• ARACNE

  • Referenced in 36 articles [sw17200]
  • algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. Background: Elucidating ... gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing...
  • SNOOPY

  • Referenced in 34 articles [sw04386]
  • biochemcial networks as metabolic, signal transduction, gene regulatory networks, compare poster ”overview on the research...
  • Celldesigner

  • Referenced in 21 articles [sw09942]
  • process diagram editor for gene-regulatory and biochemical networks. CellDesigner is a structured diagram editor ... drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with ... representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation...
  • Cytoscape

  • Referenced in 76 articles [sw09080]
  • physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models...
  • SynTReN

  • Referenced in 15 articles [sw12311]
  • algorithms to infer the structure of gene regulatory networks based on expression data...
  • SIRENE

  • Referenced in 7 articles [sw17419]
  • transcription of thousands of genes. The elucidation of transcriptional regulatory networks is thus needed ... methods have been proposed to infer gene regulatory networks from gene expression data, a recent ... method for the inference of gene regulatory networks from a compendium of expression data ... method decomposes the problem of gene regulatory network inference into a large number of local...
  • Siconos

  • Referenced in 12 articles [sw25724]
  • converter. Sliding mode control systems. Biology (Gene regulatory network). Other applications are found in Systems...
  • GNA

  • Referenced in 24 articles [sw35974]
  • genetic regulatory network using knowledge about regulatory interactions in combination with gene expression data. Genetic ... simulator of qualitative models of genetic regulatory networks in the form of piecewise-linear differential...
  • TIGRESS

  • Referenced in 9 articles [sw23826]
  • Selection. BACKGROUND: Inferring the structure of gene regulatory networks (GRN) from a collection of gene...
  • NARROMI

  • Referenced in 6 articles [sw24066]
  • redundancy reduction technique improves accuracy of gene regulatory network inference. MOTIVATION: Reconstruction of gene regulatory ... networks (GRNs) is of utmost interest to biologists and is vital for understanding the complex ... regulatory mechanisms within the cell. Despite various methods developed for reconstruction of GRNs from gene...
  • SGN Sim

  • Referenced in 8 articles [sw29325]
  • Networks Simulator’, a tool to model gene regulatory networks (GRN) where transcription and translation ... systems of chemical reactions. Perturbations, e.g. gene deletion, over-expression, copy and mutation...
  • GADDI

  • Referenced in 6 articles [sw18895]
  • represented by graphs, e.g., protein interaction networks, gene regulatory networks, etc. The need for indexing...
  • C-ImmSim

  • Referenced in 5 articles [sw34210]
  • Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based ... this work is to integrate a gene network of the TH differentiation in an agent ... gene activation and transcription. The gene regulatory network includes genes-related molecules that have been...
  • SW1PerS

  • Referenced in 7 articles [sw17206]
  • hypotheses regarding the structure of gene regulatory networks...
  • NETWORKINFERENCE

  • Referenced in 6 articles [sw06744]
  • network inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks. NETWORKINFERENCE performed well at recovering feedback ... data to recover multiple regulators of a gene. When collecting the same number of data...
  • ASIAN

  • Referenced in 3 articles [sw36771]
  • server for inferring a regulatory network framework from gene expression profiles. The standard workflow ... analysis is the inference of a gene regulatory network, and some computational methods have been ... intensively developed to deduce the gene regulatory network. Here, we describe our web server ... framework of regulatory networks from a large number of gene expression profiles, based on graphical...
  • OKVAR-Boost

  • Referenced in 3 articles [sw24063]
  • infer nonlinear dynamics and interactions in gene regulatory networks. MOTIVATION: Reverse engineering of gene regulatory...
  • Charlie

  • Referenced in 4 articles [sw12881]
  • such as metabolic, signal transduction, and gene regulatory networks. It is publicly available...
  • RegulonDB

  • Referenced in 51 articles [sw25948]
  • RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental ... offering curated knowledge of the transcriptional regulatory network of Escherichia coli K12, currently the best ... electronically encoded database of the genetic regulatory network of any free-living organism. This paper ... origin of their effectors and by gene ontology class. We have now computational predictions...
  • GlobalMIT

  • Referenced in 3 articles [sw38463]
  • modeling various biological networks including the gene regulatory network (GRN). Due to the NP-hard ... learning the globally optimal DBN structure from gene expression data. We propose using a recently...