Towards a systems biology understanding of human health: Interplay between genotype, environment and nutrition

Biotechnology Annual Review

Volumn 10, Issue SPEC. ISS., 2004, Pages 51-84

  Desiere, Frank ^a,b  

^a NESTLÉ RESEARCH CENTER   (Switzerland)

^b Institute for System Biology   (United States)

Author keywords

Bioinformatics; Cells; Diagnostics; Diet; Disease; Epigenetics; Genomics; Health; Metabolism; Metabolomics; Molecular databases; Networks; Nutrigenomics; Nutrition; Pharmacogenetics; Pharmacogenomics; Polymorphisms; Prevention; Proteomics; SNPs; Systems biology; Transcriptomics

Indexed keywords

DNA;

BIOMEDICINE; CLINICAL RESEARCH; DIETARY INTAKE; DISEASE ASSOCIATION; DNA MICROARRAY; DRUG USE; ENVIRONMENTAL FACTOR; EXPRESSED SEQUENCE TAG; FEASIBILITY STUDY; FEEDING BEHAVIOR; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENETIC TRANSCRIPTION; GENOME IMPRINTING; GENOMICS; GENOTYPE ENVIRONMENT INTERACTION; HEALTH PROMOTION; HEALTH STATUS; HEREDITY; HUMAN; HUMAN GENOME; INDIVIDUALIZATION; LIFESTYLE; NONHUMAN; NUTRITIONAL STATUS; PATIENT CARE; PATIENT COUNSELING; POLLUTANT; PROPHYLAXIS; PROTEIN INTERACTION; QUALITY OF LIFE; RAT; REVIEW; RISK ASSESSMENT; SERIAL ANALYSIS OF GENE EXPRESSION; SINGLE NUCLEOTIDE POLYMORPHISM; TECHNOLOGY;

EID: 7044223103     PISSN: 13872656     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1387-2656(04)10003-3     Document Type: Article

References (120)

