral.com)
Analytical framework3
- 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)
- In the first part of my talk, I will introduce an analytical framework dynamo ( https://github.com/aristoteleo/dynamo-release ), and highlight dynamo's power to overcome fundamental limitations of conventional splicing-based RNA velocity analyses to enable accurate velocity estimations on a metabolically labeled human hematopoiesis scRNA-seq dataset. (amillionpieces.com)
- We then interventions within the health sector analytical framework (Atun et al. (who.int)
Quantitative3
- 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)
- 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)
- In my second section of my talk, I will talk about Spateo, a general framework for quantitative spatiotemporal modeling of single-cell resolution spatial transcriptomics. (amillionpieces.com)
Theoretical3
- 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)
- This theoretical framework for analyzing science and technology in society stresses that knowledge about nature and society both conditions and is conditioned by choices about how people wish to govern themselves. (ethz.ch)
- Here we present a theoretical framework for analysing the filter of general porins in relation to translocating molecules with the aid of enhanced molecular simulations quantitatively. (ibecbarcelona.eu)
Characterize3
- Gene expression profiling has become a mainstay approach to characterize cell properties and status, unveiling links between gene activities and disease phenotypes. (biomedcentral.com)
- To these ends his team is also developing methods to characterize gene function in this nontraditional model organism. (uni-goettingen.de)
- Heterogeneous network flow and Petri nets characterize multilayer complex networks. (unifi.it)
Proteins3
- In this work, we present a different paradigm for predicting miRNA-regulated genes based on the encoded proteins. (frontiersin.org)
- Chemically induced gene expression changes were characterized by qRT-PCR, global run-on sequencing (GRO-seq) and immunoblotting, and the network of cooperative proteins of GATA4 and NKX2-5 were further explored by the examination of the GATA4 and NKX2-5 interactome by BioID. (biomedcentral.com)
- Footnote 1 If, for example, species \(s\) is an mRNA, then \(\mathbf x (t_i)\) might contain the concentrations of transcription factors (proteins), from which \(s\) is transcribed, that bind to the promoter of the gene. (biomedcentral.com)
Mathematical2
- 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)
- 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)
Interaction2
- The type of regulatory interaction depends on the species involved, e.g., f may describe mass action kinetics, Michaelis-Menten kinetics, etc. (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)
Processes4
- Logical models such as Boolean networks and Petri nets could represent the network structure but are unable to describe dynamic processes. (biomedcentral.com)
- Substrate concentration courses resulting from gene expression reflect its oscillatory behaviour utilised in a periodical trigger for subsequent processes. (springer.com)
- Regulatory practices, legal norms and even ideas of statehood were renegotiated along with new biological concepts and constructs in processes that we now recognize as having constitutional significance. (ethz.ch)
- One step in this direction is thus to understand exactly which downstream genes and cellular processes become affected in the outcome of driver alterations. (biomedcentral.com)
Effector1
- His efforts are focused on the identification of the complete set of biomineralizing effector genes in the pulmonate gastropod Lymnaea stagnalis , and on identifying the gene regulatory and cellular communication events that coordinate the initiation of shell formation in the early snail embryo. (uni-goettingen.de)
Alleles1
- 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)
Correlations1
- Our strategy starts with the calculation of drug-gene correlations and is followed by a pathway-oriented filtering and a network-diffusion analysis across the interactome. (biomedcentral.com)
Dynamics2
- 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)
- Previous methods for network inference from dynamics data may be broadly classified according to the tools involved. (biomedcentral.com)
Differential6
- Although providing a rich account of disease biology, these studies have failed to yield better drug therapies, as causality and response to drug perturbations cannot be inferred directly from two-state (diseased vs. healthy) differential gene expression analysis [ 2 , 3 ]. (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)
- In his post-doc at Whitehead Institute with Dr. Jonathan Weissman, Xiaojie developed Dynamo (aristoteleo/dynamo-release) to infers absolute RNA velocity with metabolic labeling enabled single-cell RNA-seq, reconstructs continuous vector fields that predict fates of individual cells, employs differential geometry to extract underlying gene regulatory network regulations, and ultimately predicts optimal reprogramming paths and makes nontrivial in silico perturbation predictions. (amillionpieces.com)
- GATA4-targeted compounds 3i-1000 and 3i-1103 were identified as differential modulators of atrial and ventricular gene expression. (biomedcentral.com)
- Heterogeneity is generated both passively, e.g. by differential gene expression in cells of a tissue, and actively, such as the generation of the immense variation for immunological recognition molecules. (researchsquare.com)
- A standard approach is to view a biopathway as a network of biochemical reactions, which is modelled as a system of ordinary differential equations (ODEs). (biomedcentral.com)
Phenotype1
- By functional network, we mean a network such that an experimental perturbation will likely alter the dynamical phenotype of the network. (biomedcentral.com)
Functional4
- The formula applies to any explicit functional form of the kinetic rate laws such as mass-action, Michaelis-Menten, etc. (biomedcentral.com)
