High-content phenotypic and pathway profiling to advance drug discovery in diseases of unmet need

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

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., Bork, P., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1131 · Cited by 17,749 · see citing works

Tissue-based map of the human proteome

Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science · doi:10.1126/science.1260419 · Cited by 15,286 · see citing works

STRING v10: protein–protein interaction networks, integrated over the tree of life

Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1003 · Cited by 10,436 · see citing works

Trastuzumab in combination with chemotherapy versus chemotherapy alone for treatment of HER2-positive advanced gastric or gastro-oesophageal junction cancer (ToGA): a phase 3, open-label, randomised controlled trial

Bang, Y.-J., Van Cutsem, E., Feyereislova, A., Chung, H. C., Shen, L., Sawaki, A., Lordick, F., Ohtsu, A., Omuro, Y., Satoh, T., et al. (2010) · The Lancet · doi:10.1016/s0140-6736(10)61121-x · Cited by 7,302 · see citing works

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N. T., Roth, A., Bork, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw937 · Cited by 6,980 · see citing works

Glioma stem cells promote radioresistance by preferential activation of the DNA damage response

Bao, S., Wu, Q., McLendon, R. E., Hao, Y., Shi, Q., Hjelmeland, A. B., Dewhirst, M. W., Bigner, D. D., & Rich, J. N. (2006) · Nature · doi:10.1038/nature05236 · Cited by 6,397 · 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

Network pharmacology: the next paradigm in drug discovery

Hopkins, A. L. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.118 · Cited by 4,622 · see citing works

ChEMBL: a large-scale bioactivity database for drug discovery

Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., Light, Y., McGlinchey, S., Michalovich, D., Al-Lazikani, B., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr777 · Cited by 4,382 · see citing works

Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells

Yang, W., Soares, J., Greninger, P., Edelman, E. J., Lightfoot, H., Forbes, S., Bindal, N., Beare, D., Smith, J. A., Thompson, I. R., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1111 · Cited by 4,051 · see citing works

DrugBank: a comprehensive resource for in silico drug discovery and exploration

Wishart, D. S. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj067 · Cited by 3,892 · see citing works

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles

Subramanian, A., Narayan, R., Corsello, S. M., Peck, D. D., Natoli, T. E., Lu, X., Gould, J., Davis, J. F., Tubelli, A. A., Asiedu, J. K., et al. (2017) · Cell · doi:10.1016/j.cell.2017.10.049 · Cited by 3,515 · see citing works

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders

Hamosh, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki033 · Cited by 3,443 · see citing works

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells

Klein, A. M., Mazutis, L., Akartuna, I., Tallapragada, N., Veres, A., Li, V., Peshkin, L., Weitz, D. A., & Kirschner, M. W. (2015) · Cell · doi:10.1016/j.cell.2015.04.044 · Cited by 3,356 · see citing works

Defining a Cancer Dependency Map

Tsherniak, A., Vazquez, F., Montgomery, P. G., Weir, B. A., Kryukov, G., Cowley, G. S., Gill, S., Harrington, W. F., Pantel, S., Krill-Burger, J. M., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.010 · Cited by 3,276 · see citing works

Clinical development success rates for investigational drugs

Hay, M., Thomas, D. W., Craighead, J. L., Economides, C., & Rosenthal, J. (2014) · Nature Biotechnology · doi:10.1038/nbt.2786 · Cited by 2,536 · see citing works

Relating protein pharmacology by ligand chemistry

Keiser, M. J., Roth, B. L., Armbruster, B. N., Ernsberger, P., Irwin, J. J., & Shoichet, B. K. (2007) · Nature Biotechnology · doi:10.1038/nbt1284 · Cited by 2,402 · see citing works

The mechanisms of action of metformin

Rena, G., Hardie, D. G., & Pearson, E. R. (2017) · Diabetologia · doi:10.1007/s00125-017-4342-z · Cited by 2,287 · see citing works

A restricted cell population propagates glioblastoma growth after chemotherapy

Chen, J., Li, Y., Yu, T.-S., McKay, R. M., Burns, D. K., Kernie, S. G., & Parada, L. F. (2012) · Nature · doi:10.1038/nature11287 · Cited by 2,096 · see citing works

Direct multiplexed measurement of gene expression with color-coded probe pairs

Geiss, G. K., Bumgarner, R. E., Birditt, B., Dahl, T., Dowidar, N., Dunaway, D. L., Fell, H. P., Ferree, S., George, R. D., Grogan, T., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1385 · Cited by 2,066 · see citing works

How were new medicines discovered?

