ArticlePLoS computational biology2017
Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it, 41 citations in OpenAlex.
- Plasma cortisol-linked gene networks in hepatic and adipose tissues implicate corticosteroid-binding globulin in modulating tissue glucocorticoid action and cardiovascular risk.Frontiers in endocrinology · 2023Pooled it
- NLCD: A method to discover nonlinear causal relations among genes.PLoS computational biology · 2026Article
- From Prediction to Creation: Generative Plant Design.Plants (Basel, Switzerland) · 2026Review
- Integrating multi-omic QTLs and predictive models reveals regulatory architectures at immune related GWAS loci in CD4+ T cells.medRxiv : the preprint server for health sciences · 2026Article
- Personalized gene expression prediction in the era of deep learning: a review.Briefings in bioinformatics · 2026Review
- Circulating causal protein networks linked to future risk of myocardial infarction.Nature communications · 2025Article
- Airqtl dissects cell state-specific causal gene regulatory networks with efficient single-cell eQTL mapping.Nature communications · 2025Article
- Causal network inference of cis- and trans-gene regulation of expression quantitative trait loci across human tissues.Genetics · 2025Article
- A Network-Driven Framework for Enhancing Gene-Disease Association Studies in Coronary Artery Disease.ArXiv · 2025Article
- Constructing the dynamic transcriptional regulatory networks to identify phenotype-specific transcription regulators.Briefings in bioinformatics · 2024Article
- Predicting the genetic component of gene expression using gene regulatory networks.Bioinformatics advances · 2024Article
- Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics.Nature methods · 2023Article
- eQTLs as causal instruments for the reconstruction of hormone linked gene networks.Frontiers in endocrinology · 2022Review
- A mechanistic framework for cardiometabolic and coronary artery diseases.Nature cardiovascular research · 2022Article
- The activity of human enhancers is modulated by the splicing of their associated lncRNAs.PLoS computational biology · 2022Article
- Single-cell normalization and association testing unifying CRISPR screen and gene co-expression analyses with Normalisr.Nature communications · 2021Article
- Genetic program activity delineates risk, relapse, and therapy responsiveness in multiple myeloma.NPJ precision oncology · 2021Article
- MRPC: An R Package for Inference of Causal Graphs.Frontiers in genetics · 2021Article
- Challenges Raised by Mediation Analysis in a High-Dimension Setting.Environmental health perspectives · 2020Article
- Inferring the direction of a causal link and estimating its effect via a Bayesian Mendelian randomization approach.Statistical methods in medical research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations. Findr outperformed existing methods on the DREAM5 Systems Genetics challenge and on the prediction of microRNA and transcription factor targets in human lymphoblastoid cells, while being nearly a million times faster. Findr is publicly available at https://github.com/lingfeiwang/findr.
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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.