Metabolomics, modelling and machine learning in systems biology - Towards an understanding of the languages of cells: Delivered on 3 July 2005 at the 30th FEBS Congress and 9th IUBMB conference in Budapest

FEBS Journal

Volumn 273, Issue 5, 2006, Pages 873-894

  Kell, Douglas B ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Evolutionary computing; Genetic programming; Hypothesis generation; Signal processing elements; Systems biology; Technology development

Indexed keywords

I KAPPA B; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN;

CALCULATION; CHEMICAL GENETICS; COMPUTER; CONCENTRATION RESPONSE; CONFERENCE PAPER; CYTODIAGNOSIS; ENGINEERING; EXPERIMENTATION; GENETIC LINKAGE; GENOMICS; INFORMATION PROCESSING; KINETICS; LEARNING; MATHEMATICS; MEDICAL LITERATURE; MEDICAL RESEARCH; MEDICAL TECHNOLOGY; METABOLOMICS; MICHAELIS CONSTANT; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; NANOTECHNOLOGY; NATURAL SCIENCE; PRIORITY JOURNAL; SIGNAL PROCESSING; SIGNAL TRANSDUCTION; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; HUNGARY; METABOLISM; SYSTEMS BIOLOGY; UNITED KINGDOM;

ARTIFICIAL INTELLIGENCE; GREAT BRITAIN; HUNGARY; METABOLISM; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY;

EID: 33644959172     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2006.05136.x     Document Type: Conference Paper

References (354)

1. von Bertalanffy L 1969 General System Theory George Braziller New York
2. Iberall AS 1972 Toward a General Science of Viable Systems McGraw-Hill New York
3. Kell DB 1979 On the functional proton current pathway of electron transport phosphorylation: an electrodic view Biochim Biophys Acta 549 55 99
4. Brenner S 1997 Loose Ends. Current Biology London
5. Hood L 2003 Systems biology: integrating technology, biology, and computation Mech Ageing Dev 124 9 16
6. Ideker T Galitski T Hood L 2001 A new approach to decoding life: systems biology Annu Rev Genomics Hum Genet 2 343 372
7. Kitano H 2002 Systems biology: a brief overview Science 295 1662 1664
8. Kitano H 2002 Computational systems biology Nature 420 206 210
9. Davidov E Holland J Marple E Naylor S 2003 Advancing drug discovery through systems biology Drug Discov Today 8 175 183
10. Henry CM 2003 Systems biology Chem Eng News 81 45 55
11. Westerhoff HV Palsson BO 2004 The evolution of molecular biology into systems biology Nat Biotechnol 22 1249 1252
12. Klipp E Herwig R Kowald A Wierling C Lehrach H 2005 Systems Biology in Practice: Concepts, Implementation and Clinical Application Wiley/VCH Berlin
13. Kriete A Eils R 2005 Computational Systems Biology Academic Press New York
14. Palsson BØ 2006 Systems Biology: Properties of Reconstructed Networks Cambridge University Press Cambridge
15. Kell DB 2002 Genotype: phenotype mapping: genes as computer programs Trends Genet 18 555 559
16. Kell DB Oliver SG 2004 Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era Bioessays 26 99 105
17. Kell DB 2005 Metabolomics, machine learning and modelling: towards an understanding of the language of cells Biochem Soc Trans 33 520 524
18. Ihekwaba AEC Broomhead DS Grimley R Benson N Kell DB 2004 Sensitivity analysis of parameters controlling oscillatory signalling in the NF-κB pathway: the roles of IKK and IκBα Systems Biol 1 93 103
19. Nelson DE Ihekwaba AEC Elliott M Gibney CA Foreman BE Nelson G See V Horton CA Spiller DG Edwards SW McDowell HP Unitt JF Sullivan E Grimley R Benson N Broomhead DS Kell DB White MRH 2004 Oscillations in NF-κB signalling control the dynamics of target gene expression Science 306 704 708
20. Ihekwaba AEC Broomhead DS Grimley R Benson N White MRH Kell DB 2005 Synergistic control of oscillations in the NF-κB signalling pathway IEE Systems Biol 152 153 160
21. Milo R Shen-Orr S Itzkovitz S Kashtan N Chklovskii D Alon U 2002 Network motifs: simple building blocks of complex networks Science 298 824 827
22. Tyson JJ Chen KC Novak B 2003 Sniffers, buzzers, toggles and blinkers. dynamics of regulatory and signaling pathways in the cell Curr Opin Cell Biol 15 221 231
23. Bhalla U.S. 2003 Understanding complex signaling networks through models and metaphors Prog Biophys Mol Biol 81 45 65
24. Wall ME Hlavacek WS Savageau MA 2004 Design of gene circuits: Lessons from bacteria Nat Rev Genet 5 34 42
25. Kacser H 1986 On parts and wholes in metabolism The Organization of Cell Metabolism Welch GR Clegg JS, eds), pp. 327 337 Plenum Press New York
26. Kell DB Mendes P 2000 Snapshots of systems. metabolic control analysis and biotechnology in the post-genomic era Technological and Medical Implications of Metabolic Control Analysis Cornish-Bowden A Cárdenas ML, eds), pp. 3 25 (and see ). Kluwer Academic Publishers Dordrecht
27. Kell DB 2004 Metabolomics and systems biology: making sense of the soup Curr Op Microbiol 7 296 307
28. Kacser H Burns JA 1973 The control of flux Rate Control of Biological ProcessesSymposium of the Society for Experimental Biology Vol. 27 Davies DD, ed.), pp. 65 104 Cambridge University Press Cambridge
29. Heinrich R Rapoport TA 1974 A linear steady-state treatment of enzymatic chains. General properties, control and effector strength Eur J Biochem 42 89 95
30. Kell DB Westerhoff HV 1986 Metabolic control theory: its role in microbiology and biotechnology FEMS Microbiol Rev 39 305 320
31. Heinrich R Schuster S 1996 The Regulation of Cellular Systems Chapman & Hall New York
32. Fell DA 1996 Understanding the Control of Metabolism Portland Press London
33. Savageau M 1976 Biochemical Systems Analysis: a Study of Function and Design in Molecular Biology Addison-Wesley Reading, MA
34. Voit EO 2000 Computational Analysis of Biochemical Systems Cambridge University Press Cambridge
35. Lazebnik Y 2002 Can a biologist fix a radio? - or, what I learned while studying apoptosis Cancer Cell 2 179 182
36. Kell DB Knowles JD 2005 The role of modeling in systems biology System Modeling in Cellular Biology: from Concepts to Nuts and Bolts Szallasi Z Periwal V Stelling J, eds), pp. 3 18 MIT Press Cambridge
37. Bower JM Bolouri H 2004 Computational Modeling of Genetic and Biochemical Networks Bradford Books New York
38. Mendes P Kell DB 2001 MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous cellular systems Bioinformatics 17 288 289
39. Andrews SS Bray D 2004 Stochastic simulation of chemical reactions with spatial resolution and single molecule detail Phys Biol 1 137 151
40. Salis H Kaznessis Y 2005 Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions J Chem Phys 122 54103
41. Hucka M Finney A Sauro HM Bolouri H Doyle JC Kitano H Arkin AP Bornstein BJ Bray D Cornish-Bowden A et al. 2003 The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics 19 524 531
42. Finney A Hucka M 2003 Systems biology markup language: Level 2 and beyond Biochem Soc Trans 31 1472 1473
43. Mendes P 1997 Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3 Trends Biochem Sci 22 361 363
44. Mendes P Kell DB 1998 Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation Bioinformatics 14 869 883
45. Kauffman S Lobo J Macready WG 2000 Optimal search on a technology landscape J Econ Behav Organ 43 141 166
46. Goldberg DE 2002 The Design of Innovation: Lessons from and for Competent Genetic Algorithms Kluwer Boston
47. Koza JR Keane MA Streeter MJ Mydlowec W Yu J Lanza G 2003 Genetic Programming: Routine Human-Competitive Machine Intelligence Kluwer New York
48. Raju GK Cooney CL 1998 Active learning from process data AlChE J 44 2199 2211
49. Bryant CH Muggleton SH Oliver SG Kell DB Reiser P King RD 2001 Combining inductive logic programming, active learning and robotics to discover the function of genes Electronic Transactions on Artificial Intelligence 5 1 36 ().