Swinney, D. C., & Anthony, J. (2011) · Nature Reviews Drug Discovery · doi:10.1038/nrd3480 · Cited by 1,812 · see citing works

SwissTargetPrediction: a web server for target prediction of bioactive small molecules

Gfeller, D., Grosdidier, A., Wirth, M., Daina, A., Michielin, O. A., & Zoete, V. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku293 · Cited by 1,811 · see citing works

Cancer stem cells in glioblastomaPreprint

Lathia, J. D., Mack, S. C., Mulkearns-Hubert, E. E., Valentim, C. L. L., & Rich, J. N. (2015) · Genes & Development · doi:10.1101/gad.261982.115 · Cited by 1,600 · see citing works

NCBI GEO: mining tens of millions of expression profiles--database and tools update

Barrett, T., Troup, D. B., Wilhite, S. E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I. F., Soboleva, A., Tomashevsky, M., & Edgar, R. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl887 · Cited by 1,524 · see citing works

PubChem: a public information system for analyzing bioactivities of small molecules

Wang, Y., Xiao, J., Önal-Süzek, T., Zhang, J., Wang, J., & Bryant, S. H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp456 · Cited by 1,465 · see citing works

Glioblastoma: Overview of Disease and Treatment

Davis, M. E. (2016) · Clinical journal of oncology nursing · doi:10.1188/16.cjon.s1.2-8 · Cited by 1,222 · see citing works

The IntAct molecular interaction database in 2012

Kerrien, S., Aranda, B., Breuza, L., Bridge, A. J., Broackes-Carter, F., Chen, C. C. L., Duesbury, M., Dumousseau, M., Feuermann, M., Hinz, U. G., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1088 · Cited by 1,151 · see citing works

Target identification and mechanism of action in chemical biology and drug discovery

Schenone, M., Dančík, V., Wagner, B. K., & Clemons, P. A. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1199 · Cited by 1,107 · see citing works

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

Bray, M.-A., Singh, S., Han, H., Davis, C. T., Borgeson, B., Hartland, C., Kost-Alimova, M., Gustafsdottir, S. M., Gibson, C. C., & Carpenter, A. E. (2016) · Nature Protocols · doi:10.1038/nprot.2016.105 · Cited by 1,090 · see citing works

Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in HumansPreprint

Kristiansen, T. Z., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T. K. B., Gronborg, M., et al. (2003) · Genome Research · doi:10.1101/gr.1680803 · Cited by 1,078 · see citing works

Artificial intelligence in drug development: Present status and future prospects

Mak, K.-K., & Pichika, M. R. (2019) · Drug Discovery Today · doi:10.1016/j.drudis.2018.11.014 · Cited by 1,018 · see citing works

The Genetic Association Database

Becker, K. G., Barnes, K. C., Bright, T. J., & Wang, S. A. (2004) · Nature Genetics · doi:10.1038/ng0504-431 · Cited by 971 · see citing works

Opportunities and challenges in phenotypic drug discovery: an industry perspective

Moffat, J. G., Vincent, F., Lee, J. A., Eder, J., & Prunotto, M. (2017) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2017.111 · Cited by 939 · see citing works

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

Csermely, P., Korcsmáros, T., Kiss, H., London, G., & Nussinov, R. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.016 · Cited by 889 · see citing works

Correlating chemical sensitivity and basal gene expression reveals mechanism of action

