The IBD interactome: an integrated view of aetiology, pathogenesis and therapy
Abstract
Crohn's disease and ulcerative colitis are prototypical complex diseases characterized by chronic and heterogeneous manifestations, induced by interacting environmental, genomic, microbial and immunological factors. These interactions result in an overwhelming complexity that cannot be tackled by studying the totality of each pathological component (an '-ome') in isolation without consideration of the interaction among all relevant -omes that yield an overall 'network effect'. The outcome of this effect is the 'IBD interactome', defined as a disease network in which dysregulation of individual -omes causes intestinal inflammation mediated by dysfunctional molecular modules. To define the IBD interactome, new concepts and tools are needed to implement a systems approach; an unbiased data-driven integration strategy that reveals key players of the system, pinpoints the central drivers of inflammation and enables development of targeted therapies. Powerful bioinformatics tools able to query and integrate multiple -omes are available, enabling the integration of genomic, epigenomic, transcriptomic, proteomic, metabolomic and microbiome information to build a comprehensive molecular map of IBD. This approach will enable identification of IBD molecular subtypes, correlations with clinical phenotypes and elucidation of the central hubs of the IBD interactome that will aid discovery of compounds that can specifically target the hubs that control the disease.
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IBD is considered an immune-mediated intestinal disorder resulting from complex interactions among genetics, environmental factors, and gut microbiota.
“IBD is considered to be an immune-mediated intestinal disorder, resulting from complex interactions among genetics, environmental factors, and gut microbiota (9).”
From Stress triggers flare of inflammatory bowel disease in children and adults (2019) · cites this paper as [9]
Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · see citing works
Emergence of Scaling in Random Networks
Barabási, A.-L., & Albert, R. (1999) · Science · doi:10.1126/science.286.5439.509 · Cited by 36,135 · see citing works
Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · see citing works
Lamb, J., Crawford, E. D., Peck, D., Modell, J. W., Blat, I. C., Wrobel, M. J., Lerner, J., Brunet, J.-P., Subramanian, A., Ross, K. N., et al. (2006) · Science · doi:10.1126/science.1132939 · Cited by 5,257 · see citing works
A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease
Ogura, Y., Bonen, D. K., Inohara, N., Nicolae, D. L., Chen, F. F., Ramos, R., Britton, H., Moran, T., Karaliuskas, R., Duerr, R. H., et al. (2001) · Nature · doi:10.1038/35079114 · Cited by 5,030 · see citing works
Genomic classification and prognosis in acute myeloid leukemia
Papaemmanuil, E., Gerstung, M., Bullinger, L., Gaidzik, V. I., Paschka, P., Roberts, N. D., Potter, N. E., Heuser, M., Thol, F., Bolli, N., et al. (2016) · New England Journal of Medicine · doi:10.1056/nejmoa1516192 · Cited by 4,350 · see citing works
Maere, S., Heymans, K., & Kuiper, M. (2005) · Bioinform. · doi:10.1093/bioinformatics/bti551 · Cited by 4,251 · see citing works
Genomic analyses identify molecular subtypes of pancreatic cancer
Bailey, P., Chang, D. K., Nones, K., Johns, A. L., Patch, A.-M., Gingras, M.-C., Miller, D. K., Christ, A. N., Bruxner, T. J. C., Quinn, M. C., et al. (2016) · Nature · doi:10.1038/nature16965 · Cited by 3,621 · see citing works
Human Genetics Shape the Gut Microbiome
Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J. T., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.053 · Cited by 3,164 · see citing works
Cytokines in inflammatory bowel disease
Neurath, M. F. (2014) · Nature Reviews Immunology · doi:10.1038/nri3661 · Cited by 2,706 · see citing works
Metabolomics: the apogee of the omics trilogy
Patti, G. J., Yanes, Ó., & Siuzdak, G. E. (2012) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3314 · Cited by 2,605 · see citing works
Artificial sweeteners induce glucose intolerance by altering the gut microbiota
Suez, J., Korem, T., Zeevi, D., Zilberman-Schapira, G., Thaiss, C. A., Maza, O., Israeli, D., Zmora, N., Gilad, S., Weinberger, A., et al. (2014) · Nature · doi:10.1038/nature13793 · Cited by 2,067 · see citing works
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
