Systems biology: The next frontier for bioinformatics

Advances in Bioinformatics

Volumn 2010, Issue , 2010, Pages

  Likić, Vladimir A ^a   McConville, Malcolm J ^a,b   Lithgow, Trevor ^c   Bacic, Antony ^a,b  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c MONASH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79953279638     PISSN: 16878027     EISSN: 16878035     Source Type: Journal    
DOI: 10.1155/2010/268925     Document Type: Review

References (141)

1. Ideker T., Galitski T., Hood L., A new approach to decoding life: systems biology Annual Review of Genomics and Human Genetics 2001 2 343 372 (Pubitemid 35265011)
2. Kitano H., Computational systems biology Nature 2002 420 6912 206 210 (Pubitemid 35340131)
3. Kitano H., Systems biology: a brief overview Science 2002 295 5560 1662 1664 (Pubitemid 34202893)
4. Westerhoff H. V., Palsson B. O., The evolution of molecular biology into systems biology Nature Biotechnology 2004 22 10 1249 1252 (Pubitemid 39336777)
5. Stelling J., Mathematical models in microbial systems biology Current Opinion in Microbiology 2004 7 5 513 518 (Pubitemid 39297132)
6. Lander E. S., Linton L. M., Birren B., Initial sequencing and analysis of the human genome Nature 2001 409 860 921 (Pubitemid 32165345)
7. Craig Venter J., Adams M. D., Myers E. W., Li P. W., Mural R. J., Sutton G. G., Smith H. O., Yandell M., Evans C. A., Holt R. A., Gocayne J. D., Amanatides P., Ballew R. M., Huson D. H., Wortman J. R., Zhang Q., Kodira C. D., Zheng X. H., Chen L., Skupski M., Subramanian G., Thomas P. D., Zhang J., Gabor Miklos G. L., Nelson C., Broder S., Clark A. G., Nadeau J., McKusick V. A., Zinder N., Levine A. J., Roberts R. J., Simon M., Slayman C., Hunkapiller M., Bolanos R., Delcher A., Dew I., Fasulo D., Flanigan M., Florea L., Halpern A., Hannenhalli S., Kravitz S., Levy S., Mobarry C., Reinert K., Remington K., Abu-Threideh J., Beasley E., Biddick K., Bonazzi V., Brandon R., Cargill M., Chandramouliswaran I., Charlab R., Chaturvedi K., Deng Z., Di Francesco V., Dunn P., Eilbeck K., Evangelista C., Gabrielian A. E., Gan W., Ge W., Gong F., Gu Z., Guan P., Heiman T. J., Higgins M. E., Ji R.-R., Ke Z., Ketchum K. A., Lai Z., Lei Y., Li Z., Li J., Liang Y., Lin X., Lu F., Merkulov G. V., Milshina N., Moore H. M., Naik A. K., Narayan V. A., Neelam B., Nusskern D., Rusch D. B., Salzberg S., Shao W., Shue B., Sun J., Zhen Yuan Wang, Wang A., Wang X., Wang J., Wei M.-H., Wides R., Xiao C., The sequence of the human genome Science 2001 291 5507 1304 1351 (Pubitemid 32173090)
8. Schena M., Shalon D., Davis R. W., Brown P. O., Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 1995 270 5235 467 470
9. Lashkari D. A., DeRisi J. L., Mccusker J. H., Namath A. F., Gentile C., Hwang S. Y., Brown P. O., Davis R. W., Yeast microarrays for genome wide parallel genetic and gene expression analysis Proceedings of the National Academy of Sciences of the United States of America 1997 94 24 13057 13062 (Pubitemid 27518475)
10. Patterson S. D., Aebersold R. H., Proteomics: the first decade and beyond Nature Genetics 2003 33 311 323 (Pubitemid 36278841)
11. Oliver S. G., Winson M. K., Kell D. B., Baganz F., Systematic functional analysis of the yeast genome Trends in Biotechnology 1998 16 9 373 378 (Pubitemid 28410425)
12. Fiehn O., Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks Comparative and Functional Genomics 2001 2 3 155 168 (Pubitemid 32590962)
