• ARACNE

  • Referenced in 39 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 35 articles [sw04386]
  • biochemcial networks as metabolic, signal transduction, gene regulatory networks, compare poster ”overview on the research...
  • Celldesigner

  • Referenced in 22 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 82 articles [sw09080]
  • physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models...
  • SynTReN

  • Referenced in 17 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 26 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...
  • SW1PerS

  • Referenced in 10 articles [sw17206]
  • hypotheses regarding the structure of gene regulatory networks...
  • 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...
  • NETWORKINFERENCE

  • Referenced in 8 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...
  • 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...
  • 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...
  • GeNGe

  • Referenced in 3 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...
  • OKVAR-Boost

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

  • Referenced in 3 articles [sw43051]
  • NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms. One of the long ... biology is the topology inference of gene regulatory networks from high-throughput omics data. Recently ... have been established to benchmark network inference techniques using gene expression measurements. In these challenges ... putative evidence of a regulatory link existing between both genes. The contribution of this work...
  • COXPRESdb

  • Referenced in 7 articles [sw41318]
  • analyses in Gene Ontology and in cis elements, along with interactive network analyses with Cytoscape ... analyses of functional and regulatory networks of genes in a variety of animal species...