메뉴 건너뛰기




Volumn 30, Issue 4, 2014, Pages 339-346

Systems biology in inflammatory bowel diseases: Ready for prime time

Author keywords

Data integration; High throughput analysis; Inflammatory bowel disease; Network; Systems biology

Indexed keywords

DNA; PROTEOME; TRANSCRIPTOME;

EID: 84902280684     PISSN: 02671379     EISSN: 15317056     Source Type: Journal    
DOI: 10.1097/MOG.0000000000000081     Document Type: Review
Times cited : (33)

References (91)
  • 1
    • 84862298345 scopus 로고    scopus 로고
    • IBD: Advances in pathogenesis, complications, diagnosis and therapy
    • Fiocchi C. IBD: Advances in pathogenesis, complications, diagnosis and therapy. Curr Opin Gastroenterol 2012; 28:297-300.
    • (2012) Curr Opin Gastroenterol , vol.28 , pp. 297-300
    • Fiocchi, C.1
  • 2
    • 84883412154 scopus 로고    scopus 로고
    • Recent progress on the role of gut microbiota in the pathogenesis of inflammatory bowel disease
    • Yu CG, Huang Q. Recent progress on the role of gut microbiota in the pathogenesis of inflammatory bowel disease. J Dig Dis 2013; 14:513-517.
    • (2013) J Dig Dis , vol.14 , pp. 513-517
    • Yu, C.G.1    Huang, Q.2
  • 3
    • 84881488406 scopus 로고    scopus 로고
    • Colitis, microbiota, and colon cancer: An infernal triangle
    • Vetrano S, Danese S. Colitis, microbiota, and colon cancer: An infernal triangle. Gastroenterology 2013; 144:461-463.
    • (2013) Gastroenterology , vol.144 , pp. 461-463
    • Vetrano, S.1    Danese, S.2
  • 4
    • 84866549438 scopus 로고    scopus 로고
    • Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
    • Morgan XC, Tickle TL, Sokol H, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 2012; 13:R79.
    • (2012) Genome Biol , vol.13
    • Morgan, X.C.1    Tickle, T.L.2    Sokol, H.3
  • 5
    • 84868336049 scopus 로고    scopus 로고
    • Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease
    • Jostins L, Ripke S, Weersma RK, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012; 491:119-124.
    • (2012) Nature , vol.491 , pp. 119-124
    • Jostins, L.1    Ripke, S.2    Weersma, R.K.3
  • 6
    • 79958261646 scopus 로고    scopus 로고
    • What are innate and acquired immunity, and why are they important in IBD
    • Blumberg R. What are innate and acquired immunity, and why are they important in IBD? Inflamm Bowel Dis 2008; 14 (Suppl 2):S93-S94.
    • (2008) Inflamm Bowel Dis , vol.14 , Issue.SUPPL. 2
    • Blumberg, R.1
  • 8
    • 84885658881 scopus 로고    scopus 로고
    • Recent advances in inflammatory bowel disease: Mucosal immune cells in intestinal inflammation
    • Cader MZ, Kaser A. Recent advances in inflammatory bowel disease: mucosal immune cells in intestinal inflammation. Gut 2013; 62:1653-1664.
    • (2013) Gut , vol.62 , pp. 1653-1664
    • Cader, M.Z.1    Kaser, A.2
  • 9
    • 84886094366 scopus 로고    scopus 로고
    • Advances in therapeutic interventions targeting the vascular and lymphatic endothelium in inflammatory bowel disease
    • D'Alessio S, Tacconi C, Fiocchi C, et al. Advances in therapeutic interventions targeting the vascular and lymphatic endothelium in inflammatory bowel disease. Curr Opin Gastroenterol 2013; 29:608-613.
    • (2013) Curr Opin Gastroenterol , vol.29 , pp. 608-613
    • D'alessio, S.1    Tacconi, C.2    Fiocchi, C.3
  • 10
    • 80054976356 scopus 로고    scopus 로고
    • Inflammation-induced endothelial-tomesenchymal transition: A novel mechanism of intestinal fibrosis
    • Rieder F, Kessler SP, West GA, et al. Inflammation-induced endothelial-tomesenchymal transition: A novel mechanism of intestinal fibrosis. Am J Pathol 2011; 179:2660-2673.
    • (2011) Am J Pathol , vol.179 , pp. 2660-2673
    • Rieder, F.1    Kessler, S.P.2    West, G.A.3
  • 11
    • 79956202699 scopus 로고    scopus 로고
    • Occludin S408 phosphorylation regulates tight junction protein interactions and barrier function
    • Raleigh DR, Boe DM, Yu D, et al. Occludin S408 phosphorylation regulates tight junction protein interactions and barrier function. J Cell Biol 2011; 193:565-582.
    • (2011) J Cell Biol , vol.193 , pp. 565-582
    • Raleigh, D.R.1    Boe, D.M.2    Yu, D.3
  • 12
    • 84867505323 scopus 로고    scopus 로고
    • Mechanism of interleukin-1beta inducedincrease in mouse intestinal permeability in vivo
    • Al-Sadi R, Guo S, Dokladny K, et al. Mechanism of interleukin-1beta inducedincrease in mouse intestinal permeability in vivo. J Interferon Cytokine Res 2012; 32:474-484.
