What does systems biology mean for biomarker discovery?

Expert Opinion on Medical Diagnostics

Volumn 4, Issue 1, 2010, Pages 1-10

  Azuaje, Francisco ^a  

^a Laboratory of Cardiovascular Research   (Luxembourg)

Author keywords

Biological networks; Biomarkers; Network based disease classification; Systems biology; Translational bioinformatics

Indexed keywords

BIOLOGICAL MARKER;

BIOINFORMATICS; ECOLOGICAL GENETICS; GENETIC ANALYSIS; REVIEW; SYSTEMS BIOLOGY;

EID: 77953391592     PISSN: 17530059     EISSN: 17530067     Source Type: Journal    
DOI: 10.1517/17530050903468709     Document Type: Review

References (38)

1. Hood L, Heath JR, Phelps ME, et al. Systems biology and new technologies enable predictive and preventative medicine. Science 2004;306:640-643
2. Auffray C, Chen Z, Hood L. Systems medicine: the future of medical genomics and healthcare. Genome Med 2009;1:2
3. Lemberger T. Systems biology in human health and disease. Mol Syst Biol 2007;3:136
4. Azuaje F, Devaux Y, Wagner D. Computational biology for cardiovascular biomarker discovery. Brief Bioinform 2009;10:367-377
5. Chuang HY, Lee E, Liu YT, et al. Network-based classification of breast cancer metastasis. Mol Syst Biol 2007;3:140
6. Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature 2009;461(7261):218-223
7. Brynildsen MP, Collins JJ. Systems biology makes it personal. Mol Cell 2009;34:137-138
8. Hurst RE. Does the biomarker search paradigm need re-booting? BMC Urol 2009;9:1
9. Janssens AC, van Duijn CM. Genome-based prediction of common diseases: methodological considerations for future research. Genome Med 2009;1:20
10. Zethelius B, Berglund L, Sundström J, et al. Use of multiple biomarkers to improve the prediction of death from cardiovascular causes. N Engl J Med 2008;358:2107-2116
11. Jones S, Zhang X, Parsons DW, et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 2008;321:1801-1806
12. Keller MP, Choi Y, Wang P, et al. A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility. Genome Res 2008;18:706-716
13. Chen Y, Zhu J, Lum PY, et al. Variations in DNA elucidate molecular networks that cause disease. Nature 2008;452:429-435
14. Ein-Dor L, Zuk O, Domany E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA 2006;103:5923-5928
15. Shen R, Chinnaiyan AM, Ghosh D. Pathway analysis reveals functional convergence of gene expression profiles in breast cancer. BMC Med Genomics 2008;1:28
16. Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005;102:15545-15550
17. Efron B, Tibshirani R. On testing the significance of sets of genes. Ann Appl Statistics 2007;1:107-129
18. Dobrin R, Zhu J, Molony C, et al. Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease. Genome Biol 2009;10:R55
19. Taylor IW, Linding R, Warde-Farley D, et al. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 2009;27:199-204
20. Lee E, Chuang HY, Kim JW, et al. Inferring pathway activity toward precise disease classification. PLoS Comput Biol 2008;4:e1000217
21. Edelman EJ, Guinney J, Chi JT, et al. Modeling cancer progression via pathway dependencies. PLoS Comput Biol 2008:4:e28
22. 2A.Z associated with breast cancer progression. Mol Syst Biol 2008;4:188
23. Mani KM, Lefebvre C, Wang K, et al. A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol 2008;4:169
24. Hwang D, Lee IY, Yoo H, et al. A systems approach to prion disease. Mol Syst Biol 2009;5:252
25. Chang JT, Carvalho C, Mori S, et al. A genomic strategy to elucidate modules of oncogenic pathway signaling networks. Mol Cell 2009;34:104-114
26. Lim WK, Lyashenko E, Califano A. Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput 2009:504-515
27. Basso K, Margolin AA, Stolovitzky G, et al. Reverse engineering of regulatory networks in human B cells. Nat Genet 2005;37:382-390
28. van de Vijver MJ, He YD, van't Veer LJ, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002;347:1999-2009
29. Wang Y, Klijn JG, Zhang Y, et al. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005;365:671-679
30. Aebersold R, Auffray C, Baney E, et al. Report on EU-USA workshop: how systems biology can advance cancer research. Mol Oncol 2009;3:9-17
31. Blow N. Biobanking: freezer burn. Nat Methods 2009;6:173-178
32. King RD, Rowland J, Oliver SG, et al. The automation of science. Science 2009;324:85-89
33. Krishna R, Schaefer HG, Bjerrum OJ. Effective integration of systems biology, biomarkers, biosimulation and modelling in streamlining drug development. Eur J Pharm Sci 2007;31:62-67 (Pubitemid 46601868)
34. Henney A, Superti-Furga GM. A network solution. Nature 2008;455:730-731
35. Service RF. Will biomarkers take off at last? Science 2008;321:1760
36. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008;26:1135-1145
37. Marguerat S, Wilhelm BT, Bähler J. Next-generation sequencing: applications beyond genomes. Biochem Soc Trans 2008;36:1091-1096
38. Mardis ER. New strategies and emerging technologies for massively parallel sequencing: applications in medical research. Genome Med 2009;1:40