Rees, M. G., Seashore-Ludlow, B. A., Cheah, J. H., Adams, D., Price, E. V., Gill, S., Javaid, S., Coletti, M. E., Jones, V., Bodycombe, N. E., et al. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1986 · Cited by 874 · see citing works

Reactome knowledgebase of human biological pathways and processes

Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn863 · Cited by 873 · see citing works

MINT: a Molecular INTeraction database

Zanzoni, A., Montecchi‐Palazzi, L., Quondam, M., Ausiello, G., Helmer‐Citterich, M., & Cesareni, G. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)03293-8 · Cited by 792 · see citing works

Using graph theory to analyze biological networks

Pavlopoulos, G. A., Secrier, M., Moschopoulos, C. N., Soldatos, T. G., Κοσσίδα, Σ., Aerts, J. A., Schneider, R., & Bagos, P. G. (2011) · BioData Mining · doi:10.1186/1756-0381-4-10 · Cited by 784 · see citing works

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders

Hamosh, A. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.52 · Cited by 762 · see citing works

Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials

Lin, A., Giuliano, C. J., Palladino, A. C., John, K. M., Abramowicz, C., Yuan, M. L., Sausville, E. L., Lukow, D. A., Liu, L., Chait, A. R., et al. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aaw8412 · Cited by 747 · see citing works

Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks

Lee, M. J., Ye, A. S., Gardino, A. K., Heijink, A. M., Sorger, P. K., MacBeath, G., & Yaffe, M. B. (2012) · Cell · doi:10.1016/j.cell.2012.03.031 · Cited by 681 · see citing works

Multidimensional Drug Profiling By Automated Microscopy

Perlman, Z. E., Slack, M. D., Feng, Y., Mitchison, T. J., Wu, L. F., & Altschuler, S. J. (2004) · Science · doi:10.1126/science.1100709 · Cited by 660 · see citing works

An open-source drug discovery platform enables ultra-large virtual screens

Gorgulla, C., Boeszoermenyi, A., Wang, Z., Fischer, P. D., Coote, P. W., Das, K. M., Malets, Y. S., Radchenko, D. S., Moroz, Y. S., Scott, D. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2117-z · Cited by 652 · 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

Discovery of Risdiplam, a Selective Survival of Motor Neuron-2 ( SMN2 ) Gene Splicing Modifier for the Treatment of Spinal Muscular Atrophy (SMA)

Ratni, H., Ebeling, M., Baird, J. D., Bendels, S., Bylund, J., Chen, K. S., Denk, N., Feng, Z., Green, L., Guérard, M., et al. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b00741 · Cited by 545 · see citing works

The discovery of first-in-class drugs: origins and evolution

Eder, J., Sedrani, R., & Wiesmann, C. (2014) · Nature Reviews Drug Discovery · doi:10.1038/nrd4336 · Cited by 514 · see citing works

Phenotypic screening in cancer drug discovery — past, present and future

Moffat, J. G., Rudolph, J., & Bailey, D. (2014) · Nature Reviews Drug Discovery · doi:10.1038/nrd4366 · Cited by 507 · see citing works

Open Targets: a platform for therapeutic target identification and validation

Koscielny, G., An, P., Carvalho‐Silva, D., Cham, J. A., Fumis, L., Gasparyan, R., Hasan, S., Karamanis, N., Maguire, M., Papa, E., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1055 · Cited by 500 · 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

STITCH 4: integration of protein–chemical interactions with user data

Kuhn, M., Szklarczyk, D., Pletscher-Frankild, S., Blicher, T. H., von Mering, C., Jensen, L. J., & Peer Bork, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1207 · Cited by 487 · see citing works

Open Targets Platform: new developments and updates two years on

Carvalho‐Silva, D., Pierleoni, A., Pignatelli, M., Ong, C. K., Fumis, L., Karamanis, N., Carmona, M., Faulconbridge, A., Hercules, A., McAuley, E., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1133 · Cited by 449 · see citing works

In silico activity profiling reveals the mechanism of action of antimalarials discovered in a high-throughput screen