1. Wolkenhauer O. Systems Biology: The Reincarnation of Systems Theory Applied in Biology? 2001 258-270 Columbia University Press New York
2. Rosen R Essays on life itself 1999 Columbia University Press New York
3. eLander E.S. Linton L.M. Birren B. Nusbaum C. Zody M.C. Baldwin J. Devon K. Dewar K. Doyle M. FitzHugh W. Funke R. Gage D. Harris K. Heaford A. Howland J. Kann L. Lehoczky J. LeVine R. McEwan P. McKernan K. Meldrim J. Mesirov J.P. Miranda C. Morris W. Naylor J. Raymond C. Rosetti M. Santos R. Sheridan A. Sougnez C. Stange-Thomann N. Stojanovic N. Subramanian A. Wyman D. Rogers J. Sulston J. Ainscough R. Beck S. Bentley D. Burton J. Clee C. Carter N. Coulson A. Deadman R. Deloukas P. Dunham A. Dunham I. Durbin R. French L. Grafham D. Gregory S. Hubbard T. Humphray S. Hunt A. Jones M. Lloyd C. McMurray A. Matthews L. Mercer S. Milne S. Mullikin J.C. Mungall A. Plumb R. Ross M. Shownkeen R. Sims S. Waterston R.H. Wilson R.K. Hillier L.W. McPherson J.D. Marra M.A. Mardis E.R. Fulton L.A. Chinwalla A.T. Pepin K.H. Gish W.R. Chissoe S.L. Wendl M.C. Delehaunty K.D. Miner T.L. Delehaunty A. Kramer J.B. Cook L.L. Fulton R.S. Johnson D.L. Minx P.J. Clifton S.W. Hawkins T. Branscomb E. Predki P. Richardson P. Wenning S. Slezak T. Doggett N. Cheng J.F. Olsen A. Lucas S. Elkin C. Uberbacher E. et al. Initial sequencing and analysis of the human genome Nature 409 2001 860-921
4. lVenter J.C. 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 F.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. Wang Z. Wang A. Wang X. Wang J. Wei M. Wides R. Xiao C. et al. The sequence of the human genome Science 291 2001 1304-1351
5. Stuart J.M. Segal E. Koller D. Kim S.K. A Gene-coexpression Network for global discovery of conserved genetic modules Science 302 2003 249-255
6. Zhou H. Ranish J.A. Watts J.D. Aebersold R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry Nat Biotechnol 20 2002 512-515
7. Price N.D. Reed J.L. Papin J.A. Wiback S.J. Palsson B.O. Network-based analysis of metabolic regulation in the human red blood cell J Theor Biol 225 2003 185-194
8. Arias E. Anderson R.N. Kung H.C. Murphy S.L. Kochanek K.D. Deaths: final data for 2001 Natl Vital Stat Rep 52 2003 1-115
9. Kitano H. Computational Systems Biology Nature 420 2002 206-210
10. Ideker T. Galitski T. Hood L. A new approach to decoding life: systems biology Annu Rev Genomics Hum Genet 2 2001 343-372
11. 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 292 2001 929-934
12. Poincaré, H. Science and hypothesis; with a preface by J. Larmor
13. Mungall A.J. Palmer S.A. Sims S.K. Edwards C.A. Ashurst J.L. Wilming L. Jones M.C. Horton R. Hunt S.E. Scott C.E. Gilbert J.G. Clamp M.E. Bethel G. Milne S. Ainscough R. Almeida J.P. Ambrose K.D. Andrews K.D. The DNA sequence and analysis of human chromosome 6 Nature 425 2003 805-811
14. Stein L.D. Bao Z. Blasiar D. Blumenthal T. Brent M.R. Chen N. Chinwalla A. Clarke L. Clee C. Coghlan A. Coulson A. D'Eustachio P. Fitch D.H. Fulton L.A. Fulton R.E. Griffiths-Jones S. Harris T.W. Hillier L.W. Kamath R. Kuwabara P.E. Mardis E.R. Marra M.A. Miner T.L. Minx P. Mullikin J.C. Plumb R.W. Rogers J. Schein J.E. Sohrmann M. Spieth J. Stajich J.E. Wei C. Willey D. Wilson R.K. Durbin R. Waterston R.H. The genome sequence of caenorhabditis briggsae: A platform for comparative genomics PLoS Biol 1 2003 E45
15. Pennisi E Bioinformatics, Gene counters struggle to get the right answer Science 301 2003 1040-1041
16. Hood L. Galas D. The digital code of DNA Nature 421 2003 444-448
17. Davidson E.H. Rast J.P. Oliveri P. Ransick A. Calestani C. Yuh C.H. Minokawa T. Amore G. Hinman V. Arenas-Mena C.Otim O. Brown C.T. Livi C.B. Lee P.Y. Revilla R. Rust A.G. Pan Z. Schilstra M.J. Clarke P.J. Arnone M.I. Rowen L. Cameron R.A. McClay D.R. Hood L. Bolouri H. A genomic regulatory network for development Science 295 2002 1669-1678