Zhernakova, A., Kurilshikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., Mujagic, Z., Vila, A. V., Falony, G., Vieira-Silva, S., et al. (2016) · Science · doi:10.1126/science.aad3369 · Cited by 1,914 · see citing works
Machiels, K., Joossens, M., Sabino, J., De Preter, V., Arijs, I., Eeckhaut, V., Ballet, V., Claes, K., Van Immerseel, F., Verbeke, K., et al. (2014) · Gut · doi:10.1136/gutjnl-2013-304833 · Cited by 1,904 · see citing works
The NIH Roadmap Epigenomics Mapping Consortium
Bernstein, B. E., Stamatoyannopoulos, J. A., Costello, J. F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M. A., Beaudet, A. L., Ecker, J. R., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt1010-1045 · Cited by 1,892 · see citing works
The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead
Kostic, A. D., Xavier, R. J., & Gevers, D. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.02.009 · Cited by 1,789 · see citing works
A N <scp>EW</scp> A <scp>PPROACH TO</scp> D <scp>ECODING</scp> L <scp>IFE</scp> : Systems Biology
Ideker, T., Galitski, T., & Hood, L. (2001) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.2.1.343 · Cited by 1,664 · see citing works
Transcriptional Regulation and Its Misregulation in Disease
Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.014 · Cited by 1,588 · see citing works
Darfeuille-Michaud, A., Boudeau, J., Bulois, P., Neut, C., Glasser, A.-L., Barnich, N., Bringer, M.-A., Swidsinski, A., Beaugerie, L., & Colombel, J.-F. (2004) · Gastroenterology · doi:10.1053/j.gastro.2004.04.061 · Cited by 1,566 · see citing works
Immunopathogenesis of IBD: current state of the art
de Souza, H. S. P., & Fiocchi, C. (2016) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2015.186 · Cited by 1,551 · see citing works
Self-citationHueber, W., Sands, B. E., Lewitzky, S., Vandemeulebroecke, M., Reinisch, W., Higgins, P. D. R., Wehkamp, J., Feagan, B. G., Yao, M. D., Karczewski, M., et al. (2012) · Gut · doi:10.1136/gutjnl-2011-301668 · Cited by 1,547 · see citing works
Genomewide Association Studies and Assessment of the Risk of Disease
Manolio, T. A. (2010) · New England Journal of Medicine · doi:10.1056/nejmra0905980 · Cited by 1,512 · see citing works
A travel guide to Cytoscape plugins
Saito, R., Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P.-L., Lotia, S., Pico, A., Bader, G. D., & Ideker, T. (2012) · Nature Methods · doi:10.1038/nmeth.2212 · Cited by 1,511 · see citing works
Inflammatory Bowel Disease and Mutations Affecting the Interleukin-10 Receptor
Glocker, E., Kotlarz, D., Boztuǧ, K., Gertz, E. M., Schäffer, A. A., Noyan, F., Perro, M., Diestelhorst, J., Saborowski, A. L., Murugan, D., et al. (2009) · New England Journal of Medicine · doi:10.1056/nejmoa0907206 · Cited by 1,464 · see citing works
A network-based analysis of systemic inflammation in humans
Program, I. A. H. R. T. I. L. S. C. R., Calvano, S. E., Xiao, W., Richards, D. R., Felciano, R. M., Baker, H. V., Cho, R. J., Chen, R. O., Brownstein, B. H., Cobb, J. P., et al. (2005) · Nature · doi:10.1038/nature03985 · Cited by 1,429 · see citing works
Therapeutic genome editing: prospects and challenges
Cox, D. B. T., Platt, R. J., & Zhang, F. (2015) · Nature Medicine · doi:10.1038/nm.3793 · Cited by 1,336 · see citing works
Lupp, C., Robertson, M. L., Wickham, M. E., Sekirov, I., Champion, O. L., Gaynor, E. C., & Finlay, B. B. (2007) · Cell Host & Microbe · doi:10.1016/j.chom.2007.06.010 · Cited by 1,310 · see citing works
Circular RNAs: diversity of form and function
Lasda, E. L., & Parker, R. (2014) · RNA · doi:10.1261/rna.047126.114 · Cited by 1,193 · see citing works
Manichanh, C., Borruel, N., Casellas, F., & Guarner, F. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2012.152 · Cited by 1,160 · see citing works
Precision Medicine — Personalized, Problematic, and Promising
Jameson, J. L., & Longo, D. L. (2015) · New England Journal of Medicine · doi:10.1056/nejmsb1503104 · Cited by 1,115 · see citing works
Hirsch, H. A., Iliopoulos, D., Tsichlis, P. N., & Struhl, K. (2009) · Cancer Research · doi:10.1158/0008-5472.can-09-2994 · Cited by 1,115 · see citing works
Self-citationVariations in DNA elucidate molecular networks that cause disease
Chen, Y., Zhu, J., Lum, P. Y., Yang, X., Pinto, S., MacNeil, D. J., Zhang, C., Lamb, J., Edwards, S., Sieberts, S. K., et al. (2008) · Nature · doi:10.1038/nature06757 · Cited by 887 · see citing works
