• RegulonDB

  • Referenced in 51 articles [sw25948]
  • 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 ... expands beyond transcription initiation, including RNA regulatory elements, specifically riboswitches, attenuators and small RNAs, with...
  • ARACNE

  • Referenced in 34 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 ... scale up to the complexity of regulatory networks in mammalian cells, yet general enough ... ARACNE’s ability to reconstruct transcriptional regulatory networks using both a realistic synthetic dataset...
  • Ginsim

  • Referenced in 29 articles [sw09090]
  • qualitative modelling, simulation and analysis of regulatory networks. This paper presents GINsim, a Java software ... modelling, analysis and simulation of genetic regulatory networks. Formally, our approach leans on discrete mathematical ... definition and the parameterisation of a regulatory graph, as well as a simulation engine ... model analysis of the inter-cellular regulatory network activating Notch at the dorsal–ventral boundary...
  • GNA

  • Referenced in 21 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 ... analysis of various regulatory systems, such as the networks controlling the initiation of sporulation...
  • SNOOPY

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

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

  • Referenced in 10 articles [sw23121]
  • ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Although ... surprisingly little is known about the regulatory interaction networks among the multiple classes of RNAs ... other ncRNAs from the miRNA-mediated regulatory networks. Finally, we developed interactive web implementations ... ncRNA functions and their coordinated regulatory networks...
  • Cytoscape

  • Referenced in 69 articles [sw09080]
  • physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models...
  • SynTReN

  • Referenced in 14 articles [sw12311]
  • infer the structure of gene regulatory networks based on expression data is an important subject...
  • LBS

  • Referenced in 14 articles [sw12372]
  • modular descriptions of metabolic, signalling and regulatory networks in terms of reactions between modified complexes...
  • SIRENE

  • Referenced in 7 articles [sw17419]
  • SIRENE: Supervised inference of regulatory networks. Motivation: Living cells are the product of gene expression ... genes. The elucidation of transcriptional regulatory networks is thus needed to understand the cell ... have been proposed to infer gene regulatory networks from gene expression data, a recent comparison ... propose SIRENE (Supervised Inference of Regulatory Networks), a new method for the inference of gene...
  • Siconos

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

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

  • Referenced in 8 articles [sw29325]
  • Simulator’, a tool to model gene regulatory networks (GRN) where transcription and translation are modeled...
  • SQUAD

  • Referenced in 5 articles [sw29353]
  • Method for the Qualitative Modeling of Regulatory Networks. The wealth of molecular information provided ... efforts dedicated to the reconstruction of regulatory networks in diverse biological systems. This information, however ... patterns of expression to infer the regulatory networks that generate such patterns. One of these...
  • NARROMI

  • Referenced in 5 articles [sw24066]
  • reduction technique improves accuracy of gene regulatory network inference. MOTIVATION: Reconstruction of gene regulatory networks ... vital for understanding the complex regulatory mechanisms within the cell. Despite various methods developed...
  • GADDI

  • Referenced in 6 articles [sw18895]
  • graphs, e.g., protein interaction networks, gene regulatory networks, etc. The need for indexing large graphs...
  • NETWORKINFERENCE

  • Referenced in 6 articles [sw06744]
  • inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks. NETWORKINFERENCE performed well at recovering feedback loops...
  • 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...