13. Wiener N., Cybernetics: Or Control and Communication in the Animan and the Machine 1946 Cambridge, Mass, USA MIT Press
14. Mesarovic M. D., Mesarovic M. D., Systems theory and biologyview of a theoretician Systems Theory and Biology 1968 New York, NY, USA Springer 59 87
15. von Bertalanffy L., General System Theory 1969 New York, NY, USA George Braziller
16. Kacser H., Burns J. A., The control of flux Symposia of the Society for Experimental Biology 1973 27 65 104
17. Heinrich R., Rapoport T. A., A linear steady state treatment of enzymatic chains: general properties, control and effector strength European Journal of Biochemistry 1974 42 1 89 95
18. Kacser H., Burns J. A., The molecular basis of dominance Genetics 1981 97 3-4 639 666 (Pubitemid 12224399)
19. Wolkenhauer O., Systems biology: the reincarnation of systems theory applied in biology? Briefings in Bioinformatics 2001 2 3 258 270
20. Benner S. A., Sismour A. M., Synthetic biology Nature Reviews Genetics 2005 6 7 533 543 (Pubitemid 40910430)
21. McDaniel R., Weiss R., Advances in synthetic biology: on the path from prototypes to applications Current Opinion in Biotechnology 2005 16 4 476 483 (Pubitemid 41111533)
22. Heinemann M., Panke S., Synthetic biologyputting engineering into biology Bioinformatics 2006 22 22 2790 2799
23. Barrett C. L., Kim T. Y., Kim H. U., Palsson B.., Lee S. Y., Systems biology as a foundation for genome-scale synthetic biology Current Opinion in Biotechnology 2006 17 5 488 492 (Pubitemid 44468377)
24. Mukherji S., van Oudenaarden A., Synthetic biology: understanding biological design from synthetic circuits Nature Reviews Genetics 2009 10 12 859 871
25. Vieites J. M., Guazzaroni M.-E., Beloqui A., Golyshin P. N., Ferrer M., Metagenomics approaches in systems microbiology FEMS Microbiology Reviews 2009 33 1 236 255
26. Liu E. T., Systems biology, integrative biology, predictive biology Cell 2005 121 4 505 506 (Pubitemid 40720003)
27. O'Callaghan P. M., James D. C., Systems biotechnology of mammalian cell factories Briefings in Functional Genomics and Proteomics 2008 7 2 95 110 (Pubitemid 351728951)
28. Tomlins S. A., Rubin M. A., Chinnaiyan A. M., Integrative biology of prostate cancer progression Annual Review of Pathology 2006 1 243 271
29. Liu E. T., Integrative biologya strategy for systems biomedicine Nature Reviews Genetics 2009 10 1 64 68
30. Riesenfeld C. S., Schloss P. D., Handelsman J., Metagenomics: genomic analysis of microbial communities Annual Review of Genetics 2004 38 525 552 (Pubitemid 40013737)
31. Kirschner M. W., The meaning of systems biology Cell 2005 121 4 503 504 (Pubitemid 40720002)
32. Cowley A. W. Jr., The elusive field of systems biology Physiological Genomics 2004 16 285 286
33. Kohl P., Crampin E. J., Quinn T. A., Noble D., Systems biology: an approach Clinical Pharmacology and Therapeutics 2010 88 1 25 33
34. McKusick V. A., Ruddle F. H., A new discipline, a new name, a new journal Genomics 1987 1 1 1 2
35. Maxam A. M., Gilbert W., A new method for sequencing DNA Proceedings of the National Academy of Sciences of the United States of America 1977 74 2 560 564 (Pubitemid 8038842)
36. Sanger F., Coulson A. R., A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase Journal of Molecular Biology 1975 94 3 441 448
