Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks

No abstract is available for this paper.

• Publication year

  2003

• Venue

  Bioinform.

• Publication date

  2003-11-22

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/BIOINFORMATICS/BTG313PMID 14630656
• 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.

• Local identifiability : when can genetic networks be identified from microarray data ?

  2002cited by this paper
• Modeling and Simulation of Genetic Regulatory Systems: A Literature Review

  2002cited by this paper
• From promoter sequence to expression: a probabilistic framework

  2002cited by this paper
• Modelling regulatory pathways in E. coli from time series expression profiles

  2002cited by this paper
• Evaluating functional network inference using simulations of complex biological systems

  2002cited by this paper
• Modelling biological responses using gene expression profiling and linear dynamical systems

  2001cited by this paper
• Simulation Studies for the Identification of Genetic Networks from cDNA Array and Regulatory Activity Data

  2001cited by this paper
• Inferring subnetworks from perturbed expression profiles

  2001cited by this paper
• Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models

  2001cited by this paper
• Biological rhythms: Circadian clocks limited by noise

  2000cited by this paper
• Construction of a genetic toggle switch in Escherichia coli

  2000cited by this paper
• Genome-wide location and function of DNA binding proteins.

  2000cited by this paper
• Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data

  2000cited by this paper
• Genetic network inference: from co-expression clustering to reverse engineering

  2000cited by this paper
• Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks

  2000cited by this paper
• Using Bayesian Networks to Analyze Expression Data

  2000cited by this paper
• A Tutorial on Learning with Bayesian Networks

  1999cited by this paper
• Learning probabilistic networks

  1999cited by this paper
• Modeling Gene Expression with Differential Equations

  1998cited by this paper
• Cluster analysis and display of genome-wide expression patterns.

  1998influential reference
• Learning the Structure of Dynamic Probabilistic Networks

  1998cited by this paper
• A Transformational Characterization of Equivalent Bayesian Network Structures

  1995cited by this paper
• Reversible jump Markov chain Monte Carlo computation and Bayesian model determination

  1995cited by this paper
• Understanding the Metropolis-Hastings Algorithm

  1995cited by this paper
• Introduction to the theory of neural computation

  1994cited by this paper
• The origins of order

  1993cited by this paper
• Probabilistic reasoning in intelligent systems: Networks of plausible inference

  1991cited by this paper
• Basic local alignment search tool.

  1990cited by this paper
• Monte Carlo Sampling Methods Using Markov Chains and Their Applications

  1970cited by this paper
• Metabolic stability and epigenesis in randomly constructed genetic nets.

  1969cited by this paper
• Physical Chemistry

  year unknowncited by this paper

• Signpost Testing to Navigate the Parameter Space of the Gaussian Graphical Model With High‐Dimensional Data

  2026cites this paper
• Sustainable software development in science – insights from 20 years of Vanted

  2025cites this paper
• Constraining acyclicity of differentiable Bayesian structure learning with topological ordering

  2024cites this paper
• Identifying vital nodes for yeast network by dynamic network entropy

  2024cites this paper
• Network Modeling and Control of Dynamic Disease Pathways, Review and Perspectives

  2024cites this paper
• An Integrated Approach of Learning Genetic Networks From Genome-Wide Gene Expression Data Using Gaussian Graphical Model and Monte Carlo Method

  2023cites this paper
• Differentiable Bayesian Structure Learning with Acyclicity Assurance

  2023cites this paper
• Integrated regulatory and metabolic networks of the tumor microenvironment for therapeutic target prioritization

  2023cites this paper
• Connecting the Dots: Using Machine Learning to Forge Gene Regulatory Networks from Large Biological Datasets. At the Intersection of GRNs: Where System Biology Meets Machine Learning

  2022cites this paper
• Computational systems biology in disease modeling and control, review and perspectives

  2022cites this paper
• Structure Learning for Hybrid Bayesian Networks

  2022cites this paper
• Bayesian learning of Causal Structure and Mechanisms with GFlowNets and Variational Bayes

  2022cites this paper
• Explainable Machine Learning for Longitudinal Multi-Omic Microbiome

  2022cites this paper
• Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection

  2022cites this paper
• GFlowCausal: Generative Flow Networks for Causal Discovery

  2022cites this paper
• Bayesian Structure Learning with Generative Flow Networks

  2022cites this paper
• Gene Regulatory Identification Based on the Novel Hybrid Time-Delayed Method

  2022influential citation
• A Multi-Granularity Information-Based Method for Learning High-Dimensional Bayesian Network Structures

  2021cites this paper
• Probabilistic Graphical Models Applied to Biological Networks.

