Toward whole cell modeling and simulation: Comprehensive functional genomics through the constraint-based approach

Progress in Drug Research

Volumn 64, Issue , 2007, Pages 265-309

  Joyce, Andrew R ^a   Palsson, Bernhard Ø ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Constraint based reconstruction and analysis; Extreme pathway analysis; Flux Balance Analysis (FBA); Mathematical modeling of biological systems; Systems biology

Indexed keywords

ANALYTIC METHOD; CELL STIMULATION; GENOMICS; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN SYNTHESIS; RANDOM SAMPLE; REVIEW; RNA ANALYSIS; STOICHIOMETRY; ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; DRUG DESIGN; GENETIC TRANSCRIPTION; HUMAN; SIGNAL TRANSDUCTION; THEORETICAL MODEL;

ANIMALS; COMPUTER SIMULATION; DATA COLLECTION; DRUG DESIGN; GENOMICS; HUMANS; MODELS, BIOLOGICAL; MODELS, THEORETICAL; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC;

EID: 33846912030     PISSN: 0071786X     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-7643-7567-6_11     Document Type: Review

References (106)

1. Wheeler DL, Church DM, Edgar R, Federhen S, Helmberg W, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E et al (2004) Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res 32 Database issue: D35-40
2. Joyce AR, Palsson BO (2006) The model organismas a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 7(3): 198-210
3. Arkin AP (2001) Synthetic cell biology. Curr Opin Biotechnol 12(6): 638-644
4. Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC et al (1999) E-CELL: software environment for whole-cell simulation. Bioinformatics 15(1): 72-84
5. Hoffmann A, Levchenko A, Scott ML, Baltimore D (2002) The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science 298(5596): 1241-1245
6. Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297(5584): 1183-1186
7. Arkin A, Ross J, McAdams HH (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 149(4): 1633-1648
8. Sarkar A, Franza BR (2004) A logical analysis of the process of T cell activation: different consequences depending on the state of CD28 engagement. J Theor Biol 226(4): 455-466
9. Reed JL, Famili I, Thiele I, Palsson BO (2006) Towards multidimensional genome annotation. Nat Rev Genet 7(2): 130-141
10. Price ND, Reed JL, Palsson BO (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2(11): 886-897
11. Edwards JS, Covert M, Palsson B (2002) Metabolic modelling of microbes: the flux-balance approach. Environ Microbiol 4(3): 133-140
12. Covert MW, Famili I, Palsson BO (2003) Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Biotechnol Bioeng 84(7): 763-772
13. Price ND, Papin JA, Schilling CH, Palsson BO (2003) Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol 21(4): 162-169
14. Varma A, Palsson BO (1994) Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 60(10): 3724-3731
15. Kauffman KJ, Prakash P, Edwards JS (2003) Advances in flux balance analysis. Curr Opin Biotechnol 14(5): 491-496
16. Price ND, Schellenberger J, Palsson BO (2004) Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophys J 87(4): 2172-2186
17. Thiele I, Price ND, Vo TD, Palsson BO (2005) Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J Biol Chem 280(12): 11683-11695
18. Neidhardt FC, Curtiss R (1996) Escherichia coli and Salmonella: Cellular and molecular biology. 2nd ed. ASM Press, Washington, DC, USA
19. Scheffler IE (1999) Mitochondria. Wiley-Liss, New York, USA
20. Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC (2006) The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res 34(Database issue): D332-334
21. Consortium CSAA (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437(7055): 69-87
22. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE et al (2004) Genome sequence of the Brown Norway rat yields insights intomammalian evolution. Nature 428(6982): 493-521
23. Istrail S, Sutton GG, Florea L, Halpern AL, Mobarry CM, Lippert R, Walenz B, Shatkay H, Dew I, Miller JR et al (2004) Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci USA 101(7): 1916-1921
24. Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, Rusch DB, Delcher AL, Pop M, Wang W, Fraser CM et al (2003) The dog genome: survey sequencing and comparative analysis. Science 301(5641): 1898-1903
25. Stein L (2001) Genome annotation: from sequence to biology. Nat Rev Genet 2(7): 493-503
26. Brent MR (2005) Genome annotation past, present, and future: how to define an ORF at each locus. Genome Res 15(12): 1777-1786
27. Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21(19): 3787-3793
28. Karp PD, Paley S, Romero P (2002) The Pathway Tools software. Bioinformatics 18 Suppl 1: S225-232
29. Cash P (2003) Proteomics of bacterial pathogens. Adv Biochem Eng Biotechnol 83: 93-115
30. Taylor SW, Fahy E, Ghosh SS (2003) Global organellar proteomics. Trends Biotechnol 21(2): 82-88
31. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32 Database issue: D277-280