50. Cohn DA Ghabhramani Z Jordan MI 1996 Active learning with statistical models J Artif Intell Res 4 129 145
51. Hasenjäger M Ritter H 1998 Active learning with local models Neural Proc Lett 7 110 117
52. Cohn DA Atlas L Ladner R 1994 Improving generalisation with active learning Machine Learning 15 201 221
53. Mackay D 1992 Information-based objective functions for active data selection Neural Comput 4 590 604
54. Milano M Schmidhuber J Koumoutsakos P 2001 (2001) Active learning with adaptive grids Artifical Neural Networks-ICANN Proc 2130 436 442
55. King RD Whelan KE Jones FM Reiser PGK Bryant CH Muggleton SH Kell DB Oliver SG 2004 Functional genomic hypothesis generation and experimentation by a robot scientist Nature 427 247 252
56. Whelan KE King RD 2004 Intelligent software for laboratory automation Trends Biotechnol 22 440 445
57. Olansky AS Parker LR Jr. Morgan SL Deming SN 1977 Automated development of analytical chemical methods: the determination of serum calcium by the cresolphthalein complexone method Anal Chim Acta 95 107 133
58. Olansky AS Deming SN 1978 Automated development of a kinetic method for the continuous-flow determination of creatinine Clin Chem 24 2115 2124
59. O'Hagan S Dunn WB Brown M Knowles JD Kell DB 2005 Closed-loop, multiobjective optimisation of analytical instrumentation: gas-chromatography- time-of-flight mass spectrometry of the metabolomes of human serum and of yeast fermentations Anal Chem 77 290 303
60. Daniel C Full J Gonzalez L Lupulescu C Manz J Merli A Vajda S Woste L 2003 Deciphering the reaction dynamics underlying optimal control laser fields Science 299 536 539
61. Schlesselman JJ 1982 Case-Control Studies - Design, Conduct, Analysis Oxford University Press Oxford
62. Logothetis N Wynn HP 1989 Quality Through Design: Experimental Design, Off-Line Quality Control, and Taguchi's Contribution Clarendon Press Oxford
63. Hicks CR Turner KV 1999 ) Jr. Fundamental Concepts in the Design of Experiments 5th edn Oxford University Press Oxford
64. Montgomery DC 2001 Design and Analysis of Experiments 5th edn Wiley Chichester
65. Myers RH Montgomery DC 1995 Response Surface Methodology: Process and Product Optimization Using Designed Experiments Wiley New York
66. Brent R 1999 Functional genomics: Learning to think about gene expression data Curr Biol 9 R338 R341
67. Kell DB Darby RM Draper J 2001 Genomic computing: explanatory analysis of plant expression profiling data using machine learning Plant Physiol 126 943 951
68. Kell DB 2002 Metabolomics and machine learning: explanatory analysis of complex metabolome data using genetic programming to produce simple, robust rules Mol Biol Report 29 237 241
69. Brent R Lok L 2005 A fishing buddy for hypothesis generators Science 308 504 506
70. Förster J Famili I Fu P Palsson BØ Nielsen J 2003 Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network Genome Res 13 244 253
71. Reed JL Palsson BØ 2003 Thirteen years of building constraint-based in silico models of Escherichia coli J Bacteriol 185 2692 2699
72. Borodina I Krabben P Nielsen J 2005 Genome-scale analysis of Streptomyces coelicolor A3 (2) metabolism Genome Res 15 820 829
73. Edwards JS Ibarra RU Palsson BØ 2001 In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data Nat Biotechnol 19 125 130
74. Segrè D Vitkup D Church GM 2002 Analysis of optimality in natural and perturbed metabolic networks Proc Natl Acad Sci USA 99 15112 15117
75. Segrè D Zucker J Katz J Lin X D'Haeseleer P Rindone WP Kharchenko P Nguyen DH Wright MA Church GM 2003 From annotated genomes to metabolic flux models and kinetic parameter fitting Omics 7 301 316
76. Covert MW Palsson BØ 2003 Constraints-based models: regulation of gene expression reduces the steady-state solution space J Theor Biol 221 309 325
77. Papin JA Stelling J Price ND Klamt S Schuster S Palsson BO 2004 Comparison of network-based pathway analysis methods Trends Biotechnol 22 400 405
78. Patil KR Akesson M Nielsen J 2004 Use of genome-scale microbial models for metabolic engineering Curr Opin Biotechnol 15 64 69
79. Famili I Mahadevan R Palsson BO 2005 k-Cone analysis: determining all candidate values for kinetic parameters on a network scale Biophys J 88 1616 1625
80. Patil KR Rocha I Forster J Nielsen J 2005 Evolutionary programming as a platform for in silico metabolic engineering BMC Bioinformatics 6 308
81. Fersht A 1977 Enzyme Structure and Mechanism 2nd edn W.H. Freeman San Francisco
82. Keleti T 1986 Basic Enzyme Kinetics, Akadémiai Kiadó Budapest
83. Segel IH 1993 Enzyme Kinetics Wiley New York
84. Cornish-Bowden A 1995 Fundamentals of Enzyme Kinetics 2nd edn Portland Press London
85. Wu L Wang W van Winden WA van Gulik WM Heijnen JJ 2004 A new framework for the estimation of control parameters in metabolic pathways using lin-log kinetics Eur J Biochem 271 3348 3359
86. Ljung L 1987 System Identification: Theory for the User Prentice Hall Englewood Cliffs, NJ
87. Mendes P Kell DB 1996 On the analysis of the inverse problem of metabolic pathways using artificial neural networks Biosystems 38 15 28
88. Koza JR Mydlowec W Lanza G Yu J Keane MA 2001 Reverse engineering of metabolic pathways from observed data using genetic programming Pac Symp Biocomput 434 445
89. Moles CG Mendes P Banga JR 2003 Parameter estimation in biochemical pathways: a comparison of global optimization methods Genome Res 13 2467 2474
