TY - JOUR AU - Swinney, D. C. AU - Anthony, J. PY - 2011 DA - 2011// TI - How were new medicines discovered? JO - Nat Rev Drug Discov VL - 10 UR - https://doi.org/10.1038/nrd3480 DO - 10.1038/nrd3480 ID - Swinney2011 ER - TY - JOUR AU - Nagamine, N. AU - Sakakibara, Y. PY - 2007 DA - 2007// TI - Statistical prediction of protein chemical interactions based on chemical structure and mass spectrometry data JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm266 DO - 10.1093/bioinformatics/btm266 ID - Nagamine2007 ER - TY - JOUR AU - Yamanishi, Y. AU - Araki, M. AU - Gutteridge, A. AU - Honda, W. AU - Kanehisa, M. PY - 2008 DA - 2008// TI - Prediction of drug-target interaction networks from the integration of chemical and genomic spaces JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn162 DO - 10.1093/bioinformatics/btn162 ID - Yamanishi2008 ER - TY - JOUR AU - Jacob, L. AU - Vert, J. P. PY - 2008 DA - 2008// TI - Protein-ligand interaction prediction: an improved chemogenomics approach JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn409 DO - 10.1093/bioinformatics/btn409 ID - Jacob2008 ER - TY - JOUR AU - Faulon, J. L. AU - Misra, M. AU - Martin, S. AU - Sale, K. AU - Sapra, R. PY - 2008 DA - 2008// TI - Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btm580 DO - 10.1093/bioinformatics/btm580 ID - Faulon2008 ER - TY - JOUR AU - Keiser, M. J. AU - Setola, V. AU - Irwin, J. J. AU - Laggner, C. AU - Abbas, A. I. AU - Hufeisen, S. J. PY - 2009 DA - 2009// TI - Predicting new molecular targets for known drugs JO - Nature VL - 462 UR - https://doi.org/10.1038/nature08506 DO - 10.1038/nature08506 ID - Keiser2009 ER - TY - JOUR AU - Bleakley, K. AU - Yamanishi, Y. PY - 2009 DA - 2009// TI - Supervised prediction of drug-target interactions using bipartite local models JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp433 DO - 10.1093/bioinformatics/btp433 ID - Bleakley2009 ER - TY - JOUR AU - Campillos, M. AU - Kuhn, M. AU - Gavin, A. C. AU - Jensen, L. J. AU - Bork, P. PY - 2008 DA - 2008// TI - Drug target identification using side-effect similarity JO - Science VL - 321 UR - https://doi.org/10.1126/science.1158140 DO - 10.1126/science.1158140 ID - Campillos2008 ER - TY - JOUR AU - Takarabe, M. AU - Kotera, M. AU - Nishimura, Y. AU - Goto, S. AU - Yamanishi, Y. PY - 2012 DA - 2012// TI - Drug target prediction using adverse event report systems: a pharmacogenomic approach JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts413 DO - 10.1093/bioinformatics/bts413 ID - Takarabe2012 ER - TY - JOUR AU - Yamanishi, Y. AU - Kotera, M. AU - Kanehisa, M. AU - Goto, S. PY - 2010 DA - 2010// TI - Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq176 DO - 10.1093/bioinformatics/btq176 ID - Yamanishi2010 ER - TY - JOUR AU - Edgar, R. AU - Domrachev, M. AU - Lash, A. E. PY - 2002 DA - 2002// TI - Gene Expression Omnibus: NCBI gene expression and hybridization array data repository JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.207 DO - 10.1093/nar/30.1.207 ID - Edgar2002 ER - TY - JOUR AU - Brazma, A. AU - Parkinson, H. AU - Sarkans, U. AU - Shojatalab, M. AU - Vilo, J. AU - Abeygunawardena, N. PY - 2003 DA - 2003// TI - ArrayExpress--a public repository for microarray gene expression data at the EBI JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg091 DO - 10.1093/nar/gkg091 ID - Brazma2003 ER - TY - JOUR AU - Leinonen, R. AU - Sugawara, H. AU - Shumway, M. PY - 2011 DA - 2011// TI - The sequence read archive JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq1019 DO - 10.1093/nar/gkq1019 ID - Leinonen2011 ER - TY - JOUR AU - Lamb, J. AU - Crawford, E. D. AU - Peck, D. AU - Modell, J. W. AU - Blat, I. C. AU - Wrobel, M. J. PY - 2006 DA - 2006// TI - The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease JO - Science VL - 313 UR - https://doi.org/10.1126/science.1132939 DO - 10.1126/science.1132939 