Plouffe, D., Brinker, A., McNamara, C. W., Henson, K., Kato, N., Kuhen, K., Nagle, A. S., Adrián, F., Matzen, J., Anderson, P., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802982105 · Cited by 442 · see citing works

Classifying and segmenting microscopy images with deep multiple instance learning

Kraus, O. Z., Ba, J. L., & Frey, B. J. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw252 · Cited by 407 · see citing works

Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action

Zhao, S., & Iyengar, R. (2011) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010611-134520 · Cited by 358 · see citing works

Integrating high-content screening and ligand-target prediction to identify mechanism of action

Young, D. W., Bender, A., Hoyt, J., McWhinnie, E., Chirn, G.-W., Tao, C. Y., Tallarico, J. A., Labow, M., Jenkins, J. L., Mitchison, T. J., et al. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.2007.53 · Cited by 345 · see citing works

Prediction of Biological Targets for Compounds Using Multiple-Category Bayesian Models Trained on Chemogenomics Databases

Nidhi, N., Glick, M., Davies, J. W., & Jenkins, J. L. (2006) · Journal of Chemical Information and Modeling · doi:10.1021/ci060003g · Cited by 340 · see citing works

Multiplex Cytological Profiling Assay to Measure Diverse Cellular States

Gustafsdottir, S. M., Ljosa, V., Sokolnicki, K. L., Anthony Wilson, J., Walpita, D., Kemp, M. M., Petri Seiler, K., Carrel, H. A., Golub, T. R., Schreiber, S. L., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080999 · Cited by 291 · see citing works

Multi-Target Drugs: The Trend of Drug Research and Development

Lu, J., Pan, W., Yuanjia, H., & Wang, Y. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040262 · Cited by 259 · see citing works

Zeptosens' protein microarrays: A novel high performance microarray platform for low abundance protein analysis

Pawlak, M., Schick, E., Bopp, M. A., Schneider, M. J., Oroszlan, P. L., & Ehrat, M. (2002) · PROTEOMICS · doi:10.1002/1615-9861(200204)2:4 · Cited by 258 · see citing works

Applications of Connectivity Map in drug discovery and development

Qu, X. A., & Rajpal, D. K. (2012) · Drug Discovery Today · doi:10.1016/j.drudis.2012.07.017 · Cited by 235 · see citing works

Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus

Reker, D., Rodrigues, T., Schneider, P., & Schneider, G. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320001111 · Cited by 226 · see citing works

DRUG-seq for miniaturized high-throughput transcriptome profiling in drug discovery

Ye, C., Ho, D. J., Neri, M., Yang, C., Kulkarni, T., Randhawa, R., Henault, M., Mostacci, N., Farmer, P., Renner, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06500-x · Cited by 222 · see citing works

Comparison of glioblastoma (GBM) molecular classification methods

Lee, E., Yong, R. L. M., Paddison, P. J., & Zhu, J. (2018) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2018.07.006 · Cited by 215 · see citing works

Comparison of Methods for Image-Based Profiling of Cellular Morphological Responses to Small-Molecule Treatment

Ljosa, V., Caie, P. D., ter Horst, R., Sokolnicki, K. L., Jenkins, E. L., Daya, S., Roberts, M. E., Jones, T. R., Singh, S., Genovesio, A., et al. (2013) · SLAS DISCOVERY · doi:10.1177/1087057113503553 · Cited by 183 · see citing works

A multi-scale convolutional neural network for phenotyping high-content cellular images

Godinez, W. J., Hossain, I., Lazic, S. E., Davies, J. W., & Zhang, X. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx069 · Cited by 181 · see citing works

A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay

Bray, M., Gustafsdottir, S., Rohban, M. H., Singh, S., Ljosa, V., Sokolnicki, K. L., Bittker, J. A., Bodycombe, N. E., Dančík, V., Hasaka, T. P., et al. (2017) · GigaScience · doi:10.1093/gigascience/giw014 · Cited by 173 · see citing works

Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action

McFarland, J. M., Paolella, B. R., Warren, A., Geiger-Schuller, K., Shibue, T., Rothberg, M., Kuksenko, O., Colgan, W. N., Jones, A., Chambers, E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17440-w · Cited by 173 · see citing works

High-Content Phenotypic Profiling of Drug Response Signatures across Distinct Cancer Cells

Caie, P. D., Walls, R. E., Ingleston-Orme, A., Daya, S., Houslay, T. M., Eagle, R., Roberts, M. E., & Carragher, N. O. (2010) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-09-1148 · Cited by 172 · see citing works

Realizing the Promise of Reverse Phase Protein Arrays for Clinical, Translational, and Basic Research: A Workshop Report

Akbani, R., Becker, K., Carragher, N. O., Goldstein, T., de Koning, L., Korf, U., Liotta, L. A., Mills, G. B., Nishizuka, S., Pawlak, M., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o113.034918 · Cited by 169 · see citing works

Target 2035: probing the human proteome

Carter, A. J., Kraemer, O., Zwick, M., Mueller‐Fahrnow, A., Arrowsmith, C. H., & Edwards, A. M. (2019) · Drug Discovery Today · doi:10.1016/j.drudis.2019.06.020 · Cited by 169 · see citing works

HAPPI: an online database of comprehensive human annotated and predicted protein interactions

Chen, J. Y., Mamidipalli, S., & Huan, T. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-s1-s16 · Cited by 164 · see citing works

Utility of reverse phase protein arrays: Applications to signalling pathways and human body arrays

Charboneau, L. (2002) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/1.3.305 · Cited by 112 · see citing works

HitPick: a web server for hit identification and target prediction of chemical screenings

Liu, X., Vogt, I., Haque, T., et al. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt303 · Cited by 106 · see citing works

A potential anti-tumor herbal medicine, Corilagin, inhibits ovarian cancer cell growth through blocking the TGF-β signaling pathways

Jia, L., Jin, H., Zhou, J., et al. (2013) · BMC Complementary and Alternative Medicine · doi:10.1186/1472-6882-13-33 · Cited by 98 · see citing works

Improving Phenotypic Measurements in High-Content Imaging Screens

Ando, D. M., McLean, C. Y., & Berndl, M. (2017) · doi:10.1101/161422 · Cited by 96 · see citing works

PASS: identification of probable targets and mechanisms of toxicity

Poroikov, V., Filimonov, D. A., Lagunin, A. A., et al. (2007) · SAR and QSAR in environmental research · doi:10.1080/10629360601054032 · Cited by 92 · see citing works

Off-Target Effects of Psychoactive Drugs Revealed by Genome-Wide Assays in Yeast

Ericson, E., Gebbia, M., Heisler, L. E., Wildenhain, J., Tyers, M., Giaever, G., & Nislow, C. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000151 · Cited by 89 · see citing works

“Omics” data and levels of evidence for biomarker discovery

Ghosh, D., & Poisson, L. (2008) · Genomics · doi:10.1016/j.ygeno.2008.07.006 · Cited by 89 · see citing works

The needle in the haystack: Application of breast fine-needle aspirate samples to quantitative protein microarray technology

Rapkiewicz, A., Espina, V. A., Zujewski, J. A., Lebowitz, P. F., Filie, A. C., Wulfkuhle, J. D., Camphausen, K. A., Petricoin, E. F., Liotta, L. A., & Abati, A. D. (2007) · Cancer · doi:10.1002/cncr.22686 · Cited by 82 · see citing works

Compound signature detection on LINCS L1000 big data

Liu, C., Su, J., Yang, F., Wei, K., Ma, J., & Zhou, X. (2015) · Molecular BioSystems · doi:10.1039/c4mb00677a · Cited by 81 · see citing works

Phenotypic Profiling of Reference Chemicals across Biologically Diverse Cell Types Using the Cell Painting Assay

Willis, C. M., Nyffeler, J., & Harrill, J. (2020) · SLAS DISCOVERY · doi:10.1177/2472555220928004 · Cited by 81 · see citing works