Non-linear dynamics for clinicians: chaos theory, fractals, and complexity at the bedside
Goldberger, A. L. (1996) · The Lancet · doi:10.1016/s0140-6736(96)90948-4 · Cited by 859 · see citing works
Shen, R., Olshen, A. B., & Ladanyi, M. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp543 · Cited by 849 · see citing works
The host shapes the gut microbiota via fecal microRNA
Liu, S., da Cunha, A. P., Rezende, R. M., Cialic, R., Wei, Z., Bry, L., Comstock, L. E., Gandhi, R., & Weiner, H. L. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2015.12.005 · Cited by 808 · see citing works
Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6
Zhang, Q., Zhao, K., Shen, Q., Han, Y., Gu, Y., Li, X., Zhao, D., Liu, Y., Wang, C., Zhang, X., et al. (2015) · Nature · doi:10.1038/nature15252 · Cited by 807 · see citing works
Imhann, F., Vich Vila, A., Bonder, M. J., Fu, J., Gevers, D., Visschedijk, M. C., Spekhorst, L. M., Alberts, R., Franke, L., van Dullemen, H. M., et al. (2018) · Gut · doi:10.1136/gutjnl-2016-312135 · Cited by 788 · see citing works
Vaske, C. J., Benz, S. C., Sanborn, J. Z., Earl, D., Szeto, C., Zhu, J., Haussler, D., & Stuart, J. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq182 · Cited by 786 · see citing works
Beyond GWASs: Illuminating the Dark Road from Association to Function
Edwards, S. L., Beesley, J., French, J. D., & Dunning, A. M. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.012 · Cited by 784 · see citing works
The International IBD Genetics Consortium (IIBDGC), Ellinghaus, D., International Genetics of Ankylosing Spondylitis Consortium (IGAS), International PSC Study Group (IPSCSG), Genetic Analysis of Psoriasis Consortium (GAPC), Psoriasis Association Genetics Extension (PAGE), Jostins, L., Spain, S. L., Cortes, A., Bethune, J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3528 · Cited by 751 · see citing works
Gu, H., Smith, Z. D., Bock, C., Boyle, P., Gnirke, A., & Meissner, A. (2011) · Nature Protocols · doi:10.1038/nprot.2010.190 · Cited by 750 · see citing works
Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients
Banchereau, R., Hong, S., Cantarel, B. L., Baldwin, N. E., Baisch, J. M., Edens, M., Cepika, A., Acs, P., Turner, J., Anguiano, E., et al. (2016) · Cell · doi:10.1016/j.cell.2016.03.008 · Cited by 739 · see citing works
Pathway studio—the analysis and navigation of molecular networks
Nikitin, A., Egorov, S., Daraselia, N., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg290 · Cited by 670 · see citing works
Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease
Chu, H., Khosravi, A., Kusumawardhani, I. P., Kwon, A. H. K., Vasconcelos, A. C., Cunha, L. D., Mayer, A. E., Shen, Y., Wu, W.-L., Kambal, A., et al. (2016) · Science · doi:10.1126/science.aad9948 · Cited by 647 · see citing works
Early life dynamics of the human gut virome and bacterial microbiome in infants
Lim, E. S., Zhou, Y., Zhao, G., Bauer, I. K., Droit, L., Ndao, I. M., Warner, B. B., Tarr, P. I., Wang, D., & Holtz, L. R. (2015) · Nature Medicine · doi:10.1038/nm.3950 · Cited by 644 · see citing works
Chromatin modifiers and remodellers: regulators of cellular differentiation
Chen, T., & Dent, S. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3607 · Cited by 629 · see citing works
Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease
Dudley, J. T., Sirota, M., Shenoy, M. M., Pai, R. K., Roedder, S., Chiang, A. P.-F., Morgan, A. A., Sarwal, M., Pasricha, P. J., & Butte, A. J. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3002648 · Cited by 604 · see citing works
Blocking Smad7 restores TGF-β1 signaling in chronic inflammatory bowel disease
Monteleone, G., Kumberová, A., Croft, N. M., McKenzie, C. A., Steer, H. W., & MacDonald, T. T. (2001) · Journal of Clinical Investigation · doi:10.1172/jci12821 · Cited by 602 · see citing works
Widespread macromolecular interaction perturbations in human genetic disorders
Sahni, N., Yi, S., Taipale, M., Fuxman Bass, J. I., Coulombe-Huntington, J., Yang, F., Peng, J., Weile, J., Karras, G. I., Wang, Y., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.013 · Cited by 594 · see citing works
Shen, R., Olshen, A. B., & Ladanyi, M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp659 · Cited by 566 · see citing works
Abundant Pleiotropy in Human Complex Diseases and Traits
Sivakumaran, S., Agakov, F. V., Τheodoratou, E., Prendergast, J. G. D., Zgaga, L., Manolio, T. A., Rudan, I., McKeigue, P., Wilson, J. F., & Campbell, H. J. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.10.004 · Cited by 534 · see citing works