90. Styczynski MP Stephanopoulos G 2005 Overview of computational methods for the inference of gene regulatory networks Comput Chem Eng 29 519 534
91. Patil KR Nielsen J 2005 Uncovering transcriptional regulation of metabolism by using metabolic network topology Proc Natl Acad Sci USA 102 2685 2689
92. Oliver SG Winson MK Kell DB Baganz F 1998 Systematic functional analysis of the yeast genome Trends Biotechnol 16 373 378
93. Raamsdonk LM Teusink B Broadhurst D Zhang N Hayes A Walsh M Berden JA Brindle KM Kell DB Rowland JJ et al. 2001 A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations Nat Biotechnol 19 45 50
94. Fiehn O 2002 Metabolomics: the link between genotypes and phenotypes Plant Mol Biol 48 155 171
95. Harrigan GG Goodacre R 2003 Metabolic Profiling: its Role in Biomarker Discovery and Gene Function Analysis Kluwer Academic Publishers Boston
96. Sumner LW Mendes P Dixon RA 2003 Plant metabolomics: large-scale phytochemistry in the functional genomics era Phytochemistry 62 817 836
97. Weckwerth W 2003 Metabolomics in systems biology Annu Rev Plant Biol 54 669 689
98. German JB Roberts MA Watkins SM 2003 Personal metabolomics as a next generation nutritional assessment J Nutr 133 4260 4266
99. Nicholson JK Wilson ID 2003 Understanding 'global' systems biology: Metabonomics and the continuum of metabolism Nat Rev Drug Disc 2 668 676
100. Bino RJ Hall RD Fiehn O Kopka J Saito K Draper J Nikolau BJ Mendes P Roessner-Tunali U Beale MH et al. 2004 Potential of metabolomics as a functional genomics tool Trends Plant Sci 9 418 425
101. Nicholson JK Holmes E Lindon JC Wilson ID 2004 The challenges of modeling mammalian biocomplexity Nat Biotechnol 22 1268 1274
102. Whitfield PD German AJ Noble PJ 2004 Metabolomics: an emerging post-genomic tool for nutrition Br J Nutr 92 549 555
103. Gibney MJ Walsh M Brennan L Roche HM German B van Ommen B 2005 Metabolomics in human nutrition: opportunities and challenges Am J Clin Nutr 82 497 503
104. Vaidyanathan S Harrigan GG Goodacre R 2005 Metabolome Analyses: Strategies for Systems Biology Springer New York
105. Wilson ID Nicholson JK Castro-Perez J Granger JH Johnson KA Smith BW Plumb RS 2005 High resolution 'ultra performance' liquid chromatography coupled to oa-TOF mass spectrometry as a tool for differential metabolic pathway profiling in functional genomic studies J Proteome Res 4 591 598
106. Wilson ID Brinkman UA 2003 Hyphenation and hypernation: the practice and prospects of multiple hyphenation J Chromatogr A 1000 325 356
107. Goodacre R Vaidyanathan S Dunn WB Harrigan GG Kell DB 2004 Metabolomics by numbers: acquiring and understanding global metabolite data Trends Biotechnol 22 245 252
108. Dunn WB Ellis DI 2005 Metabolomics: current analytical platforms and methodologies Trends Anal Chem 24 285 294
109. Dunn WB Bailey NJC Johnson HE 2005 Measuring the metabolome: current analytical technologies Analyst 130 606 625
110. Brown M Dunn WB Ellis DI Goodacre R Handl J Knowles JD O'Hagan S Spasic I Kell DB 2005 A metabolome pipeline: from concept to data to knowledge Metabolomics 1 35 46
111. Vaidyanathan S Broadhurst DI Kell DB Goodacre R 2003 Explanatory optimisation of protein mass spectrometry via genetic search Anal Chem 75 6679 6686
112. Barrow JD Silk J 1995 The Left Hand of Creation: the Origin and Evolution of the Expanding Universe Penguin London
113. Reeves CR 1995 Modern Heuristic Techniques for Combinatorial Problems McGraw-Hill London
114. RaywardSmith VJ Osman IH Reeves CR Smith GD 1996 Modern Heuristic Search Methods Wiley Chichester
115. Corne D Dorigo M Glover F 1999 New Ideas in Optimization McGraw-Hill London
116. Dasgupta P Chakrabarti PP DeSarkar SC 1999 Multiobjective Heuristic Search, Vieweg Braunschweig
117. Michalewicz Z Fogel DB 2000 How to Solve It: Modern Heuristics Springer-Verlag Heidelberg
118. Vaidyanathan S Kell DB Goodacre R 2004 Selective detection of proteins in mixtures using electrospray ionization mass spectrometry: influence of instrumental settings and implications for proteomics Anal Chem 76 5024 5032
119. Bäck T Fogel DB Michalewicz Z 1997 Handbook of Evolutionary Computation IOP Publishing/Oxford University Press Oxford
120. Kell DB King RD 2000 On the optimization of classes for the assignment of unidentified reading frames in functional genomics programmes: the need for machine learning Trends Biotechnol 18 93 98
121. Langley P Simon HA Bradshaw GL Zytkow JM 1987 Scientific Discovery: Computational Exploration of the Creative Processes MIT Press Cambridge, MA
122. Allen JK Davey HM Broadhurst D Heald JK Rowland JJ Oliver SG Kell DB 2003 High-throughput characterisation of yeast mutants for functional genomics using metabolic footprinting Nat Biotechnol 21 692 696
123. Allen J Davey HM Broadhurst D Rowland JJ Oliver SG Kell DB 2004 Discrimination of the modes of action of antifungal substances by use of metabolic footprinting Appl Env Micr 70 6157 6165
124. Kell DB Brown M Davey HM Dunn WB Spasic I Oliver SG 2005 Metabolic footprinting and Systems Biology: the medium is the message Nat Rev Microbiol 3 557 565
125. Kenny LC Dunn WB Ellis DI Myers J Baker PN The GOPEC Consortium & Kell DB 2005 Novel biomarkers for pre-eclampsia detected using metabolomics and machine learning Metabolomics 1 in press ). Online 10.1007/s11306-005-0003-1.
126. Catchpole GS Beckmann M Enot DP Mondhe M Zywicki B Taylor J Hardy N Smith A King RD Kell DB Fiehn O Draper J 2005 Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops Proc Natl Acad Sci USA 102 14458 14462
127. Kaderbhai NN Broadhurst DI Ellis DI Goodacre R Kell DB 2003 Functional genomics via metabolic footprinting: Monitoring metabolite secretion by Escherichia coli tryptophan metabolism mutants using FT-IR and direct injection electrospray mass spectrometry Comp Func Genomics 4 376 391
128. Marriott P Shellie R 2002 Principles and applications of comprehensive two-dimensional gas chromatography Trends Anal Chem 21 573 583
129. Ong RC Marriott PJ 2002 A review of basic concepts in comprehensive two-dimensional gas chromatography J Chromatogr Sci 40 276 291
130. Blumberg LM 2003 Comprehensive two-dimensional gas chromatography: metrics, potentials, limits J Chromatogr A 985 29 38
131. Plumb R Castro-Perez J Granger J Beattie I Joncour K Wright A 2004 Ultra-performance liquid chromatography coupled to quadrupole-orthogonal time-of-flight mass spectrometry Rapid Commun Mass Spectrom 18 2331 2337
132. Wilson ID Plumb R Granger J Major H Williams R Lenz EM 2005 HPLC-MS-based methods for the study of metabonomics J Chromatogr B Analyt Technol Biomed Life Sci 817 67 76
133. Sauro HM Kholodenko BN 2004 Quantitative analysis of signaling networks Prog Biophys Mol Biol 86 5 43
134. Hoffmann A Levchenko A Scott ML Baltimore D 2002 The IκB-NF- κB signaling module: temporal control and selective gene activation Science 298 1241 1245
135. Ghosh S Karin M 2002 Missing pieces in the NF-kappaB puzzle Cell 109 Suppl. S81 S96
136. Richmond A 2002 NF-κB, chemokine gene transcription and tumour growth Nat Rev Immunol 2 664 674
137. Tian B Brasier AR 2003 Identification of a nuclear factor kappa B-dependent gene network Recent Prog Horm Res 58 95 130
138. Tian B Nowak DE Jamaluddin M Wang S Brasier AR 2005 Identification of direct genomic targets downstream of the nuclear factor-kappaB transcription factor mediating tumor necrosis factor signalling J Biol Chem 280 17435 17448
139. Nelson G Paraoan L Spiller DG Wilde GJ Browne MA Djali PK Unitt JF Sullivan E Floettmann E White MR 2002 Multi-parameter analysis of the kinetics of NF-κB signalling and transcription in single living cells J Cell Sci 115 1137 1148
140. Mantzaris NV 2005 Single-cell gene-switching networks and heterogeneous cell population phenotypes Comput Chem Eng 29 631 643
141. Kell DB Ryder HM Kaprelyants AS Westerhoff HV 1991 Quantifying heterogeneity: Flow cytometry of bacterial cultures Antonie van Leeuwenhoek 60 145 158
142. Davey HM Kell DB 1996 Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analysis Microbiol Rev 60 641 696
143. Werner SL Barken D Hoffmann A 2005 Stimulus specificity of gene expression programs determined by temporal control of IKK activity Science 309 1857 1861
144. Covert MW Leung TH Gaston JE Baltimore D 2005 Achieving stability of lipopolysaccharide-induced NF-kappaB activation Science 309 1854 1857
145. White TA Kell DB 2004 Comparative genomic assessment of novel broad-spectrum targets for antibacterial drugs Comp Func Genomics 5 304 327
146. Wolf DM Arkin AP 2003 Motifs, modules and games in bacteria Curr Opin Microbiol 6 125 134
147. Yeger-Lotem E Sattath S Kashtan N Itzkovitz S Milo R Pinter RY Alon U Margalit H 2004 Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction Proc Natl Acad Sci USA 101 5934 5939
148. Woodward AM Rowland JJ Kell DB 2004 Fast automatic registration of images using the phase of a complex wavelet transform: application to proteome gels Analyst 129 542 552
149. Isaacs FJ Blake WJ Collins JJ 2005 Molecular biology. Signal processing in single cells Science 307 1886 1888
150. Mendes P Kell DB Welch GR 1995 Metabolic channeling in organized enzyme systems: experiments and models Enzymology in Vivo Brindle KM, ed.), pp. 1 19 JAI Press London
151. Ovádi J 1995 Cell Architecture and Metabolic Channeling Springer-Verlag New York
152. Agius L Sherratt HSA 1997 Channelling in Intermediary Metabolism Portland Press London
153. Ovádi J Srere PA 2000 Macromolecular compartmentation and channeling Int Rev Cytol 192 255 280
154. Buchler NE Gerland U Hwa T 2003 On schemes of combinatorial transcription logic Proc Natl Acad Sci USA 100 5136 5141
155. Westerhoff HV Tsong TY Chock PB Chen Y Astumian RD 1986 How enzymes can capture and transmit free energy from an oscillating electric field Proc Natl Acad Sci USA 83 4734 4738
156. Westerhoff HV Astumian RD Kell DB 1988 Mechanisms for the interaction between nonstationary electric fields and biological systems.2. Nonlinear dielectric theory and free-energy transduction Ferroelectrics 86 79 101
157. Woodward AM Kell DB 1990 On the nonlinear dielectric properties of biological systems. Saccharomyces cerevisiae Bioelectrochem Bioenerg 24 83 100
158. Woodward AM Jones A Zhang X Rowland J Kell DB 1996 Rapid and non-invasive quantification of metabolic substrates in biological cell suspensions using nonlinear dielectric spectroscopy with multivariate calibration and artificial neural networks. Principles and applications Bioelectrochem Bioenerg 40 99 132
159. Kell DB Woodward AM Davies E Todd RW Evans MF Rowland JJ 2004 Nonlinear dielectric spectroscopy of biological systems: principles and applications Nonlinear Dielectric Phenomena in Complex Liquids Rzoska SJ Zhelezny VP, eds), pp. 335 344 Kluwer, Dordrecht.
160. Mikulecky DC 1983 Network thermodynamics: a candidate for a common language for theoretical and experimental biology Am J Physiol 245 R1 R9
161. Mikulecky DC 2001 Network thermodynamics and complexity: a transition to relational systems theory Comput Chem 25 369 391
162. Westerhoff HV van Dam K 1987 Thermodynamics and Control of Biological Free Energy Transduction Elsevier Amsterdam
163. Koza JR Mydlowec W Lanza G Yu J Keane MA 2001 ) Automatic synthesis of both the topology and sizing of metabolic pathways using genetic programming. Proceedings of the. GECCO-2001. ( Spector L Goodman ED Wu A Langdon WB General M Sen S Dorigo M Pezeshk S Garzon MH Burke E, eds), pp. 57 65 Morgan Kaufmann San Francisco
164. Tyson JJ Chen K Novak B 2001 Network dynamics and cell physiology Nat Rev Mol Cell Biol 2 908 916
165. Csete ME Doyle JC 2002 Reverse engineering of biological complexity Science 295 1664 1669
166. Kramer BP Fischer C Fussenegger M 2004 BioLogic gates enable logical transcription control in mammalian cells Biotechnol Bioeng 87 478 484
167. Deckard A Sauro HM 2004 Preliminary studies on the in silico evolution of biochemical networks Chembiochem 5 1423 1431
168. Milo R Itzkovitz S Kashtan N Levitt R Shen-Orr S Ayzenshtat I Sheffer M Alon U 2004 Superfamilies of evolved and designed networks Science 303 1538 1542
169. Kashtan N Alon U 2005 Spontaneous evolution of modularity and network motifs Proc Natl Acad Sci USA 102 13773 13778
170. Endy D Brent R 2001 Modelling cellular behaviour Nat 409 391 395
171. Pethig R Kell DB 1987 The passive electrical properties of biological systems: their significance in physiology, biophysics and biotechnology Phys Med Biol 32 933 970
172. Chen W-K 1986 Passive and Active Filters: Theory and Implementations Wiley New York
173. Rosenfeld N Alon U 2003 Response delays and the structure of transcription networks J Mol Biol 329 645 654
174. Shen-Orr SS Milo R Mangan S Alon U 2002 Network motifs in the transcriptional regulation network of Escherichia coli Nat Genet 31 64 68
175. Mangan S Alon U 2003 Structure and function of the feed-forward loop network motif Proc Natl Acad Sci USA 100 11980 11985
176. Barkai N Leibler S 1997 Robustness in simple biochemical networks Nature 387 913 917
177. von Dassow G Meir E Munro EM Odell GM 2000 The segment polarity network is a robust development module Nature 406 188 192
