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Network medicine

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each protein appears only once in the interactome, whereas in reality, one protein can occur in different contexts and different cellular locations. Such signaling modules are therapeutically best targeted at several sites, which is now the new and clinically applied definition of network pharmacology. To achieve higher than current precision, patients must not be selected solely on descriptive phenotypes but also based on diagnostics that detect the module dysregulation. Moreover, such mechanism-based network pharmacology has the advantage that each of the drugs used within one module is highly synergistic, which allows for reducing the doses of each drug, which then reduces the potential of these drugs acting on other proteins outside the module and hence the chance for unwanted side effects.
35: 333:, also called the diseasome, are networks in which the nodes are diseases and the links, the strength of correlation between them. This correlation is commonly quantified based on associated cellular components that two diseases share. The first-published human disease network (HDN) looked at genes, finding that many of the disease associated genes are 536:
The development of organs and other biological systems can be modelled as network structures where the clinical (e.g., radiographic, functional) characteristics can be represented as nodes and the relationships between these characteristics are represented as the links among such nodes. Therefore, it
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in these networks and understand the role of the environment on the interactome. The human symptom-disease network (HSDN), published in June 2014, showed that the symptoms of disease and disease associated cellular components were strongly correlated and that diseases of the same categories tend to
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Recently, some researchers tended to represent medication use in form of networks. The nodes in these networks represent medications and the edges represent some sort of relationship between these medications. Cavallo et al. (2013) described the topology of a co-prescription network to demonstrate
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database. The projection of the diseases, called the human disease network (HDN), is a network of diseases connected to each other if they share a common gene. Using the HDN, diseases can be classified and analyzed through the genetic relationships between them. Network medicine has proven to be a
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which drug classes are most co-prescribed. Bazzoni et al. (2015) concluded that the DPNs of co-prescribed medications are dense, highly clustered, modular and assortative. Askar et al. (2021) created a network of the severe drug-drug interactions (DDIs) showing that it consisted of many clusters.
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have also been studied in this field. The next iteration of network pharmacology used entirely different disease definitions, defined as dysfunction in signaling modules derived from protein-protein interaction modules. The latter as well as the interactome had many conceptual shortcomings, e.g.,
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as well as the type of drug-drug interactions, thus can help design efficient and safe therapeutic strategies. In addition, the drug-target network (DTN) can play an important role in understanding the mechanisms of action of approved and experimental drugs. The network theory view of
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for disease detection. There can be a variety of ways to identifying drugs using network pharmacology; a simple example of this is the "guilt by association" method. This states if two diseases are treated by the same drug, a drug that treats one disease may treat the other.
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Schäfer, Samuel; Smelik, Martin; Sysoev, Oleg; Zhao, Yelin; Eklund, Desiré; Lilja, Sandra; Gustafsson, Mika; Heyn, Holger; Julia, Antonio; Kovács, István A.; Loscalzo, Joseph; Marsal, Sara; Zhang, Huan; Li, Xinxiu; Gawel, Danuta (20 March 2024).
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Using interactome networks, one can discover and classify diseases, as well as develop treatments through knowledge of its associations and their role in the networks. One observation is that diseases can be classified not by their principle
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Nogales C, Mamdouh ZM, List M, Kiel C, Casas AI, Schmidt HHHW. Network pharmacology: curing causal mechanisms instead of treating symptoms. Trends Pharmacol Sci. 2022 Feb;43(2):136-150. doi: 10.1016/j.tips.2021.11.004. Epub 2021 Dec 9. PMID
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Rual, J. F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., ... & Vidal, M. (2005). Towards a proteome-scale map of the human protein–protein interaction network. Nature, 437(7062),
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Scala, A. Auconi, P., Scazzocchio, M., Caldarelli, G., McNamara, J., Franchi, L. (2014). Complex networks for data-driven medicine: the case of Class III dentoskeletal disharmony, New J. Phys. 16 115017
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Catalyst (The Harvard Clinical and Translational Science Center) offers a three-day course entitled "Introduction to Network Medicine", open to clinical and science professionals with doctorate degrees.