  2021cites this paper
• Network Modeling in Biology: Statistical Methods for Gene and Brain Networks.

  2021cites this paper
• Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks

  2021cites this paper
• Application of Meta-Heuristics on Reconstructing Gene Regulatory Network: A Bayesian Model Approach

  2021cites this paper
• Optimal Finite-Horizon Perturbation Policy for Inference of Gene Regulatory Networks

  2021cites this paper
• A practical analysis of sample complexity for structure learning of discrete dynamic Bayesian networks

  2021cites this paper
• Systems biology in disease modeling and control, analysis and perspectives

  2021cites this paper
• Parameter identification of genetic regulatory network with time-varying delays via adaptive synchronization method

  2020cites this paper
• Integrating Data-Driven and Mechanistic Models of the Inflammatory Response in Sepsis and Trauma

  2020cites this paper
• Big data analytics for cycle time related feature selection in the semiconductor wafer fabrication system

  2020cites this paper
• Molecular networks in Network Medicine: Development and applications

  2020cites this paper
• Modified Half-System Based Method for Reverse Engineering of Gene Regulatory Networks

  2020cites this paper
• An order independent algorithm for inferring gene regulatory network using quantile value for conditional independence tests

  2020cites this paper
• Decomposition-based Bayesian network structure learning algorithm using local topology information

  2020cites this paper
• Review of Artificial Intelligence Applications and Algorithms for Brain Organoid Research

  2020cites this paper
• A Hybrid Methodology for the Reverse Engineering of Gene Regulatory Networks

  2020cites this paper
• DOKI: Domain knowledge-driven inference method for reverse-engineering transcriptional regulatory relationships among genes in cancer

  2020cites this paper
• PFBNet: a priori-fused boosting method for gene regulatory network inference

  2020cites this paper
• Bayesian Data Fusion of Gene Expression and Histone Modification Profiles for Inference of Gene Regulatory Network

  2020influential citation
• From graph topology to ODE models for gene regulatory networks

  2020influential citation
• Use of transcriptomic data to inform biophysical models via Bayesian networks

  2020cites this paper
• Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer’s disease

  2019cites this paper
• Modelling Non‐homogeneous Dynamic Bayesian Networks with Piecewise Linear Regression Models

  2019cites this paper
• The application of omics-based human liver platforms for investigating the mechanism of drug-induced hepatotoxicity in vitro

  2019cites this paper
• Gaussian DAGs on network data

  2019cites this paper
• Quantitative Modelling Approaches

  2019cites this paper
• An analytical threshold for combining Bayesian Networks

  2019cites this paper
• Restricted-derestricted dynamic Bayesian Network inference of transcriptional regulatory relationships among genes in cancer

  2019cites this paper
• A sparse and decomposed particle swarm optimization for inferring gene regulatory networks based on fuzzy cognitive maps

  2019cites this paper
• Overview and Evaluation of Recent Methods for Statistical Inference of Gene Regulatory Networks from Time Series Data.

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

  2018cites this paper
• Continuous Learning of the Structure of Bayesian Networks: A Mapping Study

  2018cites this paper
• Advanced non-homogeneous dynamic Bayesian network models for statistical analyses of time series data

  2018cites this paper
• HSCVFNT: Inference of Time-Delayed Gene Regulatory Network Based on Complex-Valued Flexible Neural Tree Model

  2018cites this paper
• Title Highly sensitive inference of time-delayed generegulation by network deconvolution

  2018cites this paper
• BayesPiles

  2018cites this paper
• Query Answering in Probabilistic Data and Knowledge Bases

  2018cites this paper
• Inferring Causal Gene Regulatory Networks Using Time-Delay Association Rules

  2018cites this paper
• Tractography-Based Score for Learning Effective Connectivity From Multimodal Imaging Data Using Dynamic Bayesian Networks

  2018cites this paper
• Network Structure Sampling in Bayesian Networks via Perfect Sampling from Linear Extensions

  2018cites this paper
• Inference of protein-protein networks for triple-negative breast cancer using single-patient proteomic data

  2018cites this paper
• Causal Queries from Observational Data in Biological Systems via Bayesian Networks: An Empirical Study in Small Networks.

