ArticleFrontiers in genetics2012
Statistical inference and reverse engineering of gene regulatory networks from observational expression data.
Article in Frontiers in genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Gene circuit-based sensors.Fundamental research · 2025Review
- SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data.Bioinformatics (Oxford, England) · 2025Article
- Holimap: an accurate and efficient method for solving stochastic gene network dynamics.Nature communications · 2024Article
- Conceptual breakthroughs of the long noncoding RNA functional system and its endogenous regulatory role in the cancerous regime.Exploration of targeted anti-tumor therapy · 2024Review
- Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration.PLoS computational biology · 2023Article
- Network-based approaches for modeling disease regulation and progression.Computational and structural biotechnology journal · 2023Review
- Review
- k-core genes underpin structural features of breast cancer.Scientific reports · 2021Article
- Multi-task learning for the simultaneous reconstruction of the human and mouse gene regulatory networks.Scientific reports · 2020Article
- FINET: Fast Inferring NETwork.BMC research notes · 2020Article
- A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks.BMC bioinformatics · 2020Article
- Computational models of melanoma.Theoretical biology & medical modelling · 2020Review
- Inference of Genetic Networks From Time-Series and Static Gene Expression Data: Combining a Random-Forest-Based Inference Method With Feature Selection Methods.Frontiers in genetics · 2020Article
- Gene Co-expression Is Distance-Dependent in Breast Cancer.Frontiers in oncology · 2020Article
- Fusing gene expressions and transitive protein-protein interactions for inference of gene regulatory networks.BMC systems biology · 2019Article
- High-Dimensional Bayesian Network Inference From Systems Genetics Data Using Genetic Node Ordering.Frontiers in genetics · 2019Article
- Comprehensive Review of Models and Methods for Inferences in Bio-Chemical Reaction Networks.Frontiers in genetics · 2019Review
- Extensive evaluation of the generalized relevance network approach to inferring gene regulatory networks.GigaScience · 2018Article
- Hub genes in a pan-cancer co-expression network show potential for predicting drug responses.F1000Research · 2018Article
- Informed walks: whispering hints to gene hunters inside networks' jungle.BMC systems biology · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this paper, we present a systematic and conceptual overview of methods for inferring gene regulatory networks from observational gene expression data. Further, we discuss two classic approaches to infer causal structures and compare them with contemporary methods by providing a conceptual categorization thereof. We complement the above by surveying global and local evaluation measures for assessing the performance of inference algorithms.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.