37. Smith L. M., Sanders J. Z., Kaiser R. J., Fluorescence detection in automated DNA sequence analysis Nature 1986 321 6071 674 679 (Pubitemid 16044126)
38. Hood L. E., Hunkapiller M. W., Smith L. M., Automated DNA sequencing and analysis of the human genome Genomics 1987 1 3 201 212
39. Collins F. S., Morgan M., Patrinos A., The human genome project: lessons from large-scale biology Science 2003 300 5617 286 290 (Pubitemid 36433711)
40. Hieter P., Boguski M., Functional genomics: it's all how you read it Science 1997 278 5338 601 602 (Pubitemid 27464949)
41. Rastan S., Beeley L. J., Functional genomics: going forwards from the databases Current Opinion in Genetics and Development 1997 7 6 777 783 (Pubitemid 28051020)
42. Somerville C., Somerville S., Plant functional genomics Science 1999 285 5426 380 383 (Pubitemid 29343954)
43. Brent R., Genomic biology Cell 2000 100 1 169 183 (Pubitemid 30046305)
44. Griffiths P. E., Stotz K., Genes in the postgenomic era Theoretical Medicine and Bioethics 2006 27 6 499 521 (Pubitemid 44873584)
45. Rdei G. P., Koncz C., Phillips J. D., Changing images of the gene Advances in Genetics 2006 56 53 100 (Pubitemid 43776136)
46. Gingeras T. R., Origin of phenotypes: genes and transcripts Genome Research 2007 17 6 682 690 (Pubitemid 46919706)
47. Gerstein M. B., Bruce C., Rozowsky J. S., Zheng D., Du J., Korbel J. O., Emanuelsson O., Zhang Z. D., Weissman S., Snyder M., What is a gene, post-ENCODE? History and updated definition Genome Research 2007 17 6 669 681 (Pubitemid 46919705)
48. Portin P., The elusive concept of the gene Hereditas 2009 146 3 112 117
49. Carninci P., Tagging mammalian transcription complexity Trends in Genetics 2006 22 9 501 510
50. Kapranov P., Willingham A. T., Gingeras T. R., Genome-wide transcription and the implications for genomic organization Nature Reviews Genetics 2007 8 6 413 423 (Pubitemid 46789245)
51. Avise J. C., Evolving genomic metaphors: a new look at the language of DNA Science 2001 294 5540 86 87 (Pubitemid 32952952)
52. Amaral P. P., Dinger M. E., Mercer T. R., Mattick J. S., The eukaryotic genome as an RNA machine Science 2008 319 5871 1787 1789 (Pubitemid 351451554)
53. Mattick J. S., The functional genomics of noncoding RNA Science 2005 309 5740 1527 1528 (Pubitemid 41266470)
54. Martin K. C., Ephrussi A., mRNA localization: gene expression in the spatial dimension Cell 2009 136 4 719 730
55. Lazebnik Y., Can a biologist fix a radio?Or, what I learned while studying apoptosis Cancer Cell 2002 2 3 179 182 (Pubitemid 41043973)
56. Weng G., Bhalla U. S., Iyengar R., Complexity in biological signaling systems Science 1999 284 5411 92 96 (Pubitemid 29282052)
57. Whitesides G. M., Ismagilov R. F., Complexity in chemistry Science 1999 284 5411 89 92 (Pubitemid 29282051)
58. Ross J., Arkin A. P., Complex systems: from chemistry to systems biology Proceedings of the National Academy of Sciences of the United States of America 2009 106 16 6433 6434
59. Goldenfeld N., Kadanoff L. P., Simple lessons from complexity Science 1999 284 5411 87 89 (Pubitemid 29282050)
60. Castrillo J. I., Oliver S. G., Brown A. J. P., Metabolomics and systems biology in Saccharomyces cerevisiae The Mycota: A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research 2006 Heidelberg, Germany Springer 3 18