- In a novel, automated machine learning framework, we use sequence as well as diverse functional annotations to train models on multiple organisms using experimentally validated data. (frontiersin.org)
- One of the best examples of a large functional network is the mammalian circadian oscillator, for which the current core network contains about 30 nodes. (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)
Metabolic1
- Their ability to maintain cell and tissue homeostasis is critical, with many miRNA genes implicated in human diseases such as metabolic, inflammatory, and neurodegenerative diseases ( Vishnoi and Rani, 2017 ). (frontiersin.org)
Developmental5
- 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)
- Developmental systems also afford an excellent avenue to study complex regulatory circuits designed to ensure the robust functioning of a normal process. (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)
- 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)
- Pharmacological modulation of cell fate decisions and developmental gene regulatory networks holds promise for the treatment of heart failure. (biomedcentral.com)
Promoters1
- In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms. (genomeweb.com)
Conceptual1
- However, that influence is hard to see from the traditional standpoint, so we need to encourage alternative conceptual frameworks. (uncommondescent.com)
Enrichment1
- Finally, we prove the predictive capability of the modules and demonstrate how they can be used as gene sets in conventional enrichment analyses. (biomedcentral.com)
Functionally2
- To simplify drug signatures, we have developed a network-based methodology to identify functionally coherent gene modules. (biomedcentral.com)
- This has opened up the possibility to carry out systematic studies to uncover the repertoire of functionally related groups of driver genes. (biomedcentral.com)
Analysis6
- Provided that the panel of cell lines is large enough, this approach allows for a new type of gene expression analysis where basal expression levels are correlated to drug response phenotypes. (biomedcentral.com)
- Fan, T. W. M., Bandura, L. L., Higashi, R. M. & Lane, A. N. Metabolomics-edited transcriptomics analysis of Se anticancer action in human lung cancer cells. (nature.com)
- Network analysis pinpointed several well-known flowering-related genes such as ELF , COL1 , FLT , and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. (biomedcentral.com)
- However, the comparative transcriptome analysis of two spinach accessions with different bolting times identified genome-wide gene expression profiling and large-scale discovery of flowering-related genes from vegetative and reproductive leaves [ 13 ]. (biomedcentral.com)
- Ewan led the analysis of the Human Genome gene set, mouse and chicken genomes and the ENCODE project, focusing on non-coding elements of the human genome. (nottingham.ac.uk)
- There are two main reasons why the catalogs of cancer drivers produced by the aforementioned projects and others need to be broken down into related sets of genes for deeper analysis. (biomedcentral.com)
Reconstruction3
- 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)
- My paper on reconstruction of Gene Regulatory Networks reports the SimGenex framework which can be used to in silico simulate both the wetlab and artificial life, from cell to organ to plant. (niab.com)
Heterogeneous1
- A Resilient Consensus Protocol for Networks with Heterogeneous Confidence and Byzantine Adversaries. (unifi.it)
Regulate2
- MicroRNAs (miRNAs) post-transcriptionally regulate genes across all animals and plants. (frontiersin.org)
- A largely studied class of biological systems is constituted by systems which regulate the expression of genes in an organism. (biomedcentral.com)
Coherent2
- 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)
- Our modeling approach is able to simulate some interesting temporal properties of gene regulatory network motifs: the delay in the activation and the deactivation of the "output" gene in the coherent type-1 feedforward loop, the pulse in the incoherent type-1 feedforward loop, the bistability nature of double positive and double negative feedback loops, the oscillatory behavior of the negative feedback loop, and the "lock-in" effect of positive autoregulation. (biomedcentral.com)
Analyses2
- In this respect, he is using a broad range of methods including immunohistochemical analyses, histological staining procedures and ultrastructural investigations as well as gene expression analyses and phylogenomic approaches. (uni-goettingen.de)
- The catalog of driver genes involved in the development of several malignancies has grown in recent years, as a result of whole-exome and whole-genome analyses of cohorts of tumors, mainly within the framework of large international consortia [ 3 , 4 ]. (biomedcentral.com)
Molecular4
- The integration of large-scale drug sensitivity screens and genome-wide experiments is changing the field of pharmacogenomics, revealing molecular determinants of drug response without the need for previous knowledge about drug action. (biomedcentral.com)
- 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)
- 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)
- Cellular decisions depend on the coordinated action of molecular components. (u-psud.fr)
Neural2
- 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)
- AI and its sub fields like machine learning, neural networks and deep learning. (datasciencecentral.com)
Assay2
- Transcription factor GATA4-targeted compounds that have previously shown in vivo efficacy in cardiac injury models were tested for stage-specific activation of atrial and ventricular reporter genes in differentiating pluripotent stem cells using a dual reporter assay. (biomedcentral.com)
- Effective use of hierarchical lines of evidence relies on consideration of the rele- vance and potency of assays, organization of assays by mode of action, and better assay validation. (cdc.gov)
Genome1
- Large tumor genome sequencing projects have now uncovered a few hundred genes involved in the onset of tumorigenesis, or drivers, in some two dozen malignancies. (biomedcentral.com)