ID - Lamb2006 ER - TY - JOUR AU - Babcock, J. J. AU - Du, F. AU - Xu, K. AU - Wheelan, S. J. AU - Li, M. PY - 2013 DA - 2013// TI - Integrated analysis of drug-induced gene expression profiles predicts novel hERG inhibitors JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0069513 DO - 10.1371/journal.pone.0069513 ID - Babcock2013 ER - TY - JOUR AU - Iorio, F. AU - Bosotti, R. AU - Scacheri, E. AU - Belcastro, V. AU - Mithbaokar, P. AU - Ferriero, R. PY - 2010 DA - 2010// TI - Discovery of drug mode of action and drug repositioning from transcriptional responses JO - Proc Natl Acad Sci U S A VL - 107 UR - https://doi.org/10.1073/pnas.1000138107 DO - 10.1073/pnas.1000138107 ID - Iorio2010 ER - TY - JOUR AU - Iorio, F. AU - Rittman, T. AU - Ge, H. AU - Menden, M. AU - Saez-Rodriguez, J. PY - 2013 DA - 2013// TI - Transcriptional data: a new gateway to drug repositioning? JO - Drug Discov Today VL - 18 UR - https://doi.org/10.1016/j.drudis.2012.07.014 DO - 10.1016/j.drudis.2012.07.014 ID - Iorio2013 ER - TY - JOUR AU - Iskar, M. AU - Campillos, M. AU - Kuhn, M. AU - Jensen, L. J. AU - Noort, V. AU - Bork, P. PY - 2010 DA - 2010// TI - Drug-induced regulation of target expression JO - PLoS Comput Biol VL - 6 UR - https://doi.org/10.1371/journal.pcbi.1000925 DO - 10.1371/journal.pcbi.1000925 ID - Iskar2010 ER - TY - JOUR AU - Wang, K. AU - Sun, J. AU - Zhou, S. AU - Wan, C. AU - Qin, S. AU - Li, C. PY - 2013 DA - 2013// TI - Prediction of drug-target interactions for drug repositioning only based on genomic expression similarity JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1003315 DO - 10.1371/journal.pcbi.1003315 ID - Wang2013 ER - TY - JOUR AU - Cheng, J. AU - Yang, L. AU - Kumar, V. AU - Agarwal, P. PY - 2014 DA - 2014// TI - Systematic evaluation of connectivity map for disease indications JO - Genome Med VL - 6 UR - https://doi.org/10.1186/s13073-014-0095-1 DO - 10.1186/s13073-014-0095-1 ID - Cheng2014 ER - TY - STD TI - Connectivity Map. http://www.broadinstitute.org/cmap/. UR - http://www.broadinstitute.org/cmap/ ID - ref21 ER - TY - JOUR AU - Hubbell, E. AU - Liu, W. M. AU - Mei, R. PY - 2002 DA - 2002// TI - Robust estimators for expression analysis JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.12.1585 DO - 10.1093/bioinformatics/18.12.1585 ID - Hubbell2002 ER - TY - JOUR AU - Seiler, K. P. AU - George, G. A. AU - Happ, M. P. AU - Bodycombe, N. E. AU - Carrinski, H. A. AU - Norton, S. PY - 2008 DA - 2008// TI - ChemBank: a small-molecule screening and cheminformatics resource database JO - Nucleic Acids Res VL - 36 ID - Seiler2008 ER - TY - STD TI - ChemBank. http://chembank.broadinstitute.org/. Accessed 2 June 2015. UR - http://chembank.broadinstitute.org/ ID - ref24 ER - TY - JOUR AU - Carhart, R. E. AU - Smith, D. H. AU - Venkataraghavan, R. PY - 1985 DA - 1985// TI - Atom pairs as molecular features in structure-activity studies: definition and applications JO - J Chem Inf Comput Sci VL - 25 UR - https://doi.org/10.1021/ci00046a002 DO - 10.1021/ci00046a002 ID - Carhart1985 ER - TY - JOUR AU - Apweiler, R. AU - Bairoch, A. AU - Wu, C. H. AU - Barker, W. C. AU - Boeckmann, B. AU - Ferro, S. PY - 2004 DA - 2004// TI - UniProt: the Universal Protein knowledgebase JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh131 DO - 10.1093/nar/gkh131 ID - Apweiler2004 ER - TY - STD TI - UniProt. http://www.uniprot.org/. UR - http://www.uniprot.org/ ID - ref27 ER - TY - JOUR AU - Rice, P. AU - Longden, I. AU - Bleasby, A. PY - 2000 DA - 2000// TI - EMBOSS: the European Molecular Biology Open Software Suite JO - Trends Genet VL - 16 UR - https://doi.org/10.1016/S0168-9525(00)02024-2 DO - 10.1016/S0168-9525(00)02024-2 ID - Rice2000 ER - TY - JOUR AU - Smith, T. F. AU - Waterman, M. S. PY - 1981 DA - 1981// TI - Identification of common molecular subsequences JO - J Mol Biol VL - 147 UR - https://doi.org/10.1016/0022-2836(81)90087-5 DO - 10.1016/0022-2836(81)90087-5 ID - Smith1981 ER - TY - JOUR AU - Wishart, D. S. AU - Knox, C. AU - Guo, A. C. AU - Shrivastava, S. AU - Hassanali, M. AU - Stothard, P. PY - 2006 DA - 2006// TI - DrugBank: a comprehensive resource for in silico drug discovery and exploration JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj067 DO - 10.1093/nar/gkj067 ID - Wishart2006 ER - TY - STD TI - DrugBank. http://www.drugbank.ca/. UR - http://www.drugbank.ca/ ID - ref31 ER - TY - JOUR AU - Gaulton, A. AU - Bellis, L. J. AU - Bento, A. P. AU - Chambers, J. AU - Davies, M. AU - Hersey, A. PY - 2012 DA - 2012// TI - ChEMBL: a large-scale bioactivity database for drug discovery JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr777 DO - 10.1093/nar/gkr777 ID - Gaulton2012 ER - TY - STD TI - ChEMBL. https://www.ebi.ac.uk/chembl/. UR - https://www.ebi.ac.uk/chembl/ ID - ref33 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. AU - Furumichi, M. AU - Tanabe, M. AU - Hirakawa, M. PY - 2010 DA - 2010// TI - KEGG for representation and analysis of molecular networks involving diseases and drugs JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkp896 DO - 10.1093/nar/gkp896 ID - Kanehisa2010 ER - TY - JOUR AU - Gunther, S. AU - Kuhn, M. AU - Dunkel, M. AU - Campillos, M. AU - Senger, C. AU - Petsalaki, E. PY - 2008 DA - 2008// TI - SuperTarget and Matador: resources for exploring drug-target relationships JO - Nucleic Acids Res VL - 36 ID - Gunther2008 ER - TY - JOUR AU - Roth, B. L. AU - Lopez, E. AU - Patel, S. AU - Kroeze, W. K. PY - 2000 DA - 2000// TI - The Multiplicity of Serotonin Receptors: Uselessly Diverse Molecules or an Embarrassment of Riches? JO - Neuroscientist VL - 6 UR - https://doi.org/10.1177/107385840000600408 DO - 10.1177/107385840000600408 ID - Roth2000 ER - TY - JOUR AU - Rao, S. AU - Aoyama, R. AU - Schrag, M. AU - Trager, W. F. AU - Rettie, A. AU - Jones, J. P. PY - 2000 DA - 2000// TI - A refined 3-dimensional QSAR of cytochrome P450 2C9: computational predictions of drug interactions JO - J Med Chem VL - 43 UR - https://doi.org/10.1021/jm000048n DO - 10.1021/jm000048n ID - Rao2000 ER - TY - JOUR AU - Groot, M. J. AU - Alex, A. A. AU - Jones, B. C. PY - 2002 DA - 2002// TI - Development of a combined protein and pharmacophore model for cytochrome P450 2C9 JO - J Med Chem VL - 45 UR - https://doi.org/10.1021/jm0110791 DO - 10.1021/jm0110791 ID - Groot2002 ER - TY - JOUR AU - Vempati, U. D. AU - Chung, C. AU - Mader, C. AU - Koleti, A. AU - Datar, N. AU - Vidovic, D. PY - 2014 DA - 2014// TI - Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS) JO - J Biomol Screen VL - 19 UR - https://doi.org/10.1177/1087057114522514 DO - 10.1177/1087057114522514 ID - Vempati2014 ER - TY - JOUR AU - Yang, W. AU - Soares, J. AU - Greninger, P. AU - Edelman, E. J. AU - Lightfoot, H. AU - Forbes, S. PY - 2013 DA - 2013// TI - Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1111 DO - 10.1093/nar/gks1111 ID - Yang2013 ER - TY - JOUR AU - Barretina, J. AU - Caponigro, G. AU - Stransky, N. AU - Venkatesan, K. AU - Margolin, A. A. AU - Kim, S. PY - 2012 DA - 2012// TI - The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity JO - Nature VL - 483 UR - https://doi.org/10.1038/nature11003 DO - 10.1038/nature11003 ID - Barretina2012 ER - TY - JOUR AU - Nyström-Persson, J. AU - Igarashi, Y. AU - Ito, M. AU - Morita, M. AU - Nakatsu, N. AU - Yamada, H. PY - 2013 DA - 2013// TI - Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt531 DO - 10.1093/bioinformatics/btt531 ID - Nyström-Persson2013 ER - TY - JOUR AU - Igarashi, Y. AU - Nakatsu, N. AU - Yamashita, T. AU - Ono, A. AU - Ohno, Y. AU - Urushidani, T. PY - 2015 DA - 2015// TI - Open TG-GATEs: a large-scale toxicogenomics database JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku955 DO - 10.1093/nar/gku955 ID - Igarashi2015 ER -