61. Ideker T., Thorsson V., Ranish J. A., Christmas R., Buhler J., Eng J. K., Bumgarner R., Goodlett D. R., Aebersold R., Hood L., Integrated genomic and proteomic analyses of a systematically perturbed metabolic network Science 2001 292 5518 929 934 (Pubitemid 32422490)
62. Ge H., Walhout A. J. M., Vidal M., Integrating 'omic' information: a bridge between genomics and systems biology Trends in Genetics 2003 19 10 551 560 (Pubitemid 37204914)
63. de Hoog C. L., Mann M., Proteomics Annual Review of Genomics and Human Genetics 2004 5 267 293 (Pubitemid 39362748)
64. Bruggeman F. J., Westerhoff H. V., The nature of systems biology Trends in Microbiology 2007 15 1 45 50 (Pubitemid 46043550)
65. Ideker T., Lauffenburger D., Building with a scaffold: emerging strategies for high- to low-level cellular modeling Trends in Biotechnology 2003 21 6 255 262 (Pubitemid 36645212)
66. Laubenbacher R., Jarrah A. S., Algebraic models of biochemical networks Methods in Enzymology 2009 467 C 163 196
67. Huang S., Back to the biology in systems biology: what can we learn from biomolecular networks? Brief Funct Genomic Proteomic 2004 2 4 279 297
68. O'Malley M. A., Dupr J., Fundamental issues in systems biology BioEssays 2005 27 12 1270 1276 (Pubitemid 43076170)
69. May R. M., Uses and abuses of mathematics in biology Science 2004 303 5659 790 793 (Pubitemid 38174648)
70. Tyson J. J., Chen K., Novak B., Network dynamics and cell physiology Nature Reviews Molecular Cell Biology 2001 2 12 908 916 (Pubitemid 33674090)
71. Chen K. C., Calzone L., Csikasz-Nagy A., Cross F. R., Novak B., Tyson J. J., Integrative analysis of cell cycle control in budding yeast Molecular Biology of the Cell 2004 15 8 3841 3862 (Pubitemid 38989719)
72. Klipp E., Nordlander B., Krger R., Gennemark P., Hohmann S., Integrative model of the response of yeast to osmotic shock Nature Biotechnology 2005 23 8 975 982 (Pubitemid 41114031)
73. Feist A. M., Henry C. S., Reed J. L., Krummenacker M., Joyce A. R., Karp P. D., Broadbelt L. J., Hatzimanikatis V., Palsson B., A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information Molecular Systems Biology 2007 3, article 121
74. Bakker B. M., Michels P. A. M., Opperdoes F. R., Westerhoff H. V., What controls glycolysis in bloodstream form Trypanosoma brucei? Journal of Biological Chemistry 1999 274 21 14551 14559
75. Duarte N. C., Herrgrd M. J., Palsson B.., Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model Genome Research 2004 14 7 1298 1309 (Pubitemid 39036129)
76. Teusink B., Passarge J., Reijenga C. A., Esgalhado E., Van Der Weijden C. C., Schepper M., Walsh M. C., Bakker B. M., Van Dam K., Westerhoff H. V., Snoep J. L., Can yeast glycolysis be understood terms of vitro kinetics of the constituent enzymes? Testing biochemistry European Journal of Biochemistry 2000 267 17 5313 5329
77. Smallbone K., Simeonidis E., Swainston N., Mendes P., Towards a genome-scale kinetic model of cellular metabolism BMC Systems Biology 2010 4, article 6
78. Hartwell L. H., Hopfield J. J., Leibler S., Murray A. W., From molecular to modular cell biology Nature 1999 402 6761 C47 C52
79. Hornberg J. J., Bruggeman F. J., Westerhoff H. V., Lankelma J., Cancer: a systems biology disease BioSystems 2006 83 2-3 81 90 (Pubitemid 43199809)
80. Kohl P., Noble D., Systems biology and the virtual physiological human Molecular Systems Biology 2009 5, article 292