18. Lander E.S. The new genomics: Global views of biology Science 274 1996 536-539
19. Jasny B.R. Roberts L. Are we there yet? Science 302 2003 587
20. Pirmohamed M. Park B.K. Cytochrome P450 enzyme polymorphisms and adverse drug reactions Toxicology 192 2003 23-32
21. Staddon S. Arranz M.J. Mancama D. Mata I. Kerwin R.W. Clinical applications of pharmacogenetics in psychiatry Psychopharmacology (Berl) 162 2002 18-23
22. Higashi M.K. Veenstra D.L. Kondo L.M. Wittkowsky A.K. Srinouanprachanh S.L. Farin F.M. Rettie A.E. Association between CYP2C9 genetic variants and anticoagulation-related outcomes during warfarin therapy JAMA 287 2002 1690-1698
23. Cortellino S. Turner D. Masciullo V. Schepis F. Albino D. Daniel R. Skalka A.M. Meropol N.J. Alberti C. Larue L. Bellacosa A. The base excision repair enzyme MED1 mediates DNA damage response to antitumor drugs and is associated with mismatch repair system integrity Proc Natl Acad Sci USA 2003
24. Melton L. Pharmacogenetics and genotyping: On the trail of SNPs Nature 422 2003 917
25. Johnson J.A. Pharmacogenetics: Potential for individualized drug therapy through genetics Trends Genet 19 2003 660-666
26. Dennis C. Epigenetics and disease: Altered states Nature 421 2003 686-688
27. Wolffe A.P. Matzke M.A. Epigenetics: Regulation through repression Science 286 1999 481-486
28. Waterland R.A. Jirtle R.L. Transposable elements: Targets for early nutritional effects on epigenetic gene regulation Mol Cell Biol 23 2003 5293-5300
29. Clark M.S. Edwards Y.J. Peterson D. Clifton S.W. Thompson A.J. Sasaki M. Suzuki Y. Kikuchi K. Watabe S. Kawakami K. Sugano S. Elgar G. Johnson S.L. Fugu ESTs: New resources for transcription analysis and genome annotation Genome Res 13 2003 2747-2753
30. Stears R.L. Martinsky T. Schena M. Trends in microarray analysis Nat Med 9 2003 140-145
31. Lockhart D.J. Dong H. Byrne M.C. Follettie M.T. Gallo M.V. Chee M.S. Mittmann M. Wang C. Kobayashi M. Horton H. Brown E.L. Expression monitoring by hybridization to high-density oligonucleotide arrays Nat Biotechnol 14 1996 1675-1680
32. Velculescu V.E. Zhang L. Vogelstein B. Kinzler K.W. Serial analysis of gene expression Science 270 1995 484-487
33. Hackett C.S. Hodgson J.G. Law M.E. Fridlyand J. Osoegawa K. de Jong P.J. Nowak N.J. Pinkel D. Albertson D.G. Jain A. Jenkins R. Gray J.W. Weiss W.A. Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors Cancer Res 63 2003 5266-5273
34. Howbrook D.N. van der VaA. O'Shaughnessy M.C. Sarker D.K. Baker S.C. Lloyd A.W. Developments in microarray technologies Drug Discov Today 8 2003 642-651
35. Yamada K. Lim J. Dale J.M. Chen H. Shinn P. Palm C.J. Southwick AM Wu H.C. Kim C. Nguyen M. Pham P. Cheuk R. Karlin-Newmann G. Liu S.X. Lam B. Sakano H. Wu T. Yu G. Miranda M. Quach H.L. Tripp. M. Chang C.H. Lee J.M. Toriumi M. Chan M.M. Tang C.C. Onodera C.S. Deng J.M. Akiyama K. Ansari Y. Arakawa T. Banh J. Banno F. Bowser L. Brooks S. Carninci P. Chao Q. Choy N. Enju A. Goldsmith A.D. Gurjal M. Hansen N.F. Hayashizaki Y. Johnson-Hopson C. Hsuan V.W. Iida K. Karnes M. Khan S. Koesema E. Ishida J.Jiang P.X. Jones T. Kawai J. Kamiya A. Meyers C. Nakajima M. Narusaka M.Seki M.Sakurai T. Satou M. Tamse R. Vaysberg M. Wallender E.K. Wong C. Yamamura Y. Yuan S. Shinozaki K. Davis R.W. Theologis A. Ecker J.R. Empirical analysis of transcriptional activity in the arabidopsis genome. Science 302 2003 842-846
36. Neumann N.F. Galvez F. DNA microarrays and toxicogenomics: Applications for ecotoxicology? Biotechnol Adv 20 2002 391-419
