Applications of Connectivity Map in drug discovery and development

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works

The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease

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

The human disease network

Goh, K.-I., Cusick, M. E., Valle, D., Childs, B., Vidal, M., & Barabási, A.-L. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701361104 · Cited by 3,242 · see citing works

Drug repositioning: identifying and developing new uses for existing drugs

Ashburn, T. T., & Thor, K. B. (2004) · Nature Reviews Drug Discovery · doi:10.1038/nrd1468 · Cited by 3,237 · see citing works

DrugBank: a knowledgebase for drugs, drug actions and drug targets

Wishart, D. S., Knox, C., Guo, A. C., Cheng, D., Shrivastava, S., Tzur, D., Gautam, B., & Hassanali, M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm958 · Cited by 2,852 · see citing works

Nonparametric Statistical Methods.

Knott, M. J., Hollander, M., & Wolfe, D. A. (1974) · Journal of the Royal Statistical Society Series A (General) · doi:10.2307/2344557 · Cited by 2,687 · see citing works

Drug—target network

Yıldırım, M. A., Goh, K.-I., Cusick, M. E., Barabási, A.-Ĺ., & Vidal, M. (2007) · Nature Biotechnology · doi:10.1038/nbt1338 · Cited by 1,711 · see citing works

Nonparametric Statistical Methods

Ramsey, P. H., Hollander, M., & Wolfe, D. A. (2000) · Technometrics · doi:10.2307/1271473 · Cited by 1,167 · see citing works

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

Lachmann, A., Xu, H., Krishnan, J., Berger, S., Mazloom, A. R., & Ma’ayan, A. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq466 · Cited by 997 · see citing works

Nonparametric Statistical Methods, 2nd, Ed.

Borror, C. M. (2001) · Journal of Quality Technology · doi:10.1080/00224065.2001.11980073 · Cited by 876 · see citing works

Global mapping of pharmacological space

Paolini, G. V., Shapland, R. H. B., van Hoorn, W. P., Mason, J. S., & Hopkins, A. L. (2006) · Nature Biotechnology · doi:10.1038/nbt1228 · Cited by 812 · see citing works

Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data

Sirota, M., Dudley, J. T., Kim, J., Chiang, A. P.-F., Morgan, A. A., Sweet-Cordero, A., Sage, J., & Butte, A. J. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3001318 · Cited by 801 · see citing works

Systematic discovery of multicomponent therapeutics

Borisy, A. A., Elliott, P. J., Hurst, N. W., Lee, M. S., Lehár, J., Price, E. R., Serbedzija, G., Zimmermann, G. R., Foley, M. A., Stockwell, B. R., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1337088100 · Cited by 620 · see citing works

Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators

Hieronymus, H., Lamb, J., Ross, K. N., Peng, X. P., Clement, C. C., Rodina, A., Nieto, M., Du, J., Stegmaier, K., Raj, S. M., et al. (2006) · Cancer Cell · doi:10.1016/j.ccr.2006.09.005 · Cited by 616 · 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

CLINICAL DEVELOPMENT OF HISTONE DEACETYLASE INHIBITORS AS ANTICANCER AGENTS

Drummond, D. C., Noble, C. O., Kirpotin, D. B., Guo, Z., Scott, G. K., & Benz, C. C. (2004) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.45.120403.095825 · Cited by 598 · see citing works

Exploiting drug-disease relationships for computational drug repositioning

Dudley, J. T., Deshpande, T. A., & Butte, A. J. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr013 · Cited by 526 · see citing works

Nonparametric Statistical Methods

Ramsey, P. H. (2000) · Technometrics · doi:10.1080/00401706.2000.10486020 · Cited by 522 · see citing works

Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance

Wei, G., Twomey, D., Lamb, J., Schlis, K. D., Agarwal, J., Stam, R. W., Opferman, J. T., Sallan, S. E., den Boer, M. L., Pieters, R., et al. (2006) · Cancer Cell · doi:10.1016/j.ccr.2006.09.006 · Cited by 505 · see citing works

