Systems biology of embryogenesis

Reproduction, Fertility and Development

Volumn 22, Issue 1, 2010, Pages 98-105

  Edelman, Lucas B ^a,b,d   Chandrasekaran, Sriram ^a,c   Price, Nathan D ^a,c  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b University of Illinois at Urbana Champaign   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Complex adaptive systems; Computational models; Development; Organogenesis; Regulatory networks.

Indexed keywords

BETA CATENIN; WNT PROTEIN;

ADAPTIVE BEHAVIOR; BIOLOGY; CELL COMMUNICATION; EMBRYO DEVELOPMENT; ENVIRONMENTAL CHANGE; EXTRACELLULAR MATRIX; GENE EXPRESSION; GENE INTERACTION; HUMAN; MATHEMATICAL MODEL; NONHUMAN; ORGANOGENESIS; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW; SIGNAL TRANSDUCTION;

ANIMALS; COMPUTER SIMULATION; EMBRYONIC DEVELOPMENT; HUMANS; MODELS, BIOLOGICAL; ORGANOGENESIS; SYSTEMS BIOLOGY;

EID: 73649133695     PISSN: 10313613     EISSN: None     Source Type: Journal    
DOI: 10.1071/RD09215     Document Type: Review

References (100)

1. Aboobaker, A. A., Tomancak, P., Patel, N., Rubin, G. M., and Lai, E. C. (2005). Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proc. Natl Acad. Sci. USA 102, 18 017-18 022. doi:10.1073/PNAS.0508823102 (Pubitemid 41798494)
2. Allison, D. B., Cui, X., Page, G. P., and Sabripour, M. (2006). Microarray data analysis: from disarray to consolidation and consensus. Nat. Rev. Genet. 7, 55-65. doi:10.1038/NRG1749 (Pubitemid 41828948)
3. Alon, U. (2007). 'An Introduction to Systems Biology: Design Principles of Biological Circuits.' (Chapman & Hall/CRC: Boca Raton, FL.)
4. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., and Kuster, B. (2007). Quantitative mass spectrometry in proteomics: A critical review. Anal. Bioanal. Chem. 389, 1017-1031. doi:10.1007/S00216-007-1486-6 (Pubitemid 47482251)
5. Bentley,D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P.,Milton, J., et al. (2008).Accuratewhole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59. doi:10.1038/NATURE07517
6. Bock, C., and Lengauer,T. (2008). Computational epigenetics. Bioinformatics 24, 1-10. doi:10.1093/BIOINFORMATICS/BTM546
7. Boozer, C., Kim, G., Cong, S., Guan, H. W., and Londergan, T. (2006). Looking towards label-free biomolecular interaction analysis in a high-throughput format: A review of new surface plasmon resonance technologies. Curr. Opin. Biotechnol. 17, 400-405. doi:10.1016/ J.COPBIO.2006.06.012
8. Braun, P., Tasan, M., Dreze, M., Barrios-Rodiles, M., Lemmens, I., et al. (2008). An experimentally derived confidence score for binary protein- protein interactions. Nat. Methods 6, 91-97. doi:10.1038/NMETH.1281
9. Cavin Perier, R. C., Junier, T., and Bucher, P. (1998). The eukaryotic promoter database EPD. Nucleic Acids Res. 26, 353-357. doi:10.1093/ NAR/26.1.353
10. Chang, H. H., Oh, P.Y., Ingber, D. E., and Huang, S. (2006). Multistable and multistep dynamics in neutrophil differentiation. BMC Cell Biol. 7, 11. doi:10.1186/1471-2121-7-11 (Pubitemid 43376251)
11. Chaturvedi, R., Huang, C., Kazmierczak, B., Schneider, T., Izaguirre, J. A., Glimm, T., Hentschel, H. G. E., Glazier, J. A., Newman, S. A., and Alber, M. S. (2005). On multiscale approaches to threedimensional modelling of morphogenesis. J. R. Soc. Interface 2, 237-253. doi:10.1098/RSIF.2005.0033
