The Alpha Project: A model system for systems biology research
One goal of systems biology is to understand how genome-encoded parts interact to produce quantitative phenotypes. The Alpha Project is a medium-scale, interdisciplinary systems biology effort that aims to achieve this goal by understanding fundamental quantitative behaviours of a prototypic signal...
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| Otros Autores: | , , , , , , , , , , , , , , , , |
| Formato: | Capítulo de libro |
| Lenguaje: | Inglés |
| Publicado: |
2008
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| Acceso en línea: | Registro en Scopus DOI Handle Registro en la Biblioteca Digital |
| Aporte de: | Registro referencial: Solicitar el recurso aquí |
| LEADER | 13405caa a22017537a 4500 | ||
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| 001 | PAPER-5644 | ||
| 003 | AR-BaUEN | ||
| 005 | 20230518203518.0 | ||
| 008 | 190411s2008 xx ||||fo|||| 00| 0 eng|d | ||
| 024 | 7 | |2 scopus |a 2-s2.0-54049101149 | |
| 024 | 7 | |2 cas |a mitogen activated protein kinase, 142243-02-5; Pheromones; Proteome; Saccharomyces cerevisiae Proteins | |
| 040 | |a Scopus |b spa |c AR-BaUEN |d AR-BaUEN | ||
| 100 | 1 | |a Yu, R.C. | |
| 245 | 1 | 4 | |a The Alpha Project: A model system for systems biology research |
| 260 | |c 2008 | ||
| 270 | 1 | 0 | |m Yu, R.C.; Molecular Sciences Institute, Berkeley, CA, United States |
| 506 | |2 openaire |e Política editorial | ||
| 504 | |a Kay, L.E., (1993) 'The Molecular Vision of Life: Caltech, The Rockefeller Foundation and the Rise of the New Biology', , (Oxford Univeristy Press, New York) | ||
| 504 | |a Brent, R., 'Genomic biology' (2000) Cell, 100 (1), pp. 169-183. , 10.1016/S0092-8674(00)81693-1 | ||
| 504 | |a Endy, D., Brent, R., 'Modelling cellular behaviour' (2001) Nature, 409 (6818), pp. 391-395. , 0028-0836 | ||
| 504 | |a Colman-Lerner, A., Gordon, A., Serra, E., 'Regulated cell-to-cell variation in a cell-fate decision system' (2005) Nature, 437 (7059), pp. 699-706. , 0028-0836 | ||
| 504 | |a Dohlman, H.G., Thorner, J.W., 'Regulation of G protein-initiated signal transduction in yeast: Paradigms and principles' (2001) Annu. Rev. Biochem., 70, pp. 703-754 | ||
| 504 | |a Giaever, G., Chu, A.M., Ni, L., 'Functional profiling of the Saccharomyces cerevisiae genome' (2002) Nature, 418 (6896), pp. 387-391. , 0028-0836 | ||
| 504 | |a Winzeler, E.A., Shoemaker, D.D., Astromoff, A., 'Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis' (1999) Science, 285 (5429), pp. 901-906. , 0036-8075 | ||
| 504 | |a Huh, W.K.L., Falvo, J.V., Gerke, L.C., 'Global analysis of protein localization in budding yeast' (2003) Nature, 425 (6959), pp. 686-691. , 0028-0836 | ||
| 504 | |a Ghaemmaghami, S., Huh, W.K., Bower, K., 'Global analysis of protein expression in yeast' (2003) Nature, 425 (6959), pp. 737-741. , 0028-0836 | ||
| 504 | |a Gordon, A., Colman-Lerner, A., Chin, T.E.., Benjamin, K.R., Yu, R.C., 'Single-cell quantification of molecules and rates using open-source microscope-based cytometry' (2007) Nat. Methods, 4 (2), pp. 175-181 | ||
| 504 | |a Yu, R.C., Pesce, C.G., Colman-Lerner, A., 'Feedback regulates information transmission in yeast pheromone response' (2008) Nature, , (in press) 0028-0836 | ||
| 504 | |a Colman-Lerner, A., Chin, T.E., Brent, R., 'Yeast Cbk1 and Mob2 activate daughter-specific genetic programs to induce asymmetric cell fates' (2001) Cell, 107 (6), pp. 739-750 | ||
