• DeCAF

  • Referenced in 28 articles [sw17856]
  • compare the efficacy of relying on various network levels to define a fixed feature ... convolutional activation features, along with all associated network parameters to enable vision researchers...
  • CFinder

  • Referenced in 25 articles [sw12379]
  • locating cliques and overlapping modules in biological networks. Summary: Most cellular tasks are performed ... functionally associated proteins, often referred to as modules. In a protein assocation network modules appear ... overlap with each other and form a network of their own, in which nodes (links ... show that in gene (protein) association networks CFinder can be used to predict the function...
  • GeneMANIA

  • Referenced in 12 articles [sw30022]
  • GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Background: Most ... ridge regression, to integrate multiple functional association networks and predict gene function from a single...
  • SOFAR

  • Referenced in 7 articles [sw31665]
  • SOFAR: large-scale association network learning. Many modern big data applications feature large scale ... understanding the large-scale response-predictor association network structures via layers of sparse latent factors ... constrained optimization to learn the underlying association networks, with broad applications to both unsupervised...
  • DNA

  • Referenced in 8 articles [sw26923]
  • statistical framework for differential network analysis from microarray data. It has been long well known ... computational techniques to detect such interaction or association between gene expressions ... being proposed which lead to an association network. While most microarray analyses look for genes ... greater significance to identify how entire association network structures change between two or more biological...
  • GeneNet

  • Referenced in 9 articles [sw07992]
  • 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...
  • ParaDisEO

  • Referenced in 45 articles [sw01948]
  • instantiate their associated provided classes. Their experimentation on the radio network design real-world application...
  • STRING

  • Referenced in 34 articles [sw23938]
  • STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Complete knowledge ... functional systems. Currently, protein interactions and associations are annotated at various levels of detail ... predicted associations are scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here...
  • ConsensusPathDB

  • Referenced in 6 articles [sw29342]
  • integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes...
  • ClueGO

  • Referenced in 9 articles [sw22916]
  • text file or interactively from a network of Cytoscape. The type of identifiers supported ... share similar associated genes can be fused to reduce redundancy. The ClueGO network is created ... similarity of their associated genes. On the network, the node colour can be switched between...
  • iNA

  • Referenced in 4 articles [sw17973]
  • cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software...
  • DAVID

  • Referenced in 66 articles [sw17292]
  • condense a list of genes or associated biological terms into organized classes of related genes ... efficient interpretation of gene lists in a network context...
  • ncPred

  • Referenced in 2 articles [sw17007]
  • ncPred: ncRNA-Disease Association Prediction through Tripartite Network-Based Inference. ncPred is an algorithm ... disease association based on recommendation technique. We represent our knowledge through a tripartite network, whose ... diseases. Interactions in such a network associate each ncRNA with a disease through its targets ... algorithm, starting from such a network, computes weights between each ncRNA-disease pair using...
  • phyloXML

  • Referenced in 4 articles [sw35271]
  • designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly...
  • Gaggle

  • Referenced in 4 articles [sw20341]
  • four simple data types (names, matrices, networks, and associative arrays) are sufficient to bring together...
  • SeqNet

  • Referenced in 1 article [sw40323]
  • Data from Gene-Gene Association Networks. Methods to generate random gene-gene association networks ... such that the association among gene expression profiles reflect the underlying network. A reference...
  • CAPP

  • Referenced in 9 articles [sw03233]
  • another on the network; and relational databases (RDBs) and associated structured query language (SQL) allow...
  • TinkerCell

  • Referenced in 4 articles [sw20852]
  • each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model ... their parameters and rate equations. The modular network design can be used to exchange modules...
  • MetaNet

  • Referenced in 2 articles [sw01779]
  • MetaNet supports these services over multiple heterogeneous networks. The MetaNet consists of a number ... Presence); each PoP is associated with one or more communication networks. PoPs realize the functionality ... functionality. Associated with each network is an Adapter that hides from the PoP the network...
  • GENeVis

  • Referenced in 2 articles [sw06743]
  • Interactive visualization of gene regulatory networks with associated gene expression time series data We present ... time series data in a gene regulatory network context. This is a network of regulator...