    • (2012) J Interferon Cytokine Res , vol.32 , pp. 474-484
    • Al-Sadi, R.1    Guo, S.2    Dokladny, K.3
  • 13
    • 80053581738 scopus 로고    scopus 로고
    • MicroRNA regulation of intestinal epithelial tight junction permeability
    • Ye D, Guo S, Al-Sadi R, et al. MicroRNA regulation of intestinal epithelial tight junction permeability. Gastroenterology 2011; 141:1323-1333.
    • (2011) Gastroenterology , vol.141 , pp. 1323-1333
    • Ye, D.1    Guo, S.2    Al-Sadi, R.3
  • 14
    • 84895475003 scopus 로고    scopus 로고
    • Analytical tools and databases for metagenomics in the next-generation sequencing era
    • Kim M, Lee KH, Yoon SW, et al. Analytical tools and databases for metagenomics in the next-generation sequencing era. Genomics Inform 2013; 11:102-113.
    • (2013) Genomics Inform , vol.11 , pp. 102-113
    • Kim, M.1    Lee, K.H.2    Yoon, S.W.3
  • 15
    • 84888884169 scopus 로고    scopus 로고
    • High throughput sequencing methods and analysis for microbiome research
    • Di Bella JM, Bao Y, GloorGB, et al. High throughput sequencing methods and analysis for microbiome research. J Microbiol Methods 2013; 95:401-414.
    • (2013) J Microbiol Methods , vol.95 , pp. 401-414
    • Di Bella, J.M.1    Bao, Y.2    Gloor, G.B.3
  • 16
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • Watts DJ, Strogatz SH. Collective dynamics of 'small-world' networks. Nature 1998; 393:440-442.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 17
    • 84884683078 scopus 로고    scopus 로고
    • Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis
    • Beaudoin M, Goyette P, Boucher G, et al. Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis. PLoS Genet 2013; 9:e1003723.
    • (2013) PLoS Genet , vol.9
    • Beaudoin, M.1    Goyette, P.2    Boucher, G.3
  • 18
    • 84863963644 scopus 로고    scopus 로고
    • Towards a 'cure' for IBD
    • Fiocchi C. Towards a 'cure' for IBD. Dig Dis 2012; 30:428-433.
    • (2012) Dig Dis , vol.30 , pp. 428-433
    • Fiocchi, C.1
  • 19
    • 84880595486 scopus 로고    scopus 로고
    • Beyond gene discovery in inflammatory bowel disease: The emerging role of epigenetics
    • Ventham NT, Kennedy NA, Nimmo ER, et al. Beyond gene discovery in inflammatory bowel disease: The emerging role of epigenetics. Gastroenterology 2013; 145:293-308.
    • (2013) Gastroenterology , vol.145 , pp. 293-308
    • Ventham, N.T.1    Kennedy, N.A.2    Nimmo, E.R.3
  • 20
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Consortium EP, Bernstein BE, Birney E, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Consortium, E.P.1    Bernstein, B.E.2    Birney, E.3
  • 21
    • 77950298959 scopus 로고    scopus 로고
    • Genome-wide association identifies multiple ulcerative colitis susceptibility loci
    • McGovern DP,Gardet A, Torkvist L, et al. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet 2010; 42:332-337.
    • (2010) Nat Genet , vol.42 , pp. 332-337
    • McGovern Dpgardet, A.1    Torkvist, L.2
  • 22
    • 84878829383 scopus 로고    scopus 로고
    • Large sample size, wide variant spectrum, and advanced machine-learning technique boost risk prediction for inflammatory bowel disease
    • Wei Z, Wang W, Bradfield J, et al. Large sample size, wide variant spectrum, and advanced machine-learning technique boost risk prediction for inflammatory bowel disease. Am J Hum Genet 2013; 92:1008-1012.
    • (2013) Am J Hum Genet , vol.92 , pp. 1008-1012
    • Wei, Z.1    Wang, W.2    Bradfield, J.3
  • 23
    • 84871005700 scopus 로고    scopus 로고
    • Promises, delivery, and challenges of inflammatory bowel disease risk gene discovery
    • Brant SR. Promises, delivery, and challenges of inflammatory bowel disease risk gene discovery. Clin Gastroenterol Hepatol 2013; 11:22-26.
    • (2013) Clin Gastroenterol Hepatol , vol.11 , pp. 22-26
    • Brant, S.R.1
  • 24
    • 84880617946 scopus 로고    scopus 로고
    • Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
    • Ellinghaus D, Zhang H, Zeissig S, et al. Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies. Gastroenterology 2013; 145:339-347.
    • (2013) Gastroenterology , vol.145 , pp. 339-347
    • Ellinghaus, D.1    Zhang, H.2    Zeissig, S.3
  • 25
    • 84878764878 scopus 로고    scopus 로고
    • Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes
    • Christodoulou K, Wiskin AE, Gibson J, et al. Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes. Gut 2013; 62:977-984.