157:, similarly to social and technological systems, contain many components that are connected in complicated relationships but are organized by simple principles. Relaying on the tools and principles of 393:
exceeds a predefined threshold. This does not look at the mechanism of action of diseases, but captures disease progression and how highly connected diseases correlate to higher mortality rates.
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Chiang, A. P., & Butte, A. J. (2009). Systematic evaluation of drug–disease relationships to identify leads for novel drug uses. Clinical Pharmacology & Therapeutics, 86(5), 507–510.
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Goh, K. I., Cusick, M. E., Valle, D., Childs, B., Vidal, M., & Barabási, A. L. (2007). The human disease network. Proceedings of the National Academy of Sciences, 104(21), 8685–8690.
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Roeland van Wijk et al., Non-monotonic dynamics and crosstalk in signaling pathways and their implications for pharmacology. Scientific Reports 5:11376 (2015) doi: 10.1038/srep11376
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Hidalgo, C. A., Blumm, N., Barabási, A. L., & Christakis, N. A. (2009). A dynamic network approach for the study of human phenotypes. PLoS Computational Biology, 5(4), e1000353.
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Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., & Barabási, A. L. (2002). Hierarchical organization of modularity in metabolic networks. science, 297(5586), 1551–1555.
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Mehrad Babaei et al., Biochemical reaction network topology defines dose-dependent Drug–Drug interactions. Comput Biol Med 155:106584 (2023) doi: 10.1016/j.compbiomed.2023.106584
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Liu, Y. I., Wise, P. H., & Butte, A. J. (2009). The "etiome": identification and clustering of human disease etiological factors. BMC bioinformatics, 10(Suppl 2), S14.
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P. Auconi, G. Caldarelli, A. Scala, G. Ierardo, A. Polimeni (2011). A network approach to orthodontic diagnosis, Orthodontics and Craniofacial Research 14, 189-197.
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Loscalzo, J., & Barabasi, A. L. (2011). Systems biology and the future of medicine. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 3(6), 619–627.
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Christakis, N. A., & Fowler, J. H. (2007). The spread of obesity in a large social network over 32 years. New England Journal of Medicine, 357(4), 370–379.
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Barabási, A. L., Gulbahce, N., & Loscalzo, J. (2011). Network medicine: a network-based approach to human disease. Nature Reviews Genetics, 12(1), 56–68.
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Braun, P., Rietman, E., & Vidal, M. (2008). Networking metabolites and diseases. Proceedings of the National Academy of Sciences, 105(29), 9849–9850.
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that looks at the effect of drugs on both the interactome and the diseasome. The topology of a biochemical reaction network determines the shape of drug
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Chan, S. Y., & Loscalzo, J. (2012). The emerging paradigm of network medicine in the study of human disease. Circulation research, 111(3), 359–374.
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Bazzoni, Gianfranco (April 2015). "The Drug Prescription Network: A System-Level View of Drug Co-Prescription in Community-Dwelling Elderly People".
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Yıldırım, M. A., Goh, K. I., Cusick, M. E., Barabási, A. L., & Vidal, M. (2007). Drug—target network. Nature Biotechnology, 25(10), 1119–1126.
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offers an undergraduate course called "Network Medicine: Using Systems Biology and Signaling Networks to Create Novel Cancer Therapeutics". Also,
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and that representing these as complex networks will shed light on the causes and mechanisms of diseases. It is possible, for example, to infer a
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linked together by a particular biological or molecular relationship. For networks pertaining to medicine, nodes represent biological factors (
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and social networks play a role in the spread of disease. Social networks have been used to assess the role of social ties in the spread of
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states that if a metabolic pathway is linked to two different diseases, then the two diseases likely have a shared metabolic origin (
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Pastor-Satorras, R., & Vespignani, A. (2001). Epidemic spreading in scale-free networks. Physical review letters, 86(14), 3200.
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states that if a gene is linked to two different disease phenotypes, then the two diseases likely have a common genetic origin (
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Keeling, M. J., & Eames, K. T. (2005). Networks and epidemic models. Journal of the Royal Society Interface, 2(4), 295–307.
