ArticleProceedings of the National Academy of Sciences of the United States of America2018
Predicting perturbation patterns from the topology of biological networks.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 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
113 citing papers in PubMed, 332 citations in OpenAlex.
- Adaxial-abaxial leaf surface asymmetry is a key ecological driver of the phyllosphere microbiome.Journal of experimental botany · 2026Article
- Network Topology and Interactomic Analysis Reveal the Regulatory Framework of the Humanin Protein Family (MTRNR2Lx Class).Biomolecules · 2026Article
- Balancing deterministic and stochastic assembly during needle aging shapes phyllosphere microbial community complexity and stability.Environmental microbiome · 2026Article
- Microbial community succession along the entrance to distant zone in karst cave ecosystem: community assembly and distance decay patterns in weathered rock and sediment habitats.Environmental microbiome · 2026Article
- Arbuscular Mycorrhizal Fungi Orchestrate Soil Microbial Community Assembly Along aEcology and evolution · 2026Article
- Effects of exogenous selenium treatment on the composition of endophytic bacterial and fungal communities in Amorphophallus muelleri.Scientific reports · 2026Article
- Article
- Continuous cropping drives assembly process of soil microbial community to alter keystone taxa causing challenges.BMC microbiology · 2025Article
- Divergent Response of Host-Specific Driven Gut Microbial Stability in Freshwater Gastropods to Cyanobacterial Blooms.Ecology and evolution · 2025Article
- Metagenome and metabolome study on inhaled corticosteroids in asthma patients with side effects.Journal of integrative bioinformatics · 2025Article
- Organic farming significantly improves microbial community structure, network complexity, and functional diversity in the Gannan navel orange orchard.BMC microbiology · 2025Article
- Starvation Influences the Microbiota in the Stomach of the Corallivorous Crown-of-Thorns Starfish.Biology · 2025Article
- Unstable pathogen profile in spotted seal (Phoca largha) gut microbiota and limited turnover with habitat microbiome.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Article
- Local Fungi Promote Plant Growth by Positively Affecting Rhizosphere Metabolites to Drive Beneficial Microbial Assembly.Microorganisms · 2025Article
- Microbes with plastic-degrading and pathogenic potentials are present on plastics in the final polishing pond of a wastewater treatment plant.Environmental microbiome · 2025Article
- CeONPJ microgravity · 2025Article
- Perturbation response scanning of drug-target networks: Drug repurposing for multiple sclerosis.Journal of pharmaceutical analysis · 2025Article
- Integrative approaches for predicting protein network perturbations through machine learning and structural characterization.Journal of proteomics · 2025Article
- Sensitivity analysis on protein-protein interaction networks through deep graph networks.BMC bioinformatics · 2025Article
- Exploring the Mechanism of Action and Potential Targets of Saorilao-4 Decoction in the Treatment of Pulmonary Fibrosis in Rats by Metabolomics.Food science & nutrition · 2025Article
53 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
2 authors at 1 institution in 2 countries.
Funding
Abstract
High-throughput technologies, offering an unprecedented wealth of quantitative data underlying the makeup of living systems, are changing biology. Notably, the systematic mapping of the relationships between biochemical entities has fueled the rapid development of network biology, offering a suitable framework to describe disease phenotypes and predict potential drug targets. However, our ability to develop accurate dynamical models remains limited, due in part to the limited knowledge of the kinetic parameters underlying these interactions. Here, we explore the degree to which we can make reasonably accurate predictions in the absence of the kinetic parameters. We find that simple dynamically agnostic models are sufficient to recover the strength and sign of the biochemical perturbation patterns observed in 87 biological models for which the underlying kinetics are known. Surprisingly, a simple distance-based model achieves 65% accuracy. We show that this predictive power is robust to topological and kinetic parameter perturbations, and we identify key network properties that can increase up to 80% the recovery rate of the true perturbation patterns. We validate our approach using experimental data on the chemotactic pathway in bacteria, finding that a network model of perturbation spreading predicts with ∼80% accuracy the directionality of gene expression and phenotype changes in knock-out and overproduction experiments. These findings show that the steady advances in mapping out the topology of biochemical interaction networks opens avenues for accurate perturbation spread modeling, with direct implications for medicine and drug development.
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.