81. Sang Y. L., Lee D.-Y., Tae Y. K., Systems biotechnology for strain improvement Trends in Biotechnology 2005 23 7 349 358 (Pubitemid 40835765)
82. Argmann C. A., Chambon P., Auwerx J., Mouse phenogenomics: the fast track to "systems metabolism" Cell Metabolism 2005 2 6 349 360
83. Zahn J. M., Kim S. K., Systems biology of aging in four species Current Opinion in Biotechnology 2007 18 4 355 359 (Pubitemid 47385184)
84. Yuan J. S., Galbraith D. W., Dai S. Y., Griffin P., Stewart C. N. Jr., Plant systems biology comes of age Trends in Plant Science 2008 13 4 165 171
85. Hynne F., Dan S., Srensen P. G., Full-scale model of glycolysis in Saccharomyces cerevisiae Biophysical Chemistry 2001 94 1-2 121 163 (Pubitemid 34015989)
86. Albert M.-A., Haanstra J. R., Hannaert V., Van Roy J., Opperdoes F. R., Bakker B. M., Michels P. A. M., Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei Journal of Biological Chemistry 2005 280 31 28306 28315 (Pubitemid 41105727)
87. Kim P. S., Levy D., Lee P. P., Modeling and simulation of the immune system as a self-regulating network Methods in Enzymology 2009 467 C 79 109
88. Noble D., Modeling the heartfrom genes to cells to the whole organ Science 2002 295 5560 1678 1682 (Pubitemid 34202896)
89. Schwikowski B., Uetz P., Fields S., A network of protein-protein interactions in yeast Nature Biotechnology 2000 18 12 1257 1261
90. Lee T. I., Rinaldi N. J., Robert F., Odom D. T., Bar-Joseph Z., Gerber G. K., Hannett N. M., Harbison C. T., Thompson C. M., Simon I., Zeitlinger J., Jennings E. G., Murray H. L., Benjamin Gordon D., Ren B., Wyrick J. J., Tagne J.-B., Volkert T. L., Fraenkel E., Gifford D. K., Young R. A., Transcriptional regulatory networks in Saccharomyces cerevisiae Science 2002 298 5594 799 804 (Pubitemid 35231527)
91. Gell M., van Noort V., Yus E., Chen W.-H., Leigh-Bell J., Michalodimitrakis K., Yamada T., Arumugam M., Doerks T., Khner S., Rode M., Suyama M., Schmidt S., Gavin A.-C., Bork P., Serrano L., Transcriptome complexity in a genome-reduced bacterium Science 2009 326 5957 1268 1271
92. Khner S., van Noort V., Betts M. J., Leo-Madas A., Batisse C., Rode M., Yamada T., Maier T., Bader S., Beltran-Alvarez P., Castao-Diez D., Chen W.-H., Devos D., Gell M., Norambuena T., Racke I., Rybin V., Schmidt A., Yus E., Aebersold R., Herrmann R., Bttcher B., Frangakis A. S., Russell R. B., Serrano L., Bork P., Gavin A.-C., Proteome organization in a genome-reduced bacterium Science 2009 326 5957 1235 1240
93. Yus E., Maier T., Michalodimitrakis K., Van Noort V., Yamada T., Chen W.-H., Wodke J. A. H., Gell M., Martnez S., Bourgeois R., Khner S., Raineri E., Letunic I., Kalinina O. V., Rode M., Herrmann R., Gutirrez-Gallego R., Russell R. B., Gavin A.-C., Bork P., Serrano L., Impact of genome reduction on bacterial metabolism and its regulation Science 2009 326 5957 1263 1268
94. Shen-Orr S. S., Milo R., Mangan S., Alon U., Network motifs in the transcriptional regulation network of Escherichia coli Nature Genetics 2002 31 1 64 68
95. Krogan N. J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., Li J., Pu S., Datta N., Tikuisis A. P., Punna T., Peregrn-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. Y., 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., Greenblatt J. F., Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 2006 440 7084 637 643