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Some disease networks connect diseases to associated factors outside the human cell. Networks of environmental and genetic
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Hopkins, A. L. (2008). Network pharmacology: the next paradigm in drug discovery. Nature Chemical Biology, 4(11), 682–690.
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Zhou, X., Menche, J., Barabási, A. L., & Sharma, A. (2014). Human symptoms–disease network. Nature Communications, 5.
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Pastor-Satorras, R., & Vespignani, A. (2002). Immunization of complex networks. Physical Review E, 65(3), 036104.
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are used to model the spreading of disease across populations. Network medicine is a medically focused area of
140: 185: 115:, which map relationships between diseases and biological factors, also play an important role in the field. 1247: 232:, can be used for disease identification and prevention. These networks have been technically classified as 639: 251: 193: 104: 1261: 605: 433: 309: 184:, and the social network. The network medicine is based on the idea that understanding complexity of 1277:"Network Medicine: Using Systems Biology and Signaling Networks to Create Novel Cancer Therapeutics" 176:
Barabasi suggested that understanding human disease requires us to focus on three key networks, the
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Askar, Mohsen (June 2021). "An introduction to network analysis for studies of medication use".
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and their interactions between each other as links. These maps utilize databases such as
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is based on the effect of the drug in the interactome, especially the region that the
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uses phenotypic disease networks (PDN), where two diseases are linked if the observed
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towards identifying, preventing, and treating diseases. This field focuses on using
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Sonawane, Abhijeet R.; Weiss, Scott T.; Glass, Kimberly; Sharma, Amitabh (2019).
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linked with shared diseases, called the "etiome", can be also used to assess the
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Cavallo, Pierpaolo (February 2013). "Network analysis of drug prescriptions".
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for a complex disease (polypharmacology) is suggested in this field since one
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is possible to use networks to model how organ systems dynamically interact.
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The whole set of molecular interactions in the human cell, also known as the
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Network epidemics has been built by applying network science to existing
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if they are in the same pathway. Researchers have used databases such as
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was created in 2012 to study, reclassify, and develop treatments for
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in an the article "Network Medicine – From Obesity to the 'Diseasome
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Caldarelli G. (2007). Scale-Free Networks. Oxford University Press.
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form highly connected communities, with respect to their symptoms.
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representing the connections of diseases to their associated
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towards identifying diseases and developing medical drugs.
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focuses on complex respiratory diseases, specifically
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in large, long-term epidemiology studies, such as the
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and has been recently used to model the spread of the
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in populations. Epidemic models and concepts, such as
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is extensively studied using network science as well;
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may be too technical for most readers to understand
