The Promise of Systems Biology in Clinical Applications

Y. L. Yip; Managing Editor for the IMIA Yearbook Section on Bioinformatics

doi:10.1055/s-0038-1638589

Yearbook of Medical Informatics, Inhaltsverzeichnis

Yearb Med Inform 2008; 17(01): 102-104
DOI: 10.1055/s-0038-1638589

Original Article

Georg Thieme Verlag KG Stuttgart

The Promise of Systems Biology in Clinical Applications

Findings from the Yearbook 2008 Section on Bioinformatics

Y. L. Yip

¹Swiss-Prot group, Swiss Institute of Bioinformatics, Geneva, Switzerland

²University of Geneva, Dept. of Structural Biology and Bioinformatics, Geneva, Switzerland

,

Managing Editor for the IMIA Yearbook Section on Bioinformatics

› Institutsangaben

Abstract

Summary

Objectives To summarize current excellent research in the field of bioinformatics.

Method Synopsis of the articles selected for the IMIA Yearbook 2008.

Results Current research in the field of Bioinformatics shows that the emergent field of systems biology is starting to offer innovative solutions to clinically-relevant problems. The approach used can be top-down, where models are created based on hypotheses to describe previously unexplained phenomena and then tested against experimental or clinical evidence. It can also be bottom-up, where mathematical models are built by harnessing existing information about the components (e.g. protein entities, interaction networks) of a system in order to discern critical system-level mechanisms that can be relevant for clinical applications. Progress in this area is aided by the ongoing development in data integration and management, whose current focus is on better semantics for facilitating translational research. Advances in other important areas, such as microarray technology, text mining and ontologies, are also noted.

Conclusions The best paper selection of articles on bioinformatics gives examples of original research that exploits mathematical modeling to tackle medical problems and of improved semantic solutions for data integration. As new directions are explored and the technologies mature, these approaches are expected to be increasingly integrated into clinical practice.

Keywords

International Medical Informatics Association - IMIA Yearbook - bioinformatics - systems biology

Volltext

Referenzen

References
1 Beerenwinkel N, Antal T, Dingli D, Traulsen A, Kinzler KW, Velculescu VE. et al. Genetic progression and the waiting time to cancer. PLoS Comput Biol 2007; 03: e225.
2 Filipe JAN, Riley EM, Drakeley CJ, Sutherland CJ, Ghani AC. Determination of the processes driving the acquisition of immunity to malaria using a mathematical transmission model. PLoS Comput Biol 2007; 03: e255.
3 Chan C, Kepler TB. Computational immunologyFrom bench to virtual reality. Ann Acad Med Singapore 2007; 36: 123-7.
4 Maojo V, Crespo J, de la Calle G, Barreiro J, GarciaRemesal M. Using Web services for linking genomic data to medical information systems. Methods Inf Med 2007; 46: 484-92.
5 Baross A, Delaney AD, Li HI, Nayar T, Flibotte S, Qian H. et al. Assessment of algorithms for high throughput detection of genomic copy number variation in ologonucleotide microarray data. BMC Bioinformatics 2007; 08: 368.
6 English SB, Butte AJ. Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes. Bioinformatics 2007; 23: 2910-17.
7 Nicolau M, Tibshirani Borresen-Dale AL, Jeggrey SS. Disease-specific genomic analysis: identifying the signature of pathologic biology. Bioinformatics 2007; 23: 957-65.
8 Sun Y, Goodison S, Li J, Liu L, Farmerie W. Improved breast cancer prognosis through the combination of clinical and genetic markers. Bioinformatics 2007; 23: 30-7.
9 Van Vooren S, Thienpont B, Menten B, Speleman F, De Moor B, Vermeesch J. et al. Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations. Nucleic Acid Research 2007; 35: 2533-43.
10 Hoehndorf R, Loebe F, Keiso J, Herre H. Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies. BMC Bioinformatics 2007; 08: 377.
11 Knaup P, Ammenwerth E, Brandner R, Brigl B, Fischer G, Garde S. et al. Towards clinical bioinformatics: advancing genomic medicine with informatics methods and tools. Methods Inf Med 2004; 43: 302-7.
12 Bott OJ, Ammenwerth E, Brigl B, Knaup P, Lang E, Pilgram R. et al. The challenge of ubiquitous computing in health care: technology, concepts and solutions. Findings from the IMIAYearbook of Medical Informatics 2005. Methods Inf Med 2005; 44: 473-9.
13 Lang E. Bioinformatics and its Impact on Clinical Research Methods. Methods Inf Med 2006; 45: 104-6.
14 Lang E. Integrating bioinformatics into clinical practice: progress and evaluation. Methods Inf Med 2007; 46: 106-8.
15 Kaplan S, Itzkovitz S, Shapiro E. A universal mechanism ties genotype to phenotype in trinucleotide diseases. PLoS Comput Biol 2007; 03: e235.
16 Luan D, Zai M, Varner JD. Computationally derived points of fragility of a human cascade are consistent with current therapeutic strategies. PLoS Comput Biol 2007; 03: e142.
17 Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H. et al. Advancing translational research with semantic web. BMC Bioinformatics 2007; 08: S2.
18 Sioutos N, de Coronado S, Haber MW, Hartel FW, Shaiu WL, Wright LW. NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information. J Biomed Inform 2007; 40: 30-43.