    • (2013) Gut , vol.62 , pp. 977-984
    • Christodoulou, K.1    Wiskin, A.E.2    Gibson, J.3
  • 26
    • 79958769268 scopus 로고    scopus 로고
    • Epigenetic aberrations during oncogenesis
    • Hatziapostolou M, Iliopoulos D. Epigenetic aberrations during oncogenesis. Cell Mol Life Sci 2011; 68:1681-1702.
    • (2011) Cell Mol Life Sci , vol.68 , pp. 1681-1702
    • Hatziapostolou, M.1    Iliopoulos, D.2
  • 27
    • 84859795659 scopus 로고    scopus 로고
    • Genome-wide methylation profiling in Crohn's disease identifies altered epigenetic regulation of key host defense mechanisms including the Th17 pathway
    • Nimmo ER, Prendergast JG, Aldhous MC, et al. Genome-wide methylation profiling in Crohn's disease identifies altered epigenetic regulation of key host defense mechanisms including the Th17 pathway. Inflamm Bowel Dis 2012; 18:889-899.
    • (2012) Inflamm Bowel Dis , vol.18 , pp. 889-899
    • Nimmo, E.R.1    Prendergast, J.G.2    Aldhous, M.C.3
  • 28
    • 84869216522 scopus 로고    scopus 로고
    • Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases
    • Harris RA, Nagy-Szakal D, Pedersen N, et al. Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases. Inflamm Bowel Dis 2012; 18:2334-2341.
    • (2012) Inflamm Bowel Dis , vol.18 , pp. 2334-2341
    • Harris, R.A.1    Nagy-Szakal, D.2    Pedersen, N.3
  • 29
    • 84866849405 scopus 로고    scopus 로고
    • A functional methylome map of ulcerative colitis
    • Hasler R, Feng Z, Backdahl L, et al. A functional methylome map of ulcerative colitis. Genome Res 2012; 22:2130-2137.
    • (2012) Genome Res , vol.22 , pp. 2130-2137
    • Hasler, R.1    Feng, Z.2    Backdahl, L.3
  • 30
    • 79952788617 scopus 로고    scopus 로고
    • Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
    • Gu H, Smith ZD, Bock C, et al. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 2011; 6:468-481.
    • (2011) Nat Protoc , vol.6 , pp. 468-481
    • Gu, H.1    Smith, Z.D.2    Bock, C.3
  • 31
    • 84879102821 scopus 로고    scopus 로고
    • Cytokine-induced chromatin modifications of the type i collagen alpha 2 gene during intestinal endothelial-to-mesenchymal transition
    • Sadler T, Scarpa M, Rieder F, et al. Cytokine-induced chromatin modifications of the type I collagen alpha 2 gene during intestinal endothelial-to-mesenchymal transition. Inflamm Bowel Dis 2013; 19:1354-1364.
    • (2013) Inflamm Bowel Dis , vol.19 , pp. 1354-1364
    • Sadler, T.1    Scarpa, M.2    Rieder, F.3
  • 32
    • 84878753756 scopus 로고    scopus 로고
    • Transcriptional analysis of the intestinal mucosa of patients with ulcerative colitis in remission reveals lasting epithelial cell alterations
    • Planell N, Lozano JJ, Mora-Buch R, et al. Transcriptional analysis of the intestinal mucosa of patients with ulcerative colitis in remission reveals lasting epithelial cell alterations. Gut 2013; 62:967-976.
    • (2013) Gut , vol.62 , pp. 967-976
    • Planell, N.1    Lozano, J.J.2    Mora-Buch, R.3
  • 33
    • 40449100030 scopus 로고    scopus 로고
    • Direct multiplexed measurement of gene expression with color-coded probe pairs
    • Geiss GK, Bumgarner RE, Birditt B, et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 2008; 26:317-325.
    • (2008) Nat Biotechnol , vol.26 , pp. 317-325
    • Geiss, G.K.1    Bumgarner, R.E.2    Birditt, B.3
  • 34
    • 55249119513 scopus 로고    scopus 로고
    • MicroRNAs are differentially expressed in ulcerative colitis and alter expression of macrophage inflammatory peptide-2 alpha
    • e24
    • Wu F, Zikusoka M, Trindade A, et al. MicroRNAs are differentially expressed in ulcerative colitis and alter expression of macrophage inflammatory peptide-2 alpha. Gastroenterology 2008; 135:1624-1635; e24.
    • (2008) Gastroenterology , vol.135 , pp. 1624-1635
    • Wu, F.1    Zikusoka, M.2    Trindade, A.3
  • 35
    • 84884373262 scopus 로고    scopus 로고
    • MicroRNA-124 regulates STAT3 expression and is down-regulated in colon tissues of pediatric patients with ulcerative colitis
    • e2
    • Koukos G, Polytarchou C, Kaplan JL, et al. MicroRNA-124 regulates STAT3 expression and is down-regulated in colon tissues of pediatric patients with ulcerative colitis. Gastroenterology 2013; 145:842-852; e2.
