• FANMOD

  • Referenced in 13 articles [sw26134]
  • FANMOD: a tool for fast network motif detection. Motifs are small connected subnetworks that ... FANMOD is a tool for fast network motif detection; it relies on recently developed algorithms ... improve the efficiency of network motif detection by some orders of magnitude over existing tools ... facilitates the detection of larger motifs in bigger networks than previously possible. Additional benefits...
  • Kavosh

  • Referenced in 8 articles [sw29733]
  • Kavosh: a new algorithm for finding network motifs. Background: Complex networks are studied across many ... particularly important to understand biological processes. Motifs in networks are small connected sub-graphs that ... complex networks. Existing algorithms for finding network motifs are extremely costly in CPU time ... algorithm (Kavosh), for finding k-size network motifs with less memory and CPU time...
  • NeMoFinder

  • Referenced in 4 articles [sw29732]
  • protein-protein interactions with meso-scale network motifs. Recent works in network analysis have revealed ... existence of network motifs in biological networks such as the protein-protein interaction (PPI) networks ... sufficiently scalable to find meso-scale network motifs. Also, there has been little ... work to systematically exploit the extracted network motifs for dissecting the vast interactomes.We describe...
  • MODA

  • Referenced in 4 articles [sw29734]
  • MODA: an efficient algorithm for network motif discovery in biological networks. In recent years, interest ... networks. Recently, an active research area has developed in studying local features named motifs ... building blocks of networks. Unfortunately, network motif discovery is a computationally hard problem and finding ... rely on induced subgraphs as motifs of the networks, MODA is able to extract both...
  • MAVisto

  • Referenced in 3 articles [sw29735]
  • tool for the exploration of network motifs. MAVisto is a tool for the exploration ... motifs in biological networks. It provides a flexible motif search algorithm and different views ... analysis and visualization of network motifs. These views help to explore interesting motifs: the frequency ... distribution of a particular motif in the network can be visualized using an advanced layout...
  • MFinder

  • Referenced in 2 articles [sw08095]
  • mfinder is a software tool for network motifs detection. To understand biological networks ... defined network motifs: basic interaction patterns that recur throughout biological networks, much more often than ... networks. The same small set of network motifs appears to serve as the building blocks ... networks from bacteria to mammals. Specific network motifs are also found in signal transduction networks...
  • MESSI

  • Referenced in 13 articles [sw33875]
  • post-translational modification networks are MESSI systems. For example: the motifs in [Feliu and Wiuf...
  • GraMoFoNe

  • Referenced in 3 articles [sw34237]
  • Plugin for Cytoscape. GraMoFoNe (Graph Motif For Networks) is under GPL licence, written in Java ... proteins in the motif got different colors, proteins of the network are colored with ... colors of motif proteins which are homologous. Note that a network node can have ... motif) of colored or uncolored network nodes. It uses an exact algorithm to perform this...
  • SIMBio

  • Referenced in 1 article [sw34238]
  • SIMBio: Searching and Inferring Colorful Motifs in Biological Networks. SIMBio is a tool written ... colorful motifs in vertex colored biological networks. Motifs can be topological or not and gaps...
  • RAGE

  • Referenced in 3 articles [sw24031]
  • enumerator for large networks. Counting network graphlets (and motifs) was shown to have an important ... studying a wide range of complex networks. However, when the network size is large...
  • MI-Sim

  • Referenced in 1 article [sw17108]
  • webs and other classes of ecological network motifs, are a means of describing feeding relationships...
  • tigre

  • Referenced in 1 article [sw36163]
  • expression time series from single input motif networks. The package can be used for inferring...
  • HPAM

  • Referenced in 3 articles [sw10931]
  • regulatory systems and integrating them into genetic networks. Gene expression is determined by protein-protein ... interactions, by means of the DNA motifs that characterize the regulatory factors operating ... they are connected to build genetic networks. We propose a hybrid promoter analysis methodology (HPAM ... discover complex promoter motifs that combines the neural network efficiency and ability of representing imprecise...
  • pSpatiocyte

  • Referenced in 0 articles [sw15003]
  • MAPK model, a typical reaction network motif in cell signaling pathways...
  • HubAlign

  • Referenced in 2 articles [sw34150]
  • align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have...
  • NodeXL

  • Referenced in 7 articles [sw04183]
  • NodeXL, our free and open source network analysis tool, and show examples from our research ... also discuss our recent work on motif simplification, in which common patterns are replaced with...
  • GraphWeb

  • Referenced in 2 articles [sw20147]
  • node annotation; detects gene modules from networks using a collection of algorithms; interprets discovered modules ... using Gene Ontology, pathways, and cis-regulatory motifs...
  • Seeder

  • Referenced in 2 articles [sw35336]
  • perform equally or better than other motif discovery tools. The algorithm is applied ... download on the Comprehensive Perl Archive Network (CPAN) at http://www.cpan.org...
  • MINT

  • Referenced in 1 article [sw16407]
  • huge amounts of data. We present MINT (Motif Identifier for Nucleic acids Trajectory) — an automatic ... hydrogen bonding network resolving the base pairing patterns, identifies secondary structure motifs (helices, junctions, loops...
  • multistatepdscontrol

  • Referenced in 1 article [sw31987]
  • Boolean networks, where structure-based approaches have been developed, as well as stable motif techniques ... development of control strategies for multistate networks is needed. This paper presents a control approach...