1306: 596:uses multidisciplinary approaches, including as 209:valuable tool in analyzing big biomedical data. 282:to map these networks. Others networks include 1178:Research in Social and Administrative Pharmacy 911: 909: 844: 842: 832: 830: 139:The term "network medicine" was introduced by 733: 545:The Channing Division of Network Medicine at 352:Three representations of the diseasome are: 1274: 906: 839: 827: 608:, to understand complex diseases and guide 1222: 749: 747: 745: 1231: 1189: 997: 979: 810: 792: 761: 759: 270:encompasses the biochemical reactions in 72:Learn how and when to remove this message 56:, without removing the technical details. 1248:"Channing Division of Network Medicine" 1140: 1097: 742: 541:Educational and clinical implementation 14: 1307: 756: 1175: 617:Massachusetts Institute of Technology 54:make it understandable to non-experts 1100:Pharmacoepidemiology and Drug Safety 482: 312:for a specific pathophenotype using 254:have been mapped, using proteins as 111:, are utilized by network medicine. 28: 517:Ebola virus epidemic in West Africa 150:The New England Journal of Medicine 24: 370:Shared metabolic pathway formalism 25: 1326: 531: 523:Drug prescription networks (DPNs) 519:across countries and continents. 212: 720:Targeted immunization strategies 590:, in smaller population studies. 451:active pharmaceutical ingredient 264:Human Protein Reference Database 153:, in 2007. Barabási states that 33: 1287: 1268: 1254: 1240: 1169: 1134: 1091: 1077: 1060: 1051: 1042: 1033: 1024: 1014: 954: 945: 936: 927: 918: 897: 888: 879: 580:Systems Genetics & Genomics 428:is a developing field based in 413: 870: 861: 851: 768: 557:. It focuses on three areas: 302:(pathophenotype) but by their 217: 13: 1: 1200:10.1016/j.sapharm.2021.06.021 726: 382:Disease comorbidity formalism 134: 640:Biological network inference 562:Chronic Disease Epidemiology 547:Brigham and Women's Hospital 319: 252:Protein-protein interactions 194:protein-protein interactions 105:protein-protein interactions 7: 627: 165:, which are collections of 10: 1331: 981:10.1186/s13073-024-01314-7 606:combinatorial optimization 553:using network science and 417: 323: 221: 461:, and the development of 794:10.3389/fgene.2019.00294 655:Glossary of graph theory 288:gene regulatory networks 493:transportation networks 125:transportation networks 472:drug-drug interactions 331:Human disease networks 246:betweenness centrality 141:Albert-LászlĂł Barabási 87:is the application of 1155:10.1089/rej.2014.1628 1143:Rejuvenation Research 781:Frontiers in Genetics 670:Human disease network 513:targeted immunization 407:environmental factors 358:Shared gene formalism 326:Human disease network 314:clustering algorithms 715:Systems pharmacology 574:Nurses' Health Study 430:systems pharmacology 420:Systems pharmacology 242:small-world networks 447:Combination therapy 434:dose-response curve 399:etiological factors 375:metabolic disorders 347:metabolic disorders 335:non-essential genes 190:metabolic reactions 101:Biological networks 1281:MIT OpenCourseWare 635:Biological network 272:metabolic pathways 155:biological systems 109:metabolic pathways 1275:Dr. Michael Lee. 1184:(12): 2054–2061. 1087:. 31 August 2014. 680:Metabolic network 602:dynamical systems 594:Systems Pathology 483:Network epidemics 363:genetic disorders 343:metabolic pathway 274:, connecting two 268:metabolic network 178:metabolic network 82: 81: 74: 16:(Redirected from 1322: 1299: 1298: 1291: 1285: 1284: 1272: 1266: 1265: 1258: 1252: 1251: 1244: 1238: 1235: 1229: 1226: 1220: 1219: 1193: 1173: 1167: 1166: 1138: 1132: 1131: 1112:10.1002/pds.3384 1095: 1089: 1088: 1081: 1075: 1064: 1058: 1055: 1049: 1046: 1040: 1037: 1031: 1028: 1022: 1018: 1012: 1011: 1001: 983: 958: 952: 949: 943: 940: 934: 931: 925: 922: 916: 913: 904: 901: 895: 892: 886: 883: 877: 874: 868: 865: 859: 855: 849: 846: 837: 834: 825: 824: 814: 796: 772: 766: 763: 754: 751: 740: 737: 700:Network topology 685:Network dynamics 665:Graphical models 551:complex diseases 468:Drug repurposing 244:, having a high 163:complex networks 147:", published in 146: 113:Disease networks 97:network dynamics 93:network topology 85:Network medicine 77: 70: 66: 63: 57: 37: 36: 29: 21: 18:Network Medicine 1330: 1329: 1325: 1324: 1323: 1321: 1320: 1319: 1305: 1304: 1303: 1302: 1293: 1292: 1288: 1273: 1269: 1260: 1259: 1255: 1246: 1245: 1241: 1236: 1232: 1227: 1223: 1174: 1170: 1139: 1135: 1096: 1092: 1083: 1082: 1078: 1072:Halloran, M. 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Index

Network Medicine
help improve it
make it understandable to non-experts
Learn how and when to remove this message
network science
network topology
network dynamics
Biological networks
protein-protein interactions
metabolic pathways
Disease networks
Epidemiology
social networks
transportation networks
systems biology
Albert-László Barabási
The New England Journal of Medicine
biological systems
network theory
complex networks
nodes
biomolecules
metabolic network
disease network
gene regulation
metabolic reactions
protein-protein interactions
bipartite graph
genes
OMIM

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