| 504 | |a Heiman, M.G., Walter, P., 'Prm1p, a pheromone-regulated multispanning membrane protein, facilitates plasma membrane fusion during yeast mating' (2000) J. Cell Biol., 151 (3), pp. 719-730 | ||
| 504 | |a Brun, R., Couet, O., Vandroni, C., Zanarini, O., (1989) 'PAW Physics Analysis Workstation CERN Program Library Entry Q121', , CERN, Geneva | ||
| 504 | |a Chernomoretz, A., Bush, A., Yu, R.C., Gordon, A., Colman-Lerner, A., 'Cell-ID, a software for microscope-based cytometry' (2008) Curr Protoc. Mol. Biol., , (in press) | ||
| 504 | |a Burbulis, I., Yamaguchi, K., Gordon, A., Carlson, R., Brent, R., 'Using protein-DNA chimeras to detect and count small numbers of molecules' (2005) Nat. Methods, 2 (1), pp. 31-37 | ||
| 504 | |a Burbulis, I., Yamaguchi, K., Yu, R., Resnekov, O., Brent, R., 'Quantifying small numbers of antibodies with a 'near-universal protein-DNA chimera' (2007) Nat. Methods, 4 (12), pp. 1011-1013 | ||
| 504 | |a Morton-Firth, C., (1998) 'Stochastic Simulation of Cell Signalling Pathways', pp. 1-197. , (University of Cambridge, Department of Physiology, Development and Neuroscience, Cambridge, UK) | ||
| 504 | |a Lok, L., Brent, R., 'Automatic generation of cellular reaction networks with Moleculizer 1.0' (2005) Nat. Biotechnol., 23 (1), pp. 131-136 | ||
| 504 | |a Blinov, M.L., Faeder, J.R., Goldstein, B., Hlavacek, W.S., 'BioNetGen: Software for rule-based modeling of signal transduction based on the interactions of molecular domains' (2004) Bioinformatics, 20 (17), pp. 3289-3291 | ||
| 504 | |a Meier-Schellersheim, M., Xu, X., Angermann, B., Kunkel, E.J., Jin, T., Germain, R.N., 'Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method' (2006) PLoS Comput. Biol., 2 (7), pp. e82 | ||
| 504 | |a Hucka, M., Finney, A., Bornstein, B.J., 'Evolving a lingua franca and associated software infrastructure for computational systems biology: The systems biology markup language (SBML) project' (2004) Syst. Biol., 1 (1), pp. 41-53. , 10.1049/sb:20045008 | ||
| 504 | |a Hucka, M., Finney, A., Sauro, H.M., 'The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models' (2003) Bioinformatics, 19 (4), pp. 524-531 | ||
| 504 | |a Shannon, C.E., 'A mathematical theory of communication' (1948) Bell Syst. Tech. J., 27, pp. 379-423. , 0005-8580 | ||
| 504 | |a Yi, T.M., Kitano, H., Simon, M.I., 'A quantitative characterization of the yeast heterotrimeric G protein cycle' (2003) Proc. Natl. Acad. Sci. USA, 100 (19), pp. 10764-10769. , 0027-8424 | ||
| 504 | |a Cuatrecasas, P., 'Insulin-receptor interactions in adipose tissue cells: Direct measurement and properties' (1971) Proc. Natl. Acad. Sci. USA, 68 (6), pp. 1264-1268. , 0027-8424 | ||
| 504 | |a Knauer, D.J., Wiley, H.S., Cunningham, D.D., 'Relationship between epidermal growth factor receptor occupancy and mitogenic response. Quantitative analysis using a steady state model system' (1984) J. Biol. Chem., 259 (9), pp. 5623-5631 | ||
| 504 | |a Nagashima, T., Shimodaira, H., Ide, K., 'Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiation' (2007) J. Biol. Chem., 282 (6), pp. 4045-4056 | ||
| 504 | |a Amsterdam, A., Sadler, K.C., Lai, K., 'Many ribosomal protein genes are cancer genes in zebrafish' (2004) PLoS Biol., 2 (5), pp. E139 | ||