96. Tarassov K., Messier V., Landry C. R., Radinovic S., Serna Molina M. M., Shames I., Malitskaya Y., Vogel J., Bussey H., Michnick S. W., An in vivo map of the yeast protein interactome Science 2008 320 5882 1465 1470 (Pubitemid 351929421)
97. Tang Y., Pingitore F., Mukhopadhyay A., Phan R., Hazen T. C., Keasling J. D., Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using gas chromatography-mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry Journal of Bacteriology 2007 189 3 940 949 (Pubitemid 46183869)
98. del Castillo T., Ramos J. L., Rodrguez-Herva J. J., Fuhrer T., Sauer U., Duque E., Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis Journal of Bacteriology 2007 189 14 5142 5152 (Pubitemid 47076060)
99. Schilling O., Frick O., Herzberg C., Ehrenreich A., Heinzle E., Wittmann C., Stlke J., Transcriptional and metabolic responses of Bacillus subtilis to the availability of organic acids: transcription regulation is important but not sufficient to account for metabolic adaptation Applied and Environmental Microbiology 2007 73 2 499 507 (Pubitemid 46147580)
100. Saito N., Robert M., Kochi H., Matsuo G., Kakazu Y., Soga T., Tomita M., Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli Journal of Biological Chemistry 2009 284 24 16442 16451
101. Krantz M., Ahmadpour D., Ottosson L.-G., Warringer J., Waltermann C., Nordlander B., Klipp E., Blomberg A., Hohmann S., Kitano H., Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway Molecular Systems Biology 2009 5, article 281
102. Koide T., Hayata T., Cho K. W. Y., Xenopus as a model system to study transcriptional regulatory networks Proceedings of the National Academy of Sciences of the United States of America 2005 102 14 4943 4948
103. Giot L., Bader J. S., Brouwer C., Chaudhuri A., Kuang B., Li Y., Hao Y. L., Ooi C. E., Godwin B., Vitols E., Vijayadamodar G., Pochart P., Machineni H., Welsh M., Kong Y., Zerhusen B., Malcolm R., Varrone Z., Collis A., Minto M., Burgess S., McDaniel L., Stimpson E., Spriggs F., Williams J., Neurath K., Ioime N., Agee M., Voss E., Furtak K., Renzulli R., Aanensen N., Carrolla S., Bickelhaupt E., Lazovatsky Y., DaSilva A., Zhong J., Stanyon C. A., Finley Jr. R. L., White K. P., Braverman M., Jarvie T., Gold S., Leach M., Knight J., Shimkets R. A., McKenna M. P., Chant J., Rothberg J. M., A protein interaction map of Drosophila melanogaster Science 2003 302 5651 1727 1736 (Pubitemid 37505730)
104. Tang Y. J., Chakraborty R., Martn H. G., Chu J., Hazen T. C., Keasling J. D., Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid Applied and Environmental Microbiology 2007 73 12 3859 3864 (Pubitemid 46983233)
105. Aldridge B. B., Burke J. M., Lauffenburger D. A., Sorger P. K., Physicochemical modelling of cell signalling pathways Nature Cell Biology 2006 8 11 1195 1203 (Pubitemid 44660581)
106. Ishii N., Nakahigashi K., Baba T., Robert M., Soga T., Kanai A., Hirasawa T., Naba M., Hirai K., Hoque A., Ho P. Y., Kakazu Y., Sugawara K., Igarashi S., Harada S., Masuda T., Sugiyama N., Togashi T., Hasegawa M., Takai Y., Yugi K., Arakawa K., Iwata N., Toya Y., Nakayama Y., Nishioka T., Shimizu K., Mori H., Tomita M., Multiple high-throughput analyses monitor the response of E. coli to perturbations Science 2007 316 5824 593 597 (Pubitemid 46683144)
107. Tnnler S., Fischer E., Le Coq D., Doan T., Jamet E., Sauer U., Aymerich S., CcpN controls central carbon fluxes in Bacillus subtilis Journal of Bacteriology 2008 190 18 6178 6187