Evolution of commercially available compounds for HTS

Volochnyuk, D. M., Ryabukhin, S. V., Moroz, Y. S., Savych, O., Chuprina, A., Horvath, D., Zabolotna, Y., Varnek, A. A., & Judd, D. B. (2018) · Drug Discovery Today · doi:10.1016/j.drudis.2018.10.016 · Cited by 79 · see citing works

Linking Phenotypes and Modes of Action Through High-Content Screen Fingerprints

Reisen, F., Sauty de Chalon, A., Pfeifer, M., Zhang, X., Gabriel, D., & Selzer, P. (2015) · ASSAY and Drug Development Technologies · doi:10.1089/adt.2015.656 · Cited by 76 · see citing works

Life Beyond Kinases: Structure-Based Discovery of Sorafenib as Nanomolar Antagonist of 5-HT Receptors

Lin, X., Huang, X.-P., Chen, G., Whaley, R., Peng, S., Wang, Y., Zhang, G., Wang, S. X., Wang, S., Roth, B. L., et al. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm300338m · Cited by 73 · see citing works

Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing

Lim, H., Poleksić, A., Yao, Y., Tong, H., He, D., Zhuang, L., Meng, P., & Xie, L. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005135 · Cited by 73 · see citing works

Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens

Lo, Y., Senese, S., Li, C., Hu, Q., Huang, Y., Damoiseaux, R. D., & Torres, J. Z. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004153 · Cited by 72 · see citing works

Discovery of RG7834: The First-in-Class Selective and Orally Available Small Molecule Hepatitis B Virus Expression Inhibitor with Novel Mechanism of Action

Han, X., Zhou, C., Jiang, M., Wang, Y., Wang, J., Cheng, Z., Wang, M., Liu, Y., Liang, C., Wang, J., et al. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b01245 · Cited by 71 · see citing works

Target Fishing for Chemical Compounds Using Target-Ligand Activity Data and Ranking Based Methods

Wale, N., & Karypis, G. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci9000376 · Cited by 70 · see citing works

Emerging Approaches for the Identification of Protein Targets of Small Molecules - A Practitioners’ Perspective

Comess, K. M., McLoughlin, S. M., Oyer, J. A., Richardson, P. L., Stöckmann, H., Vasudevan, A., & Warder, S. E. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b01921 · Cited by 66 · see citing works

Morphological Profiling Identifies a Common Mode of Action for Small Molecules with Different Targets

Schneidewind, T., Brause, A., Pahl, A., Burhop, A., Mejuch, T., Sievers, S., Waldmann, H., & Ziegler, S. (2020) · ChemBioChem · doi:10.1002/cbic.202000381 · Cited by 65 · see citing works

Structural coverage of the proteome for pharmaceutical applications

Somody, J. C., MacKinnon, S. S., & Windemuth, A. (2017) · Drug Discovery Today · doi:10.1016/j.drudis.2017.08.004 · Cited by 59 · see citing works

Systematic Chemogenetic Library Assembly

Canham, S. M., Wang, Y., Cornett, A., Auld, D. S., Baeschlin, D. K., Patoor, M., Skaanderup, P. R., Honda, A., Llamas, L., Wendel, G., et al. (2020) · Cell chemical biology · doi:10.1016/j.chembiol.2020.07.004 · Cited by 59 · see citing works

Brain Tumor Stem Cells Remain in Play

Parada, L. F., Dirks, P. B., & Wechsler‐Reya, R. J. (2017) · Journal of Clinical Oncology · doi:10.1200/jco.2017.73.9540 · Cited by 58 · see citing works

Hit Triage and Validation in Phenotypic Screening: Considerations and Strategies

Vincent, F., Loria, P. M., Weston, A. D., Steppan, C. M., Doyonnas, R., Wang, Y., Rockwell, K. L., & Peakman, M. (2020) · Cell chemical biology · doi:10.1016/j.chembiol.2020.08.009 · Cited by 58 · see citing works