Inhibition of proteasome deubiquitinating activity as a new cancer therapy

D’Arcy, P., Brnjic, S., Olofsson, M. H., Fryknäs, M., Lindsten, K., Cesare, M. D., Perego, P., Sadeghi, B., Hassan, M., Larsson, R. L., et al. (2011) · Nature Medicine · doi:10.1038/nm.2536 · Cited by 493 · see citing works

The contribution of gene expression profiling to breast cancer classification, prognostication and prediction: a retrospective of the last decade

Weigelt, B., Baehner, F. L., & Reis-Filho, J. S. (2009) · The Journal of Pathology · doi:10.1002/path.2648 · Cited by 482 · see citing works

Use of genome-wide association studies for drug repositioning

Sanséau, P., Agarwal, P., Barnes, M. R., Pastinen, T., Richards, J. B., Cardon, L. R., & Mooser, V. (2012) · Nature Biotechnology · doi:10.1038/nbt.2151 · Cited by 387 · see citing works

mRNA expression signatures of human skeletal muscle atrophy identify a natural compound that increases muscle mass

Kunkel, S. D., Suneja, M., Ebert, S. M., Bongers, K. S., Fox, D. K., Malmberg, S. E., Alipour, F., Shields, R. K., & Adams, C. M. (2011) · Cell Metabolism · doi:10.1016/j.cmet.2011.03.020 · Cited by 345 · see citing works

Human Disease-Drug Network Based on Genomic Expression Profiles

Hu, G., & Agarwal, P. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006536 · Cited by 304 · see citing works

Chemical combination effects predict connectivity in biological systems

Lehár, J., Zimmermann, G. R., Krueger, A. S., Molnar, R. A., Ledell, J. T., Heilbut, A. M., Short, G. F., Giusti, L. C., Nolan, G. P., Magid, O. A., et al. (2007) · Molecular Systems Biology · doi:10.1038/msb4100116 · Cited by 275 · see citing works

Systematic Drug Repositioning Based on Clinical Side-Effects

Yang, L., & Agarwal, P. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028025 · Cited by 266 · see citing works

Structural Biology and Drug Discovery of Difficult Targets: The Limits of Ligandability

Surade, S., & Blundell, T. L. (2012) · Chemistry & Biology · doi:10.1016/j.chembiol.2011.12.013 · Cited by 230 · see citing works

Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data

Hassane, D. C., Guzmán, M. L., Corbett, C. A., Li, X., Abboud, R., Young, F. M., Liesveld, J. L., Carroll, M. P., & Jordan, C. T. (2008) · Blood · doi:10.1182/blood-2007-11-126003 · Cited by 185 · see citing works

Effects of Cigarette Smoke on the Human Oral Mucosal Transcriptome

Boyle, J. O., Gumus, Z. H., Kacker, A., Choksi, V. L., Bocker, J. M., Zhou, X. K., Yantiss, R. K., Hughes, D. B., Du, B., Judson, B. L., et al. (2010) · Cancer Prevention Research · doi:10.1158/1940-6207.capr-09-0192 · Cited by 172 · see citing works

Histone Deacetylase Inhibitors: Mechanisms and Clinical Significance in Cancer: HDAC Inhibitor-Induced Apoptosis

Shankar, S., & Srivastava, R. K. (2007) · Advances in experimental medicine and biology · doi:10.1007/978-1-4020-6554-5_13 · Cited by 158 · see citing works

Drug-Induced Regulation of Target Expression

Iskar, M., Campillos, M., Kuhn, M., Jensen, L. J., van Noort, V., & Peer Bork, B. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000925 · Cited by 143 · see citing works

Discovery of Molecular Mechanisms of Traditional Chinese Medicinal Formula Si-Wu-Tang Using Gene Expression Microarray and Connectivity Map

Wen, Z., Wang, Z. K., Wang, S., Ravula, R., Yang, L., Xu, J., Wang, C., Zuo, Z., Chow, M. S. S., Shi, L. M., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018278 · Cited by 136 · see citing works

Alpha terpineol: a potential anticancer agent which acts through suppressing NF-kappaB signalling.