12. Chiellini, C., Cochet, O., Negroni, L., Samson, M., Poggi, M., Ailhaud, G., Alessi, M.-C., Dani, C., and Amri, E.-Z. (2008). Characterization of human mesenchymal stem cell secretome at early steps of adipocyte and osteoblast differentiation. BMC Mol. Biol. 9, 26. doi:10.1186/1471- 2199-9-26
13. Christiansen, J. H., Yang, Y., Venkataraman, S., Richardson, L., Stevenson, P., Burton, N., Baldock, R. A., and Davidson, D. R. (2006). EMAGE: A spatial database of gene expression patterns during mouse embryo development. Nucleic Acids Res. 34, D637-D641. doi:10.1093/NAR/ GKJ006
14. Cickovski, T., Aras, K., Alber, M. S., Izaguirre, J. A., Swat, M., et al. (2007). From genes to organisms via the cell: A problem-solving environment for multicellular development. Comput. Sci. Eng. 9, 50-60. doi:10.1109/MCSE.2007.74 (Pubitemid 47159734)
15. Coffey, D. S. (1998). Self-organization, complexity and chaos: The new biology for medicine. Nat. Med. 4, 882-885. doi:10.1038/ NM0898-882
16. Core, L. J., Waterfall, J. J., and Lis, J. T. (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848. doi:10.1126/SCIENCE.1162228
17. Davidson, E. H., and Erwin, D. H. (2006). Gene regulatory networks and the evolution of animal body plans. Science 311, 796-800. doi:10.1126/ SCIENCE.1113832
18. Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., et al. (2002). A genomic regulatory network for development. Science 295, 1669-1678. doi:10.1126/SCIENCE.1069883 (Pubitemid 34202895)
19. Dinger, M. E., Amaral, P. P., Mercer, T. R., Pang, K. C., Bruce, S. J., et al. (2008). Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 18, 1433-1445. doi:10.1101/GR.078378.108
20. Dominguez, F., Pellicer, A., and Simon, C. (2009). The human embryo proteome. Reprod. Sci. 16, 188-190. doi:10.1177/1933719108328612
21. Edgar, R., Domrachev, M., and Lash, A. E. (2002). Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210. doi:10.1093/NAR/30.1.207
22. Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., et al. (2009). Real-time DNA sequencing from single polymerase molecules. Science 323, 133-138. doi:10.1126/SCIENCE.1162986
23. El-Ali, J., Sorger, P., and Jensen, K. (2006). Cells on chips. Nature 442, 403-411. doi:10.1038/NATURE05063 (Pubitemid 44264784)
24. Eldar, A., Dorfman, R., Weiss, D., Ashe, H., Shilo, B. Z., and Barkai, N. (2002). Robustness of the BMP morphogen gradient in Drosophila embryonic patterning. Nature 419, 304-308. doi:10.1038/NATURE01061
25. Froment, C., Uttenweiler-Joseph, S., Bousquet-Dubouch, M. P., Matondo, M., Borges, J. P., Esmenjaud, C., Lacroix, C., Monsarrat, B., and Burlet-Schiltz, O. (2005). A quantitative proteomic approach using two-dimensional gel electrophoresis and isotope-coded affinity tag labeling for studying human 20S proteasome heterogeneity. Proteomics 5, 2351-2363. doi:10.1002/PMIC.200401281 (Pubitemid 40835404)
26. Gandhi, T. K. B., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., et al. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat. Genet. 38, 285-293. doi:10.1038/NG1747 (Pubitemid 43315748)
27. Gell-Mann, M. (1994). Complex adaptive systems. In 'Complexity: Metaphors, Models, and Reality'. (Eds D. P. George, A. Cowan and D. Elliott Meltzer.) pp. 17-45. (Westview Press: Boulder, CO.)