| 504 | |a McCarthy, M.I., Abecasis, G.R., Cardon, L.R., 'Genome-wide association studies for complex traits: Consensus, uncertainty and challenges' (2008) Nat. Rev. Genet., 9 (5), pp. 356-369 | ||
| 504 | |a Langefeld, C.D., Fingerlin, T.E., 'Association methods in human genetics' (2007) Methods Mol. Biol., 404, pp. 431-460 | ||
| 504 | |a Bornholdt, S., 'Systems biology. Less is more in modeling large genetic networks' (2005) Science, 310 (5747), pp. 449-451. , 0036-8075 | ||
| 504 | |a Jenness, D.D., Burkholder, A.L., Hartwell, L.H., 'Binding of alpha-factor pheromone to Saccharomyces cerevisiae a cells: Dissociation constant and number of binding sites' (1986) Mol. Cell Biol., 6 (1), pp. 318-320 | ||
| 504 | |a Bajaj, A., Celic, A., Ding, F.X., Naider, F., Becker, J.M., Dumont, M.E., 'A fluorescent alpha-factor analogue exhibits multiple steps on binding to its G protein coupled receptor in yeast' (2004) Biochemistry, 43 (42), pp. 13564-13578 | ||
| 520 | 3 | |a One goal of systems biology is to understand how genome-encoded parts interact to produce quantitative phenotypes. The Alpha Project is a medium-scale, interdisciplinary systems biology effort that aims to achieve this goal by understanding fundamental quantitative behaviours of a prototypic signal transduction pathway, the yeast pheromone response system from Saccharomyces cerevisiae. The Alpha Project distinguishes itself from many other systems biology projects by studying a tightly bounded and well-characterised system that is easily modified by genetic means, and by focusing on deep understanding of a discrete number of important and accessible quantitative behaviours. During the project, the authors have developed tools to measure the appropriate data and develop models at appropriate levels of detail to study a number of these quantitative behaviours. The authors have also developed transportable experimental tools and conceptual frameworks for understanding other signalling systems. In particular, the authors have begun to interpret system behaviours and their underlying molecular mechanisms through the lens of information transmission, a principal function of signalling systems. The Alpha Project demonstrates that interdisciplinary studies that identify key quantitative behaviours and measure important quantities, in the context of well-articulated abstractions of system function and appropriate analytical frameworks, can lead to deeper biological understanding. The author's experience may provide a productive template for systems biology investigations of other cellular systems. © The Institution of Engineering and Technology 2008. |l eng | |
| 593 | |a Molecular Sciences Institute, Berkeley, CA, United States | ||
| 593 | |a California Institute of Technology, Computation and Neural Systems, Department of Electrical Engineering, Pasadena, CA, United States | ||
| 593 | |a Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States | ||
| 593 | |a Microscale Life Sciences Center, University of Washington, Seattle, WA, United States | ||
| 593 | |a Pacific Northwest National Laboratory, Richland, WA, United States | ||
| 593 | |a Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States | ||
| 593 | |a Prosetta, San Francisco, CA, United States | ||
| 593 | |a Amyris Biotechnologies, Emeryville, CA, United States | ||
| 593 | |a Departamento de Fisiología, Biología Molecular y Cellular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina | ||
