Bayesian Inference of Signaling Network Topology in a Cancer Cell Line

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Bioinform.

• Publication date

  2012-11-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/bts514PMID 22923301PMCID PMC3476330
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• CONFLICT OF INTEREST: None declared.

  2013cited by this paper
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  2011influential reference
• Objective Bayes Criteria for Variable Selection

  2011cited by this paper
• Systems Analysis of EGF Receptor Signaling Dynamics with Micro-Western Arrays

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• An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data

  2010influential reference
• Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data

  2010cited by this paper
• Nonparametric Bayesian Sparse Factor Models with application to Gene Expression modelling

  2010influential reference
• Learning Non-Stationary Dynamic Bayesian Networks

  2010cited by this paper
• Inferring Signaling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species

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• A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches.

  2009cited by this paper
• Statistical Applications in Genetics and Molecular Biology Inferring Dynamic Genetic Networks with Low Order Independencies Inferring Dynamic Genetic Networks with Low Order Independencies ∗

  2009cited by this paper
• Consistency of Bayesian procedures for variable selection

  2009cited by this paper
• Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics

  2009cited by this paper
• Network inference using informative priors

  2008influential reference
• Gene Regulatory Network Reconstruction by Bayesian Integration of Prior Knowledge and/or Different Experimental Conditions

  2008cited by this paper
• Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge

  2007influential reference
• Oncogenic re-wiring of cellular signaling pathways

  2007influential reference
• USING REGULARIZED DYNAMIC CORRELATION TO INFER GENE DEPENDENCY NETWORKS FROM TIME-SERIES MICROARRAY DATA

  2006cited by this paper
• High-dimensional graphs and variable selection with the Lasso

  2006cited by this paper
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  2006cited by this paper
• Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells

  2006cited by this paper
• Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data

  2005cited by this paper
• Bayesian Methods for Nonlinear Classification and Regression

  2004cited by this paper
• Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks

  2003cited by this paper
• Dynamic bayesian networks: representation, inference and learning

  2002influential reference
• Nonparametric regression using linear combinations of basis functions

  2001cited by this paper
• Using Bayesian Networks to Analyze Expression Data

  2000cited by this paper
• Learning the Structure of Dynamic Probabilistic Networks

  1998cited by this paper
• Regression Shrinkage and Selection via the Lasso

  1996cited by this paper
• Bayesian Graphical Models for Discrete Data

  1995cited by this paper
• Learning Gaussian Networks

  1994cited by this paper
• Bayesian inference and decision techniques : essays in honor of Bruno de Finetti

  1986cited by this paper

• Causal models and prediction in cell line perturbation experiments

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• Navigating Cancer Complexity: Integrative Multi-Omics Methodologies for Clinical Insights

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• Uncovering Functional Gene Regulatory Networks in Bulk and Single-Cell Data through Robust Transcription Factor Activity Estimation and Model-Guided Experimental Validation

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• Multi-OMICS approaches in cancer biology: New era in cancer therapy.

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• Testing and overcoming the limitations of modular response analysis

  2024cites this paper
• Systems-level reconstruction of kinase phosphosignaling networks regulating endothelial barrier integrity using temporal data

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• Advances in computational and experimental approaches for deciphering transcriptional regulatory networks

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  2023cites this paper
• Advanced data analysis in inertial confinement fusion and high energy density physics.

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• Network inference from temporal phosphoproteomics informed by protein-protein interactions

  2023cites this paper
• Structure Learning for Hybrid Bayesian Networks

  2022cites this paper
• Integrative Multi-Omics Approaches in Cancer Research: From Biological Networks to Clinical Subtypes

  2021influential citation
• Integrated Inference of Asymmetric Protein Interaction Networks Using Dynamic Model and Individual Patient Proteomics Data

  2021cites this paper
• Prediction of Signed Protein Kinase Regulatory Circuits.

  2020cites this paper
• Inferring dynamic gene regulatory networks with low-order conditional independencies – an evaluation of the method

  2020cites this paper
• Bayesian Network Structure Learning Using Case-Injected Genetic Algorithms

  2020cites this paper
• Bayesian Inference of Stochastic Dynamic Models Using Early-Rejection Methods Based on Sequential Stochastic Simulations

  2020cites this paper
• Inferring signaling pathways with probabilistic programming

  2020cites this paper
• Statistical Genomics in Rare Cancer.

  2020cites this paper
• An Ensemble Method to Reconstruct Gene Regulatory Networks Based on Multivariate Adaptive Regression Splines

  2019cites this paper
• Towards a Hybrid Approach for Evolving Bayesian Networks Using Genetic Algorithms

  2019cites this paper
• Bayesian network models for incomplete and dynamic data

  2019cites this paper
• D3GRN: a data driven dynamic network construction method to infer gene regulatory networks

  2019cites this paper
• Network inference in systems biology: recent developments, challenges, and applications.

  2019cites this paper
• A Fast and Furious Bayesian Network and Its Application of Identifying Colon Cancer to Liver Metastasis Gene Regulatory Networks

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• Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development.

  2019cites this paper
• TIGRNCRN: Trustful inference of gene regulatory network using clustering and refining the network

  2019cites this paper
• Perturbation biology links temporal protein changes to drug responses in a melanoma cell line

  2019cites this paper
• Bayesian network hybrid learning using an elite-guided genetic algorithm

  2019cites this paper
• Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data

  2018cites this paper
• A logic-based method to build signaling networks and propose experimental plans

  2018cites this paper
• Using Regularization to Infer Cell Line Specificity in Logical Network Models of Signaling Pathways

  2018cites this paper
• Gene Regulatory Network Inference: An Introductory Survey.

  2018cites this paper
• Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases.

  2018cites this paper
• Proof and Uncertainty in Causal Claims

  2018cites this paper
• Cross-Talk Categorisations in Data-Driven Models of Signalling Networks: A System-Level View

  2018cites this paper
• Integrative Approaches for Inference of Genome-Scale Gene Regulatory Networks.

  2018cites this paper
• Statistical Network Inference for Time-Varying Molecular Data with Dynamic Bayesian Networks.

  2018cites this paper
• Bayesian networks established functional differences between breast cancer subtypes

  2018cites this paper
• Resource Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

  2018influential citation
• Inference of cell type specific regulatory networks on mammalian lineages.

  2017cites this paper
• Methods for Estimating Hidden Structure and Network Transitions in Genomics

  2017cites this paper
• Development of dynamic Bayesian network for the analysis of high-dimensional biomedical data

  2017cites this paper
• Understanding the mTOR signaling pathway via mathematical modeling

  2017cites this paper
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  2017cites this paper
• A novel method for Bayesian networks structure learning based on Breeding Swarm algorithm

  2017cites this paper
• Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling

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• Dynamic network model with continuous valued nodes for longitudinal brain morphometry

  2017cites this paper
• Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

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• SiGNet: A signaling network data simulator to enable signaling network inference

  2017cites this paper
• Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response

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• Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data

  2015cites this paper
• Pathway and network analysis of cancer genomes

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• Inferring Biological Networks from Time-Course Observations Using a Non-linear Vector Autoregressive Model

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• Pathway and Network Approaches for Identification of Cancer Signature Markers from Omics Data

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• Development of Bioinformatics Tools for Biomedical High-Throughput Analyses

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• Inferring network structure from interventional time-course experiments

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• Structural Prediction of Dynamic Bayesian Network With Partial Prior Information

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• Computational Methods in Systems Biology

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• Joint Structure Learning of Multiple Non-Exchangeable Networks

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• Causal network inference using biochemical kinetics

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