• SIRENE

  • Referenced in 7 articles [sw17419]
  • Supervised inference of regulatory networks. Motivation: Living cells are the product of gene expression programs ... 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...
  • Cytoscape

  • Referenced in 81 articles [sw09080]
  • recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium ... interface to detailed stochastic/kinetic gene regulatory models...
  • NARROMI

  • Referenced in 6 articles [sw24066]
  • reduction technique improves accuracy of gene regulatory network inference. MOTIVATION: Reconstruction of gene regulatory networks ... regulatory mechanisms within the cell. Despite various methods developed for reconstruction of GRNs from gene ... dataset with a large number of genes but a small number of samples. RESULTS ... NARROMI, to improve the accuracy of GRN inference by combining ordinary differential equation-based recursive...
  • SynTReN

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

  • Referenced in 29 articles [sw36999]
  • inference of genetic network architectures. Given the immanent gene expression mapping covering whole genomes during ... possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns ... networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression ... output states, one is able to infer the sets of input elements controlling each element...
  • NETWORKINFERENCE

  • Referenced in 8 articles [sw06744]
  • Bayesian network inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks. NETWORKINFERENCE performed well at recovering ... data to recover multiple regulators of a gene. When collecting the same number of data ... sampling covered propagation of regulation through the network but not so long such that intervals ... elucidate the possibilities and limitations of network inference based on biological data...
  • bc3net

  • Referenced in 2 articles [sw17708]
  • package bc3net: Gene Regulatory Network Inference with Bc3net. Implementation of the BC3NET algorithm for gene ... regulatory network inference (de Matos Simoes and Frank Emmert-Streib, Bagging Statistical Network Inference from ... Large-Scale Gene Expression Data, PLoS ONE 7(3): e33624...
  • TIGRESS

  • Referenced in 9 articles [sw23826]
  • using Stability Selection. BACKGROUND: Inferring the structure of gene regulatory networks (GRN) from a collection ... RESULTS: In this paper, we formulate GRN inference as a sparse regression problem and investigate...
  • ASIAN

  • Referenced in 3 articles [sw36771]
  • server for inferring a regulatory network framework from gene expression profiles. The standard workflow ... challenging analysis is the inference of a gene regulatory network, and some computational methods have ... deduce the gene regulatory network. Here, we describe our web server for inferring a framework ... Inferring A Network) web server provides an initial basis for inferring regulatory relationships, in that...
  • NetBenchmark

  • Referenced in 2 articles [sw29311]
  • package for reproducible benchmarks of gene regulatory network inference. Background: In the last decade ... great number of methods for reconstructing gene regulatory networks from expression data have been proposed ... fully reproducible, evaluation of transcriptional network inference methods. Results: Our open-source and freely available...
  • BGRMI

  • Referenced in 2 articles [sw29320]
  • BGRMI: A method for inferring gene regulatory networks from time-course gene expression data ... breast cancer research. Reconstructing gene regulatory networks (GRNs) from gene expression data is a challenging ... propose Bayesian Gene Regulation Model Inference (BGRMI), a model-based method for inferring GRNs from ... prior knowledge to reconstruct transcription regulatory networks of proliferating and differentiating breast cancer (BC) cells...
  • grndata

  • Referenced in 1 article [sw40326]
  • grndata: Synthetic Expression Data for Gene Regulatory Network Inference. Simulated expression data for five large...
  • SPINE

  • Referenced in 6 articles [sw29309]
  • that connect causal to affected genes on a network of physical interactions. Results: We present ... regulatory Pathway INferencE. The framework aims at explaining gene expression experiments in which a gene ... causal gene to the affected genes are searched for in this network. The reconstruction problem ... entire yeast network to predict protein effects and reconstruct signaling and regulatory pathways. Overall...
  • GENIE3

  • Referenced in 1 article [sw40328]
  • implements the GENIE3 algorithm for inferring gene regulatory networks from expression data...
  • CSI

  • Referenced in 1 article [sw13904]
  • Bayesian approach to network inference from multiple perturbed time series gene expression data. Here ... Gaussian process based approach to inferring gene regulatory networks (GRNs) from multiple time series data...
  • sparseSEM

  • Referenced in 1 article [sw33244]
  • structural equation models in inferring gene regulatory networks...
  • SINCERITIES

  • Referenced in 1 article [sw29321]
  • SINCERITIES is a tool for inferring gene regulatory networks from time-stamped cross-sectional single ... relationships among genes by analyzing the evolution of the distribution of gene expression levels over ... using distribution distances. We formulated the GRN inference as a regularised linear regression problem with...
  • optPBN

  • Referenced in 2 articles [sw32145]
  • optPBN: An optimisation toolbox for probabilistic boolean networks. SUMMARY: The optPBN toolbox provides a simple ... biological studies such as the inference of gene regulatory networks or the identification...
  • GeneSPIDER

  • Referenced in 1 article [sw29318]
  • GeneSPIDER - gene regulatory network inference benchmarking with controlled network and data properties. A key question...
  • PyPanda

  • Referenced in 1 article [sw14828]
  • Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate...