Graph-based methods for analysing networks in cell biology - PubMed (original) (raw)
Review
doi: 10.1093/bib/bbl022. Epub 2006 Jul 30.
Affiliations
- PMID: 16880171
- DOI: 10.1093/bib/bbl022
Review
Graph-based methods for analysing networks in cell biology
Tero Aittokallio et al. Brief Bioinform. 2006 Sep.
Abstract
Availability of large-scale experimental data for cell biology is enabling computational methods to systematically model the behaviour of cellular networks. This review surveys the recent advances in the field of graph-driven methods for analysing complex cellular networks. The methods are outlined on three levels of increasing complexity, ranging from methods that can characterize global or local structural properties of networks to methods that can detect groups of interconnected nodes, called motifs or clusters, potentially involved in common elementary biological functions. We also briefly summarize recent approaches to data integration and network inference through graph-based formalisms. Finally, we highlight some challenges in the field and offer our personal view of the key future trends and developments in graph-based analysis of large-scale datasets.
Similar articles
- Computational intelligence approaches for pattern discovery in biological systems.
Fogel GB. Fogel GB. Brief Bioinform. 2008 Jul;9(4):307-16. doi: 10.1093/bib/bbn021. Epub 2008 May 5. Brief Bioinform. 2008. PMID: 18460474 Review. - Graph theoretic modeling of large-scale semantic networks.
Bales ME, Johnson SB. Bales ME, et al. J Biomed Inform. 2006 Aug;39(4):451-64. doi: 10.1016/j.jbi.2005.10.007. Epub 2005 Dec 15. J Biomed Inform. 2006. PMID: 16442849 Review. - A multi-layered approach to protein data integration for diabetes research.
McGarry K, Chambers J, Oatley G. McGarry K, et al. Artif Intell Med. 2007 Oct;41(2):129-43. doi: 10.1016/j.artmed.2007.07.009. Epub 2007 Sep 14. Artif Intell Med. 2007. PMID: 17869073 - H-CORE: enabling genome-scale Bayesian analysis of biological systems without prior knowledge.
Jung S, Lee KH, Lee D. Jung S, et al. Biosystems. 2007 Jul-Aug;90(1):197-210. doi: 10.1016/j.biosystems.2006.08.004. Epub 2006 Aug 22. Biosystems. 2007. PMID: 17005318 - Mining coherent dense subgraphs across massive biological networks for functional discovery.
Hu H, Yan X, Huang Y, Han J, Zhou XJ. Hu H, et al. Bioinformatics. 2005 Jun;21 Suppl 1:i213-21. doi: 10.1093/bioinformatics/bti1049. Bioinformatics. 2005. PMID: 15961460
Cited by
- ORCO: Ollivier-Ricci Curvature-Omics - an unsupervised method for analyzing robustness in biological systems.
Simhal AK, Weistuch C, Murgas K, Grange D, Zhu J, Oh JH, Elkin R, Deasy JO. Simhal AK, et al. bioRxiv [Preprint]. 2024 Oct 11:2024.10.06.616915. doi: 10.1101/2024.10.06.616915. bioRxiv. 2024. PMID: 39416154 Free PMC article. Preprint. - Targeting Lactobacillus johnsonii to reverse chronic kidney disease.
Miao H, Liu F, Wang YN, Yu XY, Zhuang S, Guo Y, Vaziri ND, Ma SX, Su W, Shang YQ, Gao M, Zhang JH, Zhang L, Zhao YY, Cao G. Miao H, et al. Signal Transduct Target Ther. 2024 Aug 5;9(1):195. doi: 10.1038/s41392-024-01913-1. Signal Transduct Target Ther. 2024. PMID: 39098923 Free PMC article. - From calcium imaging to graph topology.
Blevins AS, Bassett DS, Scott EK, Vanwalleghem GC. Blevins AS, et al. Netw Neurosci. 2022 Oct 1;6(4):1125-1147. doi: 10.1162/netn_a_00262. eCollection 2022. Netw Neurosci. 2022. PMID: 38800465 Free PMC article. Review. - Application of Artificial Intelligence at All Stages of Bone Tissue Engineering.
Kolomenskaya E, Butova V, Poltavskiy A, Soldatov A, Butakova M. Kolomenskaya E, et al. Biomedicines. 2023 Dec 28;12(1):76. doi: 10.3390/biomedicines12010076. Biomedicines. 2023. PMID: 38255183 Free PMC article. Review. - A comparative NMR-based metabolomics study of lung parenchyma of severe COVID-19 patients.
Hurtado JI, López-Radcenco A, Izquierdo-García JL, Rodríguez F, Moyna G, Greif G, Nin N. Hurtado JI, et al. Front Mol Biosci. 2023 Nov 15;10:1295216. doi: 10.3389/fmolb.2023.1295216. eCollection 2023. Front Mol Biosci. 2023. PMID: 38033387 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources