ArticlePLoS computational biology2021
Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Article
- Challenges and Opportunities in Single-Sample Network Modeling.bioRxiv : the preprint server for biology · 2026Article
- Personalized transcriptional network analysis links age-related loss of gene coordination to individual biological aging.Genome medicine · 2025Article
- Sample-specific network analysis identifies gene co-expression patterns of immunotherapy response in clear cell renal cell carcinoma.iScience · 2025Article
- DNFE: Directed network flow entropy for detecting tipping points during biological processes.PLoS computational biology · 2025Article
- TARGET-SL: precision essential gene prediction using driver prioritisation and synthetic lethality.Briefings in bioinformatics · 2025Article
- Multimodal multiobjective optimization with structural network control principles to optimize personalized drug targets for drug discovery of individual patients.Briefings in bioinformatics · 2024Article
- Inference of single-cell network using mutual information for scRNA-seq data analysis.BMC bioinformatics · 2024Article
- Module control of network analysis in psychopathology.iScience · 2024Article
- Integrating multi-omics data of childhood asthma using a deep association model.Fundamental research · 2024Article
- Using single-sample networks to identify the contrasting patterns of gene interactions and reveal the radiation dose-dependent effects in multiple tissues of spaceflight mice.NPJ microgravity · 2024Article
- Evaluation of single-sample network inference methods for precision oncology.NPJ systems biology and applications · 2024Article
- Edge and modular significance assessment in individual-specific networks.Scientific reports · 2023Article
- SWEET: a single-sample network inference method for deciphering individual features in disease.Briefings in bioinformatics · 2023Article
- Article
- Identifying the critical state of complex biological systems by the directed-network rank score method.Bioinformatics (Oxford, England) · 2022Article
- Network Control Models With Personalized Genomics Data for Understanding Tumor Heterogeneity in Cancer.Frontiers in oncology · 2022Review
- Noninvasive detection and interpretation of gastrointestinal diseases by collaborative serum metabolite and magnetically controlled capsule endoscopy.Computational and structural biotechnology journal · 2022Article
- Development of a dynamic network biomarkers method and its application for detecting the tipping point of prior disease development.Computational and structural biotechnology journal · 2022Review
Corrections and comments
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
In the past few years, a wealth of sample-specific network construction methods and structural network control methods has been proposed to identify sample-specific driver nodes for supporting the Sample-Specific network Control (SSC) analysis of biological networked systems. However, there is no comprehensive evaluation for these state-of-the-art methods. Here, we conducted a performance assessment for 16 SSC analysis workflows by using the combination of 4 sample-specific network reconstruction methods and 4 representative structural control methods. This study includes simulation evaluation of representative biological networks, personalized driver genes prioritization on multiple cancer bulk expression datasets with matched patient samples from TCGA, and cell marker genes and key time point identification related to cell differentiation on single-cell RNA-seq datasets. By widely comparing analysis of existing SSC analysis workflows, we provided the following recommendations and banchmarking workflows. (i) The performance of a network control method is strongly dependent on the up-stream sample-specific network method, and Cell-Specific Network construction (CSN) method and Single-Sample Network (SSN) method are the preferred sample-specific network construction methods. (ii) After constructing the sample-specific networks, the undirected network-based control methods are more effective than the directed network-based control methods. In addition, these data and evaluation pipeline are freely available on https://github.com/WilfongGuo/Benchmark_control.
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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.