Hassan, S. B., Gali‐Muhtasib, H. U., Göransson, H., & Larsson, R. L. (2010) · PubMed · Cited by 130 · see citing works

Diurnal variation of the human adipose transcriptome and the link to metabolic disease

Loboda, A., Kraft, W. K., Fine, B., Joseph, J., Nebozhyn, M., Zhang, C., He, Y., Yang, X., Wright, C., Morris, M., et al. (2009) · BMC Medical Genomics · doi:10.1186/1755-8794-2-7 · Cited by 124 · see citing works

Gene Expression Signature Analysis Identifies Vorinostat as a Candidate Therapy for Gastric Cancer

Claerhout, S., Lim, J. Y., Choi, W., Park, Y.-Y., Kim, K., Kim, S.-B., Lee, J., Mills, G. B., & Choi, Y. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024662 · Cited by 117 · see citing works

Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses

Slonim, D. K., Koide, K., Johnson, K. L., Tantravahi, U., Cowan, J. M., Jarrah, Z., & Bianchi, D. W. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903909106 · Cited by 117 · see citing works

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Zhang, S.-D., & Gant, T. W. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-258 · Cited by 115 · see citing works

Network analysis of FDA approved drugs and their targets

Ma’ayan, A., Jenkins, S. L., Goldfarb, J., & Iyengar, R. (2007) · Mount Sinai Journal of Medicine A Journal of Translational and Personalized Medicine · doi:10.1002/msj.20002 · Cited by 115 · 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

Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome — Clozapine-Induced Agranulocytosis as a Case Study

Yang, L., Wang, K., Chen, J., Jegga, A. G., Luo, H., Shi, L. M., Wan, C., Guo, X., Qin, S., He, G., et al. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002016 · Cited by 104 · see citing works

Proteomic and transcriptomic study on the action of a cytotoxic saponin (Polyphyllin D): Induction of endoplasmic reticulum stress and mitochondria‐mediated apoptotic pathways

Siu, F., Ma, D., Cheung, Y., Lok, C., Yan, K. H., Yang, Z., Yang, M., Xu, S., Ko, B. C. B., He, Q., et al. (2008) · PROTEOMICS · doi:10.1002/pmic.200700829 · Cited by 102 · see citing works

Identifying Network of Drug Mode of Action by Gene Expression Profiling

Iorio, F., Tagliaferri, R., & di Bernardo, D. (2009) · Journal of Computational Biology · doi:10.1089/cmb.2008.10tt · Cited by 101 · see citing works

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Zhang, S., & Gant, T. W. (2008) · Figshare · Cited by 98 · see citing works

Old drugs – new uses

Aronson, J. K. (2007) · British Journal of Clinical Pharmacology · doi:10.1111/j.1365-2125.2007.03058.x · Cited by 91 · see citing works

A gene signature-based approach identifies thioridazine as an inhibitor of phosphatidylinositol-3′-kinase (PI3K)/AKT pathway in ovarian cancer cells

Rho, S. B., Kim, B.-R., & Kang, S. (2010) · Gynecologic Oncology · doi:10.1016/j.ygyno.2010.10.003 · Cited by 89 · see citing works

Coordinated posttranscriptional mRNA population dynamics during T‐cell activation

Mukherjee, N., Lager, P. J., Friedersdorf, M. B., Thompson, M. A., & Keene, J. D. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.44 · Cited by 86 · see citing works

sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

Zhang, S., & Gant, T. W. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-236 · Cited by 81 · see citing works

Gene Expression-Based Chemical Genomics Identifies Potential Therapeutic Drugs in Hepatocellular Carcinoma

