ReviewPLoS computational biology2012
Ten years of pathway analysis: current approaches and outstanding challenges.
Review in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 856 papers.
What it found
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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.
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Who cites it
856 citing papers in PubMed.
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- Knowledge-driven interpretable neural networks provide mechanistic insight.Genome research · 2026Article
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- Molecular characterization in elite rock climbers: insights from multi-omics analysis.BMC genomics · 2026Article
- Functional Depth Biomarkers Distinguish Lung Squamous Cell Carcinoma from Lung Adenocarcinoma.Research square · 2026Article
- OmicsTransformer: self-supervised masked consistency and uncertainty-aware fusion for robust multi-omics prediction.Bioinformatics (Oxford, England) · 2026Article
- BrainEnrich: Revealing Biological Insights for Imaging-Derived Phenotypes Through Transcriptomic Enrichment.Human brain mapping · 2026Article
- Hyperpathway: visualizing organization of pathway-molecule enriched interactions in omics studies via hyperbolic bipartite network embedding.NPJ systems biology and applications · 2026Article
- Helminth infection induces RELMα-dependent adipose tissue transcriptional reprogramming and protection against diet-induced obesity.bioRxiv : the preprint server for biology · 2026Article
- Review
- A literature-guided integrative transcriptomic analysis framework for prioritizing angiogenesis-associated genes across cancers.Discover oncology · 2026Article
- Weak supervision of H&E slides reveals systems-level biology and functional states that govern therapeutic resistance.bioRxiv : the preprint server for biology · 2026Article
- GEDO: topology-based inference of gene module activity in Sjögren's disease.Briefings in bioinformatics · 2026Article
- Continuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity.Briefings in bioinformatics · 2026Article
796 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
3 authors.
Funding
Abstract
Pathway analysis has become the first choice for gaining insight into the underlying biology of differentially expressed genes and proteins, as it reduces complexity and has increased explanatory power. We discuss the evolution of knowledge base-driven pathway analysis over its first decade, distinctly divided into three generations. We also discuss the limitations that are specific to each generation, and how they are addressed by successive generations of methods. We identify a number of annotation challenges that must be addressed to enable development of the next generation of pathway analysis methods. Furthermore, we identify a number of methodological challenges that the next generation of methods must tackle to take advantage of the technological advances in genomics and proteomics in order to improve specificity, sensitivity, and relevance of pathway analysis.
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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.