37. Pedrioli P.G.A. Eng J. Hubley R. Pratt B. Nilsson E. Aebersold R. A standard open representation of mass spectrometry data and its application in a proteomics research environment 2004
38. Taylor C.F. Paton N.W. Garwood K.L. Kirby P.D. Stead D.A. Yin Z. Deutsch E.W. Selway L. Walker J. Riba-Garcia I. Mohammed S. Deery M.J. Howard J.A. Dunkley T. Aebersold R. Kell D.B. Lilley K.S. Roepstorff K.S. A systematic approach to modeling, capturing and disseminating proteomics experimental data Nat Biotechnol 21 2003 247-254
39. Lee C. Atanelov L. Modrek B. Xing Y. ASAP: The alternative splicing annotation project Nucleic Acids Res 31 2003 101-105
40. Huang H.D. Horng J.T. Lee C.C. Liu B.J. ProSplicer: A database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data Genome Biol 4 2003
41. Kipps T.J. Advances in classification and therapy of indolent B-cell malignancies Semin Oncol 29 2002 98-104
42. al Khaldi S.F. Martin S.A. Rasooly A. Evans J.D. DNA microarray technology used for studying foodborne pathogens and microbial habitats: Minireview J AOAC Int 85 2002 906-910
43. Soini H. Musser J.M. Molecular diagnosis of mycobacteria Clin Chem 47 2001 809-814
44. Paweletz C.P. Charboneau L. Bichsel V.E. Simone N.L. Chen T. Gillespie J.W. Emmert-Buck M.R. Roth M.J. Petricoin EFIII Liotta LA Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front Oncogene 20 2001 1981-1989
45. Beaucage S.L. Strategies in the preparation of DNA oligonucleotide arrays for diagnostic applications Curr Med Chem 8 2001 1213-1244
46. Chizhikov V. Rasooly A. Chumakov K. Levy D.D. Microarray analysis of microbial virulence factors Appl Environ Microbiol 67 2001 3258-3263
47. Gene chip for viral discovery. PLoS Biol 2003;1:139-140
48. Covitz P.A. Class struggle: Expression profiling and categorizing cancer Pharmacogenomics J 3 2003 257-260
49. Berger A. Mutch D.M. Bruce G.J. Roberts M.A. Unraveling lipid metabolism with microarrays: Effects of arachidonate and docosahexaenoate acid on murine hepatic and hippocampal gene expression Lipids Health Dis 1 2002 2
50. Hanash S. Creighton C. Making sense of microarray data to classify cancer Pharmacogenomics J 2003
51. Aebersold R. Mann M. Mass spectrometry-based proteomics Nature 422 2003 198-207
52. Rabilloud T. Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains Proteomics 2 2002 3-10
53. Unlu M. Morgan M.E. Minden J.S. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts Electrophoresis 18 1997 2071-2077
54. Gauss C. Kalkum M. Lowe M. Lehrach H. Klose J. Analysis of the mouse proteome. (I) Brain proteins: Separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation Electrophoresis 20 1999 575-600
55. Link A.J. Eng J. Schieltz D.M. Carmack E. Mize G.J. Morris D.R. Garvik B.M. Yates J.R. Direct analysis of protein complexes using mass spectrometry Nat Biotechnol 17 1999 676-682
56. Han D.K. Eng J. Zhou H. Aebersold R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry Nat Biotechnol 19 2001 946-951
57. Washburn M.P. Wolters D. Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat Biotechnol 19 2001 242-247
58. Keller A. Nesvizhskii A.I. Kolker E. Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal Chem 74 2002 5383-5392
59. Nesvizhskii A.I. Keller A. Kolker E. Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry Anal Chem 75 2003 4646-4658
60. Conrads T.P. Issaq H.J. Hoang V.M. Current strategies for quantitative proteomics Adv Protein Chem 65 2003 133-159
61. Mirgorodskaya O.A. Kozmin Y.P. Titov M.I. Korner R. Sonksen C.P. Roepstorff P. Quantitation of peptides and proteins by matrix-assisted laser desorption/ionization mass spectrometry using (18)O-labeled internal standards Rapid Commun Mass Spectrom 14 2000 1226-1232