Chen, M., Yang, W.-L. R., Lin, K., Liu, C.-H., Liu, Y.-W., Huang, K., Chang, P. M., Lai, J.-M., Hsu, C.-N., Chao, K., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027186 · Cited by 75 · see citing works

Chemical genomic screening reveals synergism between parthenolide and inhibitors of the PI-3 kinase and mTOR pathways

Hassane, D. C., Sen, S., Minhajuddin, M., Rossi, R. M., Corbett, C. A., Balys, M. M., Wei, L., Crooks, P. A., Guzmán, M. L., & Jordan, C. T. (2010) · Blood · doi:10.1182/blood-2010-04-278044 · Cited by 75 · see citing works

Evaluation of Phenoxybenzamine in the CFA Model of Pain following Gene Expression Studies and Connectivity Mapping

Chang, M., Smith, S. E., Thorpe, A., Barratt, M. J., & Karim, F. (2010) · Molecular Pain · doi:10.1186/1744-8069-6-56 · Cited by 75 · see citing works

Modulation of Wnt/β-catenin signaling and proliferation by a ferrous iron chelator with therapeutic efficacy in genetically engineered mouse models of cancer

Coombs, G. S., Schmitt, A., Canning, C. A., Alok, A., Low, I. C. C., Banerjee, N., Kaur, S. J., Utomo, V., Jones, C. M., Pervaiz, S., et al. (2011) · Oncogene · doi:10.1038/onc.2011.228 · Cited by 69 · see citing works

Expectations, validity, and reality in gene expression profiling

Kim, K., Zakharkin, S. O., & Allison, D. B. (2010) · Journal of Clinical Epidemiology · doi:10.1016/j.jclinepi.2010.02.018 · Cited by 68 · see citing works

Identifying Inhibitors of Epithelial-Mesenchymal Transition by Connectivity Map–Based Systems Approach

Reka, A. K., Kuick, R. D., Kurapati, H., Standiford, T. J., Omenn, G. S., & Keshamouni, V. G. (2011) · Journal of Thoracic Oncology · doi:10.1097/jto.0b013e31822adfb0 · Cited by 66 · see citing works

Gene Expression Patterns in Mismatch Repair-Deficient Colorectal Cancers Highlight the Potential Therapeutic Role of Inhibitors of the Phosphatidylinositol 3-Kinase-AKT-Mammalian Target of Rapamycin Pathway

Vilar, E., Mukherjee, B., Kuick, R. D., Raskin, L., Misek, D. E., Taylor, J. M. G., Giordano, T. J., Hanash, S., Fearon, E. R., Rennert, G., et al. (2009) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-08-2432 · Cited by 66 · see citing works

Epigenetic therapy in cancer: molecular background and clinical development of histone deacetylase and DNA methyltransferase inhibitors.

Schneider‐Stock, R., & Ocker, M. (2007) · PubMed · Cited by 61 · see citing works

Bayesian approach to transforming public gene expression repositories into disease diagnosis databases

Huang, H., Liu, C.-C., & Zhou, X. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912043107 · Cited by 51 · see citing works

An Integrated Bioinformatics Approach Identifies Elevated Cyclin E2 Expression and E2F Activity as Distinct Features of Tamoxifen Resistant Breast Tumors

Huang, L., Zhao, S., Frasor, J. M., & Dai, Y. D. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022274 · Cited by 43 · see citing works

Expression-Based In Silico Screening of Candidate Therapeutic Compounds for Lung Adenocarcinoma

Wang, G., Ye, Y., Yang, X., Liao, H., Zhao, C., & Liang, S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0014573 · Cited by 43 · see citing works

Expression profiling identifies epoxy anthraquinone derivative as a DNA topoisomerase inhibitor