178. Ma L Iglesias PA 2002 Quantifying robustness of biochemical network models BMC Bioinformatics 3..
179. Morohashi M Winn AE Borisuk MT Bolouri H Doyle J Kitano H 2002 Robustness as a measure of plausibility in models of biochemical networks J Theor Biol 216 19 30
180. Ebenhoh O Heinrich R 2003 Stoichiometric design of metabolic networks: multifunctionality, clusters, optimization, weak and strong robustness Bull Math Biol 65 323 357
181. Aldana M Cluzel P 2003 A natural class of robust networks Proc Natl Acad Sci USA 100 8710 8714
182. Kitano H 2004 Biological robustness Nat Rev Genet 5 826 837
183. Schmitt BM 2004 The concept of 'buffering' in systems and control theory: from metaphor to math Chembiochem 5 1384 1392
184. Stelling J Sauer U Szallasi Z Doyle FJ 2004 3rd & Doyle, J. Robustness of cellular functions Cell 118 675 685
185. Chaves M Albert R Sontag ED 2005 Robustness and fragility of Boolean models for genetic regulatory networks J Theor Biol 235 431 449
186. Chen BS Wang YC Wu WS Li WH 2005 A new measure of the robustness of biochemical networks Bioinformatics 21 2698 2705
187. Wagner A 2005 Circuit topology and the evolution of robustness in two-gene circadian oscillators Proc Natl Acad Sci USA 102 11775 11780
188. Strömbäck L Lambrix P 2005 Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX Bioinformatics 21 4401 4407
189. Cornell M Paton NW Hedeler C Kirby P Delneri D Hayes A Oliver SG 2003 GIMS: an integrated data storage and analysis environment for genomic and functional data Yeast 20 1291 1306
190. Spellman P Miller M Stewart J Troup C Sarkans U Chervitz S Bernhart D Sherlock G Ball C Lepage M et al. 2002 Design and implementation of microarray gene expression markup language (MAGE-ML) Genome Biol 3, research0046.1-0046.9.
191. Hermjakob H Montecchi-Palazzi L Bader G Wojcik J Salwinski L Ceol A Moore S Orchard S Sarkans U von Mering C et al. 2004 The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data Nat Biotechnol 22 177 183
192. Garwood KL McLaughlin T Garwood C Joens S Morrison N Taylor CF Carroll K Evans C Whetton AD Hart S et al. 2004 PEDRo: a database for storing, searching and disseminating experimental proteomics data BMC Genomics doi:10.1186/1471- 2164-5-68.q4
193. Orchard S Hermjakob H Apweiler R 2003 The proteomics standards initiative Proteomics 3 1374 1376
194. Orchard S Hermjakob H Julian RK Jr. Runte K Sherman D Wojcik J Zhu W Apweiler R 2004 Common interchange standards for proteomics data: public availability of tools and schema Proteomics 4 490 491
195. Jenkins H Hardy N Beckmann M Draper J Smith AR Taylor J Fiehn O Goodacre R Bino R Hall R et al. 2004 A proposed framework for the description of plant metabolomics experiments and their results Nat Biotechnol 22 1601 1606
196. Lindon JC Nicholson JK Holmes E Keun HC Craig A Pearce JT Bruce SJ Hardy N Sansone SA Antti H et al. 2005 Summary recommendations for standardization and reporting of metabolic analyses Nat Biotechnol 23 833 838
197. Xirasagar S Gustafson S Merrick BA Tomer KB Stasiewicz S Chan DD Yost KJ 3rd Yates JR 3rd Sumner S Xiao N Waters MD 2004 CEBS object model for systems biology data, SysBio-OM Bioinformatics 20 15
198. Achard F Vaysseix G Barillot E 2001 XML, bioinformatics and data integration Bioinformatics 17 115 125
199. Jones AR Paton NW 2005 An analysis of extensible modelling for functional genomics data BMC Bioinformatics 6 235 ff
200. Soldatova LN King RD 2005 Are the current ontologies in biology good ontologies? Nat Biotechnol 23 1095 1098
201. Goble CA Stevens R Ng G Bechhofer S Paton NW Baker PG Peim M Brass A 2001 Transparent access to multiple bioinformatics information sources IBM Syst J 40 532 551
202. Sauro HM Hucka M Finney A Wellock C Bolouri H Doyle J Kitano H 2003 Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration Omics 7 355 372
203. Oinn T Addis M Ferris J Marvin D Senger M Greenwood M Carver T Glover K Pocock MR Wipat A Li P 2004 Taverna. a tool for the composition and enactment of bioinformatics workflows Bioinformatics 20 3045 3054
204. Lu Q Hao P Curcin V He W Li YY Luo QM Guo YK Li YX 2005 KDE Bioscience: Platform for bioinformatics analysis workflows J Biomed Informq5 doi:10.1016/j.jbi.2005.09.001
205. Wilkinson MD Links M 2002 BioMOBY: an open source biological web services proposal Brief Bioinform 3 331 341
206. Curcin V Ghanem M Guo Y 2005 Web services in the life sciences Drug Discov Today 10 865 871
207. Wilkinson M Schoof H Ernst R Haase D 2005 BioMOBY successfully integrates distributed heterogeneous bioinformatics Web Services. The PlaNet exemplar case Plant Physiol 138 5 17
208. Arkin AP 2001 Synthetic cell biology Curr Opin Biotechnol 12 638 644
209. Blake WJ Isaacs FJ 2004 Synthetic biology evolves Trends Biotechnol 22 321 324
210. Ferber D 2004 Synthetic biology. Microbes made to order Science 303 158 161
211. Gibbs WW 2004 Synthetic life Sci Am 290 74 81
212. Sismour AM Benner SA 2005 Synthetic biology Expert Opin Biol Ther 5 1409 1414
213. Benner SA Sismour AM 2005 Synthetic biology Nat Rev Genet 6 533 543
214. Hasty J Isaacs F Dolnik M McMillen D Collins JJ 2001 Designer gene networks: Towards fundamental cellular control Chaos 11 207 220
215. Hasty J McMillen D Collins JJ 2002 Engineered gene circuits Nature 420 224 230
216. Kærn M Blake WJ Collins JJ 2003 The engineering of gene regulatory networks Annu Rev Biomed Eng 5 179 206
217. Bailey JE 1991 Toward a science of metabolic engineering Science 252 1668 1675
218. Stephanopoulos G Vallino JJ 1991 Network rigidity and metabolic engineering in metabolite overproduction Science 252 1675 1681
219. Stephanopoulos G Sinskey AJ 1993 Metabolic engineering - methodologies and future prospects Trends Biotechnol 11 392 396
220. Keasling JD 1999 Gene-expression tools for the metabolic engineering of bacteria Trends Biotechnol 17 452 460