| 593 | |a Physics Department, Brookhaven National Laboratory, Upton, NY, United States | ||
| 593 | |a Biodesign Institute, Arizona State University, Tempe, AZ, United States | ||
| 593 | |a Synopsys, Sunnyvale, CA, United States | ||
| 593 | |a Centre de Genètica Mèdica i Molecular, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Barcelona, Spain | ||
| 690 | 1 | 0 | |a DATA STRUCTURES |
| 690 | 1 | 0 | |a MATHEMATICAL MODELS |
| 690 | 1 | 0 | |a PROBABILITY DENSITY FUNCTION |
| 690 | 1 | 0 | |a SIGNAL TRANSDUCTION |
| 690 | 1 | 0 | |a CELLULAR SYSTEMS |
| 690 | 1 | 0 | |a CONCEPTUAL FRAMEWORKS |
| 690 | 1 | 0 | |a DISCRETE NUMBERS |
| 690 | 1 | 0 | |a INFORMATION TRANSMISSIONS |
| 690 | 1 | 0 | |a INTERDISCIPLINARY STUDIES |
| 690 | 1 | 0 | |a INTERDISCIPLINARY SYSTEMS |
| 690 | 1 | 0 | |a LEVELS OF DETAILS |
| 690 | 1 | 0 | |a MODEL SYSTEMS |
| 690 | 1 | 0 | |a MOLECULAR MECHANISMS |
| 690 | 1 | 0 | |a PRINCIPAL FUNCTIONS |
| 690 | 1 | 0 | |a QUANTITATIVE |
| 690 | 1 | 0 | |a RESPONSE SYSTEMS |
| 690 | 1 | 0 | |a SACCHAROMYCES CEREVISIAE |
| 690 | 1 | 0 | |a SIGNAL TRANSDUCTION PATHWAYS |
| 690 | 1 | 0 | |a SIGNALLING SYSTEMS |
| 690 | 1 | 0 | |a SYSTEM BEHAVIOURS |
| 690 | 1 | 0 | |a SYSTEM FUNCTIONS |
| 690 | 1 | 0 | |a SYSTEMS BIOLOGIES |
| 690 | 1 | 0 | |a BIOLOGY |
| 690 | 1 | 0 | |a G PROTEIN COUPLED RECEPTOR |
| 690 | 1 | 0 | |a MITOGEN ACTIVATED PROTEIN KINASE |
| 690 | 1 | 0 | |a PHEROMONE |
| 690 | 1 | 0 | |a ACCESS TO INFORMATION |
| 690 | 1 | 0 | |a ALPHA PROJECT |
| 690 | 1 | 0 | |a COMPUTER NETWORK |
| 690 | 1 | 0 | |a CONCEPTUAL FRAMEWORK |
| 690 | 1 | 0 | |a CONFERENCE PAPER |
| 690 | 1 | 0 | |a CYTOLOGY |
| 690 | 1 | 0 | |a DATA ANALYSIS SOFTWARE |
| 690 | 1 | 0 | |a DATA EXTRACTION |
| 690 | 1 | 0 | |a IMAGE CYTOMETRY |
| 690 | 1 | 0 | |a INFORMATION PROCESSING |
| 690 | 1 | 0 | |a MATHEMATICAL MODEL |
| 690 | 1 | 0 | |a MOLECULAR INTERACTION |
| 690 | 1 | 0 | |a NONHUMAN |
| 690 | 1 | 0 | |a PHENOMENOLOGY |
| 690 | 1 | 0 | |a PROTEIN DATABASE |
| 690 | 1 | 0 | |a PROTEIN EXPRESSION |
| 690 | 1 | 0 | |a PROTEIN MODIFICATION |
| 690 | 1 | 0 | |a QUANTITATIVE ANALYSIS |
| 690 | 1 | 0 | |a SACCHAROMYCES CEREVISIAE |
| 690 | 1 | 0 | |a SIGNAL TRANSDUCTION |
| 690 | 1 | 0 | |a STOCHASTIC MODEL |
| 690 | 1 | 0 | |a SYSTEM ANALYSIS |
| 690 | 1 | 0 | |a SYSTEMS BIOLOGY |
| 690 | 1 | 0 | |a COMPUTER SIMULATION |
| 690 | 1 | 0 | |a MODELS, BIOLOGICAL |
| 690 | 1 | 0 | |a PHEROMONES |
| 690 | 1 | 0 | |a PROTEIN INTERACTION MAPPING |
| 690 | 1 | 0 | |a PROTEOME |
| 690 | 1 | 0 | |a RESEARCH |
| 690 | 1 | 0 | |a SACCHAROMYCES CEREVISIAE |
| 690 | 1 | 0 | |a SACCHAROMYCES CEREVISIAE PROTEINS |
| 690 | 1 | 0 | |a SIGNAL TRANSDUCTION |
| 690 | 1 | 0 | |a SACCHAROMYCES CEREVISIAE |
| 700 | 1 | |a Resnekov, O. | |
| 700 | 1 | |a Abola, A.P. | |
| 700 | 1 | |a Andrews, S.S. | |
| 700 | 1 | |a Benjamin, K.R. | |
| 700 | 1 | |a Bruck, J. | |
| 700 | 1 | |a Burbulis, I.E. | |
| 700 | 1 | |a Colman-Lerner, A. | |
| 700 | 1 | |a Endy, D. | |
| 700 | 1 | |a Gordon, A. | |
| 700 | 1 | |a Holl, M. | |
| 700 | 1 | |a Lok, L. | |
| 700 | 1 | |a Pesce, C.G. | |
| 700 | 1 | |a Serra, E. | |
| 700 | 1 | |a Smith, R.D. | |
| 700 | 1 | |a Thomson, T.M. | |
| 700 | 1 | |a Tsong, A.E. | |
| 700 | 1 | |a Brent, R. | |
| 773 | 0 | |d 2008 |g v. 2 |h pp. 222-233 |k n. 5 |p IET Syst. Biol. |x 17518849 |t IET Systems Biology | |
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