ArticleNature communications2023
NetBID2 provides comprehensive hidden driver analysis.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed, 27 citations in OpenAlex.
- Single-cell multi-omic profiling of heterogeneous PROCRiScience · 2026Article
- Benchmarking methods for inferring single-cell transcription factor activity using large-scale perturbation sequencing data.Briefings in bioinformatics · 2026Article
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
- Genomic Subtype Influences BH3 Mimetic Drug Sensitivity and Synergy with Cytotoxic Chemotherapeutics in T-cell Acute Lymphoblastic Leukemia.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Protein phosphatase 2A regulates senescence and immunogenicity in medulloblastoma models.The Journal of clinical investigation · 2026Article
- Network-based analysis reveals potential microRNA regulation of oncogenic pathways in SOX10-depleted uveal melanoma.Cellular and molecular life sciences : CMLS · 2026Article
- Defining PI3K Signaling as a Key Regulator of Molecular Heterogeneity and Inflammation in Glomerular Lupus Nephritis.Immune network · 2026Article
- NFATc1 and NFATc2 regulate glucocorticoid resistance in pediatric T-cell acute lymphoblastic leukemia through modulation of cholesterol biosynthesis and the WNT/β-catenin pathway.Haematologica · 2026Article
- Antigen Specificity and Cell Engineering Determine CAR T Cell Efficacy in Group 3 Medulloblastoma.Research square · 2026Article
- lncAPNet enables the deciphering of lncRNA-mRNA connections in patient transcriptomic data.Bioinformatics advances · 2026Article
- Activated signaling pathways and metabolic processes in disseminating myxoid glioneuronal tumors.Journal of neuropathology and experimental neurology · 2025Article
- Clinically associated genomic landscape of pediatric non-Down Syndrome acute megakaryoblastic leukemia in Chinese patients.Leukemia · 2025Article
- TEAD switches interacting partners along neural progenitor lineage progression to execute distinct functions.Genes & development · 2025Article
- scMINER: a mutual information-based framework for clustering and hidden driver inference from single-cell transcriptomics data.Nature communications · 2025Article
- GPR65 Inactivation in Tumor Cells Drives Antigen-Independent CAR T-cell Resistance via Macrophage Remodeling.Cancer discovery · 2025Article
- Latent epigenetic programs in Müller glia contribute to stress and disease response in the retina.Developmental cell · 2025Article
- Spotiphy enables single-cell spatial whole transcriptomics across an entire section.Nature methods · 2025Article
- APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19.Bioinformatics (Oxford, England) · 2025Article
- In-depth inference of transcriptional regulatory networks reveals NPM1 as a therapeutic ribosomal regulator in MYC-amplified medulloblastoma.NPJ precision oncology · 2025Article
- A mini-review on perturbation modelling across single-cell omic modalities.Computational and structural biotechnology journal · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
19 authors at 1 institution in 2 countries.
Funding
Abstract
Many signaling and other genes known as "hidden" drivers may not be genetically or epigenetically altered or differentially expressed at the mRNA or protein levels, but, rather, drive a phenotype such as tumorigenesis via post-translational modification or other mechanisms. However, conventional approaches based on genomics or differential expression are limited in exposing such hidden drivers. Here, we present a comprehensive algorithm and toolkit NetBID2 (data-driven network-based Bayesian inference of drivers, version 2), which reverse-engineers context-specific interactomes and integrates network activity inferred from large-scale multi-omics data, empowering the identification of hidden drivers that could not be detected by traditional analyses. NetBID2 has substantially re-engineered the previous prototype version by providing versatile data visualization and sophisticated statistical analyses, which strongly facilitate researchers for result interpretation through end-to-end multi-omics data analysis. We demonstrate the power of NetBID2 using three hidden driver examples. We deploy NetBID2 Viewer, Runner, and Cloud apps with 145 context-specific gene regulatory and signaling networks across normal tissues and paediatric and adult cancers to facilitate end-to-end analysis, real-time interactive visualization and cloud-based data sharing. NetBID2 is freely available at https://jyyulab.github.io/NetBID .
Indexed as
Identifiers
What OpenQuestion holds
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.