108. Ochman H., Raghavan R., Systems biology. Excavating the functional landscape of bacterial cells Science 2009 326 5957 1200 1201
109. Stephanopoulos G., Metabolic fluxes and metabolic engineering Metabolic Engineering 1999 1 1 1 11 (Pubitemid 129499367)
110. Sauer U., Metabolic networks in motion: 13C-based flux analysis Molecular Systems Biology 2006 2, article 62
111. Gianchandani E. P., Brautigan D. L., Papin J. A., Systems analyses characterize integrated functions of biochemical networks Trends in Biochemical Sciences 2006 31 5 284 291 (Pubitemid 43674361)
112. Grning N.-M., Lehrach H., Ralser M., Regulatory crosstalk of the metabolic network Trends in Biochemical Sciences 2010 35 4 220 227
113. Nielsen J., Oliver S., The next wave in metabolome analysis Trends in Biotechnology 2005 23 11 544 546 (Pubitemid 41483770)
114. Zamboni N., Sauer U., Novel biological insights through metabolomics and 13C-flux analysis Current Opinion in Microbiology 2009 12 5 553 558
115. Wiechert W., Nh K., From stationary to instationary metabolic flux analysis Advances in Biochemical Engineering/Biotechnology 2005 92 145 172 (Pubitemid 44617157)
116. Tang Y. J., Martin H. G., Myers S., Rodriguez S., Baidoo E. E. K., Keasling J. D., Advances in analysis of microbial metabolic fluxes via 13C isotopic labeling Mass Spectrometry Reviews 2009 28 2 362 375
117. Antoniewicz M. R., Kelleher J. K., Stephanopoulos G., Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions Metabolic Engineering 2007 9 1 68 86 (Pubitemid 44960874)
118. Young J. D., Walther J. L., Antoniewicz M. R., Yoo H., Stephanopoulos G., An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis Biotechnology and Bioengineering 2008 99 3 686 699 (Pubitemid 351158266)
119. Hucka M., Finney A., Bornstein B. J., Keating S. M., Shapiro B. E., Matthews J., Kovitz B. L., Schilstra M. J., Funahashi A., Doyle J. C., Kitano H., Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project Systems Biology 2004 1 1 41 53
120. Novre N. L., Hucka M., Mi H., Moodie S., Schreiber F., Sorokin A., Demir E., Wegner K., Aladjem M. I., Wimalaratne S. M., Bergman F. T., Gauges R., Ghazal P., Kawaji H., Li L., Matsuoka Y., Villger A., Boyd S. E., Calzone L., Courtot M., Dogrusoz U., Freeman T. C., Funahashi A., Ghosh S., Jouraku A., Kim S., Kolpakov F., Luna A., Sahle S., Schmidt E., Watterson S., Wu G., Goryanin I., Kell D. B., Sander C., Sauro H., Snoep J. L., Kohn K., Kitano H., The systems biology graphical notation Nature Biotechnology 2009 27 8 735 741
121. Sauro H. M., Hucka M., Finney A., Wellock C., Bolouri H., Doyle J., Kitano H., Next generation simulation tools: the systems biology workbench and BioSPICE integration OMICS 2003 7 4 355 372 (Pubitemid 38018642)
122. Funahashi A., Morohashi M., Kitano H., Tanimura N., CellDesigner: a process diagram editor for gene-regulatory and biochemical networks BIOSILICO 2003 1 159 162
123. Mendes P., Hoops S., Sahle S., Gauges R., Dada J., Kummer U., Computational modeling of biochemical networks using COPASI Methods in Molecular Biology 2009 500 17 59
124. Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J., Sayers E. W., GenBank Nucleic Acids Research 2010 37 1 D26 D31
125. Kouranov A., Xie L., de la Cruz J., Chen L., Westbrook J., Bourne P. E., Berman H. M., The RCSB PDB information portal for structural genomics Nucleic Acids Research 2006 34 D302 D305
