• target genes
  • GRNsight automatically lays out either an unweighted or weighted network graph based on an Excel spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows, a Simple Interaction Format (SIF) text file, or a GraphML XML file. (peerj.com)
  • However accurately inferring target genes of TFs is a complex task as different types of data are often not in good agreement. (utoronto.ca)
  • biomarkers
  • With this assumption in mind, we develop statistical algorithms and machine-learning methods to explain -omics data, discover cancer driver genes and predictive biomarkers, interpret cancer mutations, and infer master gene regulators of cellular processes. (utoronto.ca)
  • reveals
  • This network reveals a new model of PD regulation which we call the "crossover model", because the proximal morphogen (RA) controls the distal boundary of Hoxa11, while conversely the distal morphogens (FGFs) control the proximal boundary. (embopress.org)
  • Study further reveals the role of cytochrome P450, xyloglucan endotransglucosylase/hydrolase, glutamate dehydrogenase, methyl crotonoyl carboxylase and of thaumatin-like genes in herbicide resistance. (frontiersin.org)
  • organism
  • For example, learning when nutrients are going to be present in the environment allows the organism to selectively express genes that will take up the food source, thus allowing the organism to harvest energy. (wikipedia.org)
  • Bioinformatics
  • SIB also promotes a PhD Training Network in bioinformatics, which is open to graduate students at Swiss schools of higher education. (wikipedia.org)
  • The objectives of this network are two-fold: To offer graduate students in bioinformatics a set of cutting-edge courses that provide both the theoretical and the practical knowledge necessary to work on a successful PhD research project in bioinformatics. (wikipedia.org)
  • algorithms
  • Most of Gene Regulatory Network (GRN) studies are based on crisp and parametric algorithms, despite inherent fuzzy nature of gene co-regulation. (open.ac.uk)
  • The framework of the models, which provides algorithms for discovering and analyzing structure in complex distributions to describe them succinctly and extract the unstructured information, allows them to be constructed and utilized effectively. (wikipedia.org)
  • The target sequences and the regulated genes can be listed for each TF, which can be used as benchmark for TFBS recognition tools or as training sets for new TFBS recognition algorithms. (wikipedia.org)
  • biology
  • The simulation based on this model, though currently limited in scope in terms of the biology it represents, supports the utility of the Halley and Winkler branching process model in describing the behaviour of stem cell gene regulatory networks. (york.ac.uk)
  • GRNsight has general applicability for displaying any small, unweighted or weighted network with directed edges for systems biology or other application domains. (peerj.com)
  • These network-driven approaches help us find cancer driver mutations but also propose how they function in cancer biology. (utoronto.ca)
  • Results are discussed in a context relative to outstanding questions on termite developmental biology, particularly on regulatory gene networks that respond to JH-, colony- and environmental-cues. (biologists.org)
  • Analysis BioTapestry can create Systems Biology Markup Language files for a subset of networks. (wikipedia.org)
  • Gene regulatory network Systems biology Longabaugh WJR, Davidson EH, Bolouri H (2005). (wikipedia.org)
  • The fields of developmental biology, epigenetics, and DNA repair constitute the framework of IMB's research. (wikipedia.org)
  • PINs are the most intensely analyzed networks in biology. (wikipedia.org)
  • Boolean networks have been used in biology to model regulatory networks. (wikipedia.org)
  • In particular her research group: Teichmann's research has been funded by the European Research Council (ERC), the Medical Research Council (MRC), the Biotechnology and Biological Sciences Research Council (BBSRC), the Wellcome Trust, the European Molecular Biology Organization (EMBO), the Framework Programmes for Research and Technological Development and the European Cooperation in Science and Technology (COST). (wikipedia.org)
  • dynamics
  • For over a decade, researchers examined the dynamics of selection on network modularity. (wikipedia.org)
  • Usually, the dynamics of the system is taken as a discrete time series where the state of the entire network at time t+1 is determined by evaluating each variable's function on the state of the network at time t. (wikipedia.org)
  • Since a Boolean network has only 2N possible states, a trajectory will sooner or later reach a previously visited state, and thus, since the dynamics are deterministic, the trajectory will fall into a steady state or cycle called an attractor (though in the broader field of dynamical systems a cycle is only an attractor if perturbations from it lead back to it). (wikipedia.org)
  • States which occur only at the beginning of trajectories (no trajectories lead to them), are called garden-of-Eden states and the dynamics of the network flow from these states towards attractors. (wikipedia.org)
  • Cell-based mechanics models are often coupled to models describing the intracellular dynamics, such as an ODE representation of a relevant gene regulatory network. (wikipedia.org)
  • genetic
  • propose that genetic information might provide "constraints" on how a dynamic network responds to the environment during learning. (wikipedia.org)
  • Although Boolean networks are a crude simplification of genetic reality where genes are not simple binary switches, there are several cases where they correctly capture the correct pattern of expressed and suppressed genes. (wikipedia.org)
  • Bayesian
  • Four main network model architectures can be distinguished: i) information theory models, ii) boolean network models, iii) differential and difference equation models, iv) Bayesian models. (biomedcentral.com)
  • Bayesian models, or more generally graphical models, make use of Bayes rules and consider gene expressions as random variables. (biomedcentral.com)
  • Two branches of graphical representations of distributions are commonly used, namely, Bayesian networks and Markov random fields. (wikipedia.org)
  • Local independences and global independences are equivalent in Bayesian networks. (wikipedia.org)
  • This type of graphical model is known as a directed graphical model, Bayesian network, or belief network. (wikipedia.org)
  • Both directed acyclic graphs and undirected graphs are special cases of chain graphs, which can therefore provide a way of unifying and generalizing Bayesian and Markov networks. (wikipedia.org)
  • model
  • For example, IRIS [ 8 ] is a software tool that infers the regulatory functions of a gene network by means of a factor graph model. (biomedcentral.com)
  • If the network structure of the model is a directed acyclic graph, the model represents a factorization of the joint probability of all random variables. (wikipedia.org)
  • A Markov random field, also known as a Markov network, is a model over an undirected graph. (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)
  • data
  • The second part of my thesis is about the development of GNRevealer, a method for reverse engineering of gene regulatory networks from temporal data. (hu-berlin.de)
  • It also considers approximate validation methods based on data for which the generating network is not known, the kind of situation one faces when using real data. (eurekaselect.com)
  • A supervised method that can be trained using only positive and unlabeled data, as presented in this paper, is especially beneficial for the task of inferring gene regulatory networks, because only an incomplete set of known regulatory connections is available in public databases such as RegulonDB, TRRD, KEGG, Transfac, and IPA. (biomedcentral.com)
  • They gathered the measurement data of medical laboratory tests (e.g. hemoglobin level ) for a number of patients and they calculated the Pearson correlation between the results for each pair of tests and the pairs of tests which showed a correlation higher than a certain level were connected in the network (e.g. insulin level with blood sugar). (wikipedia.org)
  • Gelenbe has contributed pioneering research concerning the performance of multiprogramming computer systems, virtual memory management, data base reliability optimisation, distributed systems and network protocols. (wikipedia.org)
  • data can be provided during the simulation run, for example by a sensor network. (wikipedia.org)
  • functional
  • BioTapestry was initially made public in late 2003 as a web-based, read-only interactive viewer for the sea urchin network, with the first fully functional editor released in August 2004 (v0.94.1). (wikipedia.org)
  • mutational
  • We applied ActiveDriver in the TCGA pan-cancer project to characterise the mutational landscape of signalling networks and to detect known and candidate cancer driver genes (8,9). (utoronto.ca)
  • The mutational status of rearranged immunoglobulin heavy chain variable (IGVH) genes in CLL is a feature that is widely recognized for dividing patients into groups that are related to their prognoses. (biomedcentral.com)
  • molecular
  • Two major molecular subtypes are recognized, which are characterized by a high or low number of somatic hypermutations in the variable region of the immunoglobulin genes. (biomedcentral.com)
  • Recent studies have indicated conservation of molecular networks through deep evolutionary time. (wikipedia.org)
  • boolean
  • A Boolean network consists of a discrete set of Boolean variables each of which has a Boolean function (possibly different for each variable) assigned to it which takes inputs from a subset of those variables and output that determines the state of the variable it is assigned to. (wikipedia.org)
  • A Boolean network is a particular kind of sequential dynamical system, where time and states are discrete, i.e. both the set of variables and the set of states in the time series each have a bijection onto an integer series. (wikipedia.org)
  • clarification needed] A random Boolean network (RBN) is one that is randomly selected from the set of all possible boolean networks of a particular size, N. One then can study statistically, how the expected properties of such networks depend on various statistical properties of the ensemble of all possible networks. (wikipedia.org)
  • Cognitive
  • His inventions include the design of the first random access fibre-optics local area network, a patented admission control technique for ATM networks, a neural network based anomaly detector for brain magnetic resonance scans, and the cognitive packet network routing protocol to offer quality of service to users. (wikipedia.org)
  • graph
  • When a user uploads an input file specifying an unweighted network, GRNsight automatically lays out the graph using black lines and pointed arrowheads. (peerj.com)
  • Degree (or connectivity, a distinct usage from that used in graph theory) is the number of edges that connect a node, while betweenness is a measure of how central a node is in a network. (wikipedia.org)
  • signals
  • Signals are transduced within cells or in between cells and thus form complex signaling networks. (wikipedia.org)
  • Also, the inductive signals and the genes involved are different from those that control animal development. (wikipedia.org)