ArticleBiotech (Basel (Switzerland))2022
Challenges and Limitations of Biological Network Analysis.
Article in Biotech (Basel (Switzerland)), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- GATSBI: improving context-aware protein embeddings through biologically motivated data splits.Bioinformatics (Oxford, England) · 2026Article
- GATSBI: Improving context-aware protein embeddings through biologically motivated data splits.bioRxiv : the preprint server for biology · 2026Article
- OncoBERT: Context-Aware Modeling of Somatic Mutations for Precision Oncology.bioRxiv : the preprint server for biology · 2026Article
- Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation.BMC bioinformatics · 2025Article
- Amyloid-β, Tau, and α-Synuclein Protein Interactomes as Therapeutic Targets in Neurodegenerative Diseases.Cellular and molecular neurobiology · 2025Article
- Discovering subnetworks in SBML models.Bioinformatics (Oxford, England) · 2025Article
- Bisphenol A causes melatonin biosynthesis epigenetic reprogramming of melatonin biosynthesis genes in arabidopsis thaliana.Communications biology · 2025Article
- A Hypergraph powered approach to Phenotype-driven Gene Prioritization and Rare Disease Prediction.Scientific reports · 2025Article
- Biological Activity of Biomarkers Associated With Metastasis in Osteosarcoma Cell Lines.Cancer medicine · 2025Article
- Novel target identification towards drug repurposing based on biological activity profiles.PloS one · 2025Article
- Bioinformatic challenges for pharmacogenomic study: tools for genomic data analysis.Frontiers in pharmacology · 2025Article
- Enzymatic Metabolic Switches of Astrocyte Response to Lipotoxicity as Potential Therapeutic Targets for Nervous System Diseases.Pharmaceuticals (Basel, Switzerland) · 2024Article
- Complex Networks and Interacting Particle Systems.Entropy (Basel, Switzerland) · 2023Article
- An Exploratory Application of Multilayer Networks and Pathway Analysis in Pharmacogenomics.Genes · 2023Article
- Aligning Cross-Species Interactomes for Studying Complex and Chronic Diseases.Life (Basel, Switzerland) · 2023Article
- Identification of Potential Molecular Mechanisms and Prognostic Markers for Oral Squamous Cell Carcinoma: A Bioinformatics Analysis.Journal of International Society of Preventive & Community DentistryArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-Throughput technologies are producing an increasing volume of data that needs large amounts of data storage, effective data models and efficient, possibly parallel analysis algorithms. Pathway and interactomics data are represented as graphs and add a new dimension of analysis, allowing, among other features, graph-based comparison of organisms' properties. For instance, in biological pathway representation, the nodes can represent proteins, RNA and fat molecules, while the edges represent the interaction between molecules. Otherwise, biological networks such as Protein-Protein Interaction (PPI) Networks, represent the biochemical interactions among proteins by using nodes that model the proteins from a given organism, and edges that model the protein-protein interactions, whereas pathway networks enable the representation of biochemical-reaction cascades that happen within the cells or tissues. In this paper, we discuss the main models for standard representation of pathways and PPI networks, the data models for the representation and exchange of pathway and protein interaction data, the main databases in which they are stored and the alignment algorithms for the comparison of pathways and PPI networks of different organisms. Finally, we discuss the challenges and the limitations of pathways and PPI network representation and analysis. We have identified that network alignment presents a lot of open problems worthy of further investigation, especially concerning pathway alignment.
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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.