    • (2013) Gastroenterology , vol.145 , pp. 842-852
    • Koukos, G.1    Polytarchou, C.2    Kaplan, J.L.3
  • 36
    • 77951579490 scopus 로고    scopus 로고
    • Increased expression of microRNA in the inflamed colonic mucosa of patients with active ulcerative colitis
    • Takagi T, Naito Y, Mizushima K, et al. Increased expression of microRNA in the inflamed colonic mucosa of patients with active ulcerative colitis. J Gastroenterol Hepatol 2010; 25 (Suppl 1):S129-S133.
    • (2010) J Gastroenterol Hepatol , vol.25 , Issue.SUPPL. 1
    • Takagi, T.1    Naito, Y.2    Mizushima, K.3
  • 37
    • 78649231641 scopus 로고    scopus 로고
    • Identification of microRNAs associated with ileal and colonic Crohn's disease
    • Wu F, Zhang S, Dassopoulos T, et al. Identification of microRNAs associated with ileal and colonic Crohn's disease. Inflamm Bowel Dis 2010; 16:1729-1738.
    • (2010) Inflamm Bowel Dis , vol.16 , pp. 1729-1738
    • Wu, F.1    Zhang, S.2    Dassopoulos, T.3
  • 38
    • 84882613920 scopus 로고    scopus 로고
    • Translational utility of next-generation sequencing
    • Ong FS, Lin JC, Das K, et al. Translational utility of next-generation sequencing. Genomics 2013; 102:137-139.
    • (2013) Genomics , vol.102 , pp. 137-139
    • Ong, F.S.1    Lin, J.C.2    Das, K.3
  • 39
    • 0037434980 scopus 로고    scopus 로고
    • From genomics to proteomics
    • Tyers M, Mann M. From genomics to proteomics. Nature 2003; 422:193-197.
    • (2003) Nature , vol.422 , pp. 193-197
    • Tyers, M.1    Mann, M.2
  • 40
    • 78650130580 scopus 로고    scopus 로고
    • Protein-protein interactions: Interactome under construction
    • Bonetta L. Protein-protein interactions: interactome under construction. Nature 2010; 468:851-854.
    • (2010) Nature , vol.468 , pp. 851-854
    • Bonetta, L.1
  • 41
    • 67650189497 scopus 로고    scopus 로고
    • Applications of proteomics in the study of inflammatory bowel diseases: Current status and future directions with available technologies
    • Alex P, Gucek M, Li X. Applications of proteomics in the study of inflammatory bowel diseases: current status and future directions with available technologies. Inflamm Bowel Dis 2009; 15:616-629.
    • (2009) Inflamm Bowel Dis , vol.15 , pp. 616-629
    • Alex, P.1    Gucek, M.2    Li, X.3
  • 42
    • 0036244045 scopus 로고    scopus 로고
    • Proteomic analysis of cytokine induced proteins in human intestinal epithelial cells: Implications for inflammatory bowel diseases
    • Barcelo-Batllori S, Andre M, Servis C, et al. Proteomic analysis of cytokine induced proteins in human intestinal epithelial cells: implications for inflammatory bowel diseases. Proteomics 2002; 2:551-560.
    • (2002) Proteomics , vol.2 , pp. 551-560
    • Barcelo-Batllori, S.1    Andre, M.2    Servis, C.3
  • 43
    • 2442542310 scopus 로고    scopus 로고
    • Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli
    • Hardwidge PR, Rodriguez-Escudero I, Goode D, et al. Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli. J Biol Chem 2004; 279:20127-20136.
    • (2004) J Biol Chem , vol.279 , pp. 20127-20136
    • Hardwidge, P.R.1    Rodriguez-Escudero, I.2    Goode, D.3
  • 44
    • 33644871640 scopus 로고    scopus 로고
    • Analysis of NOD2-mediated proteome response to muramyl dipeptide in HEK293 cells
    • Weichart D, Gobom J, Klopfleisch S, et al. Analysis of NOD2-mediated proteome response to muramyl dipeptide in HEK293 cells. J Biol Chem 2006; 281:2380-2389.
    • (2006) J Biol Chem , vol.281 , pp. 2380-2389
    • Weichart, D.1    Gobom, J.2    Klopfleisch, S.3
  • 45
    • 33947603233 scopus 로고    scopus 로고
    • Differential protein expression profile in the intestinal epithelium from patients with inflammatory bowel disease
    • Shkoda A, Werner T, Daniel H, et al. Differential protein expression profile in the intestinal epithelium from patients with inflammatory bowel disease. J Proteome Res 2007; 6:1114-1125.
    • (2007) J Proteome Res , vol.6 , pp. 1114-1125
    • Shkoda, A.1    Werner, T.2    Daniel, H.3
  • 46
    • 79952480645 scopus 로고    scopus 로고
    • Proteomic profiling of mucosal and submucosal colonic tissues yields protein signatures that differentiate the inflammatory colitides
    • M'Koma AE, Seeley EH, Washington MK, et al. Proteomic profiling of mucosal and submucosal colonic tissues yields protein signatures that differentiate the inflammatory colitides. Inflamm Bowel Dis 2011; 17:875-883.