62. Yao X. Freas A. Ramirez J. Demirev P.A. Fenselau C. Proteolytic 18O labeling for comparative proteomics: Model studies with two serotypes of adenovirus Anal Chem 73 2001 2836-2842
63. Uetz P. Giot L. Cagney G. Mansfield T.A. Judson R.S. Knight J.R. Lockshon D. Narayan V. Srinivasan M. Pochart P. Qureshi-Emili A. Li Y. Godwin B. Conover D. Kalbfleisch T. Vijayadamodar G. Yang M. Johnston M. Johnston I. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 403 2000 623-627
64. Ho Y.P. Hsu P.H. Investigating the effects of protein patterns on microorganism identification by high-performance liquid chromatography-mass spectrometry and protein database searches J Chromatogr A 976 2002 103-111
65. Gavin A.C. Bosche M. Krause R. Grandi P. Marzioch M. Bauer A. Schultz J. Rick J.M. Michon A.M. Cruciat C.M. Remor M. Hofert C. Schelder M. Brajenovic M. Ruffner H. Merino A. Klein K. Hudak M. Dickson D. Rudi D. Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 415 2002 141-147
66. Rout M.P. Aitchison J.D. The nuclear pore complex as a transport machine J Biol Chem 276 2001 16593-16596
67. Neubauer G. Gottschalk A. Fabrizio P. Seraphin B. Luhrmann R. Mann M. Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry Proc Natl Acad Sci USA 94 2001 385-390
68. Mann M. Jensen O.N. Proteomic analysis of post-translational modifications Nat Biotechnol 21 2003 255-261
69. Griffin T.J. Gygi S.P. Ideker T. Rist B. Eng J. Hood L. Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae Mol Cell Proteomics 1 2002 323-333
70. Betts J.C. Lukey P.T. Robb L.C. McAdam R.A. Duncan K. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling Mol Microbiol 43 2002 717-731
71. Guina T. Purvine S.O. Yi E.C. Eng J. Goodlett D.R. Aebersold R. Miller S.I. Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways Proc Natl Acad Sci USA 100 2003 2771-2776
72. Zhang H. Li X.J. Martin D.B. Aebersold R. Identification and Quantification of N-linked Glycoproteins Using Hydrazide Chemistry, Stable Isotope Labeling and Mass Spectrometry 2003 660-666 Springer-Verlag Berlin, New York
73. Liotta L.A. Ferrari M. Petricoin E. Clinical proteomics: Written in blood Nature 425 2003 905
74. Petricoin E.F. Ardekani A.M. Hitt B.A. Levine P.J. Fusaro V.A. Steinberg S.M. Mills G.B. Simone C. Fishman D.A. Kohn E.C. Liotta L.A. Use of proteomic patterns in serum to identify ovarian cancer Lancet 359 2002 572-577
75. Nicholson J.K. Wilson I.D. Opinion: Understanding 'global' systems biology: Metabonomics and the continuum of metabolism Nat Rev Drug Discov 2 2003 668-676
76. Watkins S.M. German J.B. Toward the implementation of metabolomic assessments of human health and nutrition Curr Opin Biotechnol 13 2002 512-516
77. German J.B. Roberts M.A. Fay L. Watkins S.M. Metabolomics and individual metabolic assessment: The next great challenge for nutrition J Nutr 132 2002 2486-2487
78. German J.B. Roberts M.A. Watkins S.M. Personal metabolomics as a next generation nutritional assessment J Nutr 133 2003 4260-4266
79. Kauffman K.J. Prakash P. Edwards J.S. Advances in flux balance analysis Curr Opin Biotechnol 14 2003 491-496
80. Takahashi K. Ishikawa N. Sadamoto Y. Sasamoto H. Ohta S. Shiozawa A. Miyoshi F. Naito Y. Nakayama Y. Tomita M. E-Cell 2: Multi-platform E-Cell simulation system Bioinformatics 19 2003 1727-1729
81. Segre D. Zucker J. Katz J. Lin X. D'Haeseleer P. Rindone W.P. Kharchenko P. Nguyen D.H. Wright M.A. Church G.M. From annotated genomes to metabolic flux models and kinetic parameter fitting OMICS 7 2003 301-316
82. Ge H. Walhout A.J. Vidal M. Integrating 'omic' information: A bridge between genomics and systems biology Trends Genet 19 2003 551-560