221. Stafford DE Yanagimachi KS Lessard PA Rijhwani SK Sinskey AJ Stephanopoulos G 2002 Optimizing bioconversion pathways through systems analysis and metabolic engineering Proc Natl Acad Sci USA 99 1801 1806
222. Khosla C Keasling JD 2003 Metabolic engineering for drug discovery and development Nat Rev Drug Discov 2 1019 1025
223. Sweetlove LJ Last RL Fernie AR 2003 Predictive metabolic engineering: a goal for systems biology Plant Physiol 132 420 425
224. Ulmer KM 1983 Protein engineering Science 219 666 671
225. Richardson JS Richardson DC 1989 The de novo design of protein structures Trends Biochem Sci 14 304 309
226. Jones DT 1994 De novo protein design using pairwise potentials and a genetic algorithm Protein Sci 3 567 574
227. Tuchscherer G Mutter M 1995 Templates in protein de novo design J Biotechnol 41 197 210
228. Dahiyat BI Mayo SL 1997 De novo protein design: fully automated sequence selection Science 278 82 87
229. Liu LP Deber CM 1998 Guidelines for membrane protein engineering derived from de novo designed model peptides Biopolymers 47 41 62
230. Hill RB Raleigh DP Lombardi A DeGrado WF 2000 De novo design of helical bundles as models for understanding protein folding and function Acc Chem Res 33 745 754
231. Park S Xi Y Saven JG 2004 Advances in computational protein design Curr Opin Struct Biol 14 487 494
232. Park S Kono H Wang W Boder ET Saven JG 2005 Progress in the development and application of computational methods for probabilistic protein design Comput Chem Eng 29 407 421
233. Schueler-Furman O Wang C Bradley P Misura K Baker D 2005 Progress in modeling of protein structures and interactions Science 310 638 642
234. Bradley P Misura KM Baker D 2005 Toward high-resolution de novo structure prediction for small proteins Science 309 1868 1871
235. Gellman SH 1998 Foldamers: a manifesto Acc Chem Res 31 173 180
236. Cubberley MS Iverson BL 2001 Models of higher-order structure: foldamers and beyond Curr Opin Chem Biol 5 650 653
237. Hill DJ Mio MJ Prince RB Hughes TS Moore JS 2001 A field guide to foldamers Chem Rev 101 3893 4012
238. Cheng RP 2004 Beyond de novo protein design - de novo design of non-natural folded oligomers Curr Opin Struct Biol 14 512 520
239. Stemmer WPC 1994 Rapid evolution of a protein in vivo by DNA shuffling Nature 370 389 391
240. Stemmer WPC 1994 DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution Proc Natl Acad Sci USA 91 10747 10751
241. Colas P Cohen B Jessen T Grishina I McCoy J Brent R 1996 Genetic selection of peptide aptamers that recognize and inhibit cyclin-dependent kinase 2 Nature 380 548 550
242. Boder ET Midelfort KS Wittrup KD 2000 Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity Proc Natl Acad Sci USA 97 10701 10705
243. Reetz MT Jaeger K-E 2000 Enantioselective enzymes for organic synthesis created by directed evolution Chemistry - A Eur J 6 407 412
244. Arnold FH Wintrode PL Miyazaki K Gershenson A 2001 How enzymes adapt: lessons from directed evolution Trends Biochem Sci 26 100 106
245. Arnold FH 2001 Combinatorial and computational challenges for biocatalyst design Nature 409 253 257
246. Alexeeva M Carr R Turner NJ 2003 Directed evolution of enzymes: new biocatalysts for asymmetric synthesis Org Biomol Chem 1 4133 4137
247. Oates MJ Corne DW Kell DB 2003 The bimodal feature at large population sizes and high selection pressure: implications for directed evolution Recent Advances in Simulated Evolution and Learning Tan KC Lim MH Yao X Wang L, eds), pp. 215 240 World Scientific, Singapore.
248. Joyce GF 2004 Directed evolution of nucleic acid enzymes Annu Rev Biochem 73 791 836
249. Lutz S Patrick WM 2004 Novel methods for directed evolution of enzymes: quality, not quantity Curr Opin Biotechnol 15 291 297
250. Williams GJ Nelson AS Berry A 2004 Directed evolution of enzymes for biocatalysis and the life sciences Cell Mol Life Sci 61 3034 3046
251. Otten LG Quax WJ 2005 Directed evolution: selecting today's biocatalysts Biomol Eng 22 1 9
252. Reetz MT Bocola M Carballeira JD Zha D Vogel A 2005 Expanding the range of substrate acceptance of enzymes: combinatorial active-site saturation test Angew Chem Int Ed Engl 44 4192 4196
253. Conrad RC Giver L Tian Y Ellington AD 1996 In vitro selection of nucleic acid aptamers that bind proteins Methods Enzymol 267 336 367
254. Brody EN Willis MC Smith JD Jayasena S Zichi D Gold L 1999 The use of aptamers in large arrays for molecular diagnostics Mol Diagn 4 381 388
255. Jayasena SD 1999 Aptamers: an emerging class of molecules that rival antibodies in diagnostics Clin Chem 45 1628 1650
256. Famulok M Mayer G Blind M 2000 Nucleic acid aptamers-from selection in vitro to applications in vivo Acc Chem Res 33 591 599
257. Hermann T Patel DJ 2000 Adaptive recognition by nucleic acid aptamers Science 287 820 825
258. Jhaveri SD Kirby R Conrad R Maglott EJ Bowser M Kennedy RT Glick G Ellington AD 2000 Designed signaling aptamers that transduce molecular recognition to changes in fluorescence intensity JACS 122 2469 2473
259. Stojanovic MN de Prada P Landry DW 2001 Aptamer-based folding fluorescent sensor for cocaine J Am Chem Soc 123 4928 4931
260. Gold L Brody E Heilig J Singer B 2002 One, two, infinity: genomes filled with aptamers Chem Biol 9 1259 1264
261. Cox JC Hayhurst A Hesselberth J Bayer TS Georgiou G Ellington AD 2002 Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer Nucl Acids Res 30 e108
262. Clark SL Remcho VT 2002 Aptamers as analytical reagents Electrophoresis 23 1335 1340
263. Luzi E Minunni M Tombelli S Mascini M 2003 New trends in affinity sensing: aptamers for ligand binding Trac 22 810 818
264. Rimmele M 2003 Nucleic acid aptamers as tools and drugs: recent developments Chembiochem 4 963 971
265. Nutiu R Yu JM Li Y 2004 Signaling aptamers for monitoring enzymatic activity and for inhibitor screening Chembiochem 5 1139 1144
266. Stojanovic MN Kolpashchikov DM 2004 Modular aptameric sensors J Am Chem Soc 126 9266 9270