    • (2011) Inflamm Bowel Dis , vol.17 , pp. 875-883
    • M'koma, A.E.1    Seeley, E.H.2    Washington, M.K.3
  • 47
    • 33749638414 scopus 로고    scopus 로고
    • Comparative proteomic studies on the pathogenesis of human ulcerative colitis
    • Hsieh SY, Shih TC, Yeh CY, et al. Comparative proteomic studies on the pathogenesis of human ulcerative colitis. Proteomics 2006; 6:5322-5331.
    • (2006) Proteomics , vol.6 , pp. 5322-5331
    • Hsieh, S.Y.1    Shih, T.C.2    Yeh, C.Y.3
  • 48
    • 33947505382 scopus 로고    scopus 로고
    • Biomarker discovery for inflammatory bowel disease, using proteomic serum profiling
    • Meuwis MA, Fillet M, Geurts P, et al. Biomarker discovery for inflammatory bowel disease, using proteomic serum profiling. Biochem Pharmacol 2007; 73:1422-1433.
    • (2007) Biochem Pharmacol , vol.73 , pp. 1422-1433
    • Meuwis, M.A.1    Fillet, M.2    Geurts, P.3
  • 49
    • 47049105521 scopus 로고    scopus 로고
    • Proteomics for prediction and characterization of response to infliximab in Crohn's disease: A pilot study
    • Meuwis MA, Fillet M, Lutteri L, et al. Proteomics for prediction and characterization of response to infliximab in Crohn's disease: A pilot study. Clin Biochem 2008; 41:960-967.
    • (2008) Clin Biochem , vol.41 , pp. 960-967
    • Meuwis, M.A.1    Fillet, M.2    Lutteri, L.3
  • 50
    • 37649017918 scopus 로고    scopus 로고
    • Serum protein profiling in patients with inflammatory bowel diseases using selective solid-phase bulk extraction, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and chemometric data analysis
    • Nanni P, Parisi D, Roda G, et al. Serum protein profiling in patients with inflammatory bowel diseases using selective solid-phase bulk extraction, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and chemometric data analysis. Rapid Commun Mass Spectrom 2007; 21:4142-4148.
    • (2007) Rapid Commun Mass Spectrom , vol.21 , pp. 4142-4148
    • Nanni, P.1    Parisi, D.2    Roda, G.3
  • 51
    • 84856645840 scopus 로고    scopus 로고
    • Proteomic analysis of colon tissue from interleukin-10 gene-deficient mice fed polyunsaturated fatty acids with comparison to transcriptomic analysis
    • Cooney JM, Barnett MP, Brewster D, et al. Proteomic analysis of colon tissue from interleukin-10 gene-deficient mice fed polyunsaturated fatty acids with comparison to transcriptomic analysis. J Proteome Res 2012; 11:1065-1077.
    • (2012) J Proteome Res , vol.11 , pp. 1065-1077
    • Cooney, J.M.1    Barnett, M.P.2    Brewster, D.3
  • 52
    • 84858790233 scopus 로고    scopus 로고
    • Innovation: Metabolomics: The apogee of the omics trilogy
    • Patti GJ, Yanes O, Siuzdak G. Innovation: metabolomics: The apogee of the omics trilogy. Nat Rev Mol Cell Biol 2012; 13:263-269.
    • (2012) Nat Rev Mol Cell Biol , vol.13 , pp. 263-269
    • Patti, G.J.1    Yanes, O.2    Siuzdak, G.3
  • 53
    • 84858386087 scopus 로고    scopus 로고
    • Biomarkers in inflammatory bowel disease: Current practices and recent advances
    • Iskandar HN, Ciorba MA. Biomarkers in inflammatory bowel disease: current practices and recent advances. Transl Res 2012; 159:313-325.
    • (2012) Transl Res , vol.159 , pp. 313-325
    • Iskandar, H.N.1    Ciorba, M.A.2
  • 55
    • 33847378014 scopus 로고    scopus 로고
    • Rapid and noninvasive metabonomic characterization of inflammatory bowel disease
    • Marchesi JR, Holmes E, Khan F, et al. Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 2007; 6:546-551.
    • (2007) J Proteome Res , vol.6 , pp. 546-551
    • Marchesi, J.R.1    Holmes, E.2    Khan, F.3
  • 56
    • 80052481927 scopus 로고    scopus 로고
    • Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome
    • Le Gall G, Noor SO, Ridgway K, et al. Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome. J Proteome Res 2011; 10:4208-4218.
    • (2011) J Proteome Res , vol.10 , pp. 4208-4218
    • Le Gall, G.1    Noor, S.O.2    Ridgway, K.3
  • 57
    • 84876477982 scopus 로고    scopus 로고
    • 1H NMR-based spectroscopy detects metabolic alterations in serum of patients with early-stage ulcerative colitis
    • Zhang Y, Lin L, Xu Y, et al. 1H NMR-based spectroscopy detects metabolic alterations in serum of patients with early-stage ulcerative colitis. Biochem Biophys Res Commun 2013; 433:547-551.