  2018cites this paper
• Automated identification and reduction of artifacts in cine four-dimensional computed tomography (4DCT) images using respiratory motion model

  2017cites this paper
• Generating Time Series Simulation Dataset Derived from Dynamic Time-Varying Bayesian Network

  2017cites this paper
• Use of prior knowledge in biological systems modelling

  2017cites this paper
• On learning the structure of Bayesian Networks and submodular function maximization

  2017cites this paper
• Active inference for dynamic Bayesian networks with an application to tissue engineering

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

  2017cites this paper
• Ecological Network Inference From Long-Term Presence-Absence Data

  2017cites this paper
• Computational inference of gene regulatory networks: Approaches, limitations and opportunities.

  2017cites this paper
• An empirical comparison of popular structure learning algorithms with a view to gene network inference

  2017cites this paper
• Machine Learning Methods for Cancer Immunology

  2017cites this paper
• Disease Risk Assessment Using a Voronoi-Based Network Analysis of Genes and Variants Scores

  2017cites this paper
• USING DYNAMIC BAYESIAN NETWORKS FOR THE AUTOMATED VISUAL INSPECTION AND ANALYSIS OF AN INDUSTRIAL LASER PROCESS ESAUTHOR: ALBERTO OGBECHIE CONDÉS IADVISORS: PEDRO LARRAÑAGA MUGICA CONCHA BIELZA LOZOYA

  2017cites this paper
• Learning effective connectivity from fMRI using autoregressive hidden Markov model with missing data.

  2017cites this paper
• Identifying Regulators from Multiple Types of Biological Data in Cancer

  2017influential citation
• The dynamic programming high-order Dynamic Bayesian Networks learning for identifying effective connectivity in human brain from fMRI.

  2017cites this paper
• Robust stability of interactional genetic regulatory networks with reaction-diffusion terms

  2017cites this paper
• Predicting Ascospore Release of Monilinia vaccinii-corymbosi of Blueberry with Machine Learning.

  2017cites this paper
• Parallel Exact Dynamic Bayesian Network Structure Learning with Application to Gene Networks

  2017cites this paper
• Experimental design trade-offs for gene regulatory network inference: An in silico study of the yeast Saccharomyces cerevisiae cell cycle

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

  2017cites this paper
• Inferring causal molecular networks: empirical assessment through a community-based effort

  2016cites this paper
• Advances in MCMC Methods with Applications to Particle Filtering, DSMC, and Bayesian Networks

  2016cites this paper
• Hybrid Modeling of Cancer Drug Resistance Mechanisms

  2016cites this paper
• Understanding the Behaviour of Complex Biomolecular Networks by Combining Logical and Semantic Modeling

  2016cites this paper
• Data-based reconstruction of complex geospatial networks, nodal positioning and detection of hidden nodes

  2016cites this paper
• Using node ordering to improve Structure MCMC for Bayesian Model Averaging

  2016influential citation
• The Max-Min High-Order Dynamic Bayesian Network for Learning Gene Regulatory Networks with Time-Delayed Regulations

  2016cites this paper
• Understanding transcriptional regulatory networks using computational models.

  2016cites this paper
• Controllability and stability analysis of large transcriptomic dynamic systems for host response to influenza infection in human

  2016cites this paper
• CAUSAL INFERENCE IN SEMIPARAMETRIC AND NONPARAMETRIC STRUCTURAL EQUATION MODELS

  2016cites this paper
• Differential Regulatory Analysis Based on Coexpression Network in Cancer Research

  2016cites this paper
• Dynamic Bayesian Network-Based Anomaly Detection for In-Process Visual Inspection of Laser Surface Heat Treatment

  2016cites this paper
• Context-specificity in causal signaling networks revealed by phosphoprotein profiling

  2016cites this paper
• Data Based Identification and Prediction of Nonlinear and Complex Dynamical Systems

  2016cites this paper
• Linear system identifiability from distributional and time series data

  2016cites this paper
• Understanding of ‘Networks’ In Vitro and/or In Vivo

  2016cites this paper
• Inference of Gene Regulatory Network Based on Local Bayesian Networks

  2016cites this paper
• Construction of Gene Regulatory Networks Using Recurrent Neural Networks and Swarm Intelligence

  2016cites this paper
• A BIRTH AND DEATH PROCESS FOR BAYESIAN NETWORK STRUCTURE INFERENCE

  2016cites this paper
• Biological Network Inference at Multiple Scales: From Gene Regulation to Species Interactions

  2015cites this paper