ArticleNucleic acids research2016
Personalized characterization of diseases using sample-specific networks.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 174 papers.
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Who cites it
174 citing papers in PubMed, 335 citations in OpenAlex.
- Innate [European journal of nuclear medicine and molecular imaging · 2025Trial
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- Therapeutic Potential of Cucurbitacin I in Colon Adenocarcinoma Is Mediated by Modulation of SDHA Expression.Journal of cellular and molecular medicine · 2026Article
- ssNetShift: single-sample metabolic network rewiring reveals hidden prognostic subtypes beyond clinical staging in gastric cancer.Briefings in bioinformatics · 2026Article
- Network-Based Analysis for the Quantification of Brain and Body Immune Axes with Total-Body PET Imaging.Journal of nuclear medicine : official publication, Society of Nuclear Medicine · 2026Article
- MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.BMC bioinformatics · 2026Article
- Network-based disease fingerprinting with neuroinflammation PET imaging.Journal of neuroinflammation · 2026Article
- A gene interaction network-based molecular taxonomy of dilated cardiomyopathy highlighting immune and inflammatory heterogeneity.Clinical and experimental medicine · 2026Article
- Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response.Cancer immunology, immunotherapy : CII · 2026Article
- Hallmarks of the pre-disease state: prevention and control of the pre-disease state, a tipping point between health and disease.Cell discovery · 2026Article
- Challenges and Opportunities in Single-Sample Network Modeling.bioRxiv : the preprint server for biology · 2026Article
- Mapping individual molecular connectomes in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Multimodal bioinformatic analyses of genome-scale expression beyond gene-centric differential expression.Briefings in bioinformatics · 2026Review
- Tracking early cognitive decline in preclinical AD with brain MRI similarity.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Similar minds age alike: an MRI similarity approach for predicting age-related cognitive decline.npj aging · 2026Article
- GABAMolecular psychiatry · 2026Article
- Early diagnosis of Alzheimer's Disease: Graph theoretical analysis of cerebellar network features based on 18F-AV45 PET.PloS one · 2026Article
- A squamous epithelial gene interaction perturbation network index for risk stratification in esophageal squamous cell carcinoma.Journal of Cancer · 2026Article
114 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A complex disease generally results not from malfunction of individual molecules but from dysfunction of the relevant system or network, which dynamically changes with time and conditions. Thus, estimating a condition-specific network from a single sample is crucial to elucidating the molecular mechanisms of complex diseases at the system level. However, there is currently no effective way to construct such an individual-specific network by expression profiling of a single sample because of the requirement of multiple samples for computing correlations. We developed here with a statistical method, i.e. a sample-specific network (SSN) method, which allows us to construct individual-specific networks based on molecular expressions of a single sample. Using this method, we can characterize various human diseases at a network level. In particular, such SSNs can lead to the identification of individual-specific disease modules as well as driver genes, even without gene sequencing information. Extensive analysis by using the Cancer Genome Atlas data not only demonstrated the effectiveness of the method, but also found new individual-specific driver genes and network patterns for various types of cancer. Biological experiments on drug resistance further validated one important advantage of our method over the traditional methods, i.e. we can even identify such drug resistance genes that actually have no clear differential expression between samples with and without the resistance, due to the additional network information.
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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.