ArticlePloS one2013
Passing messages between biological networks to refine predicted interactions.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 160 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
160 citing papers in PubMed, 310 citations in OpenAlex.
- Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma.The Journal of allergy and clinical immunology · 2018Trial
- Inferring Gene Regulatory Networks in Stem Cells: Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2027Review
- MGCLSyn: multimodal graph contrastive learning for drug synergy prediction.Journal of computer-aided molecular design · 2026Article
- Molecular programs in human locus coeruleus link APOE and neuromelanin to Alzheimer's vulnerability.Acta neuropathologica · 2026Article
- BLOBFISH: bipartite limited subnetworks from multiple observations using breadth-first search with constrained hops.Bioinformatics (Oxford, England) · 2026Article
- Leiomodin 1 deficiency promotes lipid accumulation and redirects gene regulatory programs in smooth muscle cells exposed to oxidized LDL.Research square · 2026Article
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
- FERRET: Framework to Evaluate Robustness in Regulatory Networks Using Heterogeneous Cell Types.bioRxiv : the preprint server for biology · 2026Article
- Large-scale, interpretable gene regulatory network inference through biologically informed matrix factorization.bioRxiv : the preprint server for biology · 2026Article
- Network-based discovery of regulatory drivers of cognitive decline in alzheimer's disease.npj aging · 2026Article
- PARROT: Phase-Altering Regulatory Rewiring Over Time.bioRxiv : the preprint server for biology · 2026Article
- Context-dependent correlations mislead transcriptomic network inference in bulk and single-cell data.bioRxiv : the preprint server for biology · 2026Article
- Computational blueprints for cell fate programming.Stem cell reports · 2026Review
- Temporal changes in gene regulation during human tissue repair.Scientific reports · 2026Article
- Gene regulatory network analysis identifies dysregulation of hypoxia pathways as contributing to glioblastoma treatment resistance in females.Biology of sex differences · 2026Article
- Article
- Personalized Morphology, Replication Timing, and RNA based Gene Expression Networks for Basal-like and Classical subtyping genes in Pancreatic Adenocarcinoma.bioRxiv : the preprint server for biology · 2026Article
- Pharmacological stabilization of hypoxia-inducible factor 1-α dampens the interferon response and promotes glycolysis in Aicardi-Goutières syndrome.Nature communications · 2026Article
- Challenges and Opportunities in Single-Sample Network Modeling.bioRxiv : the preprint server for biology · 2026Article
- Multimodal bioinformatic analyses of genome-scale expression beyond gene-centric differential expression.Briefings in bioinformatics · 2026Review
100 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks using multiple, independent datasets obtained from complementary sources, but methods for this integration are lacking. We developed PANDA (Passing Attributes between Networks for Data Assimilation), a message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast as a model. The resulting networks were not only more accurate than those produced using individual data sets and other existing methods, but they also captured information regarding specific biological mechanisms and pathways that were missed using other methodologies. PANDA is scalable to higher eukaryotes, applicable to specific tissue or cell type data and conceptually generalizable to include a variety of regulatory, interaction, expression, and other genome-scale data. An implementation of the PANDA algorithm is available at www.sourceforge.net/projects/panda-net.
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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.