• ARACNE

  • Referenced in 30 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 31 articles [sw04386]
  • biochemcial networks as metabolic, signal transduction, gene regulatory networks, compare poster ”overview on the research...
  • Celldesigner

  • Referenced in 19 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 59 articles [sw09080]
  • physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models...
  • SynTReN

  • Referenced in 13 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 10 articles [sw25724]
  • converter. Sliding mode control systems. Biology (Gene regulatory network). Other applications are found in Systems...
  • 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...
  • TIGRESS

  • Referenced in 8 articles [sw23826]
  • Selection. BACKGROUND: Inferring the structure of gene regulatory networks (GRN) from a collection of gene...
  • NARROMI

  • Referenced in 5 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...
  • GADDI

  • Referenced in 5 articles [sw18895]
  • represented by graphs, e.g., protein interaction networks, gene regulatory networks, etc. The need for indexing...
  • 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...
  • SW1PerS

  • Referenced in 5 articles [sw17206]
  • hypotheses regarding the structure of gene regulatory networks...
  • OKVAR-Boost

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

  • Referenced in 46 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...
  • GeNGe

  • Referenced in 2 articles [sw29326]
  • GeNGe: systematic generation of gene regulatory networks. Summary: The analysis of gene regulatory networks (GRNs ... have developed the web application GeNGe (GEne Network GEnerator), a controlled framework for the automatic...
  • Charlie

  • Referenced in 3 articles [sw12881]
  • such as metabolic, signal transduction, and gene regulatory networks. It is publicly available...
  • BNArray

  • Referenced in 2 articles [sw30810]
  • BNArray: An R package for constructing gene regulatory networks from microarray data by using Bayesian ... facilitates the construction of gene regulatory networks from DNA microarray data by using Bayesian network...
  • Ginsim

  • Referenced in 27 articles [sw09090]
  • model analysis of the inter-cellular regulatory network activating Notch at the dorsal–ventral boundary ... focus on the cross-regulations between five genes (within and between two cells), which implements...
  • maigesPack

  • Referenced in 1 article [sw25800]
  • statistical method for measuring activation of gene regulatory networks. Motivation: Gene expression data analysis ... model for the activation measuring of gene regulatory networks, instead of the traditional gene ... statistical procedure for testing hypothesis regarding gene regulatory network activation. The real probability distribution ... hypothetical network and the activation measuring of two KEGG networks, both based on gene expression...