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Drug repositioning: identifying and developing new uses for existing drugs
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1 Ashburn, T.T., Thor, K.B., Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov 3 (2004), 673–683.
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Ashburn, T.T.1
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Network pharmacology for cancer drug discovery: are we there yet?
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2 Azmi, A.S., Network pharmacology for cancer drug discovery: are we there yet?. Future Med Chem 4 (2012), 939–941.
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Azmi, A.S.1
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Drug repositioning: re-investigating existing drugs for new therapeutic indications
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3 Padhy, B.M., Gupta, Y.K., Drug repositioning: re-investigating existing drugs for new therapeutic indications. JPGM 57 (2011), 153–160.
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Padhy, B.M.1
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Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review
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This paper proposes two strategies for using molecular network analysis for discovering novel drug targets, a central hit strategy and a network influence strategy.
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4• Csermely, P., Korcsmaros, T., Kiss, H.J., London, G., Nussinov, R., Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 138 (2013), 333–408 This paper proposes two strategies for using molecular network analysis for discovering novel drug targets, a central hit strategy and a network influence strategy.
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Csermely, P.1
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Drug repurposing through nonhypothesis driven phenotypic screening
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5 Reaume, A.G., Drug repurposing through nonhypothesis driven phenotypic screening. Drug Discov Today: Therap Strat 8 (2011), 85–88.
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The emergence of genome-based drug repositioning
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6 Lussier, Y.A., Chen, J.L., The emergence of genome-based drug repositioning. Sci Transl Med, 3, 2011, 96ps35.
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Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease
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8 Dudley, J.T., Sirota, M., Shenoy, M., Pai, R.K., Roedder, S., Chiang, A.P., Morgan, A.A., Sarwal, M.M., Pasricha, P.J., Butte, A.J., Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med, 3, 2011, 96ra76.
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Dudley, J.T.1
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Sarwal, M.M.8
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Butte, A.J.10
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9
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Discovery and preclinical validation of drug indications using compendia of public gene expression data
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9 Sirota, M., Dudley, J.T., Kim, J., Chiang, A.P., Morgan, A.A., Sweet-Cordero, A., Sage, J., Butte, A.J., Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med, 3, 2011, 96ra77.
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Sirota, M.1
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Gene expression signature-based screening identifies new broadly effective influenza A antivirals
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10 Josset, L., Textoris, J., Loriod, B., Ferraris, O., Moules, V., Lina, B., N'Guyen, C., Diaz, J.-J., Rosa-Calatrava, M., Gene expression signature-based screening identifies new broadly effective influenza A antivirals. PLoS ONE, 5, 2010, e13169.
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11
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84879571351
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Cell host response to infection with novel human coronavirus EMC predicts potential antivirals and important differences with SARS coronavirus
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This is the first use of the inverse genomic signature approach for an emerging infectious disease.
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11• Josset, L., Menachery, V.D., Gralinski, L.E., Agnihothram, S., Sova, P., Carter, V.S., Yount, B.L., Graham, R.L., Baric, R.S., Katze, M.G., Cell host response to infection with novel human coronavirus EMC predicts potential antivirals and important differences with SARS coronavirus. mBio, 2013, 4 This is the first use of the inverse genomic signature approach for an emerging infectious disease.
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mBio
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Josset, L.1
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Network biology: understanding the cell's functional organization
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12 Barabasi, A.L., Oltvai, Z.N., Network biology: understanding the cell's functional organization. Nat Rev Genet 5 (2004), 101–113.
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A multi-omic systems approach to elucidating Yersinia virulence mechanisms
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13 Ansong, C., Schrimpe-Rutledge, A.C., Mitchell, H.D., Chauhan, S., Jones, M.B., Kim, Y.M., McAteer, K., Deatherage Kaiser, B.L., Dubois, J.L., Brewer, H.M., et al. A multi-omic systems approach to elucidating Yersinia virulence mechanisms. Mol Biosyst 9 (2013), 44–54.
