Network medicine

FEBS Letters

Volumn 582, Issue 8, 2008, Pages 1266-1270

  Pawson, Tony ^a   Linding, Rune ^b  

^a MOUNT SINAI HOSPITAL   (Canada)

^b INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

Computational biology; Network biology; Network medicine; Proteomics; Quantitative mass spectrometry; Systems biology

Indexed keywords

ALGORITHM; DIABETES MELLITUS; NEOPLASM; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEOMICS; QUANTITATIVE ANALYSIS; SCHIZOPHRENIA; SHORT SURVEY; SIGNAL TRANSDUCTION;

PHOSPHORYLATION; PROTEOMICS; SYSTEMS BIOLOGY;

EID: 41149167511     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2008.02.011     Document Type: Short Survey

References (47)

1. Wood A.J.J. A proposal for radical changes in the drug-approval process. New Eng. J. Med. 355 6 (2006) 618-624
2. Hoffman J.M., Shah N.D., Vermeulen L.C., Schumock G.T., Grim P., Hunkler R.J., and Hontz K.M. Projecting future drug expenditures - 2007. Am. J. Health-Syst. Pharm. 64 (2007) 298-314
3. Reichert J.M. Trends in US approvals: new biopharmaceuticals and vaccines. Trends Biotechnol. 24 7 (2006) 293-298 Jul
4. Reichert J.M. Trends in development and approval times for new therapeutics in the United States. Nat. Rev. Drug Discov. 2 (2003) 695-702
5. Grabowski H.G., and Wang Y.R. The quantity and quality of worldwide new drug introductions, 1982-2003. Health Aff. (Millwood) 25 2 (2006) 452-460
6. DiMasi J.A., and Grabowski H.G. Economics of new oncology drug development. J. Clin. Oncol. 25 2 (2007) 209-216
7. Keyhani S., Diener-West M., and Powe N. Are development times for pharmaceuticals increasing or decreasing?. Trend. Health Affair 25 2 (2006) 461-468
8. Yildirim M.A., Goh K.I., Cusick M.E., Barabasi A.L., and Vidal M. Drug-target network. Nat. Biotechnol. 25 10 (2007) 1119-1126
9. Seet B.T., Dikic I., Zhou M.M., and Pawson T. Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol. 7 7 (2006) 473-483
10. Linding R., Jensen L.J., Ostheimer G.J., van Vugt M.A., Jorgensen C., Miron I.M., Diella F., Colwill K., Taylor L., Elder K., Metalnikov P., Nguyen V., Pasculescu A., Jin J., Park J.G., Samson L.D., Woodgett J.R., Russell R.B., Bork P., Yaffe M.B., and Pawson T. Systematic discovery of in vivo phosphorylation networks. Cell 129 7 (2007) 1415-1426
11. Miller, M.L., Jensen, L.J., Diella, F., Jørgensen, C., Tinti, M., Li, L., Hsiung, M., Parker, S.A., Bordeaux, J., Sicheritz-Ponten, T., Knapp, S., Blom, N., Bork, P., Li, S., Cesareni, G., Pawson, T., Turk, B.E., Yaffe, M.B., Brunak, S. and Linding, R. Linear motif atlas for phosphorylation-dependent signalling (submitted for publication).
12. Gavin A.C., Aloy P., Grandi P., Krause R., Boesche M., Marzioch M., Rau C., Jensen L.J., Bastuck S., Dumpelfeld B., Edelmann A., Heurtier M.A., Hoffman V., Hoefert C., Klein K., Hudak M., Michon A.M., Schelder M., Schirle M., Remor M., Rudi T., Hooper S., Bauer A., Bouwmeester T., Casari G., Drewes G., Neubauer G., Rick J.M., Kuster B., Bork P., Russell R.B., and Superti-Furga G. Proteome survey reveals modularity of the yeast cell machinery. Nature 440 7084 (2006) 631-636 Epub 2006 Jan 22, Mar 30
13. Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., Li J., Pu S., Datta N., Tikuisis A.P., Punna T., Peregrin-Alvarez J.M., Shales M., Zhang X., Davey M., Robinson M.D., Paccanaro A., Bray J.E., Sheung A., Beattie B., Richards D.P., Canadien V., Lalev A., Mena F., Wong P., Starostine A., Canete M.M., Vlasblom J., Wu S., Orsi C., Collins S.R., Chandran S., Haw R., Rilstone J.J., Gandi K., Thompson N.J., Musso G., St Onge P., Ghanny S., Lam M.H., Butland G., Altaf-Ul A.M., Kanaya S., Shilatifard A., O'Shea E., Weissman J.S., Ingles C.J., Hughes T.R., Parkinson J., Gerstein M., Wodak S.J., Emili A., and Greenblatt J.F. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440 7084 (2006) 637-643 Epub 2006 Mar 22, Mar 30
14. Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., and Mann M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127 3 (2006) 635-648
15. Blagoev B., Ong S.E., Kratchmarova I., and Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol. 22 9 (2004) 1139-1145
16. Cox J., and Mann M. Is proteomics the new genomics?. Cell 130 3 (2007) 395-398
17. Huang P.H., Mukasa A., Bonavia R., Flynn R.A., Brewer Z.E., Cavenee W.K., Furnari F.B., and White F.M. Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc. Natl. Acad. Sci. USA 104 31 (2007) 12867-12872
18. Wolf-Yadlin A., Hautaniemi S., Lauffenburger D.A., and White F.M. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc. Natl. Acad. Sci. USA 104 14 (2007) 5860-5865 Epub 2007 Mar 26, Apr 3
19. Huang P.H., Cavenee W.K., Furnari F.B., and White F.M. Uncovering therapeutic targets for glioblastoma: a systems biology approach. Cell Cycle 6 22 (2007) 2750-2754 Epub 2007 Aug 20, Aug