83. Desiere F. German B. Watzke H. Pfeifer A. Saguy S. Bioinformatics and data knowledge: The new frontiers for nutrition and foods Trends Food Sci Technol 12 2002 215-229
84. Altschul S.F. Gish W. Miller W. Myers E.W. Lipman DJ Basic local alignment search tool J Mol Biol 215 1990 403-410
85. Benson D.A. Karsch-Mizrachi I. Lipman D.J. Ostell J. Wheeler D.L. GenBank Nucleic Acids Res 31 2003 23-27
86. Xenarios I. Salwinski L. Duan X.J. Higney P. Kim S.M. Eisenberg D. DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions Nucleic Acids Res 30 2002 303-305
87. Bader G.D. Betel D. Hogue C.W. BIND: The Biomolecular Interaction Network Database Nucleic Acids Res 31 2003 248-250
88. Suzuki H. Saito R. Kanamori M. Kai C. Schonbach C. Nagashima T. Hosaka J. Hayashizaki Y. The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer Genome Res 13 2003 1534-1541
89. Zanzoni A. Montecchi-Palazzi L. Quondam M. Ausiello G. Helmer-Citterich M. Cesareni G. MINT: A Molecular INTeraction database FEBS Lett 513 2002 135-140
90. Breitkreutz B.J. Stark C. Tyers M. Osprey: A network visualization system Genome Biol 4 2003
91. Ho Y. Gruhler A. Heilbut A. Bader G.D. Moore L. Adams S.L. Millar A. Taylor P. Bennett K. Boutilier K. Yang L. Wolting C. Donaldson I. Schandorff S. Shewnarane J. Vo M. Taggart J. Goudreault M. Muskat B. Alfarano C. Dewar D. Lin Z. Michalickova K. Willems A.R. Sassi H. Nielsen P.A. Rasmussen K.J. Andersen J.R. Johansen L.E. Hansen L.H. Jespersen H. Podtelejnikov A. Nielsen E. Crawford J. Poulsen V. Sorensen B.D. Matthiesen J. Hendrickson R.C. Gleeson F.Pawson T. Moran M.F. Durocher D. Mann M. Hogue C.W. Figeys D. Tyers M. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 415 2002 180-183
92. 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 R.L. Jr. 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 302 2003 1727-1736
93. Matys V. Fricke E. Geffers R. Gossling E. Haubrock M. Hehl R. Hornischer K. Karas D. Kel A.E. Kel-Margoulis O.V. Kloos D.U. Land S. Lewicki-Potapov B. Michael H. Munch R. Reuter I. Rotert S. Saxel H. Scheer M. TRANSFAC: Transcriptional regulation, from patterns to profiles Nucleic Acids Res 31 2003 374-378
94. Zhu J. Zhang M.Q. SCPD: A promoter database of the yeast Saccharomyces cerevisiae Bioinformatics 15 1999 607-611
95. Karp P.D. Riley M. Saier M. Paulsen I.T. Collado-Vides J. Paley S.M. Pellegrini-Toole A. Bonavides C. Gama-Castro S. The EcoCyc database Nucleic Acids Res 30 2002 56-58
96. Kanehisa M. Goto S. Kawashima S. Nakaya A. The KEGG databases at GenomeNet Nucleic Acids Res 30 2002 42-46
97. Overbeek R. Larsen N. Pusch G.D. D'Souza M. Selkov E. Kyrpides N. Fonstein M. Maltsev N. Selkov E. WIT: Integrated system for high-throughput genome sequence analysis and metabolic reconstruction Nucleic Acids Res 28 2000 123-125
98. Brazma A. Parkinson H. Sarkans U. Shojatalab M. Vilo J. Abeygunawardena N. Holloway E. Kapushesky M. Kemmeren P. Lara G.G. Oezcimen A. Rocca-Serra P. Sansone S.A. ArrayExpress-a public repository for microarray gene expression data at the EBI Nucleic Acids Res 31 2003 68-71
99. Edgar R. Domrachev M. Lash A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res 30 2002 207-210
100. Sherlock G. Hernandez-Boussard T. Kasarskis A. Binkley G. Matese J.C. Dwight S.S. Kaloper M. Weng S. Jin H. Ball C.A. Eisen M.B. Spellman P.T. Brown P.O. Botstein D. Cherry J.M. The stanford microarray database Nucleic Acids Res 29 2001 152-155