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Ansong, C.1
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14
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Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis
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14 McDermott, J.E., Diamond, D.L., Corley, C., Rasmussen, A.L., Katze, M.G., Waters, K.M., Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis. BMC Syst Biol, 6, 2012, 28.
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15
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Systems virology: host-directed approaches to viral pathogenesis and drug targeting
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15 Law, G.L., Korth, M.J., Benecke, A.G., Katze, M.G., Systems virology: host-directed approaches to viral pathogenesis and drug targeting. Nat Rev Microbiol 11 (2013), 455–466.
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Law, G.L.1
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16
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Network medicine: a network-based approach to human disease
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16 Barabasi, A.L., Gulbahce, N., Loscalzo, J., Network medicine: a network-based approach to human disease. Nat Rev Genet 12 (2011), 56–68.
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17
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Network-based drug repositioning
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17 Wu, Z., Wang, Y., Chen, L., Network-based drug repositioning. Mol Biosyst 9 (2013), 1268–1281.
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Wu, Z.1
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18
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Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms
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18 Barrenas, F., Chavali, S., Alves, A.C., Coin, L., Jarvelin, M.R., Jornsten, R., Langston, M.A., Ramasamy, A., Rogers, G., Wang, H., et al. Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms. Genome Biol, 13, 2012, R46.
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NCBI GEO: archive for functional genomics data sets — update
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19 Barrett, T., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M., Holko, M., et al. NCBI GEO: archive for functional genomics data sets — update. Nucleic Acids Res 41 (2013), D991–D995.
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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
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20 Hindorff, L.A., Sethupathy, P., Junkins, H.A., Ramos, E.M., Mehta, J.P., Collins, F.S., Manolio, T.A., Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci 106 (2009), 9362–9367.
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Opportunities in systems biology to discover mechanisms and repurpose drugs for CNS diseases
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21 Mei, H., Xia, T., Feng, G., Zhu, J., Lin, S.M., Qiu, Y., Opportunities in systems biology to discover mechanisms and repurpose drugs for CNS diseases. Drug Discov Today 17 (2012), 1208–1216.
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Drug repositioning through incomplete bi-cliques in an integrated drug–target–disease network
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The novel computational approach described in this paper is an excellent example of integrating two data types into a single topological network.
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22• Daminelli, S., Haupt, V.J., Reimann, M., Schroeder, M., Drug repositioning through incomplete bi-cliques in an integrated drug–target–disease network. Integr Biol 4 (2012), 778–788 The novel computational approach described in this paper is an excellent example of integrating two data types into a single topological network.
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Daminelli, S.1
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Quercetin transiently increases energy expenditure but persistently decreases circulating markers of inflammation in C57BL/6J mice fed a high-fat diet
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23 Stewart, L.K., Soileau, J.L., Ribnicky, D., Wang, Z.Q., Raskin, I., Poulev, A., Majewski, M., Cefalu, W.T., Gettys, T.W., Quercetin transiently increases energy expenditure but persistently decreases circulating markers of inflammation in C57BL/6J mice fed a high-fat diet. Metabolism 57:Suppl 1 (2008), S39–S46.
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25 Oi, N., Jeong, C.-H., Nadas, J., Cho, Y.-Y., Pugliese, A., Bode, A.M., Dong, Z., Resveratrol, a red wine polyphenol, suppresses pancreatic cancer by inhibiting leukotriene A4 hydrolase. Cancer Res 70 (2010), 9755–9764.
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28 Aderem, A., Adkins, J.N., Ansong, C., Galagan, J., Kaiser, S., Korth, M.J., Law, G.L., McDermott, J.G., Proll, S.C., Rosenberger, C., et al. A systems biology approach to infectious disease research: innovating the pathogen–host research paradigm. mBio, 2, 2011 e00325–00310.
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Drug repurposing from an academic perspective
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29 Oprea, T.I., Bauman, J.E., Bologa, C.G., Buranda, T., Chigaev, A., Edwards, B.S., Jarvik, J.W., Gresham, H.D., Haynes, M.K., Hjelle, B., et al. Drug repurposing from an academic perspective. Drug Discov Today: Therap Strat 8 (2011), 61–69.
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