Connectivity Mapping: Methods and Applications

Keenan, A. B., Wojciechowicz, M. L., Wang, Z., Jagodnik, K. M., Jenkins, S. L., Lachmann, A., & Ma’ayan, A. (2019) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-072018-021211 · Cited by 57 · see citing works

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis

Martínez-Jiménez, F., Papadatos, G., Yang, L., Wallace, I. M., Kumar, V. D., Pieper, U., Šali, A., Brown, J. R., Overington, J. P., & Martı́-Renom, M. A. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003253 · Cited by 55 · see citing works

Tracing pathway activities with kinase inhibitors and reverse phase protein arrays

van Oostrum, J., Calonder, C., Rechsteiner, D., et al. (2008) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.200800070 · Cited by 54 · see citing works

Predicted Biological Activity of Purchasable Chemical Space

Irwin, J. J., Gaskins, G., Sterling, T., Mysinger, M. M., & Keiser, M. J. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00316 · Cited by 54 · see citing works

Next-Generation Phenotypic Screening

Warchal, S. J., Unciti‐Broceta, A., & Carragher, N. O. (2016) · Future Medicinal Chemistry · doi:10.4155/fmc-2016-0025 · Cited by 46 · see citing works

The New Paradigms in Clinical Research: From Early Access Programs to the Novel Therapeutic Approaches for Unmet Medical Needs

Scavone, C., di Mauro, G., Mascolo, A., Berrino, L., Rossi, F., & Capuano, A. (2019) · Frontiers in Pharmacology · doi:10.3389/fphar.2019.00111 · Cited by 44 · see citing works

Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology

Aguirre‐Plans, J., Piñero, J., Menche, J., Sanz, F., Furlong, L. I., Schmidt, H. H. H. W., Oliva, B., & Güney, E. (2018) · Pharmaceuticals · doi:10.3390/ph11030061 · Cited by 43 · see citing works

Modeling drug mechanism of action with large scale gene-expression profiles using GPAR, an artificial intelligence platform

Gao, S., Han, L., Luo, D., Liu, G., Xiao, Z., Shan, G., Zhang, Y., & Zhou, W. (2021) · BMC Bioinformatics · doi:10.1186/s12859-020-03915-6 · Cited by 42 · see citing works

Prediction of the P. falciparum Target Space Relevant to Malaria Drug Discovery

Spitzmüller, A., & Mestres, J. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003257 · Cited by 39 · see citing works

De-orphaning the marine natural product (±)-marinopyrrole A by computational target prediction and biochemical validation

Schneider, P., & Schneider, G. (2017) · Chemical Communications · doi:10.1039/c6cc09693j · Cited by 38 · see citing works

High-Content Phenotypic Profiling in Esophageal Adenocarcinoma Identifies Selectively Active Pharmacological Classes of Drugs for Repurposing and Chemical Starting Points for Novel Drug Discovery

Hughes, R. E., Elliott, R. J. R., Munro, A. F., Makda, A., O’Neill, J. R., Hupp, T. R., & Carragher, N. O. (2020) · SLAS DISCOVERY · doi:10.1177/2472555220917115 · Cited by 38 · see citing works

DITOP: drug-induced toxicity related protein database

Zhang, J., Huang, W., Zeng, J., Huang, W.-H., Wang, Y., Zhao, R., Han, B., Liu, Q., Chen, Y., & Ji, Z. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm139 · Cited by 36 · see citing works

High-Throughput Gene Expression Profiles to Define Drug Similarity and Predict Compound Activity

Wolf, H. D., Cougnaud, L., Hoorde, K. V., Bondt, A. D., Wegner, J. K., Ceulemans, H., & Göhlmann, H. W. H. (2018) · Assay and Drug Development Technologies · doi:10.1089/adt.2018.845 · Cited by 33 · see citing works

A Synergistic Anticancer FAK and HDAC Inhibitor Combination Discovered by a Novel Chemical–Genetic High-Content Phenotypic Screen