126. Finn R. D., Mistry J., Tate J., Coggill P., Heger A., Pollington J. E., Gavin O. L., Gunasekaran P., Ceric G., Forslund K., Holm L., Sonnhammer E. L.L., Eddy S. R., Bateman A., The Pfam protein families database Nucleic Acids Research 2010 38 supplement 1 D211 D222
127. Caspi R., Altman T., Dale J. M., Dreher K., Fulcher C. A., Gilham F., Kaipa P., Karthikeyan A. S., Kothari A., Krummenacker M., Latendresse M., Mueller L. A., Paley S., Popescu L., Pujar A., Shearer A. G., Zhang P., Karp P. D., The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Nucleic Acids Research 2010 38 supplement 1 D473 D479
128. Matthews L., Gopinath G., Gillespie M., Caudy M., Croft D., de Bono B., Garapati P., Hemish J., Hermjakob H., Jassal B., Kanapin A., Lewis S., Mahajan S., May B., Schmidt E., Vastrik I., Wu G., Birney E., Stein L., D'eustachio P., Reactome knowledgebase of human biological pathways and processes Nucleic Acids Research 2009 37 1 D619 D622
129. Kuhn M., Szklarczyk D., Franceschini A., Campillos M., Von Mering C., Jensen L. J., Beyer A., Bork P., STITCH 2: an interaction network database for small molecules and proteins Nucleic Acids Research 2010 38 supplement 1 D552 D556
130. Lehne B., Schlitt T., Protein-protein interaction databases: keeping up with growing interactomes Human Genomics 2009 3 3 291 297
131. Le Novre N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J. L., Hucka M., BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems Nucleic Acids Research 2006 34 D689 D691
132. Shannon P., Markiel A., Ozier O., Baliga N. S., Wang J. T., Ramage D., Amin N., Schwikowski B., Ideker T., Cytoscape: a software Environment for integrated models of biomolecular interaction networks Genome Research 2003 13 11 2498 2504 (Pubitemid 37428274)
133. Karp P. D., Paley S. M., Krummenacker M., Latendresse M., Dale J. M., Lee T. J., Kaipa P., Gilham F., Spaulding A., Popescu L., Altman T., Paulsen I., Keseler I. M., Caspi R., Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology Briefings in Bioinformatics 2009 11 1 40 79
134. Reed J. L., Palsson B.., Thirteen years of building constraint-based in silico models of Escherichia coli Journal of Bacteriology 2003 185 9 2692 2699 (Pubitemid 36514580)
135. Schilling C. H., Edwards J. S., Palsson B. O., Toward metabolic phenomics: analysis of genomic data using flux balances Biotechnology Progress 1999 15 3 288 295 (Pubitemid 29270672)
136. Dolezal P., Likic V., Tachezy J., Lithgow T., Evolution of the molecular machines for protein import into mitochondria Science 2006 313 5785 314 318 (Pubitemid 44480948)
137. Nielsen J., Systems biology of lipid metabolism: from yeast to human FEBS Letters 2009 583 24 3905 3913
138. Ohashi Y., Hirayama A., Ishikawa T., Nakamura S., Shimizu K., Ueno Y., Tomita M., Soga T., Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMS Molecular BioSystems 2008 4 2 135 147
139. Brazhnik P., de la Fuente A., Mendes P., Gene networks: how to put the function in genomics Trends in Biotechnology 2002 20 11 467 472 (Pubitemid 35292359)
140. Alm E., Arkin A. P., Biological networks Current Opinion in Structural Biology 2003 13 2 193 202 (Pubitemid 36515147)
141. Wullschleger S., Loewith R., Hall M. N., TOR signaling in growth and metabolism Cell 2006 124 3 471 484 (Pubitemid 43199434)