Wu, F., Zikusoka, M. N., Trindade, A. J., Dassopoulos, T., Harris, M. L., Bayless, T. M., Brant, S. R., Chakravarti, S., & Kwon, J. H. (2008) · Gastroenterology · doi:10.1053/j.gastro.2008.07.068 · Cited by 509 · see citing works
Identifying personal microbiomes using metagenomic codes
Franzosa, E. A., Huang, K. H., Meadow, J. F., Gevers, D., Lemon, K. P., Bohannan, B. J. M., & Huttenhower, C. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1423854112 · Cited by 502 · see citing works
Pattern discovery and cancer gene identification in integrated cancer genomic data
Mo, Q., Wang, S., Seshan, V. E., Olshen, A. B., Schultz, N., Sander, C., Powers, R. S., Ladanyi, M., & Shen, R. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208949110 · Cited by 474 · see citing works
Widespread RNA and DNA Sequence Differences in the Human Transcriptome
Li, M., Wang, I. X., Li, Y., Bruzel, A., Richards, A. L., Toung, J. M., & Cheung, V. G. (2011) · Science · doi:10.1126/science.1207018 · Cited by 463 · see citing works
High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics
Humphrey, S. J., Azimifar, S. B., & Mann, M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3327 · Cited by 460 · see citing works
Iliopoulos, D., Hirsch, H. A., & Struhl, K. (2011) · Cancer Research · doi:10.1158/0008-5472.can-10-3471 · Cited by 451 · see citing works
Self-citationGenetics of Inflammatory Bowel Diseases
McGovern, D. P. B., Kugathasan, S., & Cho, J. H. (2015) · Gastroenterology · doi:10.1053/j.gastro.2015.08.001 · Cited by 428 · see citing works
Mutations in NOD2 are associated with fibrostenosing disease in patients with Crohn's disease
Abreu, M. T., Taylor, K. D., Lin, Y.-C., Hang, T., Gaiennie, J., Landers, C. J., Vasiliauskas, E. A., Kam, L. Y., Rojany, M., Papadakis, K. A., et al. (2002) · Gastroenterology · doi:10.1053/gast.2002.35393 · Cited by 428 · see citing works
CellMiner: a relational database and query tool for the NCI-60 cancer cell lines
Shankavaram, U. T., Varma, S., Kane, D. W., Sunshine, M., Chary, K., Reinhold, W. C., Pommier, Y. G., & Weinstein, J. N. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-277 · Cited by 401 · see citing works
Going global by adapting local: A review of recent human adaptation
Fan, S., Hansen, M. E. B., Lo, Y., & Tishkoff, S. A. (2016) · Science · doi:10.1126/science.aaf5098 · Cited by 378 · see citing works
Transgenerational inheritance: Models and mechanisms of non–DNA sequence–based inheritance
Miska, E. A., & Ferguson-Smith, A. C. (2016) · Science · doi:10.1126/science.aaf4945 · Cited by 367 · see citing works
Variation and genetic control of protein abundance in humans
Wu, L., Candille, S. I., Choi, Y., Xie, D., Jiang, L., Li-Pook-Than, J., Tang, H., & Snyder, M. (2013) · Nature · doi:10.1038/nature12223 · Cited by 364 · see citing works
Elucidating Compound Mechanism of Action by Network Perturbation Analysis
Woo, J. H., Shimoni, Y., Yang, W. S., Subramaniam, P., Iyer, A., Nicoletti, P., Rodríguez Martínez, M., López, G., Mattioli, M., Realubit, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.056 · Cited by 351 · see citing works
Le Gall, G., Noor, S. O., Ridgway, K., Scovell, L., Jamieson, C., Johnson, I. T., Colquhoun, I. J., Kemsley, E. K., & Narbad, A. (2011) · Journal of Proteome Research · doi:10.1021/pr2003598 · Cited by 348 · see citing works
Unveiling the role of network and systems biology in drug discovery
Pujol, A., Mosca, R., Farrés, J., & Aloy, P. (2010) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2009.11.006 · Cited by 343 · see citing works
Extensive Variation in Chromatin States Across Humans
Kasowski, M., Kyriazopoulou-Panagiotopoulou, S., Grubert, F., Zaugg, J. B., Kundaje, A., Liu, Y., Boyle, A. P., Zhang, Q. C., Zakharia, F., Spacek, D. V., et al. (2013) · Science · doi:10.1126/science.1242510 · Cited by 339 · see citing works
Beyond Gene Discovery in Inflammatory Bowel Disease: The Emerging Role of Epigenetics
Ventham, N. T., Kennedy, N. A., Nimmo, E. R., & Satsangi, J. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.05.050 · Cited by 321 · see citing works
The cellular composition of the human immune system is shaped by age and cohabitation
Carr, E. J., Dooley, J., Garcia‐Perez, J. E., Lagou, V., Lee, J. C., Wouters, C. H., Meyts, I., Goris, A., Boeckxstaens, G. E., Linterman, M. A., et al. (2016) · Nature Immunology · doi:10.1038/ni.3371 · Cited by 318 · see citing works