267. Blank M Blind M 2005 Aptamers as tools for target validation Curr Opin Chem Biol 9 336 342
268. Famulok M Mayer G 2005 Intramers and aptamers. applications in protein-function analyses and potential for drug screening Chembiochem 6 19 26
269. Famulok M 2005 Allosteric aptamers and aptazymes as probes for screening approaches Curr Opin Mol Ther 7 137 143
270. Nutiu R Li Y 2005 In vitro selection of structure-switching signaling aptamers Angew Chem Int Ed Engl 44 1061 1065
271. Nutiu R Li Y 2005 Aptamers with fluorescence- signaling properties Methods 37 16 25
272. Stojanovic MN Semova S Kolpashchikov D Macdonald J Morgan C Stefanovic D 2005 Deoxyribozyme-based ligase logic gates and their initial circuits J Am Chem Soc 127 6914 6915
273. Tombelli S Minunni M Mascini M 2005 Analytical applications of aptamers Biosens Bioelectron 20 2424 2434
274. Proske D Blank M Buhmann R Resch A 2005 Aptamers-basic research, drug development, and clinical applications Appl Microbiol Biotechnol 69 367 374
275. Hitchens GD Kell DB 1983 Uncouplers can shuttle rapidly between localised energy coupling sites during photophosphorylation by chromatophores of Rhodopseudomonas capsulata N22 Biochem J 212 25 30
276. Westerhoff HV Kell DB 1988 A control theoretical analysis of inhibitor titrations of metabolic channelling Comments Mol Cell Biophys 5 57 107
277. Schreiber SL 1998 Chemical genetics resulting from a passion for synthetic organic chemistry Bioorg Medical Chem 6 1127 1152
278. Crews CM Splittgerber U 1999 Chemical genetics: exploring and controlling cellular processes with chemical probes Trends Biochem Sci 24 317 320
279. Stockwell BR 2000 Chemical genetics: ligand-based discovery of gene function Nat Rev Genet 1 116 125
280. Stockwell BR 2000 Frontiers in chemical genetics Trends Biotechnol 18 449 455
281. Zheng XF Chan TF 2002 Chemical genomics: a systematic approach in biological research and drug discovery Curr Issues Mol Biol 4 33 43
282. Carroll PM Dougherty B Ross-Macdonald P Browman K FitzGerald K 2003 Model systems in drug discovery: chemical genetics meets genomics Pharmacol Ther 99 183 220
283. Zanders ED Bailey DS Dean PM 2002 Probes for chemical genomics by design Drug Discovery Today 7 711 718
284. Giaever G 2003 A chemical genomics approach to understanding drug action Trends Pharmacol Sci 24 444 446
285. Salemme FR 2003 Chemical genomics as an emerging paradigm for postgenomic drug discovery Pharmacogenomics 4 257 267
286. Brenner C 2004 Chemical genomics in yeast Genome Biol 5 240
287. Darvas F Dorman G Krajcsi P Puskas LG Kovari Z Lorincz Z Urge L 2004 Recent advances in chemical genomics Curr Medical Chem 11 3119 3145
288. Meisner NC Hintersteiner M Uhl V Weidemann T Schmied M Gstach H Auer M 2004 The chemical hunt for the identification of drugable targets Curr Opin Chem Biol 8 424 431
289. Shim JS Kwon HJ 2004 Chemical genetics for therapeutic target mining Expert Opin Ther Targets 8 653 661
290. Wagner BK Haggarty SJ Clemons PA 2004 Chemical genomics: probing protein function using small molecules Am J Pharmacogenomics 4 313 320
291. Spring DR 2005 Chemical genetics to chemical genomics: small molecules offer big insights Chem Soc Rev 34 472 482
292. Smukste I Stockwell BR 2005 Advances in chemical genetics Annu Rev Genomics Hum Genet 6 261 286
293. Haggarty SJ Clemons PA Wong JC Schreiber SL 2004 Mapping chemical space using molecular descriptors and chemical genetics: deacetylase inhibitors Comb Chem High Throughput Screen 7 669 676
294. Fan QW Specht KM Zhang C Goldenberg DD Shokat KM Weiss WA 2003 Combinatorial efficacy achieved through two-point blockade within a signaling pathway-a chemical genetic approach Cancer Res 63 8930 8938
295. Tochtrop GP King RW 2004 Target identification strategies in chemical genetics Comb Chem High Throughput Screen 7 677 688
296. Hastie T Tibshirani R Friedman J 2001 The Elements of Statistical Learning: Data Mining, Inference and Prediction Springer-Verlag Berlin
297. Han J Kamber M 2001 Data Mining: Concepts and Techniques Morgan Kaufmann San Francisco
298. Ananiadou S McNaught J 2006 Text Mining in Biology and Biomedicine. Artech House London
299. Swanson DR 1990 Medical literature as a potential source of new knowledge Bull Medical Libr Assoc 78 29 37
300. Hirschman L Park JC Tsujii J Wong L Wu CH 2002 Accomplishments and challenges in literature data mining for biology Bioinformatics 18 1553 1561
301. Nenadic G Spasic I Ananiadou S 2003 Terminology-driven mining of biomedical literature Bioinformatics 19 938 943
302. Corney DP Buxton BF Langdon WB Jones DT 2004 BioRAT: extracting biological information from full-length papers Bioinformatics 20 3206 3213
303. Daraselia N Yuryev A Egorov S Novichkova S Nikitin A Mazo I 2004 Extracting human protein interactions from MEDLINE using a full-sentence parser Bioinformatics 20 604 611
304. Hakenberg J Schmeier S Kowald A Klipp E Leser U 2004 Finding kinetic parameters using text mining Omics 8 131 152
305. Rzhetsky A Iossifov I Koike T Krauthammer M Kra P Morris M. Yu H Duboue PA Weng W Wilbur WJ Hatzivassiloglou V Friedman C 2004 GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data J Biomed Inform 37 43 53
306. Hoffmann R Krallinger M Andres E Tamames J Blaschke C Valencia A 2005 Text mining for metabolic pathways, signaling cascades, and protein networks Sci STKE pe21
307. Vailaya A Bluvas P Kincaid R Kuchinsky A Creech M Adler A 2005 An architecture for biological information extraction and representation Bioinformatics 21 430 438
308. Spasic I Ananiadou S McNaught J Kumar A 2005 Text mining and ontologies in biomedicine: Making sense of raw text Briefings in Bioinformatics 6 239 251
309. Chalfie M Kain S 1998 Green Fluorescent Protein: Properties, Applications, and Protocols Wiley-Liss New York
310. Uhlen M Ponten F 2005 Antibody-based proteomics for human tissue profiling Mol Cell Proteomics 4 384 393