Gheeya, J., Johansson, P. A., Chen, Q., Dexheimer, T. S., Metaferia, B. B., Song, Y., Wei, J. S., He, J., Pommier, Y. G., & Khan, J. I. (2010) · Cancer Letters · doi:10.1016/j.canlet.2010.01.004 · Cited by 30 · see citing works

Identification of novel hair‐growth inducers by means of connectivity mapping

Ishimatsu‐Tsuji, Y., Soma, T., & Kishimoto, J. (2009) · The FASEB Journal · doi:10.1096/fj.09-145292 · Cited by 30 · see citing works

A chemical genetic approach identifies piperazine antipsychotics as promoters of CNS neurite growth on inhibitory substrates

Johnstone, A. L., Reierson, G. W., Smith, R. P., Goldberg, J. L., Lemmon, V., & Bixby, J. L. (2012) · Molecular and Cellular Neuroscience · doi:10.1016/j.mcn.2012.04.008 · Cited by 30 · see citing works

Similar compounds searching system by using the gene expression microarray database

Toyoshiba, H., Sawada, H., Naeshiro, I., & Horinouchi, A. (2008) · Toxicology Letters · doi:10.1016/j.toxlet.2008.08.009 · Cited by 20 · see citing works

Characterization of AKT independent effects of the synthetic AKT inhibitors SH-5 and SH-6 using an integrated approach combining transcriptomic profiling and signaling pathway perturbations

Krech, T., Thiede, M., Hilgenberg, E., Schäfer, R., & Jürchott, K. (2010) · BMC Cancer · doi:10.1186/1471-2407-10-287 · Cited by 18 · see citing works

Integrated Genomic and Pharmacological Approaches to Identify Synthetic Lethal Genes as Cancer Therapeutic Targets

Mizuarai, S., Irie, H., Schmatz, D. M., & Kotani, H. (2008) · Current Molecular Medicine · doi:10.2174/156652408786733676 · Cited by 18 · see citing works

Downstream Gene Activation of the Receptor ALX by the Agonist Annexin A1

Renshaw, D. W., Montero‐Melendez, T., Dalli, J., Kamal, A. M., Brancaleone, V., D’Acquisto, F., Cirino, G., & Perretti, M. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012771 · Cited by 17 · see citing works

Phenotype-based drug screening in primary ovarian carcinoma cultures identifies intracellular iron depletion as a promising strategy for cancer treatment

Gullbo, J., Fryknäs, M., Rickardson, L., D’Arcy, P., Hägg, M., Wickström, M., Hassan, S., Westman, G., Brnjic, S., Nygren, P., et al. (2011) · Biochemical Pharmacology · doi:10.1016/j.bcp.2011.04.003 · Cited by 14 · see citing works

Systematic integration of biomedical knowledge prioritizes drugs for repurposing

Himmelstein, D. S., Lizee, A., Hessler, C., Brueggeman, L., Chen, S. L., Hadley, D., Green, A., Khankhanian, P., & Baranzini, S. E. (2017) · eLife · doi:10.7554/elife.26726 · Cited by 666 · see citing works

Network pharmacology applications to map the unexplored target space and therapeutic potential of natural products

Kibble, M., Saarinen, N., Tang, J. P., Wennerberg, K., Mäkelä, S., & Aittokallio, T. A. (2015) · Natural Product Reports · doi:10.1039/c5np00005j · Cited by 503 · see citing works

Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders

Parikshak, N. N., Gandal, M. J., & Geschwind, D. H. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3934 · Cited by 430 · see citing works

Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines

Jin, G., & Wong, S. T. C. (2013) · Drug Discovery Today · doi:10.1016/j.drudis.2013.11.005 · Cited by 416 · see citing works

Multi-target pharmacology: possibilities and limitations of the “skeleton key approach” from a medicinal chemist perspective

Talevi, A. (2015) · Frontiers in Pharmacology · doi:10.3389/fphar.2015.00205 · Cited by 397 · see citing works