    • (2013) Biochem Biophys Res Commun , vol.433 , pp. 547-551
    • Zhang, Y.1    Lin, L.2    Xu, Y.3
  • 58
    • 84872457485 scopus 로고    scopus 로고
    • Urinary NMR metabolomic profiles discriminate inflammatory bowel disease from healthy
    • Stephens NS, Siffledeen J, Su X, et al. Urinary NMR metabolomic profiles discriminate inflammatory bowel disease from healthy. J Crohns Colitis 2013; 7:e42-e48.
    • (2013) J Crohns Colitis , vol.7
    • Stephens, N.S.1    Siffledeen, J.2    Su, X.3
  • 59
    • 84861808541 scopus 로고    scopus 로고
    • Quantitative metabolomic profiling of serum, plasma, and urine by (1)H NMR spectroscopy discriminates between patients with inflammatory bowel disease and healthy individuals
    • Schicho R, Shaykhutdinov R, Ngo J, et al. Quantitative metabolomic profiling of serum, plasma, and urine by (1)H NMR spectroscopy discriminates between patients with inflammatory bowel disease and healthy individuals. J Proteome Res 2012; 11:3344-3357.
    • (2012) J Proteome Res , vol.11 , pp. 3344-3357
    • Schicho, R.1    Shaykhutdinov, R.2    Ngo, J.3
  • 60
    • 84856420259 scopus 로고    scopus 로고
    • Novel, objective, multivariate biomarkers composed of plasma amino acid profiles for the diagnosis and assessment of inflammatory bowel disease
    • Hisamatsu T, Okamoto S, Hashimoto M, et al. Novel, objective, multivariate biomarkers composed of plasma amino acid profiles for the diagnosis and assessment of inflammatory bowel disease. PLoS One 2012; 7:e31131.
    • (2012) PLoS One , vol.7
    • Hisamatsu, T.1    Okamoto, S.2    Hashimoto, M.3
  • 61
    • 80052062107 scopus 로고    scopus 로고
    • GC/MS-based profiling of amino acids and TCA cycle-related molecules in ulcerative colitis
    • Ooi M, Nishiumi S, Yoshie T, et al. GC/MS-based profiling of amino acids and TCA cycle-related molecules in ulcerative colitis. Inflamm Res 2011; 60:831-840.
    • (2011) Inflamm Res , vol.60 , pp. 831-840
    • Ooi, M.1    Nishiumi, S.2    Yoshie, T.3
  • 62
    • 46749119859 scopus 로고    scopus 로고
    • Molecular analysis of the gut microbiota of identical twins with Crohn's disease
    • Dicksved J, Halfvarson J, Rosenquist M, et al. Molecular analysis of the gut microbiota of identical twins with Crohn's disease. ISME J 2008; 2:716-727.
    • (2008) ISME J , vol.2 , pp. 716-727
    • Dicksved, J.1    Halfvarson, J.2    Rosenquist, M.3
  • 63
    • 82755181915 scopus 로고    scopus 로고
    • Metabolic phenotyping of the Crohn's disease-like IBD etiopathology in the TNF(DeltaARE/WT) mouse model
    • Baur P, Martin FP, Gruber L, et al. Metabolic phenotyping of the Crohn's disease-like IBD etiopathology in the TNF(DeltaARE/WT) mouse model. J Proteome Res 2011; 10:5523-5535.
    • (2011) J Proteome Res , vol.10 , pp. 5523-5535
    • Baur, P.1    Martin, F.P.2    Gruber, L.3
  • 64
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • Tavazoie S, Hughes JD, Campbell MJ, et al. Systematic determination of genetic network architecture. Nat Genet 1999; 22:281-285.
    • (1999) Nat Genet , vol.22 , pp. 281-285
    • Tavazoie, S.1    Hughes, J.D.2    Campbell, M.J.3
  • 65
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: Simple building blocks of complex networks
    • Milo R, Shen-Orr S, Itzkovitz S, et al. Network motifs: simple building blocks of complex networks. Science 2002; 298:824-827.
    • (2002) Science , vol.298 , pp. 824-827
    • Milo, R.1    Shen-Orr, S.2    Itzkovitz, S.3
  • 66
    • 34249079154 scopus 로고    scopus 로고
    • Network motifs: Theory and experimental approaches
    • Alon U. Network motifs: Theory and experimental approaches. Nat Rev Genet 2007; 8:450-461.
    • (2007) Nat Rev Genet , vol.8 , pp. 450-461
    • Alon, U.1
  • 67
    • 77950672269 scopus 로고    scopus 로고
    • Targeting multiple kinase pathways: A change in paradigm
    • Gossage L, Eisen T. Targeting multiple kinase pathways: A change in paradigm. Clin Cancer Res 2010; 16:1973-1978.
    • (2010) Clin Cancer Res , vol.16 , pp. 1973-1978
    • Gossage, L.1    Eisen, T.2
  • 68
    • 18744409361 scopus 로고    scopus 로고
    • Correlated random networks
    • Berg J, Lassig M. Correlated random networks. Phys Rev Lett 2002; 89:228701.