Biological systems1
- We present a Statecharts-based approach for the modeling of gene regulatory network motifs in biological systems. (biomedcentral.com)
Chromatin2
- Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. (nature.com)
- Exploiting the aforementioned catalogs of driver genes, for example, we recently revealed the mutational landscape of chromatin regulatory factors (CRFs) in cancer [ 5 ]. (biomedcentral.com)
Computational2
- We strive to provide computational frameworks for understanding how observable biological properties arise from complex systems. (iospress.com)
- Recently, a great effort has been devoted to give gene regulatory networks a formal semantics based on existing computational frameworks. (biomedcentral.com)
Systems4
- A central objective of current systems biology research is explaining the actions among components in biopathways. (biomedcentral.com)
- The latest regulatory systems for preventing and control- of animal or human rabies, such as the cases in 2006, and ling rabies provide an effective model for elimination of the recent increases in the international movement of people disease worldwide. (cdc.gov)
- Health systems framework (WHO, 2007). (who.int)
- National Action Alliance for Suicide Prevention: Transforming Health Systems Initiative Work Group. (msdmanuals.com)
Therapies1
- One of the most exciting areas of innovation is Cell and Gene Therapy, with many therapies already changing the industry and patients' lives. (accenture.com)
Temporal1
- We find previously proposed learning objectives for GFlowNets, flow matching and detailed balance, which are analogous to temporal difference learning, to be prone to inefficient credit propagation across long action sequences. (nips.cc)
Integrate2
- Network biology offers means to integrate a large amount of omics data [ 18 ]. (biomedcentral.com)
- Interpersonal neurobiology (IPNB) or relational neurobiology is an interdisciplinary framework that was developed in the 1990s by Daniel J. Siegel, who sought to bring together scientific disciplines to demonstrate how the mind, brain, and relationships integrate. (wikipedia.org)
20221
- Title: Malaria action plan for the Eastern Mediterranean Region, 2022-2030 / World Health Organization. (who.int)
Pathway1
- To further validate the results pathway study was performed to identify the involvement of the coding genes in type II diabetes. (researchgate.net)
Morphogenesis1
- 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)
Transcription factors1
- 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)
Innovation1
- Is regulatory innovation fit for purpose? (repec.org)
Assays2
- Reporter gene assays were conducted to examine combinatorial effects of GATA-targeted compounds and bromodomain and extraterminal domain (BET) inhibition on chamber-specific gene expression. (biomedcentral.com)
- In this line, reporter gene assays with combinatorial treatment of 3i-1000 and the BET bromodomain inhibitor (+)-JQ1 demonstrated the cooperative role of GATA4 and BRD4 in the modulation of chamber-specific cardiac gene expression. (biomedcentral.com)
Characterization3
- Network biology strategies like module detection are able to digest the outcome of large-scale pharmacogenomic initiatives, thereby contributing to their interpretability and improving the characterization of the drugs screened. (biomedcentral.com)
- 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)
- Hazard characterization the best features of existing guidance, frameworks, and models using a weight-of-evidence (WoE) approach. (cdc.gov)
Models6
- The SGD method proposed in the paper presents a general framework of inferring parameters for stochastic kinetic models. (biomedcentral.com)
- 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)
- Previous models have proposed that Shh acts as a temporally integrated morphogen to instruct digit development by promoting digits from anterior to posterior (A-P) identities over extended time of action. (nih.gov)
- Fully exploiting these data, however, requires kinetic models capable of unveiling governing regulatory functions. (amillionpieces.com)
- We present an improved method for modeling gene regulatory network motifs using Statecharts and we describe the successful modeling of several motifs, including those which could not be modeled or whose models could not be distinguished using the method of a previous proposal. (biomedcentral.com)
- On convergence for hybrid models of gene regulatory networks under polytopic uncertainties: a Lyapunov approach. (unifi.it)
DYNAMO1
- Leveraging the least-action-path method, dynamo accurately predicts drivers of numerous hematopoietic transitions. (amillionpieces.com)
Regulations2
- more than thirty percent of the modeled regulations, based entirely on gene expression files, were found to be consistent with previous discoveries from known databases. (biomedcentral.com)
- In Africa and Asia, human rabies is contracted primar- ing on the latest legal regulations and plans of action. (cdc.gov)
Coherence1
- Policy coherence versus regulatory governance. (repec.org)
NCDs1
- First, we briefly present the ana- include both the delivery of health- municable diseases (NCDs) includ- lytical framework used in this chap- care services and broader individu- ing cancer (UN, 2015). (who.int)
Target gene1
- Time delay is the time lag during which expression change of the regulator is transmitted to change in target gene expression. (biomedcentral.com)
Legal framework1
- Our licenses are issued by the Government of Antigua and Barbuda and provide the legal framework that governs online casino gambling within the British West Indies region. (thebestdiaper.pk)
Mutation1
- 2.To comparatively study the effect of sous vide fish on non-haem iron absorption from vegetables in a group of women with either the G277S/G277S or G277S/G277G genotype (preferably homozygous) versus a control group that do not present the indicated mutation in the transferrin gene but the wild type G277G/G277G. (europa.eu)