28. Gunderson, K. L., Steemers, F. J., Lee, G., Mendoza, L. G., and Chee, M. S. (2005).Agenome-wide scalable SNP genotyping assay using microarray technology. Nat. Genet. 37, 549-554. doi:10.1038/NG1547 (Pubitemid 40617286)
29. Gupta, N., Tanner, S., Jaitly, N., Adkins, J. N., Lipton, M., et al. (2007). Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation. Genome Res. 17, 1362-1377. doi:10.1101/GR.6427907 (Pubitemid 47360911)
30. Haudry,Y., Berube, H., Letunic, I.,Weeber, P.-D., Gagneur, J., et al. (2008). 4DXpress: A database for cross-species expression pattern comparisons. Nucleic Acids Res. 36, D847-D853. doi:10.1093/NAR/GKM797 (Pubitemid 351149834)
31. Hood, L., Heath, J. R., Phelps, M. E., and Lin,B. (2004). Systems biology and new technologies enable predictive and preventative medicine. Science 306, 640-643. doi:10.1126/SCIENCE.1104635 (Pubitemid 39440903)
32. Hornstein, E., and Shomron, N. (2006). Canalization of development by microRNAs. Nat. Genet. 38(Suppl.), S20-S24. doi:10.1038/ NG1803
33. Huang, S., Eichler, G., Bar-Yam, Y., and Ingber, D. E. (2005). Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys. Rev. Lett. 94, 128701. doi:10.1103/PHYSREVLETT.94. 128701
34. Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., et al. (2003). The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531. doi:10.1093/BIOINFORMATICS/BTG015 (Pubitemid 36336519)
35. Imai, K. S., Levine, M., Satoh, N., and Satou, Y. (2006). Regulatory blueprint for a chordate embryo. Science 312, 1183-1187. doi:10.1126/ SCIENCE.1123404
36. Johnston, R. J., Chang, S., Etchberger, J. F., Ortiz, C. O., and Hobert, O. (2005). MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc. Natl Acad. Sci. USA 102, 12 449- 12 454. doi:10.1073/PNAS.0505530102 (Pubitemid 41266379)
37. Jones, P. A., and Martienssen, R. (2005).A blueprint for a human epigenome project: The AACR human epigenome workshop. Cancer Res. 65, 11241-11246.
38. Kaiser, J. (2008).DNAsequencing: A plan to capture human diversity in 1000 genomes. Science 319, 395. [Abstract] doi:10.1126/SCIENCE.319. 5862.395 (Pubitemid 351160548)
39. Kashiwagi, A., Urabe, I., Kaneko, K., and Yomo,T. (2006).Adaptive response of a gene network to environmental changes by fitness-induced attractor selection. PLoS One 1, e49. doi:10.1371/JOURNAL.PONE.0000049
40. Katz-Jaffe, M. G., Gardner, D. K., and Schoolcraft,W. B. (2006). Proteomic analysis of individual human embryos to identify novel biomarkers of development and viability. Fertil. Steril. 85, 101-107. doi:10.1016/ J.FERTNSTERT.2005.09.011
41. Katz-Jaffe, M. G., McReynolds, S., Gardner, D. K., and Schoolcraft, W. B. (2009). The role of proteomics in defining the human embryonic secretome. Mol. Hum. Reprod. 15, 271-277. doi:10.1093/MOLEHR/GAP012
42. Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., et al. (2008). Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56-64. doi:10.1038/NATURE06862 (Pubitemid 351630326)
43. Kitano, H. (2004). Biological robustness. Nat. Rev. Genet. 5, 826-837. doi:10.1038/NRG1471 (Pubitemid 39457498)
44. Kolkman, A., Dirksen, E. H. C., Slijper,M., and Heck, A. J. R. (2005). Double standards in quantitative proteomics direct comparative assessment of difference in gel electrophoresis and metabolic stable isotope labeling. Mol. Cell. Proteomics 4, 255-266. doi:10.1074/MCP.M400121- MCP200
45. Kuntz, S. G., Schwarz, E. M., DeModena, J. A., De Buysscher, T., Trout, D., Shizuya, H., Sternberg, P.W., andWold, B. J. (2008). Multigenome DNA sequence conservation identifies Hox cis-regulatory elements. Genome Res. 18, 1955-1968. doi:10.1101/GR.085472.108
46. Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., et al. (2007). A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401-1414. doi:10.1016/J.CELL.2007.04.040 (Pubitemid 46970709)
47. Langton, T. (2008). Leading U. S. bioscience pioneers enter international collaboration with government of Luxembourg to accelerate biomedical research. Available at: http://www.systemsbiology.org/Press-Release- 60608 [Verified 23 September 2009].
48. Lausted, C., Hu, Z., and Hood, L. (2008). Quantitative serum proteomics from surface plasmon resonance imaging. Mol. Cell. Proteomics 7, 2464-2474. doi:10.1074/MCP.M800121-MCP200
49. Levine, M., and Davidson, E. H. (2005). Gene regulatory networks for development. Proc. Natl Acad. Sci. USA 102, 4936-4942. doi:10.1073/ PNAS.0408031102
50. Lewis, J. (2008). From signals to patterns: Space, time, and mathematics in developmental biology. Science 322, 399-403. doi:10.1126/ SCIENCE.1166154
51. Li, L., Zhu, Q., He, X., Sinha, S., and Halfon, M. S. (2007). Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biol. 8, R101. doi:10.1186/ GB-2007-8-6-R101
52. Lloyd, C. M., Halstead, M. D. B., and Nielsen, P. F. (2004). CellML: Its future, present and past. Prog. Biophys. Mol. Biol. 85, 433-450. doi:10.1016/J.PBIOMOLBIO.2004.01.004 (Pubitemid 38629921)
53. Longabaugh, W. J. R., Davidson, E. H., and Bolouri, H. (2005). Computational representation of developmental genetic regulatory networks. Dev. Biol. 283, 1-16. doi:10.1016/J.YDBIO.2005.04.023 (Pubitemid 40828838)
54. Lott, S. E., Kreitman, M., Palsson, A., Alekseeva, E., and Ludwig, M. Z. (2007). Canalization of segmentation and its evolution in Drosophila. Proc. NatlAcad. Sci. USA 104, 10 926-10 931. doi:10.1073/ PNAS.0701359104
55. Mardis, E. R. (2008). The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133-141.
56. Martens, L., Hermjakob, H., Jones, P., Adamski, M., and Taylor, C. (2005). PRIDE: The proteomics identifications database. Proteomics 5, 3537-3545. doi:10.1002/PMIC.200401303 (Pubitemid 41192059)
57. Matsuda, T. (2005).Visible embryo: A 3D image database of human embryo collection at Kyoto University. IEICE Technical Report 105, 3-4.
58. Mattick, J. S. (2007). A new paradigm for developmental biology. J. Exp. Biol. 210, 1526-1547. doi:10.1242/JEB.005017 (Pubitemid 46841958)
59. Meir, E., Von Dassow, G., Munro, E., and Odell, G. M. (2002). Robustness, flexibility, and the role of lateral inhibition in the neurogenic network. Curr. Biol. 12, 778-786. doi:10.1016/S0960-9822(02)00839-4 (Pubitemid 34514363)
60. Mir, K. U., Qi, H., Salata, O., and Scozzafava, G. (2009). Sequencing by cyclic ligation and cleavage (CycLiC) directly on a microarray captured template. Nucleic Acids Res. 37, e5. doi:10.1093/NAR/GKN906
61. Nesvizhskii, A. I., Vitek, O., and Aebersold, R. (2007). Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 4, 787-797. doi:10.1038/NMETH1088 (Pubitemid 350055575)
62. Nykter, M., Price, N. D., Aldana, M., Ramsey, S. A., Kauffman, S. A., Hood, L. E., Yli-Harja, O., and Shmulevich, I. (2008). Gene expression dynamics in the macrophage exhibit criticality. Proc. Natl Acad. Sci. USA 105, 1897-1900. doi:10.1073/PNAS.0711525105
63. Pan, Q., Shai, O., Lee, L. J., Frey, B. J., and Blencowe, B. J. (2008). Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413-1415. doi:10.1038/NG.259
64. Peirce, S., Skalak, T., and Papin, J. (2006). Multiscale biosystems integration: Coupling intracellular network analysis with tissue-patterning simulations. Syst. Biol. 50, 601-615.
65. Peng, H., Long, F., Zhou, J., Leung, G., Eisen, M., and Myers, E. (2007). Automatic image analysis for gene expression patterns of fly embryos. BMC Cell Biol. 8, S7. doi:10.1186/1471-2121-8-S1-S7 (Pubitemid 351837298)
66. Pisarev, A., Poustelnikova, E., Samsonova, M., and Reinitz, J. (2009). FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. Nucleic Acids Res. 37, D560-D566. doi:10.1093/NAR/GKN717
67. Price, N. D., Edelman, L. B., Lee, I.,Yoo, H., Hwang, D., Carlson, G., Galas, D. J., Heath, J. R., and Hood, L. (2009). Systems biology and systems medicine. In 'Genomic and Personalized Medicine: From Principles to Practice'. (Eds G. Ginsburg and H. Willard.) pp. 74-85. (Elsevier: Amsterdam.)
68. Quail, M. A., Kozarewa, I., Smith, F., Scally, A., Stephens, P. J., Durbin, R., Swerdlow, H., andTurner, D. J. (2008).A large genome center's improvements to the Illumina sequencing system. Nat. Methods 5, 1005-1010. doi:10.1038/NMETH.1270
69. Reeves, G. T., Muratov, C. B., Schüpbach, T., and Shvartsman, S.Y. (2006). Quantitative models of developmental pattern formation. Dev. Cell 11, 289-300. doi:10.1016/J.DEVCEL.2006.08.006
70. Robertson, S. H., Smith, C. K., Langhans,A. L., McLinden, S. E., Oberhardt, M.A., et al. (2007). Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior.BMCSyst. Biol. 1, 46. doi:10.1186/1752-0509-1-46
71. Rothberg, J. M., and Leamon, J. H. (2008). The development and impact of 454 sequencing. Nat. Biotechnol. 26, 1117-1124. doi:10.1038/NBT1485
72. Rual, J. F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., et al. (2005). Towards a proteome-scale map of the human protein- protein interaction network. Nature 437, 1173-1178. doi:10.1038/ NATURE04209
73. Sandmann, T., Girardot, C., Brehme, M., Tongprasit, W., Stolc, V., and Furlong, E. E. M. (2007). A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes Dev. 21, 436-449. doi:10.1101/GAD.1509007 (Pubitemid 46316025)
74. Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470. doi:10.1126/SCIENCE.270. 5235.467
75. Schinköthe, T., Bloch, W., and Schmidt, A. (2008). In vitro secreting profile of human mesenchymal stem cells. Stem Cells Dev. 17, 199-206. doi:10.1089/SCD.2007.0175 (Pubitemid 351271619)
76. Schwab, E.D., and Pienta, K. J. (1996). Cancer as a complex adaptive system. Med. Hypotheses 47, 235-241. doi:10.1016/S0306-9877(96)90086-9
77. Seila, A. C., Calabrese, J. M., Levine, S. S., Yeo, G. W., Rahl, P. B., Flynn, R. A., Young, R. A., and Sharp, P. A. (2008). Divergent transcription from active promoters. Science 322, 1849-1851. doi:10.1126/ SCIENCE.1162253
78. Setty,Y., Cohen, I. R., Dor,Y., and Harel, D. (2008). Four-dimensional realistic modeling of pancreatic organogenesis. Proc. Natl Acad. Sci. USA 105, 20 374-20 379. doi:10.1073/PNAS.0808725105
79. Shalgi, R., Lieber,D., Oren, M., and Pilpel,Y. (2007). Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLOS Comput. Biol. 3, e131. doi:10.1371/JOURNAL.PCBI. 0030131
80. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker,T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504. doi:10.1101/GR.1239303 (Pubitemid 37428274)
81. Shannon, P. T., Reiss, D. J., Bonneau, R., and Baliga, N. S. (2006). The Gaggle: An open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics 7, 176. doi:10.1186/1471-2105-7-176 (Pubitemid 43750371)
82. Shendure, J., and Ji, H. (2008). Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135-1145. doi:10.1038/NBT1486
83. Sherlock, G., Hernandez-Boussard, T., Kasarskis, A., Binkley, G., Matese, J. C., et al. (2001). The Stanford Microarray Database. Nucleic Acids Res. 29, 152-155. doi:10.1093/NAR/29.1.152
84. Stelling, J., Sauer, U., Szallasi, Z., Doyle, F. J., and Doyle, J. (2004). Robustness of cellular functions. Cell 118, 675-685. doi:10.1016/ J.CELL.2004.09.008
85. Taft, R. J., Pheasant, M., and Mattick, J. S. (2007). The relationship between non-protein-coding DNA and eukaryotic complexity. BioEssays 29, 288-299. doi:10.1002/BIES.20544 (Pubitemid 46384167)
86. Theise, N. D. (2006). Implications of 'postmodern biology' for pathology: The cell doctrine. Lab. Invest. 86, 335-344. doi:10.1038/LABINVEST. 3700401
87. Theise, N. D., and d'Inverno, M. (2004). Understanding cell lineages as complex adaptive systems. Blood Cells Mol. Dis. 32, 17-20. doi:10.1016/ J.BCMD.2003.09.010
88. Tomancak, P., Berman, B., Beaton, A., Weiszmann, R., Kwan, E., Hartenstein, V., Celniker, S., and Rubin, G. (2007). Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 8, R145. doi:10.1186/GB-2007-8-7-R145 (Pubitemid 351903192)
89. Tomlin, C. J., and Axelrod, J. D. (2007). Biology by numbers: mathematical modelling in developmental biology. Nat. Rev. Genet. 8, 331-340. doi:10.1038/NRG2098 (Pubitemid 46625810)
90. Tsang, J., Zhu, J., and van Oudenaarden, A. (2007). MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol. Cell 26, 753-767. doi:10.1016/J.MOLCEL.2007.05.018 (Pubitemid 46856248)
91. Usui-Aoki, K., Shimada, K., Nagano, M., Kawai, M., and Koga, H. (2005). Anovel approach to protein expression profiling using antibody microarrays combined with surface plasmon resonance technology. Proteomics 5, 2396-2401. doi:10.1002/PMIC.200401171 (Pubitemid 40835409)
92. Van Loo, P., Aerts, S., Thienpont, B., De Moor, B., Moreau, Y., and Marynen, P. (2008). ModuleMiner-improved computational detection of cis-regulatory modules: Are there different modes of gene regulation in embryonic development and adult tissues? Genome Biol. 9, R66. doi:10.1186/GB-2008-9-4-R66 (Pubitemid 351974311)
93. von Dassow, G., Meir, E., Munro, E. M., and Odell, G. M. (2000). The segment polarity network is a robust developmental module. Nature 406, 188-192. doi:10.1038/35018085 (Pubitemid 30469001)
94. Walker, D. C., and Southgate, J. (2009). The virtual cell: A candidate co-ordinator for 'middle-out' modelling of biological systems. Brief. Bioinform. 10, 450-461. doi:10.1093/BIB/BBP010
95. Walker, D., Wood, S., Southgate, J., Holcombe, M., and Smallwood, R. (2006). An integrated agent-mathematical model of the effect of intercellular signalling via the epidermal growth factor receptor on cell proliferation. J. Theor. Biol. 242, 774-789. doi:10.1016/J.JTBI.2006.04.020 (Pubitemid 44291701)
96. Wang, J., Wang, W., Li, R., Li, Y., Tian, G., et al. (2008). The diploid genome sequence of an Asian individual. Nature 456, 60-65. doi:10.1038/ NATURE07484
97. Wei, Z., Angerer, R., and Angerer, L. (2006). A database of mRNA expression patterns for the sea urchin embryo. Dev. Biol. 300, 476-484. doi:10.1016/J.YDBIO.2006.08.034 (Pubitemid 44826997)
98. Wheeler, D. A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., et al. (2008). The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872-876. doi:10.1038/NATURE06884 (Pubitemid 351550870)
99. Xiao, Z., Blonder, J., Zhou, M., and Veenstra, T. (2009). Proteomic analysis of extracellular matrix and vesicles. J. Proteomics 72, 34-45. doi:10.1016/J.JPROT.2008.11.011
100. Zhao, F., Xuan, Z., Liu, L., and Zhang, M.Q. (2005).TRED: A transcriptional regulatory element database and a platform for in silico gene regulation studies. Nucleic Acids Res. 33, D103-D107. doi:10.1093/NAR/GKI004 (Pubitemid 40207839)