• REVEAL

  • Referenced in 28 articles [sw36999]
  • reverse engineering algorithm for inference of genetic network architectures. Given the immanent gene expression mapping ... possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns ... this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean ... output states, one is able to infer the sets of input elements controlling each element...
  • SIRENE

  • Referenced in 7 articles [sw17419]
  • SIRENE: Supervised inference of regulatory networks. Motivation: Living cells are the product of gene expression ... methods have been proposed to infer gene regulatory networks from gene expression data, a recent ... Results: We propose SIRENE (Supervised Inference of Regulatory Networks), a new method for the inference ... method decomposes the problem of gene regulatory network inference into a large number of local...
  • Cytoscape

  • Referenced in 82 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 ... vital for understanding the complex regulatory mechanisms within the cell. Despite various methods developed ... 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...
  • SCODE

  • Referenced in 3 articles [sw29314]
  • SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. Results ... novel and efficient algorithm SCODE to infer regulatory networks, based on ordinary differential equations ... dynamics. We evaluated SCODE by comparing its inferred networks with use of a DNaseI-footprint...
  • ARACNE

  • Referenced in 38 articles [sw17200]
  • regulatory networks in mammalian cells, yet general enough to address a wider range of network ... interactions inferred by co-expression methods. Results: We prove that ARACNE reconstructs the network exactly ... ARACNE’s ability to reconstruct transcriptional regulatory networks using both a realistic synthetic dataset ... Relevance Networks and Bayesian Networks. Application to the deconvolution of genetic networks in human...
  • ASIAN

  • Referenced in 3 articles [sw36771]
  • ASIAN: a web server for inferring a regulatory network framework from gene expression profiles ... challenging analysis is the inference of a gene regulatory network, and some computational methods have ... server for inferring a framework of regulatory networks from a large number of gene expression ... Inferring A Network) web server provides an initial basis for inferring regulatory relationships, in that...
  • 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...
  • SCENIC

  • Referenced in 3 articles [sw29313]
  • SCENIC: Single-cell regulatory network inference and clustering. We present SCENIC, a computational method...
  • SQUAD

  • Referenced in 5 articles [sw29353]
  • efforts dedicated to the reconstruction of regulatory networks in diverse biological systems. This information, however ... about patterns of expression to infer the regulatory networks that generate such patterns...
  • NETWORKINFERENCE

  • Referenced in 7 articles [sw06744]
  • Bayesian network inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks. NETWORKINFERENCE performed well at recovering ... 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...
  • 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...
  • NetBenchmark

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

  • Referenced in 1 article [sw40326]
  • grndata: Synthetic Expression Data for Gene Regulatory Network Inference. Simulated expression data for five large...
  • 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 ... Gene Regulation Model Inference (BGRMI), a model-based method for inferring GRNs from time-course ... prior knowledge to reconstruct transcription regulatory networks of proliferating and differentiating breast cancer (BC) cells...
  • SPINE

  • Referenced in 6 articles [sw29309]
  • SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Motivation: The complex ... interactions allow us to begin to uncover regulatory and signaling pathways within the cell that ... novel framework, SPINE, for Signaling-regulatory Pathway INferencE. The framework aims at explaining gene expression ... entire yeast network to predict protein effects and reconstruct signaling and regulatory pathways. Overall...
  • 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...
  • ARACNe-AP

  • Referenced in 3 articles [sw34267]
  • adaptive partitioning inference of mutual information. The accurate reconstruction of gene regulatory networks from large ... Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) represents one of the most effective ... Mutual Information estimator and the Network inference accuracy of the original algorithm. Given that ... modest computational resources to build complex regulatory networks from hundreds of gene expression profiles. Availability...