• RegulonDB

  • Referenced in 53 articles [sw25948]
  • offering curated knowledge of the transcriptional regulatory network of Escherichia coli K12, currently the best ... known electronically encoded database of the genetic regulatory network of any free-living organism. This...
  • GNA

  • Referenced in 26 articles [sw35974]
  • modeling and simulation of genetic regulatory networks. The aim of GNA is to assist biologists ... constructing a model of a genetic regulatory network using knowledge about regulatory interactions in combination ... simulator of qualitative models of genetic regulatory networks in the form of piecewise-linear differential...
  • Ginsim

  • Referenced in 29 articles [sw09090]
  • qualitative modelling, simulation and analysis of regulatory networks. This paper presents GINsim, a Java software ... qualitative modelling, analysis and simulation of genetic regulatory networks. Formally, our approach leans on discrete...
  • RoVerGeNe

  • Referenced in 13 articles [sw10954]
  • tool for the analysis of genetic regulatory networks under parameter uncertainty. Genetic regulatory networks...
  • REVEAL

  • Referenced in 28 articles [sw36999]
  • reverse engineering algorithm for inference of genetic network architectures. Given the immanent gene expression mapping ... principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables ... investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables...
  • ASP-G

  • Referenced in 2 articles [sw34356]
  • based method for finding attractors in genetic regulatory networks. To allow for a more flexible...
  • Jimena

  • Referenced in 1 article [sw29354]
  • computing and system state identification for genetic regulatory networks. Background: Boolean networks capture switching behavior ... many naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states ... high degree polynomial interpolation of Boolean genetic regulatory networks (GRNs) in cellular processes such...
  • MGraph

  • Referenced in 1 article [sw21099]
  • interface allows the user to predict genetic regulatory networks by a graphical gaussian model ... valuable aid in the prediction of genetic regulatory networks, as well as in investigations...
  • Cytoscape

  • Referenced in 80 articles [sw09080]
  • databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans ... layout and query the network; to visually integrate the network with expression profiles, phenotypes ... other molecular states; and to link the network to databases of functional annotations. The Core ... physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models...
  • ARACNE

  • Referenced in 38 articles [sw17200]
  • ARACNE’s ability to reconstruct transcriptional regulatory networks using both a realistic synthetic dataset ... Relevance Networks and Bayesian Networks. Application to the deconvolution of genetic networks in human...
  • KINSOLVER

  • Referenced in 1 article [sw00488]
  • ways to measure the state of these networks. The goal here is being able ... arbitrary ensemble of hypothesized biochemical and genetic regulatory networks to predict what a cell...
  • HPAM

  • Referenced in 3 articles [sw10931]
  • identifying regulatory systems and integrating them into genetic networks. Gene expression is determined by protein ... motifs that characterize the regulatory factors operating in the transcription of a gene, becomes crucial ... they are connected to build genetic networks. We propose a hybrid promoter analysis methodology (HPAM ... complex promoter motifs that combines the neural network efficiency and ability of representing imprecise...
  • gNCA

  • Referenced in 4 articles [sw08821]
  • transcription network analysis by incorporating regulatory signal constraints arising from genetic knockouts. The theoretical bases ... uniqueness of solution and distinguishability between networks are derived. In addition, numerical techniques for robust...
  • SGN Sim

  • Referenced in 8 articles [sw29325]
  • stochastic genetic networks simulator. We present SGNSim, ’Stochastic Gene Networks Simulator’, a tool to model ... gene regulatory networks (GRN) where transcription and translation are modeled as multiple time delayed events...
  • DYVIPAC

  • Referenced in 1 article [sw41442]
  • dynamics of signalling and gene regulatory networks caused by genetic alternations. Elucidating the network dynamics...
  • DREAM4

  • Referenced in 5 articles [sw36908]
  • DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models. Conclusion/Significance ... test based method proved powerful at ranking regulatory interactions, tying for first ... DREAM4 100-gene in-silico network inference challenge. We demonstrate complementarity between this method ... genetic perturbations). Our evaluation of the performance of multiple methods for network inference suggests avenues...
  • SPINE

  • Referenced in 6 articles [sw29309]
  • allows the cell to cope with changing genetic, developmental and environmental conditions. The accumulating large ... interactions allow us to begin to uncover regulatory and signaling pathways within the cell that ... connect causal to affected genes on a network of physical interactions. Results: We present...
  • VirtualLeaf

  • Referenced in 4 articles [sw28766]
  • multilevel regulatory mechanisms complicate classic molecular genetics or functional genomics approaches to biological development, because ... roles of gene products in regulatory networks, the conditions of gene expression, etc. This interplay...
  • GlobalMIT

  • Referenced in 3 articles [sw38463]
  • regulatory network (GRN). Due to the NP-hard nature of learning static Bayesian network structure ... meta stochastic global optimization framework such as genetic algorithm or simulated annealing. Results: This article...
  • trigger

  • Referenced in 1 article [sw36166]
  • construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage ... pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal...