Animal cells and systems

  • 제12권4호
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  • Pages.181-191
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  • 2008
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  • 1976-8354(pISSN)
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  • 2151-2485(eISSN)
한국통합생물학회 (The Korean Society for Integrative Biology)
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Current Research Trends in Systems Biology

  • 발행 : 2008.12.31
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  1. Albeck JG, MacBeath G, White FM, Sorger PK, Lauffenburger DA, and Gaudet S (2006) Collecting and organizing systematic sets of protein data. Nat Rev Mol Cell Biol 7: 803-812 https://doi.org/10.1038/nrm2042
  2. Albert R, Jeong H, and Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406: 378-382 https://doi.org/10.1038/35019019
  3. Aldridge BB, Burke JM, Lauffenburger DA, and Sorger PK (2006) Physicochemical modelling of cell signalling pathways. Nat cell biol 8: 1195-1203 https://doi.org/10.1038/ncb1497
  4. Aloy P, Bottcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, and Russell RB (2004) Structure-based assembly of protein complexes in yeast. Science 303: 2026-2029
  5. Aloy P and Russell RB (2002) Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci U S A. 99: 5896-5901
  6. Aloy P and Russell RB (2006) Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 7: 188-197 https://doi.org/10.1038/nrm1859
  7. Alves R, Antunes F, and Salvador A (2006) Tools for kinetic modeling of biochemical networks. Nat biotechnol 24: 667-672 https://doi.org/10.1038/nbt0606-667
  8. Andersen MR, Nielsen ML, and Nielsen J (2008) Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol syst biol 4: 178
  9. Bansal M, Belcastro V, Ambesi-Impiombato A, and di Bernardo D (2007) How to infer gene networks from expression profiles. Mol syst biol 3: 78
  10. Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, and Gifford DK (2003) Computational discovery of gene modules and regulatory networks. Nat biotechnol 21: 1337-1342 https://doi.org/10.1038/nbt890
  11. Bard JB and Rhee SY (2004) Ontologies in biology: design, applications and future challenges. Nat Rev Genet 5: 213-222 https://doi.org/10.1038/nrg1295
  12. Blake JA and Bult CJ (2006) Beyond the data deluge: data integration and bio-ontologies. J Biomed Inform 39: 314-320 https://doi.org/10.1016/j.jbi.2006.01.003
  13. Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, de Lichtervelde L, Mul JD, van de Peut D, Devos M, et al. (2008) A protein domain-based interactome network for C. elegans early embryogenesis. Cell 134: 534-545 https://doi.org/10.1016/j.cell.2008.07.009
  14. Bray D (2001) Reasoning for results. Nature 412: 863 https://doi.org/10.1038/35091132
  15. Brosh R, Shalgi R, Liran A, Landan G, Korotayev K, Nguyen GH, Enerly E, Johnsen H, Buganim Y, Solomon H, et al. (2008) p53-repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation. Mol syst biol 4: 229
  16. Busch H, Camacho-Trullio D, Rogon Z, Breuhahn K, Angel P, Eils R, and Szabowski A (2008) Gene network dynamics controlling keratinocyte migration. Mol syst biol 4: 199
  17. Cerami EG, Bader GD, Gross BE, and Sander C (2006) cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics 7: 497 https://doi.org/10.1186/1471-2105-7-497
  18. Chechik G, Oh E, Rando O, Weissman J, Regev A, and Koller D (2008) Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Nat biotechnol 26: 1251-1259 https://doi.org/10.1038/nbt.1499
  19. Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D, Winkler J, Lockhart DJ, Morris MS, and Fodor SP (1996) Accessing genetic information with high-density DNA arrays. Science 274: 610-614 https://doi.org/10.1126/science.274.5287.610
  20. Choi C, R Munch et al. (2007) SYSTOMONAS-an integrated database for systems biology analysis of Pseudomonas Nucleic Acids Res 35: D533-7 https://doi.org/10.1093/nar/gkl823
  21. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2: 2366-2382 https://doi.org/10.1038/nprot.2007.324
  22. Cox B, Kislinger T, and Emili A (2005) Integrating gene and protein expression data: pattern analysis and profile mining. Methods 35: 303-314 https://doi.org/10.1016/j.ymeth.2004.08.021
  23. De Keersmaecker SC, Thijs IM, Vanderleyden J, and Marchal K (2006) Integration of omics data: how well does it work for bacteria? Mol Microbiol 62: 1239-1250 https://doi.org/10.1111/j.1365-2958.2006.05453.x
  24. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, and Palsson BO (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 104: 1777-1782
  25. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, et al. (2008) Ensembl 2008. Nucleic Acids Res 36: D707-714 https://doi.org/10.1093/nar/gkm988
  26. Funahashi A, Jouraku A, Matsuoka Y, and Kitano H (2007) Integration of CellDesigner and SABIO-RK. In silico biol 7: S81-90
  27. Gray JJ (2006) High-resolution protein-protein docking. Curr Opin Struct Biol. 16: 183-193 https://doi.org/10.1016/j.sbi.2006.03.003
  28. Guerrero C, Milenkovic T, Przulj N, Kaiser P, and Huang L (2008) Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis. Proc Natl Acad Sci USA. 105: 13333-13338
  29. Guerrero C, Tagwerker C, Kaiser P, and Huang L (2006) An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo crosslinked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol Cell Proteomics 5: 366-378 https://doi.org/10.1074/mcp.M500303-MCP200
  30. Hall DA, Ptacek J, and Snyder M (2007) Protein microarray technology. Mech Ageing Dev 128: 161-167 https://doi.org/10.1016/j.mad.2006.11.021
  31. Hardiman G (2004) Microarray platforms--comparisons and contrasts. Pharmacogenomics 5: 487-502 https://doi.org/10.1517/14622416.5.5.487
  32. Hartwell LH, Hopfield JJ, Leibler S, and Murray AW (1999) From molecular to modular cell biology. Nature 402: C47-52 https://doi.org/10.1038/46972
  33. Holden M, Deng S, Wojnowski L, and Kulle B (2008) GSEASNP: applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics 24: 2784-2785 https://doi.org/10.1093/bioinformatics/btn516
  34. Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF, and Bolouri H (2005a) A data integration methodology for systems biology. Proc Natl Acad Sci U S A 102: 17296-17301
  35. Hwang D, Smith JJ, Leslie DM, Weston AD, Rust AG, Ramsey S, de Atauri P, Siegel AF, Bolouri H, Aitchison JD, and Hood L (2005b) A data integration methodology for systems biology: experimental verification. Proc Natl Acad Sci U S A 102: 17302-17307
  36. Ideker T and D Lauffenburger (2003) Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol 21(6): 255-62 https://doi.org/10.1016/S0167-7799(03)00115-X
  37. Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, and Barkai N (2002) Revealing modular organization in the yeast transcriptional network. Nat Genet. 31: 370-377 https://doi.org/10.1038/ng941
  38. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, et al. (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316: 593-597 https://doi.org/10.1126/science.1132067
  39. Jaqaman K and Danuser G (2006) Linking data to models: data regression. Nat Rev Mol Cell Biol 7: 813-819 https://doi.org/10.1038/nrm2030
  40. Jeong H, Tombor B, Albert R, Oltvai ZN, and Barabasi AL (2000) The large-scale organization of metabolic networks. Nature 407: 651-654 https://doi.org/10.1038/35036627
  41. Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic acids res 33: D428-432 https://doi.org/10.1093/nar/gki072
  42. Joyce AR and Palsson BO (2006) The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 7: 198-210 https://doi.org/10.1038/nrm1857
  43. Kahlem P and Birney E (2007) ENFIN a network to enhance integrative systems biology. Ann N Y Acad Sci 1115: 23-31 https://doi.org/10.1196/annals.1407.016
  44. Kell DB (2004) Metabolomics and systems biology: making sense of the soup. Curr Opin Microbiol. 7: 296-307 https://doi.org/10.1016/j.mib.2004.04.012
  45. Kitano H (2002) Systems biology: a brief overview. Science 295: 1662-1664 https://doi.org/10.1126/science.1069492
  46. Kwon YK and Cho KH (2008) Coherent coupling of feedback loops: a design principle of cell signaling networks. Bioinformatics 24: 1926-1932 https://doi.org/10.1093/bioinformatics/btn337
  47. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804 https://doi.org/10.1126/science.1075090
  48. Legewie S, Herzel H, Westerhoff HV, and Bluthgen N (2008) Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol syst biol 4: 190
  49. Lenhard B, Wahlestedt C, and Wasserman WW (2003) GeneLynx mouse: integrated portal to the mouse genome. Genome Res 13: 1501-1504 https://doi.org/10.1101/gr.951403
  50. Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, et al. (2006) The RNA Ontology Consortium: an open invitation to the RNA community. RNA 12: 533-541 https://doi.org/10.1261/rna.2343206
  51. Lin R, Dai S, Irwin RD, Heinloth AN, Boorman GA, and Li L (2008) Gene set enrichment analysis for non-monotone association and multiple experimental categories. BMC Bioinformatics 9: 481 https://doi.org/10.1186/1471-2105-9-481
  52. Liu Y and Zhao H (2004) A computational approach for ordering signal transduction pathway components from genomics and proteomics Data. BMC Bioinformatics 5: 158 https://doi.org/10.1186/1471-2105-5-158
  53. Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan THW, Shah N, et al. (2008) InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 4
  54. Lu L, Arakaki AK, Lu H, Skolnick J (2003) Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. Genome Res. 13:1146-1154 https://doi.org/10.1101/gr.1145203
  55. Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O, and Goryanin I (2007) The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol 3: 135
  56. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, and Eisenberg D (1999) A combined algorithm for genome-wide prediction of protein function. Nature 402: 83-86 https://doi.org/10.1038/47048
  57. Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, and Baumeister W (2002) Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 298: 1209-1213 https://doi.org/10.1126/science.1076184
  58. Melo RC, Dvorak AM, and Weller PF (2008) Electron tomography and immunonanogold electron microscopy for investigating intracellular trafficking and secretion in human eosinophils. J Cell Mol Med 12: 1416-1419 https://doi.org/10.1111/j.1582-4934.2008.00346.x
  59. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, and Alon U (2002) Network motifs: simple building blocks of complex networks. Science 298: 824-827 https://doi.org/10.1126/science.298.5594.824
  60. Muller SA, Aebi U, and Engel A (2008) What transmission electron microscopes can visualize now and in the future. J Struct Biol 163: 235-245 https://doi.org/10.1016/j.jsb.2008.05.008
  61. Murray DB, Beckmann M, and Kitano H (2007) Regulation of yeast oscillatory dynamics. Proc Natl Acad Sci USA 104: 2241-2246
  62. Neduva V, Linding R, Su-Angrand I, Stark A, de Masi F, Gibson TJ, Lewis J, Serrano L, and Russell RB (2005) Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS biology 3: e405 https://doi.org/10.1371/journal.pbio.0030405
  63. Nickell S, Kofler C, Leis AP, and Baumeister W (2006) A visual approach to proteomics. Nat Rev Mol Cell Biol 7: 225-230 https://doi.org/10.1038/nrm1861
  64. Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, et al. (2004) MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic acids res 32: D217-222 https://doi.org/10.1093/nar/gkh095
  65. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, and Barabasi AL (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555 https://doi.org/10.1126/science.1073374
  66. Rousseau F and Schymkowitz J (2005) A systems biology perspective on protein structural dynamics and signal transduction. Curr Opin Struct Biol 15: 23-30 https://doi.org/10.1016/j.sbi.2005.01.007
  67. Rubin DL, Shah NH, and Noy NF (2008) Biomedical ontologies: a functional perspective. Brief Bioinform 9: 75-90
  68. Safran M, Solomon I, Shmueli O, Lapidot M, Shen-Orr S, Adato A, Ben-Dor U, Esterman N, Rosen N, Peter I, et al. (2002) GeneCards 2002: towards a complete, object-oriented, human gene compendium. Bioinformatics 18: 1542-1543 https://doi.org/10.1093/bioinformatics/18.11.1542
  69. Sali A, Glaeser R, Earnest T, and Baumeister W (2003) From words to literature in structural proteomics. Nature 422: 216-225 https://doi.org/10.1038/nature01513
  70. Sauer U, Heinemann M, and Zamboni N (2007) Genetics. Getting closer to the whole picture. Science 316: 550-551 https://doi.org/10.1126/science.1142502
  71. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, et al. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res
  72. Schena M, Shalon D, Davis RW, and Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470 https://doi.org/10.1126/science.270.5235.467
  73. Shah AR, Singhal M, Klicker KR, Stephan EG, Wiley HS, and Waters KM (2007) Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager. Bioinformatics 23: 906-909 https://doi.org/10.1093/bioinformatics/btm031
  74. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, et al. (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24: 1151-1161 https://doi.org/10.1038/nbt1239
  75. Shreenivasaiah PK, Rho SH, Kim T, and Kim DH (2008) An overview of cardiac systems biology. J Mol Cell Cardiol 44: 460-469 https://doi.org/10.1016/j.yjmcc.2007.12.005
  76. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25: 1251-1255 https://doi.org/10.1038/nbt1346
  77. Sprinzak E and Margalit H (2001) Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 311: 681-692 https://doi.org/10.1006/jmbi.2001.4920
  78. Stein LD (2003) Integrating biological databases. Nat Rev Genet 4: 337-345
  79. Stemke-Hale K, Gonzalez-Angulo AM, Lluch A, Neve RM, Kuo WL, Davies M, Carey M, Hu Z, Guan Y, Sahin A, et al. (2008) An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer. Cancer Res 68: 6084-6091 https://doi.org/10.1158/0008-5472.CAN-07-6854
  80. Sugawara H, Ogasawara O, Okubo K, Gojobori T, and Tateno Y (2008) DDBJ with new system and face. Nucleic Acids Res 36: D22-24 https://doi.org/10.1093/nar/gkm848
  81. 't Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, and den Dunnen JT (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 36: e141 https://doi.org/10.1093/nar/gkn705
  82. Templin MF, Stoll D, Schwenk JM, Potz O, Kramer S, and Joos TO (2003) Protein microarrays: promising tools for proteomic research. Proteomics 3: 2155-2166 https://doi.org/10.1002/pmic.200300600
  83. Toyoda T, Mochizuki Y, Player K, Heida N, Kobayashi N, and Sakaki Y (2007) OmicBrowse: a browser of multidimensional omics annotations. Bioinformatics 23: 524-526 https://doi.org/10.1093/bioinformatics/btl523
  84. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627 https://doi.org/10.1038/35001009
  85. Van Dien S and Schilling CH (2006) Bringing metabolomics data into the forefront of systems biology. Mol Syst Biol 2: 2006 0035
  86. Wang E (Edwin Wang) MicroRNA systems biology. RNA Technologies in Cardiovascular Medicine and Research, Springer-Verlag: 69-80
  87. Waters KM, Pounds JG, and Thrall BD (2006) Data merging for integrated microarray and proteomic analysis. Brief Funct Genomic Proteomic 5: 261-272 https://doi.org/10.1093/bfgp/ell019
  88. Wright J and Wagner A (2008) The Systems Biology Research Tool: evolvable open-source software. BMC Syst Biol 2: 55 https://doi.org/10.1186/1752-0509-2-55
  89. Wu X, Jiang R, Zhang MQ, and Li S (2008) Network-based global inference of human disease genes. Mol Syst Biol 4: 189
  90. Xia T and Dickerson JA (2008) OmicsViz: Cytoscape plug-in for visualizing omics data across species. Bioinformatics 24: 2557-2558 https://doi.org/10.1093/bioinformatics/btn473
  91. Yang K, Bai H, Ouyang Q, Lai L, and Tang C (2008) Finding multiple target optimal intervention in disease-related molecular network. Mol Syst Biol 4: 228
  92. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322: 104-110 https://doi.org/10.1126/science.1158684
  93. Zhang W, Zhang Y, Zheng H, Zhang C, Xiong W, Olyarchuk JG, Walker M, Xu W, Zhao M, Zhao S, et al. (2007) SynDB: a Synapse protein DataBase based on synapse ontology. Nucleic Acids Res 35: D737-741 https://doi.org/10.1093/nar/gkl876