• ARACNE

  • Referenced in 38 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...
  • DAVID

  • Referenced in 66 articles [sw17292]
  • modules for efficient interpretation of gene lists in a network context...
  • KEGG

  • Referenced in 281 articles [sw13866]
  • system, consisting of molecular building blocks of genes and proteins (genomic information) and chemical substances ... wiring diagrams of interaction, reaction and relation networks (systems information). It also contains disease...
  • SNOOPY

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

  • Referenced in 81 articles [sw09080]
  • other molecular states; and to link the network to databases of functional annotations. The Core ... interaction pathways correlating with changes in gene expression, a study of protein complexes involved ... physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models...
  • 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...
  • REVEAL

  • Referenced in 29 articles [sw36999]
  • inference of genetic network architectures. Given the immanent gene expression mapping covering whole genomes during ... principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables ... networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression ... elements controlling each element or gene in the network. This process is unequivocal and exact...
  • RoVerGeNe

  • Referenced in 13 articles [sw10954]
  • tool for the Robust Verification of Gene Networks. Rovergene is a tool for the analysis ... regulatory networks under parameter uncertainty. Genetic regulatory networks are described by a class of piecewise ... robustness of dynamical properties of gene networks with respect to parameter variations ... tuning of synthetic gene networks...
  • BiNGO

  • Referenced in 14 articles [sw13896]
  • biological networks. Summary: The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java ... list of genes, pasted as text, or interactively on subgraphs of biological networks visualized...
  • GeneNet

  • Referenced in 9 articles [sw07992]
  • GeneNet: Modeling and Inferring Gene Networks. GeneNet is a package for analyzing gene expression (time ... with focus on the inference of gene networks. In particular, GeneNet implements the methods ... learning large-scale gene association networks (including assignment of putative directions...
  • GNA

  • Referenced in 26 articles [sw35974]
  • regulatory interactions in combination with gene expression data. Genetic Network Analyzer consists of a simulator...
  • NEURON

  • Referenced in 189 articles [sw03059]
  • connection delay. The performance of three published network models with very different spike patterns exhibits ... speed cache. On the EPFL IBM Blue Gene, almost linear speedup was obtained ... magnitude makes practical the running of large network simulations that could otherwise not be explored...
  • TIGRESS

  • Referenced in 9 articles [sw23826]
  • Selection. BACKGROUND: Inferring the structure of gene regulatory networks (GRN) from a collection of gene ... inference methods in the DREAM5 gene network inference challenge. In particular, TIGRESS was evaluated...
  • CFinder

  • Referenced in 25 articles [sw12379]
  • overlap with each other and form a network of their own, in which nodes (links ... groups. We show that in gene (protein) association networks CFinder can be used to predict...
  • GeneRank

  • Referenced in 17 articles [sw27064]
  • gene expression information with a network structure derived from gene annotations (gene ontologies) or expression ... algorithm offers an improved ranking of genes compared to pure expression change rankings. Conclusion ... underlying network. GeneRank offers an improvement compared to assessing the importance of a gene based...
  • 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...
  • SGN Sim

  • Referenced in 8 articles [sw29325]
  • 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 ... systems of chemical reactions. Perturbations, e.g. gene deletion, over-expression, copy and mutation ... simulation based on the yeast transcriptional network. AVAILABILITY: SGNSim program, instructions and examples available...
  • SynTReN

  • Referenced in 17 articles [sw12311]
  • algorithms to infer the structure of gene regulatory networks based on expression data...
  • GeneMANIA

  • Referenced in 12 articles [sw30022]
  • real-time multiple association network integration algorithm for predicting gene function. Background: Most successful computational ... integrate multiple functional association networks and predict gene function from a single process-specific network ... Conclusion: GeneMANIA is fast enough to predict gene function on-the-fly while achieving state...
  • 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...