The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2
Davidovich, C., & Cech, T. R. (2015) · RNA · doi:10.1261/rna.053918.115 · Cited by 295 · see citing works
Tackling Chronic Disease in Europe: Strategies, Interventions and Challenges
Busse, R. (2010) · Cited by 285 · see citing works
Planell, N., Lozano, J. J., Mora‐Buch, R., Masamunt, M. C., Jimeno, M., Ordás, Í., Esteller, M., Ricart, E., Piqué, J. M., Panés, J., et al. (2012) · Gut · doi:10.1136/gutjnl-2012-303333 · Cited by 274 · see citing works
A Bronchial Genomic Classifier for the Diagnostic Evaluation of Lung Cancer
Silvestri, G. A., Vachani, A., Whitney, D. H., Elashoff, M. R., Smith, K. P., Ferguson, J. S., Parsons, E., Mitra, N., Brody, J. S., Lenburg, M. E., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1504601 · Cited by 271 · see citing works
Exposing the exposures responsible for type 2 diabetes and obesity
Franks, P. W., & McCarthy, M. I. (2016) · Science · doi:10.1126/science.aaf5094 · Cited by 265 · see citing works
VisANT: an online visualization and analysis tool for biological interaction data
Hu, Z., Mellor, J. C., Wu, J., & DeLisi, C. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-17 · Cited by 258 · see citing works
Integrative Subtype Discovery in Glioblastoma Using iCluster
Shen, R., Mo, Q., Schultz, N. D., Seshan, V., Olshen, A. B., Huse, J. T., Ladanyi, M., & Sander, C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035236 · Cited by 258 · see citing works
Schicho, R., Shaykhutdinov, R. A., Ngo, J., Nazyrova, A., Schneider, C., Panaccione, R., Kaplan, G. G., Vogel, H. J., & Storr, M. (2012) · Journal of Proteome Research · doi:10.1021/pr300139q · Cited by 248 · see citing works
Metformin in early breast cancer: a prospective window of opportunity neoadjuvant study
Niraula, S., Dowling, R. J. O., Ennis, M., Chang, M. C., Done, S. J., Hood, N., Escallón, J., Leong, W. L., McCready, D. R., Reedijk, M., et al. (2012) · Breast Cancer Research and Treatment · doi:10.1007/s10549-012-2223-1 · Cited by 238 · see citing works
Κούκος, Γ., Polytarchou, C., Kaplan, J. L., Morley-Fletcher, A., Gras-Miralles, B., Kokkotou, E. G., Baril‐Dore, M., Pothoulakis, C., Winter, H. S., & Iliopoulos, D. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.07.001 · Cited by 232 · see citing works
Self-citationGao, J., Tarcea, V. G., Karnovsky, A., Mirel, B. R., Weymouth, T. E., Beecher, C., Cavalcoli, J. D., Athey, B. D., Omenn, G. S., Burant, C., et al. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq048 · Cited by 231 · see citing works
From Genotype to Phenotype: Systems Biology Meets Natural Variation
Benfey, P. N., & Mitchell‐Olds, T. (2008) · Science · doi:10.1126/science.1153716 · Cited by 214 · see citing works
Inhibition of IFN‐γ transcription by site‐specific methylation during T helper cell development
Jones, B. T., & Chen, J. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601148 · Cited by 213 · see citing works
Paull, E., Carlin, D. E., Niepel, M., et al. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt471 · Cited by 210 · see citing works
Distinct inflammatory mechanisms mediate early versus late colitis in mice
Spencer, D. M., Veldman, G. M., Banerjee, S., Willis, J., & Levine, A. D. (2002) · Gastroenterology · doi:10.1053/gast.2002.30308 · Cited by 209 · see citing works
Ohkusa, T., Sato, N., Ogihara, T., Morita, K., Ogawa, M., & Okayasu, I. (2002) · Journal of Gastroenterology and Hepatology · doi:10.1046/j.1440-1746.2002.02834.x · Cited by 198 · see citing works
Mucosal T-cell immunoregulation varies in early and late inflammatory bowel disease
Kugathasan, S., Saubermann, L. J., Smith, L. A., Kou, D., Itoh, J., Binion, D. G., Levine, A. D., Blumberg, R. S., & Fiocchi, C. (2007) · Gut · doi:10.1136/gut.2006.116467 · Cited by 192 · see citing works
Self-citationNimmo, E. R., Prendergast, J. G. D., Aldhous, M. C., Kennedy, N. A., Henderson, P., Drummond, H. E., Ramsahoye, B. H., Wilson, D. C., Semple, C. A. M., & Satsangi, J. (2011) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21912 · Cited by 179 · see citing works
Reinisch, W., Hommes, D. W., Assche, G. V., Colombel, J.-F., Jp, G., Oldenburg, B., Teml, A., Geboes, K., Ding, H., Zhang, L., et al. (2006) · Gut · doi:10.1136/gut.2005.079434 · Cited by 175 · see citing works