101. Peri S Navarro J.D. Amanchy R. Kristiansen T.Z. Jonnalagadda C.K. Surendranath V. Niranjan V. Muthusamy B. Gandhi T.K. Gronborg M. Ibarrola N. Deshpande N. Shanker K. Shivashankar H.N. Rashmi B.P. Ramya M.A. Zhao Z. Chandrika K.N. Padma N. Harsha H.C. Yatish A.J. Kavitha M.P. Menezes M. Choudhury D.R. Suresh S. Ghosh N. Saravana R. Chandran S. Krishna S. Joy M. Anand S.K. Madavan V. Joseph A. Wong G.W. Schiemann W.P. Constantinescu S.N. Huang L. Khosravi-Far R. Steen H. Tewari M. Ghaffari S. Blobe G.C. Dang C.V. Garcia J.G. Pevsner J. Jensen O.N. Roepstorff P. Deshpande K.S. Chinnaiyan A.M. Hamosh A. Chakravarti A. Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans Genome Res 13 2003 2363-2371
102. Hucka M. Finney A. Sauro H.M. Bolouri H. Doyle J.C. Kitano H. Arkin A.P. Bornstein B.J. Bray D. Cornish-Bowden A. Cuellar A.A. Dronov S. Gilles E.D. Ginkel M. Gor V. Goryanin I.I. Hedley W.J. Hodgman T.C. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics 19 2003 524-531
103. Vidal M. A biological atlas of functional maps Cell 104 2001 333-339
104. 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 Res 13 2003 2498-2504
105. Collins F.S. Watson J.D. Genetic discrimination: Time to act Science 302 2003 745
106. Collins F.S. Green E.D. Guttmacher A.E. Guyer M.S. US National Human Genome Research Institute. A vision for the future of genomics research Nature 422 2003 835-847
107. Lederberg J. Getting in tune with the enemy - Microbes The Scientist 17 2003 20
108. Xu J. Gordon J.I. Inaugural article: Honor thy symbionts Proc Natl Acad Sci USA 100 2003 10452-10459
109. Xu J. Bjursell M.K. Himrod J. Deng S. Carmichael L.K. Chiang H.C. Hooper L.V. Gordon J.I. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis Science 299 2003 2074-2076
110. Schell M.A. Karmirantzou M. Snel B. Vilanova D. Berger B. Pessi G. Zwahlen M.C. Desiere F. Bork P. Delley M. Pridmore R.D. Arigoni F. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract Proc Natl Acad Sci USA 99 2002 14422-14427
111. Paulsen I.T. Banerjei L. Myers G.S. Nelson K.E. Seshadri R. Read T.D. Fouts D.E. Eisen J.A. Gill S.R. Heidelberg J.F. Tettelin H. Dodson R.J. Umayam L. Brinkac L. Beanan M. Daugherty S. DeBoy R.T. Durkin S. Kolonay J. Madupu R. Nelson W. Vamathevan J. Tran B. Upton J. Hansen T. Shetty J. Khouri H. Utterback T. Radune D. Ketchum K.A. Dougherty B.A. Fraser C.M. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis Science 299 2003 2071-2074
112. Pridmore R.D. Berger B. Desiere F. Vilanova D. Barretto C. Pittet A.C. Zwahlen M.C. Rouvet M. Altermann E. Barrangou R. Proc Natl Acad Sci U.S.A. 101 2004 2512-2517
113. Oliveira M.J. Van Damme J. Lauwaet T. De C.V. De Bruyne G. Verschraegen G. Vaneechoutte M. Goethals M. Ahmadian M.R. Muller O. Vandekerckhove J. Mareel M. Leroy A. beta-casein-derived peptides, produced by bacteria, stimulate cancer cell invasion and motility EMBO J 22 2003 6161-6173
114. Savage DC Gastrointestinal microflora in mammalian nutrition Annu Rev Nutr 6:155-78. 1986 155-178
115. Berg R.D. The indigenous gastrointestinal microflora Trends Microbiol 4 1996 430-435
116. Urso M.L. Clarkson P.M. Oxidative stress, exercise and antioxidant supplementation Toxicology 189 2003 41-54
117. Goodman G.E. Schaffer S. Omenn G.S. Chen C. King I. The association between lung and prostate cancer risk and serum micronutrients: results and lessons learned from beta-carotene and retinol efficacy trial Cancer Epidemiol Biomarkers Prev 12 2003 518-526
118. Gann P.H. Khachik F. Tomatoes or lycopene versus prostate cancer: Is evolution anti-reductionist? JNCI Cancer Spectrum 95 2003 1563-1565
119. Hursting S.D. Lavigne J.A. Berrigan D. Perkins S.N. Barrett J.C. Calorie restriction, aging and cancer prevention: Mechanisms of action and applicability to humans Annu Rev Med 54:131-52 2003 131-152
120. Omenn G.S. Genetic advances will influence the practice of medicine: examples from cancer research and care of cancer patients Genet Med 4 2002 15S-20S