20. Barrios-Rodiles M., Brown K.R., Ozdamar B., Bose R., Liu Z., Donovan R.S., Shinjo F., Liu Y., Dembowy J., Taylor I.W., Luga V., Przulj N., Robinson M., Suzuki H., Hayashizaki Y., Jurisica I., and Wrana J.L. High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307 5715 (2005) 1621-1625
21. Rual J.F., Venkatesan K., Hao T., et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437 7062 (2005) 1173-1178 Epub 2005 Sep 28, Oct 20
22. Bakal C., Aach J., Church G., and Perrimon N. Quantitative morphological signatures define local signaling networks regulating cell morphology. Science 316 5832 (2007) 1753-1756
23. Janes K.A., Albeck J.G., Gaudet S., Sorger P.K., Lauffenburger D.A., and Yaffe M.B. A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310 5754 (2005) 1646-1653
24. Miller-Jensen K., Janes K.A., Brugge J.S., and Lauffenburger D.A. Common effector processing mediates cell-specific responses to stimuli. Nature 448 7153 (2007) 604-608 Epub 2007 Jul 18, Aug 2
25. Janes K.A., and Yaffe M.B. Data-driven modelling of signal-transduction networks. Nat. Rev. Mol. Cell Biol. 7 11 (2006) 820-828
26. Wolf-Yadlin A., Kumar N., Zhang Y., Hautaniemi S., Zaman M., Kim H.D., Grantcharova V., Lauffenburger D.A., and White F.M. Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol. Syst. Biol. 2 (2006) 54 Epub 2006 Oct 3
27. Kumar N., Wolf-Yadlin A., White F.M., and Lauffenburger D.A. Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput. Biol. 3 1 (2007) e4 Epub 2006 Nov 21, Jan 5
28. Reinhardt H.C., Aslanian A.S., Lees J.A., and Yaffe M.B. p53-deficient cells rely on ATM- and ATR-mediated checkpoint signaling through the p38MAPK/MK2 pathway for survival after DNA damage. Cancer Cell 11 2 (2007) 175-189
29. Stommel J.M., Kimmelman A.C., Ying H., et al. Coactivation of receptor tyrosine kinases affects the response of tumor cells to targeted therapies. Science 318 5848 (2007) 287-290
30. Irish J.M., Hovland R., Krutzik P.O., Perez O.D., Bruserud Ø., Gjertsen B.T., and Nolan G.P. Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell 118 2 (2004) 217-228
31. Goh K.I., Cusick M.E., Valle D., Childs B., Vidal M., and Barabasi A.L. The human disease network. Proc. Natl. Acad. Sci. USA 104 21 (2007) 8685-8690
32. Chuang H.Y., Lee E., Liu Y.T., Lee D., and Ideker T. Network-based classification of breast cancer metastasis. Mol. Syst. Biol. 3 (2007) 140 Epub 2007 Oct 16
33. Boehm J.S., Zhao J.J., Yao J., et al. Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell 129 6 (2007) 1065-1079
34. Pujana M.A., Han J.D., Starita L.M., et al. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat. Genet. 39 11 (2007) 1338-1349 Epub 2007 Oct 7, Nov
35. von Mering C., Jensen L.J., Kuhn M., Chaffron S., Doerks T., Krüger B., Snel B., and Bork P. STRING 7 - recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35 Database issue (2007) D358-D362
36. Kuhn M., von Mering C., Campillos M., Jensen L.J., and Bork P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res. 36 Database issue (2008) D684-D688 Epub 2007 Dec 15
37. Diella F., Gould C.M., Chica C., Via A., and Gibson T.J. Phospho.ELM: a database of phosphorylation sites update 2008. Nucleic Acids Res. 36 Database issue (2008) D240-D244 Epub 2007 Oct 25
38. Pawson T., and Linding R. Synthetic modular systems-reverse engineering of signal transduction. FEBS Lett. 579 8 (2005) 1808-1814
39. Howard P.L., Chia M.C., Del Rizzo S., Liu F.F., and Pawson T. Redirecting tyrosine kinase signaling to an apoptotic caspase pathway through chimeric adaptor proteins. Proc. Natl. Acad. Sci. USA 100 20 (2003) 11267-11272
40. Yeh B.J., Rutigliano R.J., Deb A., Bar-Sagi D., and Lim W.A. Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors. Nature 447 7144 (2007) 596-600
41. Schoeberl B., Nielsen U.B., and Riccardo P. Model-based design approaches in drug discovery: a parallel to traditional engineering approaches. IBM J. Res. Develop. 50 6 (2006) 645 10.1147/rd.506.0645
42. Irish J.M., Kotecha N., and Nolan G.P. Mapping normal and cancer cell signaling networks: towards single-cell proteomics. Nat. Rev. Cancer 6 (2006) 146-155
43. Irish J.M., Hovland R., Krutznik P.O., et al. Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell 118 (2004) 217-2846
44. Janes K., Albreck J.G., Gaudet S., et al. A systems model of signaling identified a molecular basis set for cytokines-induced apoptosis. Science 310 (2005) 1646-1653
45. Janes K.A., Albreck J.G., Peng L.X., et al. A high-throughput quantitative multiplex kinase assay for monitoring information flow in signaling networks: application to sepsis-apoptosis. Mol. Cell Proteom. 2 (2003) 463-473
46. Shults M.D., Janse K.A., Lauffenburger D., et al. A multiplexed homogeneous fluorescence-based assay for protein kinase assay in cell lysates. Nat. Methods 2 (2005) 1-7
47. Janes K., Albreck J.G., Gaudet S., et al. A systems model of signaling identified a molecular basis set for cytokines-induced apoptosis. Science 310 (2005) 1646-1653