32. Karp PD, Riley M, Saier M, Paulsen IT, Collado-Vides J, Paley SM, Pellegrini-Toole A, Bonavides C, Gama-Castro S (2002) The EcoCyc Database. Nucleic Acids Res 30(1): 56-58
33. Mewes HW, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G, Munsterkotter M, Pagel P, Strack N, Stumpflen V et al (2004) MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res 32 Database issue: D41-44
34. Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE et al (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res 32 Database issue: D311-314
35. Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY et al (2006) MetaCyc: amultiorganism database ofmetabolic pathways and enzymes. Nucleic Acids Res 34(Database issue): D511-516
36. Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33(19): 6083-6089
37. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C et al (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32 Database issue: D258-261
38. (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Res 34(Database issue): D322-326
39. Serres MH, Goswami S, Riley M (2004) GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. Nucleic Acids Res 32 Database issue: D300-302
40. Coulton G (2004) Are histochemistry and cytochemistry 'Omics'? J Mol Histol 35(6): 603-613
41. Arita M, Robert M, Tomita M (2005) All systems go: launching cell simulation fueled by integrated experimental biology data. Curr Opin Biotechnol 16(3): 344-349
42. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK (2003) Global analysis of protein localization in budding yeast. Nature 425(6959): 686-691
43. Guda C, Subramaniam S (2005) pTARGET: a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics 21(21): 3963-3969
44. Fields S (2005) High-throughput two-hybrid analysis. The promise and the peril. Febs J 272(21): 5391-5399
45. Deeds EJ, Ashenberg O, Shakhnovich EI (2006) A simple physical model for scaling in protein-protein interaction networks. Proc Natl Acad Sci USA 103(2): 311-316
46. Sprinzak E, Sattath S, Margalit H (2003) How reliable are experimental protein-protein interaction data? J Mol Biol 327(5): 919-923
47. Palsson B (2004) Two-dimensional annotation of genomes. Nat Biotechnol 22(10): 1218-1219
48. Beard DA, Liang SD, Qian H (2002) Energy balance for analysis of complex metabolic networks. Biophys J 83(1): 79-86
49. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429(6987): 92-96
50. Covert MW, Palsson BO (2003) Constraints-based models: regulation of gene expression reduces the steady-state solution space. J Theor Biol 221(3): 309-325
51. Covert MW, Schilling CH, Palsson B (2001) Regulation of gene expression in flux balance models of metabolism. J Theor Biol 213(1): 73-88
52. Covert MW, Palsson BO (2002) Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem 277(31): 28058-28064
53. Chvatal V (1983) Linear Programming. WH Freeman and Company, New York, USA
54. Reed JL, Palsson BO (2004) Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Res 14(9): 1797-1805
55. Vo TD, Greenberg HJ, Palsson BO (2004) Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J Biol Chem 279(38): 39532-39540
56. Barrett CL, Herring CD, Reed JL, Palsson BO (2005) The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. Proc Natl Acad Sci USA 102(52): 19103-19108
57. Neidhardt FC, Ingraham JL, Schaechter M (1990) Physiology of the bacterial cell. Sinauer Associates, Inc., Sunderland, MA, USA
58. Reed JL, Vo TD, Schilling CH, Palsson BO (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4(9): R54
59. Reed JL, Palsson BO (2003) Thirteen years of building constraint-based in silico models of Escherichia coli. J Bacteriol 185(9): 2692-2699
60. Edwards JS, Palsson BO (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97(10): 5528-5533
61. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO (2002) Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol 184(16): 4582-4593
62. Thiele I, Vo TD, Price ND, Palsson B (2005) An expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): An in silico genome-scale characterization of single and double deletion mutants. J Bacteriol 187(16): 5818-5830
63. Becker SA, Palsson BO (2005) Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol 5(1): 8
64. Mahadevan R, Bond DR, Butler JE, Esteve-Nunez A, Coppi MV, Palsson BO, Schilling CH, Lovley DR (2006) Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl Environ Microbiol 72(2): 1558-1568
65. Borodina I, Krabben P, Nielsen J (2005) Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res 15(6): 820-829
66. Feist AM, Scholten JCM, Palsson BO, Brockman FJ, Ideker T (2006) Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol 2(1): msb4100046-E1-msb4100046-E14
67. Forster J, Famili I, Fu P, Palsson BO, Nielsen J (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13(2): 244-253
68. Duarte NC, Herrgard MJ, Palsson BO (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14(7): 1298-1309
69. Kuepfer L, Sauer U, Blank LM (2005) Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res 15(10): 1421-1430
