• ARACNE

  • Referenced in 35 articles [sw17200]
  • ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context ... methods. Results: We prove that ARACNE reconstructs the network exactly (asymptotically) if the effect ... assess ARACNE’s ability to reconstruct transcriptional regulatory networks using both a realistic synthetic dataset ... misestimation of mutual information on network reconstruction, and show that algorithms based on mutual information...
  • PhyloNet

  • Referenced in 9 articles [sw20725]
  • among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed ... reticulate evolutionary events, result in networks, rather than trees, of relationships. Various software tools have ... maximum parsimony criterion; and (4) evolutionary network reconstruction: reconstructing an evolutionary network from a species ... studying the performance of evolutionary network reconstruction methods. Further, the software package supports the proposed...
  • BiGG

  • Referenced in 10 articles [sw17247]
  • experimental data. As the number of such reconstructions and analysis methods increases, there ... Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks ... high quality curated metabolic models and reconstructions. It is freely available for academic...
  • BoolNet

  • Referenced in 14 articles [sw07365]
  • synchronous, asynchronous, and probabilistic Boolean networks Provides methods to reconstruct and generate synchronous, asynchronous...
  • T-REX

  • Referenced in 8 articles [sw20724]
  • visualizing phylogenetic trees and networks. T-REX (Tree and reticulogram REConstruction ... server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference ... matrices as well as for reconstructing reticulograms and HGT networks, including the detection and validation...
  • NARROMI

  • Referenced in 6 articles [sw24066]
  • improves accuracy of gene regulatory network inference. MOTIVATION: Reconstruction of gene regulatory networks (GRNs ... cell. Despite various methods developed for reconstruction of GRNs from gene expression profiles, they...
  • COBRA Toolbox

  • Referenced in 13 articles [sw32083]
  • COBRA Toolbox: The COnstraint-Based Reconstruction and Analysis Toolbox is a MATLAB software suite ... quantitative prediction of cellular and multicellular biochemical networks with constraint-based modelling. It implements ... basic and advanced modelling methods, including reconstruction and model generation as well as biased ... metabolic phenotypes using genome-scale biochemical networks...
  • SPINE

  • Referenced in 5 articles [sw29309]
  • genes are searched for in this network. The reconstruction problem is translated into that ... entire yeast network to predict protein effects and reconstruct signaling and regulatory pathways. Overall...
  • EDISON

  • Referenced in 2 articles [sw08266]
  • EDISON: Software for network reconstruction and changepoint detection. Package EDISON (Estimation of Directed Interactions from ... expression) runs an MCMC simulation to reconstruct networks from time series data, using...
  • GeneNetwork

  • Referenced in 2 articles [sw35671]
  • GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data. Inferring genetic network ... GeneNetwork enables a user to readily reconstruct genetic networks based on microarray data without having ... intuitive mapping and analysis of the reconstructed network allowing biologists to explore gene relationships...
  • MetNetAligner

  • Referenced in 2 articles [sw25791]
  • MetNetAligner: a web service tool for metabolic network alignments. The accumulation of high-throughput genomic ... data allows for increasingly accurate modeling and reconstruction ... metabolic networks. Alignment of the reconstructed networks can help to catch model inconsistencies and infer...
  • INLOCANDA

  • Referenced in 1 article [sw34288]
  • Exploiting causality in gene network reconstruction based on graph embedding. Gene network reconstruction ... analyze gene expression data. However, the reconstructed networks often suffer from a high amount ... inductive predictive model for gene network reconstruction and overcomes all the mentioned limitations. In particular ... multiple dimensions of analysis on benchmark, real networks of two organisms ( extit{E. coli...
  • netrd

  • Referenced in 1 article [sw35821]
  • netrd: A library for network reconstruction and graph distances. Over the last two decades, alongside ... that have been inferred or reconstructed from non-network data---in particular, using time series ... challenging problem in network science. Different reconstruction techniques usually have different assumptions, and their performance ... most extensive collection of both network reconstruction techniques and network comparison techniques (often referred...
  • ANAT

  • Referenced in 1 article [sw29310]
  • ANAT 2.0: reconstructing functional protein subnetworks. BACKGROUND: ANAT is a graphical, Cytoscape-based tool ... tool allows the user to perform network reconstruction under several scenarios in a number ... updates as well as several new network reconstruction algorithms that greatly extend the applicability ... date network reconstruction tool that addresses several reconstruction challenges across multiple species...
  • 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...
  • anNET

  • Referenced in 2 articles [sw35331]
  • reaction to a complete genome-wide network reconstruction including compartments. anNET can (i) test quantitative ... active regulation in the metabolic reaction network, and (iv) help in localizing errors in data...
  • ARACNe-AP

  • Referenced in 3 articles [sw34267]
  • mutual information. The accurate reconstruction of gene regulatory networks from large scale molecular profile datasets ... Biology. The Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) represents...
  • BoostGAPFILL

  • Referenced in 1 article [sw34262]
  • BoostGAPFILL: improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods ... BoostGAPFILL uses metabolite patterns in the incomplete network captured using a matrix factorization formulation ... metabolic network. We formulate a testing framework based on the available metabolic reconstructions and demonstrate ... fill gaps. For most metabolic network reconstructions tested, BoostGAPFILL shows above 60% precision and recall...
  • F2c2

  • Referenced in 3 articles [sw17352]
  • detecting dependencies between reaction fluxes of metabolic networks at steady-state. On the one hand ... help in the curation of reconstructed metabolic networks by verifying whether the coupling between reactions...
  • BGRMI

  • Referenced in 1 article [sw29320]
  • application in breast cancer research. Reconstructing gene regulatory networks (GRNs) from gene expression data ... sources of prior knowledge to reconstruct transcription regulatory networks of proliferating and differentiating breast cancer ... time-course gene expression data. The reconstructed networks revealed key driver genes of proliferation...