311. Fehr M Lalonde S Lager I Wolff MW Frommer WB 2003 In vivo imaging of the dynamics of glucose uptake in the cytosol of COS-7 cells by fluorescent nanosensors J Biol Chem 278 19127 19133
312. Famulok M 2004 Green fluorescent RNA Nature 430 976 977
313. Rosi NL Mirkin CA 2005 Nanostructures in biodiagnostics Chem Rev 105 1547 1562
314. Rotman B 1961 Measurement of activity of single molecules of β -D-galactosidase Proc Natl Acad Sci 47 1981 1991
315. Xie XS Lu HP 1999 Single-molecule enzymology J Biol Chem 274 15967 15970
316. Moore KJ Turconi S Ashman S Ruediger M Haupts U Emerick V Pope AJ 1999 Single molecule detection technologies in miniaturized high throughput screening: fluorescence correlation spectroscopy J Biomolecular Screening 4 335 353
317. Haupts U Rüdiger M Ashman S Turconi S Bingham R Wharton C Hutchinson J Carey C Moore KJ Pope AJ 2003 Single-molecule detection technologies in miniaturized high-throughput screening: fluorescence intensity distribution analysis J Biomol Screening 8 19 33
318. Bannai M Higuchi K Akesaka T Furukawa M Yamaoka M Sato K Tokunaga K 2004 Single-nucleotide-polymorphism genotyping for whole-genome-amplified samples using automated fluorescence correlation spectroscopy Anal Biochem 327 215 221
319. Twist CR Winson MK Rowland JJ Kell DB 2004 SNP detection using nanomolar nucleotides and single molecule fluorescence Anal Biochem 327 35 44
320. Bennett ST Barnes C Cox A Davies L Brown C 2005 Toward the $1000 human genome Pharmacogenomics 6 373 382
321. Margulies M Egholm M Altman WE Attiya S Bader JS Bemben LA Berka J Braverman MS Chen YJ Chen Z et al. 2005 Genome sequencing in microfabricated high-density picolitre reactors Nature 437 376 380
322. Shendure J Porreca GJ Reppas NB Lin X McCutcheon JP Rosenbaum AM Wang MD Zhang K Mitra RD Church GM 2005 Accurate multiplex polony sequencing of an evolved bacterial genome Science 309 1728 1732
323. Prigogine I 1980 From Being to Becoming: Time and Complexity in the Physical Sciences W.H. Freeman San Francisco
324. Coveney P Highfield R 1990 The Arrow of Time W.H. Allen London
325. Nicolis G Prigogine I 1977 Self-organization in Nonequilibrium Systems: From Dissipative Structures to Order Through Fluctuations Wiley New York
326. Kauffman SA 1993 The Origins of Order Oxford University Press Oxford
327. Holland JH 1998 Emergence Helix Reading, MA
328. Johnson S 2001 Emergence: the Connected Lives of Ants, Brains, Cities and Software Scribner New York
329. Barabási A-L 2002 Linked: the New Science of Networks Perseus Publishing Cambridge, MA
330. Buchanan M 2002 Nexus: Small Worlds and the Groundbreaking Science of Networks W.W. Norton New York
331. Coveney PV Highfield RR 1995 Frontiers of Complexity. Faber & Faber London
332. Kauffman SA 1995 At Home in the Universe: the Search for Laws of Self-Organization and Complexity Oxford University Press Oxford
333. Solé R Goodwin B 2000 Signs of Life: How Complexity Pervades Biology Basic Books New York
334. Lipton P 1991 Inference to the Best Explanation Routledge London
335. Pearl J 2000 Causality: Models, Reasoning and Inference Cambridge University Press Cambridge
336. Shipley B 2001 Cause and Correlation in BiologyA User's Guide to Path Analysis, Structural Equations and Causal Inference Cambridge University Press Cambridge
337. Mackay DJC 2003 Information Theory, Inference and Learning Algorithms Cambridge University Press Cambridge
338. Laughlin RB 2005 A Different Universe: Reinventing Physics from the Bottom Down Basic Books New York
339. Kell DB Welch GR 1991 No turning back, Reductonism and Biological Complexity Times Higher Educational Suppl. ) 9th August, p. 15
340. Westerhoff HV 2001 The silicon cell, not dead but live! Metab Eng 3 207 210
341. Pe'er D Regev A Elidan G Friedman N 2001 Inferring subnetworks from perturbed expression profiles Bioinformatics 17 Suppl. 1 S215 S224
342. de la Fuente A Brazhnik P Mendes P 2002 Linking the genes: inferring quantitative gene networks from microarray data Trends Genet 18 395 398
343. Kholodenko BN Kiyatkin A Bruggeman FJ Sontag E Westerhoff HV Hoek JB 2002 Untangling the wires: a strategy to trace functional interactions in signaling and gene networks Proc Natl Acad Sci USA 99 12841 12846
344. Stark J Callard R Hubank M 2003 From the top down: towards a predictive biology of signalling networks Trends Biotechnol 21 290 293
345. Segal E Shapira M Regev A Pe'er D Botstein D Koller D Friedman N 2003 Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data Nat Genet 34 166 176
346. King RD Garrett SM Coghill GM 2005 On the use of qualitative reasoning to simulate and identify metabolic pathways Bioinformatics 21 2017 2026
347. Sachs K Perez O Pe'er D Lauffenburger DA Nolan GP 2005 Causal protein-signaling networks derived from multiparameter single-cell data Science 308 523 529
348. Corne D Jerram NR Knowles J Oates M 2001 ) PESA-II: Region-based selection in evolutionary multiobjective optimization. Paper presented at the GECCO - Proceedings of the Genetic and Evolutionary Computation Conference, San Francisco. CA.
349. Cornish-Bowden A Hofmeyr J-HS Cárdenas ML 1995 Strategies for manipulating metabolic fluxes in biotechnology Bioorg Chem 23 439 449
350. Fell DA Thomas S 1995 Physiological control of metabolic flux: the requirement for multisite modulation Biochem J 311 35 39
351. Fell DA 1998 Increasing the flux in metabolic pathways: a metabolic control analysis perspective Biotechnol Bioeng 58 121 124
352. Cascante M Boros LG Comin-Anduix B de Atauri P Centelles JJ Lee PW 2002 Metabolic control analysis in drug discovery and disease Nat Biotechnol 20 243 249
353. McCafferty DG Cudic P Yu MK Behenna DC Kruger R 1999 Synergy and duality in peptide antibiotic mechanisms Curr Opin Chem Biol 3 672 680
354. Borisy AA Elliott PJ Hurst NW Lee MS Lehar J Price ER Serbedzija G Zimmermann GR Foley MA Stockwell BR Keith CT 2003 Systematic discovery of multicomponent therapeutics Proc Natl Acad Sci USA 100 7977 7982