70. Almaas E, Oltvai ZN, Barabasi AL (2005) The activity reaction core and plasticity of metabolic networks. PLoS Comput Biol 1(7): e68
71. Segre D, DeLuna A, Church GM, Kishnoy R (2005) Modular epistasis in yeast metabolism. Nat Genet 37(1): 77-83
72. Sheikh K, Forster J, Nielsen LK (2005) Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus. Biotechnol Prog 21(1): 112-121
73. Wiback SJ, Palsson BO (2002) Extreme pathway analysis of human red blood cell metabolism. Biophys J 83(2): 808-818
74. 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(4): 524-531
75. Novere NL, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P et al (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 23(12): 1509-1515
76. Schilling CH, Palsson BO (2000) Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor Biol 203(3): 249-283
77. Forster J, Famili I, Palsson BO, Nielsen J (2003) Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. Omics 7(2): 193-202
78. Hartwell L (2004) Genetics. Robust interactions. Science 303(5659): 774-775
79. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M et al (2004) Global mapping of the yeast genetic interaction network. Science 303(5659): 808-813
80. Heinemann M, Kummel A, Ruinatscha R, Panke S (2005) In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnol Bioeng 92(7): 850-864
81. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. 2(1): msb4100050-E1-msb4100050-E11
82. Glasner JD, Liss P, Plunkett G 3rd, Darling A, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR et al (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 31(1): 147-151
83. Salgado H, Gama-Castro S, Martinez-Antonio A, Diaz-Peredo E, Sanchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jimenez-Jacinto V, Santos-Zavaleta A, Bonavides-Martinez C et al (2004) RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res 32 Database issue: D303-306
84. Palsson BO (2006) Systems Biology: Properties of Reconstructed Networks. Cambridge University Press, UK
85. Price ND, Thiele I, Palsson BO (2006) Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of loop law thermodynamic constraints. Biophys J 90(11): 3919-3928
86. Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL (2004) Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427(6977): 839-843
87. Allen TE, Palsson BO (2003) Sequence-based analysis of metabolic demands for protein synthesis in prokaryotes. J Theor Biol 220(1): 1-18
88. Papin JA, Hunter T, Palsson BO, Subramaniam S (2005) Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 6(2): 99-111
89. Varma A, Palsson BO (1993) Metabolic capabilities of Escherichia coli: II. Optimal growth patterns. J Theor Biol 165(4): 503-522
90. Papin JA, Palsson BO (2004) Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. J Theor Biol 227(2): 283-297
91. Papin JA, Palsson BO (2004) The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophys J 87(1): 37-46
92. Schilling CH, Palsson BO (2000) Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway Analysis. J Theor Biol 203(3): 249-283
93. Bell SL, Palsson BO (2005) Expa: a program for calculating extreme pathways in biochemical reaction networks. Bioinformatics 21(8): 1739-1740
94. Herrgard MJ, Lee BS, Portnoy V, Palsson BO (2006) Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res 16(5): 627-635
95. Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO (2006) Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol 2(8): e101
96. Papin JA, Price ND, Palsson BO (2002) Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res 12(12): 1889-1900
97. Price ND, Reed JL, Papin JA, Famili I, Palsson BO (2003) Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophys J 84(2 Pt 1): 794-804
98. Price ND, Papin JA, Palsson BO (2002) Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res 12(5): 760-769
99. Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO (2005) In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 91(5): 643-648
100. Burgard AP, Pharkya P, Maranas CD (2003) Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84(6): 647-657
101. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S et al (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 34(Database issue): D173-180
102. Park SM, Schilling CH, Palsson BO (2003) Compositions and methods for modeling Bacillus subtilis metabolism. US Patent and Trademark Office, USA
103. Edwards JS, Palsson BO (1999) Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem 274(25): 17410-17416
104. Oliveira AP, Nielsen J, Forster J (2005) Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol 5: 39
105. Hong SH, Kim JS, Lee SY, In YH, Choi SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ (2004) The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat Biotechnol 22(10): 1275-1281
106. Taylor SW, Fahy E, Zhang B, Glenn GM, Warnock DE, Wiley S, Murphy AN, Gaucher SP, Capaldi RA, Gibson BW et al (2003) Characterization of the human heart mitochondrial proteome. Nat Biotechnol 21(3): 281-286