Danese, S., Rudziński, J., Brandt, W., Dupas, J., Peyrin‐Biroulet, L., Bouhnik, Y., Kleczkowski, D., Uebel, P., Lukáš, M., Knutsson, M., et al. (2014) · Gut · doi:10.1136/gutjnl-2014-308004 · Cited by 158 · see citing works
Foran, E., Garrity-Park, M. M., Mureau, C., Newell, J., Smyrk, T. C., Limburg, P. J., & Egan, L. J. (2010) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-09-0496 · Cited by 155 · see citing works
iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data
Wang, W., Baladandayuthapani, V., Morris, J. S., Broom, B. M., Manyam, G. C., & Do, K.-A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts655 · Cited by 154 · see citing works
Sanchez, C., Lachaize, C., Janody, F., et al. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.89 · Cited by 150 · see citing works
ProViz: protein interaction visualization and exploration
Iragne, F., Nikolski, M., Mathieu, B., et al. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth494 · Cited by 142 · see citing works
Choung, R. S., Princen, F., Stockfisch, T. P., Torres, J., Maue, A. C., Porter, C. K., Leon, F., Vroey, B. D., Singh, S., Riddle, M. S., et al. (2016) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.13641 · Cited by 139 · see citing works
Rogler (2015) · doi:10.1097/mib.0000000000000229 · Cited by 137 · see citing works
VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies
Hu, Z., Chang, Y.-C., Wang, Y., Huang, C. L., Liu, Y., Tian, F., Granger, B. R., & DeLisi, C. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt401 · Cited by 130 · see citing works
Polytarchou, C., Hommes, D. W., Palumbo, T., Hatziapostolou, M., Κουτσιούμπα, Μ., Κούκος, Γ., Jong, A. E. V. D. M., Oikonomopoulos, A., van Deen, W. K., Vorvis, C., et al. (2015) · Gastroenterology · doi:10.1053/j.gastro.2015.05.057 · Cited by 128 · see citing works
Self-citationUrinary NMR metabolomic profiles discriminate inflammatory bowel disease from healthy
Stephens, N. S., Siffledeen, J. S., Su, X., Murdoch, T. B., Fedorak, R. N., & Slupsky, C. M. (2012) · Journal of Crohn s and Colitis · doi:10.1016/j.crohns.2012.04.019 · Cited by 125 · see citing works
DNA methylation of colon mucosa in ulcerative colitis patients: Correlation with inflammatory status
Saito, S., Kato, J., Hiraoka, S., et al. (2011) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21573 · Cited by 111 · see citing works
A modular approach for integrative analysis of large-scale gene-expression and drug-response data
Kutalik, Z., Beckmann, J. S., & Bergmann, S. (2008) · Nature Biotechnology · doi:10.1038/nbt1397 · Cited by 110 · see citing works
Crohn disease: A current perspective on genetics, autophagy and immunity
Stappenbeck, T. S., Rioux, J. D., Mizoguchi, A., Saitoh, T., Huett, A. S., Darfeuille–Michaud, A., Wileman, T., Mizushima, N., Carding, S. R., Parkes, M., et al. (2011) · Autophagy · doi:10.4161/auto.7.4.13074 · Cited by 109 · see citing works
T cells of the human intestinal lamina propria are high producers of interleukin-10
Braunstein, J., Qiao, L., Autschbach, F., Schürmann, G., & Meuer, S. C. (1997) · Gut · doi:10.1136/gut.41.2.215 · Cited by 96 · see citing works
Adams, A. T., Kennedy, N. A., Hansen, R., Ventham, N. T., O’Leary, K. R., Drummond, H. E., Noble, C. L., El-Omar, E. M., Russell, R. K., Wilson, D. C., et al. (2014) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000179 · Cited by 93 · see citing works
Genetic variation in IBD: progress, clues to pathogenesis and possible clinical utility
Ye, B. D., & McGovern, D. P. B. (2016) · Expert Review of Clinical Immunology · doi:10.1080/1744666x.2016.1184972 · Cited by 89 · see citing works
Starr, A. E., Deeke, S. A., Ning, Z., Chiang, C., Zhang, X., Mottawea, W., Singleton, R., Benchimol, E. I., Wen, M., Mack, D. R., et al. (2016) · Gut · doi:10.1136/gutjnl-2015-310705 · Cited by 87 · see citing works
Endophenotype Network Models: Common Core of Complex Diseases
Ghiassian, S. D., Menche, J., Chasman, D. I., Giulianini, F., Wang, R., Ricchiuto, P., Aikawa, M., Iwata, H., Müller, C., Zeller, T., et al. (2016) · Scientific Reports · doi:10.1038/srep27414 · Cited by 87 · see citing works
Environmental Immunology: Lessons Learned from Exposure to a Select Panel of Immunotoxicants
Kreitinger, J. M., Beamer, C. A., & Shepherd, D. M. (2016) · The Journal of Immunology · doi:10.4049/jimmunol.1502149 · Cited by 86 · see citing works
(2017) · Harvard University Press eBooks · doi:10.4159/9780674545533 · Cited by 86 · see citing works