Computational Drug Repositioning: From Data to Therapeutics

Hurle, M. R., Yang, L., Xie, Q. S., Rajpal, D. K., Sanséau, P., & Agarwal, P. (2013) · Clinical Pharmacology & Therapeutics · doi:10.1038/clpt.2013.1 · Cited by 375 · see citing works

Giving Drugs a Second Chance: Overcoming Regulatory and Financial Hurdles in Repurposing Approved Drugs As Cancer Therapeutics

Hernández, J. J., Pryszlak, M., Smith, L., Yanchus, C., Kurji, N., Shahani, V. M., & Molinski, S. V. (2017) · Frontiers in Oncology · doi:10.3389/fonc.2017.00273 · Cited by 281 · see citing works

A circRNA–miRNA–mRNA network identification for exploring underlying pathogenesis and therapy strategy of hepatocellular carcinoma

Xiong, D., Dang, Y., Lin, P., Wen, D., He, R., Luo, D., Feng, Z., & Chen, G. (2018) · Journal of Translational Medicine · doi:10.1186/s12967-018-1593-5 · Cited by 280 · see citing works

A review of connectivity map and computational approaches in pharmacogenomics

Musa, A., Ghoraie, L. S., Zhang, S., Galzko, G., Yli-Harja, O. P., Dehmer, M., Haibe‐Kains, B., & Emmert‐Streib, F. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbw112 · Cited by 275 · see citing works

The phytochemical hyperforin triggers thermogenesis in adipose tissue via a Dlat-AMPK signaling axis to curb obesity

Chen, S., Liu, X., Peng, C., Tan, C., Sun, H., Liu, H., Zhang, Y., Wu, P., Cui, C., Liu, C., et al. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2021.02.007 · Cited by 235 · see citing works

CLC-Pred: A freely available web-service for in silico prediction of human cell line cytotoxicity for drug-like compounds

Lagunin, A. A., Dubovskaja, V., Rudik, A. V., Pogodin, P. V., Druzhilovskiy, D. S., Gloriozova, T. A., Filimonov, D. A., Sastry, N. G., & Poroikov, V. (2018) · PLoS ONE · doi:10.1371/journal.pone.0191838 · Cited by 201 · see citing works

Role of the ERO1-PDI interaction in oxidative protein folding and disease

Shergalis, A. G., Hu, S., Bankhead, A., & Neamati, N. (2020) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2020.107525 · Cited by 194 · see citing works

Drug repurposing in oncology: Compounds, pathways, phenotypes and computational approaches for colorectal cancer

Nowak-Sliwinska, P. M., Scapozza, L., & Altaba, A. R. I. (2019) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2019.04.005 · Cited by 183 · see citing works

Drug Repositioning: New Approaches and Future Prospects for Life-Debilitating Diseases and the COVID-19 Pandemic Outbreak

Low, Z. Y., Farouk, I. A., & Lal, S. K. (2020) · Viruses · doi:10.3390/v12091058 · Cited by 180 · see citing works

Systems biology approaches for advancing the discovery of effective drug combinations

Ryall, K. A., & Tan, A. C. (2015) · Journal of Cheminformatics · doi:10.1186/s13321-015-0055-9 · Cited by 160 · see citing works

In silico polypharmacology of natural products

Fang, J., Liu, C., Wang, Q., Lin, P., & Cheng, F. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx045 · Cited by 164 · see citing works

Advances in identification and validation of protein targets of natural products without chemical modification

Chang, J., Kim, Y., & Kwon, H. J. (2016) · Natural Product Reports · doi:10.1039/c5np00107b · Cited by 151 · see citing works

mTOR Inhibitors Suppress Homologous Recombination Repair and Synergize with PARP Inhibitors via Regulating SUV39H1 in BRCA-Proficient Triple-Negative Breast Cancer

Mo, W., Liu, Q., Lin, C. C.-J., Dai, H., Peng, Y., Liang, Y., Peng, G., Meric‐Bernstam, F., Mills, G. B., Li, K., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-1772 · Cited by 137 · see citing works