    • (2002) Phys Rev Lett , vol.89 , pp. 228701
    • Berg, J.1    Lassig, M.2
  • 69
    • 84891359051 scopus 로고    scopus 로고
    • BooleSim: An interactive Boolean network simulator
    • Bock M, Scharp T, Talnikar C, et al. BooleSim: An interactive Boolean network simulator. Bioinformatics 2014; 30:131-132.
    • (2014) Bioinformatics , vol.30 , pp. 131-132
    • Bock, M.1    Scharp, T.2    Talnikar, C.3
  • 70
    • 84882999414 scopus 로고    scopus 로고
    • The complex fluctuations of probabilistic Boolean networks
    • Gao YM, Xu P, Wang XH, et al. The complex fluctuations of probabilistic Boolean networks. Biosystems 2013; 114:78-84.
    • (2013) Biosystems , vol.114 , pp. 78-84
    • Gao, Y.M.1    Xu, P.2    Wang, X.H.3
  • 71
    • 84893308174 scopus 로고    scopus 로고
    • A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation
    • Liepe J, Kirk P, Filippi S, et al. A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation. Nat Protoc 2014; 9:439-456.
    • (2014) Nat Protoc , vol.9 , pp. 439-456
    • Liepe, J.1    Kirk, P.2    Filippi, S.3
  • 72
    • 84891907251 scopus 로고    scopus 로고
    • Mathematical modeling of primary succession of murine intestinal microbiota
    • Marino S, Baxter NT, Huffnagle GB, et al. Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci U S A 2014; 111:439-444.
    • (2014) Proc Natl Acad Sci U S A , vol.111 , pp. 439-444
    • Marino, S.1    Baxter, N.T.2    Huffnagle, G.B.3
  • 73
    • 84890083793 scopus 로고    scopus 로고
    • Parameter estimation of partial differential equation models
    • Xun X, Cao J, Mallick B, et al. Parameter estimation of partial differential equation models. J Am Stat Assoc 2013; 108:1009-1020.
    • (2013) J Am Stat Assoc , vol.108 , pp. 1009-1020
    • Xun, X.1    Cao, J.2    Mallick, B.3
  • 74
    • 84885332835 scopus 로고    scopus 로고
    • Jimena: Efficient computing and system state identification for genetic regulatory networks
    • Karl S, Dandekar T. Jimena: efficient computing and system state identification for genetic regulatory networks. BMC Bioinformatics 2013; 14:306.
    • (2013) BMC Bioinformatics , vol.14 , pp. 306
    • Karl, S.1    Dandekar, T.2
  • 75
    • 84860508659 scopus 로고    scopus 로고
    • Hub-centered gene network reconstruction using automatic relevance determination
    • Bock M, Ogishima S, Tanaka H, et al. Hub-centered gene network reconstruction using automatic relevance determination. PLoS One 2012; 7:e35077.
    • (2012) PLoS One , vol.7
    • Bock, M.1    Ogishima, S.2    Tanaka, H.3
  • 76
    • 61949441759 scopus 로고    scopus 로고
    • Advances in semantic representation for multiscale biosimulation: A case study in merging models
    • Neal ML, Gennari JH, Arts T, et al. Advances in semantic representation for multiscale biosimulation: A case study in merging models. Pac Symp Biocomput 2009; 14:304-315.
    • (2009) Pac Symp Biocomput , vol.14 , pp. 304-315
    • Neal, M.L.1    Gennari, J.H.2    Arts, T.3
  • 77
    • 83355177254 scopus 로고    scopus 로고
    • BioPAX support in CellDesigner
    • Mi H, Muruganujan A, Demir E, et al. BioPAX support in CellDesigner. Bioinformatics 2011; 27:3437-3438.
    • (2011) Bioinformatics , vol.27 , pp. 3437-3438
    • Mi, H.1    Muruganujan, A.2    Demir, E.3
  • 78
    • 0033031386 scopus 로고    scopus 로고
    • E-CELL: Software environment for whole-cell simulation
    • Tomita M, Hashimoto K, Takahashi K, et al. E-CELL: software environment for whole-cell simulation. Bioinformatics 1999; 15:72-84.
    • (1999) Bioinformatics , vol.15 , pp. 72-84
    • Tomita, M.1    Hashimoto, K.2    Takahashi, K.3
  • 79
    • 37849009181 scopus 로고    scopus 로고
    • Emerging applications of network and pathway analysis in drug discovery and development
    • Ganter B, Giroux CN. Emerging applications of network and pathway analysis in drug discovery and development. Curr Opin Drug Discov Devel 2008; 11:86-94.
    • (2008) Curr Opin Drug Discov Devel , vol.11 , pp. 86-94
    • Ganter, B.1    Giroux, C.N.2
  • 80
    • 65249149643 scopus 로고    scopus 로고
    • Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla
    • Mahowald MA, Rey FE, Seedorf H, et al. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A 2009; 106:5859-5864.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 5859-5864
    • Mahowald, M.A.1    Rey, F.E.2    Seedorf, H.3
  • 81
    • 79953748870 scopus 로고    scopus 로고
    • Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives
    • Joossens M, Huys G, Cnockaert M, et al. Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut 2011; 60:631-637.