Kabakchiev, B., & Silverberg, M. S. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.03.001 · Cited by 84 · see citing works
Luker, G. D., & Piwnica-Worms, D. (2001) · Academic Radiology · doi:10.1016/s1076-6332(03)80738-9 · Cited by 81 · see citing works
Li‐Pook‐Than, J., & Snyder, M. P. (2013) · Chemistry & Biology · doi:10.1016/j.chembiol.2013.05.001 · Cited by 80 · see citing works
Inflammatory Bowel Disease in Chinese Children
Wang, X., Zhang, Y., Xu, C., Jiang, L., Huang, Y., Du, H., & Wang, X. (2013) · Inflammatory Bowel Diseases · doi:10.1097/mib.0b013e318286f9f2 · Cited by 77 · see citing works
Meuwis, M., Fillet, M., Lutteri, L., Marée, R., Geurts, P., de Seny, D., Malaise, M., Chapelle, J.-P., Wehenkel, L. A., Bélaïche, J., et al. (2008) · Clinical Biochemistry · doi:10.1016/j.clinbiochem.2008.04.021 · Cited by 69 · see citing works
M’Koma, A. E., Seeley, E. H., Washington, M. K., Schwartz, D. A., Muldoon, R. L., Herline, A. J., Wise, P. E., & Caprioli, R. M. (2010) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21442 · Cited by 64 · see citing works
Complex diseases require complex therapies
Iyengar, R. (2013) · EMBO Reports · doi:10.1038/embor.2013.177 · Cited by 61 · see citing works
A MicroRNA Signature in Pediatric Ulcerative Colitis
Κούκος, Γ., Polytarchou, C., Kaplan, J. L., Oikonomopoulos, A., Ziring, D., Hommes, D. W., Wahed, R., Kokkotou, E. G., Pothoulakis, C., Winter, H. S., et al. (2015) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000339 · Cited by 61 · see citing works
Self-citationCytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks
Moni, M. A., Xu, H., & Lió, P. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu731 · Cited by 57 · see citing works
GenePro: a cytoscape plug-in for advanced visualization and analysis of interaction networks
Vlasblom, J., Wu, S., Pu, S., Superina, M., Liu, G., Orsi, C., & Wodak, S. J. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl356 · Cited by 52 · see citing works
Writ large: Genomic dissection of the effect of cellular environment on immune response
Yosef, N., & Regev, A. (2016) · Science · doi:10.1126/science.aaf5453 · Cited by 50 · see citing works
Meddens, C., Harakaľová, M., van den Dungen, N. A. M., Asl, H. F., Hijma, H. J., Cuppen, E. P. J. G., Björkegren, J., Asselbergs, F. W., Nieuwenhuis, E. E. S., & Mokrý, M. (2016) · Genome biology · doi:10.1186/s13059-016-1100-3 · Cited by 48 · see citing works
Chakravarti, A. (2011) · Science · doi:10.1126/science.1214458 · Cited by 44 · see citing works
Network medicine : complex systems in human disease and therapeutics
Loscalzo, J., Barabási, A.-Ĺ., & Silverman, E. K. (2017) · Cited by 43 · see citing works
Multiple Molecular Data Sets and the Classification of Adult Diffuse Gliomas
Ellison, D. W. (2015) · New England Journal of Medicine · doi:10.1056/nejme1506813 · Cited by 36 · see citing works
Personalizing medicine for autoimmune and inflammatory diseases
Chan, A. C., & Behrens, T. W. (2013) · Nature Immunology · doi:10.1038/ni.2473 · Cited by 35 · see citing works
Systems biology in inflammatory bowel diseases
Polytarchou, C., Κούκος, Γ., & Iliopoulos, D. (2014) · Current Opinion in Gastroenterology · doi:10.1097/mog.0000000000000081 · Cited by 35 · see citing works
Self-citationThe genetic architecture of inflammatory bowel disease
Cleynen, I., & Vermeire, S. (2015) · Current Opinion in Gastroenterology · doi:10.1097/mog.0000000000000215 · Cited by 35 · see citing works
iFad: an integrative factor analysis model for drug-pathway association inference†
Ma, H., & Zhao, H. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts285 · Cited by 30 · see citing works
A mathematics for medicine: The Network Effect
West, B. J. (2014) · Frontiers in Physiology · doi:10.3389/fphys.2014.00456 · Cited by 22 · see citing works
A Novel Approach to Detect Cumulative Genetic Effects and Genetic Interactions in Crohn’s Disease
Wang, M., Fiocchi, C., Ripke, S., Zhu, X., Duerr, R. H., & Achkar, J. (2013) · Inflammatory Bowel Diseases · doi:10.1097/mib.0b013e31828706a0 · Cited by 20 · see citing works
Self-citationElectronic Sorting of Immune Cell Subpopulations Based on Highly Plastic Genes
Wang, P., Han, W., & Ma, D. (2016) · The Journal of Immunology · doi:10.4049/jimmunol.1502552 · Cited by 18 · see citing works
Berg, J. M. (2016) · Science · doi:10.1126/science.aal0219 · Cited by 15 · see citing works
Hygiene hypothesis in inflammatory bowel disease.