DIGEP-Pred: web service for in silico prediction of drug-induced gene expression profiles based on structural formula

Lagunin, A. A., Ivanov, S. M., Rudik, A. V., Filimonov, D. A., & Poroikov, V. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt322 · Cited by 133 · see citing works

Systematic evaluation of connectivity map for disease indications

Cheng, J., Yang, L., Kumar, V. D., & Agarwal, P. (2014) · Genome Medicine · doi:10.1186/s13073-014-0095-1 · Cited by 131 · see citing works

Characterization of drug‐induced transcriptional modules: towards drug repositioning and functional understanding

Iskar, M., Zeller, G., Blattmann, P., Campillos, M., Kuhn, M., Kaminska, K. H., Runz, H., Gavin, A., Pepperkok, R., van Noort, V., et al. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.20 · Cited by 118 · see citing works

Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies

Moni, M. A., & Lió, P. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-333 · Cited by 106 · see citing works

Novel Drug Candidates for the Treatment of Metastatic Colorectal Cancer through Global Inverse Gene-Expression Profiling

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Thioridazine inhibits autophagy and sensitizes glioblastoma cells to temozolomide

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A network-based method for mechanistic investigation of Shexiang Baoxin Pill’s treatment of cardiovascular diseases

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Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes

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Target deconvolution of bioactive small molecules: the heart of chemical biology and drug discovery

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Identification of circRNA–miRNA–mRNA networks contributes to explore underlying pathogenesis and therapy strategy of gastric cancer

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Using the Connectivity Map to discover compounds influencing human osteoblast differentiation

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A pre-clinical model of resistance to induction therapy in pediatric acute lymphoblastic leukemia

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Assessing compound carcinogenicity in vitro using connectivity mapping

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Probabilistic drug connectivity mapping

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Analysis of Infected Host Gene Expression Reveals Repurposed Drug Candidates and Time-Dependent Host Response Dynamics for COVID-19Preprint

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How Not To Drown in Data: A Guide for Biomaterial Engineers

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Identification of repaglinide as a therapeutic drug for glioblastoma multiforme

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Transcriptome-based identification of lovastatin as a breast cancer stem cell-targeting drug

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The opportunities of mining historical and collective data in drug discovery

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Current progress and future perspectives of polypharmacology : From the view of non-small cell lung cancer

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Computational Identification of Potential Multitarget Inhibitors of Nipah Virus by Molecular Docking and Molecular Dynamics

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Phenotypic chemical biology for predicting safety and efficacy

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Identification of Prognostic Signature and Gliclazide as Candidate Drugs in Lung Adenocarcinoma

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Phenotypic Screens Targeting Neurodegenerative Diseases

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Connectivity mapping using a combined gene signature from multiple colorectal cancer datasets identified candidate drugs including existing chemotherapies

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Using Pharmacogenomic Databases for Discovering Patient-Target Genes and Small Molecule Candidates to Cancer Therapy

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High-throughput Drug Repositioning for the Discovery of New Treatments for Chagas Disease

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Connectivity map identifies HDAC inhibition as a treatment option of high-risk hepatoblastoma

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Promising targets and drugs in rheumatoid arthritis

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The Neuroimmune Transcriptome and Alcohol Dependence: Potential for Targeted Therapies

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The Advantages of Connectivity Map Applied in Traditional Chinese Medicine

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Discovery of potential drugs for COVID-19 based on the connectivity mapPreprint

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Computational Drug Repositioning and Experimental Validation of Ivermectin in Treatment of Gastric Cancer

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Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post- chemotherapy tissues

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Indirubin, a small molecular deriving from connectivity map (CMAP) screening, ameliorates obesity-induced metabolic dysfunction by enhancing brown adipose thermogenesis and white adipose browning

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Connectivity Map

(2008) · Springer eBooks · doi:10.1007/978-1-4020-6754-9_3532