    • (2011) Gut , vol.60 , pp. 631-637
    • Joossens, M.1    Huys, G.2    Cnockaert, M.3
  • 82
    • 80054078496 scopus 로고    scopus 로고
    • Analytical metabolomics: Nutritional opportunities for personalized health
    • McNiven EM, German JB, Slupsky CM. Analytical metabolomics: nutritional opportunities for personalized health. J Nutr Biochem 2011; 22:995-1002.
    • (2011) J Nutr Biochem , vol.22 , pp. 995-1002
    • McNiven, E.M.1    German, J.B.2    Slupsky, C.M.3
  • 83
    • 84873853757 scopus 로고    scopus 로고
    • Host genotype, intestinal microbiota and inflammatory disorders
    • Olivares M, Laparra JM, Sanz Y. Host genotype, intestinal microbiota and inflammatory disorders. Br J Nutr 2013; 109 (Suppl 2):S76-S80.
    • (2013) Br J Nutr , vol.109 , Issue.SUPPL. 2
    • Olivares, M.1    Laparra, J.M.2    Sanz, Y.3
  • 84
    • 81455145738 scopus 로고    scopus 로고
    • Host-microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosalluminal interface
    • Presley LL, Ye J, Li X, et al. Host-microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosalluminal interface. Inflamm Bowel Dis 2012; 18:409-417.
    • (2012) Inflamm Bowel Dis , vol.18 , pp. 409-417
    • Presley, L.L.1    Ye, J.2    Li, X.3
  • 85
    • 84893686882 scopus 로고    scopus 로고
    • Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships
    • McHardy IH, Goudarzi M, Tong M, et al. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome 2013; 1:17.
    • (2013) Microbiome , vol.1 , pp. 17
    • McHardy, I.H.1    Goudarzi, M.2    Tong, M.3
  • 86
    • 58649111743 scopus 로고    scopus 로고
    • VEGF-A links angiogenesis and inflammation in inflammatory bowel disease pathogenesis
    • Scaldaferri F, Vetrano S, Sans M, et al. VEGF-A links angiogenesis and inflammation in inflammatory bowel disease pathogenesis. Gastroenterology 2009; 136:585-595; e5.
    • (2009) Gastroenterology , vol.136 , pp. 585-595
    • Scaldaferri, F.1    Vetrano, S.2    Sans, M.3
  • 87
    • 84884609221 scopus 로고    scopus 로고
    • Blockade of VEGF receptor-3 aggravates inflammatory bowel disease and lymphatic vessel enlargement
    • Jurisic G, Sundberg JP, Detmar M. Blockade of VEGF receptor-3 aggravates inflammatory bowel disease and lymphatic vessel enlargement. Inflamm Bowel Dis 2013; 19:1983-1989.
    • (2013) Inflamm Bowel Dis , vol.19 , pp. 1983-1989
    • Jurisic, G.1    Sundberg, J.P.2    Detmar, M.3
  • 88
    • 84888263186 scopus 로고    scopus 로고
    • TNF-alpha modulation of intestinal epithelial tight junction barrier is regulated by ERK1/2 activation of Elk-1
    • Al-Sadi R, Guo S, Ye D, et al. TNF-alpha modulation of intestinal epithelial tight junction barrier is regulated by ERK1/2 activation of Elk-1. Am J Pathol 2013; 183:1871-1884.
    • (2013) Am J Pathol , vol.183 , pp. 1871-1884
    • Al-Sadi, R.1    Guo, S.2    Ye, D.3
  • 89
    • 73949105149 scopus 로고    scopus 로고
    • Epithelial NF-kappaB enhances transmucosal fluid movement by altering tight junction protein composition after T cell activation
    • Tang Y, Clayburgh DR, Mittal N, et al. Epithelial NF-kappaB enhances transmucosal fluid movement by altering tight junction protein composition after T cell activation. Am J Pathol 2010; 176:158-167.
    • (2010) Am J Pathol , vol.176 , pp. 158-167
    • Tang, Y.1    Clayburgh, D.R.2    Mittal, N.3
  • 90
    • 70350509805 scopus 로고    scopus 로고
    • Intestinal mucosal barrier function in health and disease
    • Turner JR. Intestinal mucosal barrier function in health and disease. Nat Rev Immunol 2009; 9:799-809.
    • (2009) Nat Rev Immunol , vol.9 , pp. 799-809
    • Turner, J.R.1
  • 91
    • 33749335282 scopus 로고    scopus 로고
    • The connectivity map: Using geneexpression signatures to connect small molecules, genes and disease
    • Lamb J, Crawford ED, Peck D, et al. The connectivity map: using geneexpression signatures to connect small molecules, genes and disease. Science 2006; 29:1929-1935.
    • (2006) Science , vol.29 , pp. 1929-1935
    • Lamb, J.1    Crawford, E.D.2    Peck, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.