Saidel‐Odes, L., & Odes, S. H. (2014) · PubMed · Cited by 14 · see citing works
(2015) · Nature · doi:10.1038/518273a · Cited by 14 · see citing works
Graph-representation of oxidative folding pathways
Ágoston, V., Čemažar, M., Kaján, L., et al. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-19 · Cited by 12 · see citing works
OmicsViz: Cytoscape plug-in for visualizing omics data across species
Xia, T., & Dickerson, J. A. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn473 · Cited by 9 · see citing works
Integration, Warehousing, and Analysis Strategies of Omics Data
Gedela, S. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-027-0_18 · Cited by 9 · see citing works
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The vagus nerve at the interface of the microbiota-gut-brain axis
Bonaz, B., Bazin, T., & Pellissier, S. (2018) · Frontiers in Neuroscience · doi:10.3389/fnins.2018.00049 · Cited by 1,397 · see citing works
Pott, J., Kabat, A. M., & Maloy, K. J. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2017.12.017 · Cited by 205 · see citing works
Stress triggers flare of inflammatory bowel disease in children and adults
Sun, Y., Li, L., Xie, R., Wang, B., Jiang, K., & Cao, H. (2019) · Frontiers in Pediatrics · doi:10.3389/fped.2019.00432 · Cited by 171 · see citing works
Big data in IBD: a look into the future
Olivera, P., Danese, S., Jay, N., Natoli, G., & Peyrin-Biroulet, L. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0102-5 · Cited by 151 · see citing works
New insights into IL-6 family cytokines in metabolism, hepatology and gastroenterology
Giraldez, M. D., Carneros, D., Garbers, C., Rose-John, S., & Bustos, M. (2021) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-021-00473-x · Cited by 156 · see citing works
Gubatan, J., Levitte, S., Patel, A., Balabanis, T., Wei, M. T., & Sinha, S. R. (2021) · World Journal of Gastroenterology · doi:10.3748/wjg.v27.i17.1920 · Cited by 121 · see citing works
Bourgonje, A. R., Roo-Brand, G., Lisotto, P., Sadaghian Sadabad, M., Reitsema, R. D., de Goffau, M. C., Faber, K. N., Dijkstra, G., & Harmsen, H. J. M. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.842911 · Cited by 47 · see citing works
- Authors
- de Souza, H. S. P., Fiocchi, C., & Iliopoulos, D.
- Affiliations
- Cleveland Clinic (US)
- University of California, Los Angeles (US)
- Corresponding author
- Fiocchi, Claudio
- Venue
- Nature Reviews Gastroenterology & Hepatology
- Published
- 2017-08-23
- Volume
- 14
- Issue
- 12
- Pages
- 739-749
- ISSN
- 1759-5045 (ISSN-L)
- 1759-5053
- OpenAlex
- W2749616891
- Cited by
- 447
- References
- 136
- Citations by year
- 2026: 27 · 2025: 49 · 2024: 44 · 2023: 55 · 2022: 84 · 2021: 64 · 2020: 41 · 2019: 47 · 2018: 31 · 2017: 4 · 2015: 1
- FWCI
- 4.31
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Gastroenterology & Hepatology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Inflammatory Bowel Disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- inflammatory bowel disease, Crohn's disease, ulcerative colitis, systems biology, multi-omics integration, molecular networks, intestinal inflammation, dysbiosis, molecular subtypes, targeted therapy, central hub, etiology, pathogenesis
- MeSH terms
- Gastrointestinal Microbiome, Gastrointestinal Agents, Humans, Inflammatory Bowel Diseases, Genetic Predisposition to Disease, Proteomics, Systems Biology, Drug Discovery, Epigenomics, Transcriptome, Gene-Environment Interaction
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