Dawson, J. C., Serrels, B., Byron, A., Muir, M., Makda, A., García-Muñoz, A., von Kriegsheim, A., Lietha, D., Carragher, N. O., & Frame, M. C. (2019) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-19-0330 · Cited by 31 · see citing works

Fully unsupervised deep mode of action learning for phenotyping high-content cellular images

Janssens, R., Zhang, X., Kauffmann, A., de Weck, A., & Durand, E. Y. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab497 · Cited by 31 · 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

Discovery of a Novel Inhibitor of the Hedgehog Signaling Pathway through Cell‐based Compound Discovery and Target Prediction

Kremer, L., Schultz‐Fademrecht, C., Baumann, M., Habenberger, P., Choidas, A., Klebl, B., Kordes, S., Schöler, H. R., Sterneckert, J. L., Ziegler, S., et al. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201707394 · Cited by 26 · see citing works

Extending In Silico Mechanism-of-Action Analysis by Annotating Targets with Pathways: Application to Cellular Cytotoxicity Readouts

Liggi, S., Drakakis, G., Koutsoukas, A., Cortés‐Ciriano, I., Martínez–Alonso, P., Malliavin, T. E., Velázquez‐Campoy, A., Brewerton, S. C., Bodkin, M. J., Evans, D. A. P., et al. (2014) · Future Medicinal Chemistry · doi:10.4155/fmc.14.137 · Cited by 19 · see citing works

A Chemocentric Approach to the Identification of Cancer Targets

Flachner, B., Lőrincz, Z., Carotti, A., Nicolotti, O., Kuchipudi, P., Remez, N., Sanz, F., Tóvári, J., Szabó, M. J., Bertók, B., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035582 · Cited by 19 · see citing works

Systems Biology Approach for New Target and Biomarker Identification

Wang, I., Stone, D. J., Nickle, D. C., Loboda, A. P., Puig, Ó., & Roberts, C. (2012) · Current topics in microbiology and immunology · doi:10.1007/82_2012_252 · Cited by 19 · see citing works

Evaluation of Machine Learning Classifiers to Predict Compound Mechanism of Action When Transferred across Distinct Cell Lines

Warchal, S. J., Dawson, J. C., & Carragher, N. O. (2019) · SLAS DISCOVERY · doi:10.1177/2472555218820805 · Cited by 18 · see citing works

Mauritian Endemic Medicinal Plant Extracts Induce G2/M Phase Cell Cycle Arrest and Growth Inhibition of Oesophageal Squamous Cell Carcinoma in Vitro

Rummun, N., Hughes, R. E., Beesoo, R., et al. (2019) · Acta Naturae · doi:10.32607/20758251-2019-11-1-81-90 · Cited by 14 · see citing works

Systematic Identification of Pharmacological Targets from Small-Molecule Phenotypic Screens

Liu, X., Baarsma, H. A., Thiam, C. H., Montrone, C., Brauner, B., Fobo, G., Heier, J.-S., Duscha, S., Königshoff, M., Angeli, V., et al. (2016) · Cell chemical biology · doi:10.1016/j.chembiol.2016.08.011 · Cited by 11 · see citing works

Global initiative seeks 1,000 new cancer models

Ledford, H. K. (2016) · Nature · doi:10.1038/nature.2016.20242 · Cited by 5 · see citing works

The Triple‐Agonist Revolution: Retatrutide and the Paradigm Shift in Multi‐Hormonal Pharmacotherapy for Obesity and Cardiometabolic Comorbidities

Ganamurali, N., & Sabarathinam, S. (2026) · Clinical Pharmacology in Drug Development · doi:10.1002/cpdd.70001 · Cited by 8 · see citing works

Approaches to Protozoan Drug Discovery: Phenotypic Screening

Sykes, M. L., & Avery, V. M. (2013) · Journal of Medicinal Chemistry · doi:10.1021/jm4004279 · Cited by 76 · see citing works

Applications of chemogenomic library screening in drug discovery

Jones, L. H., & Bunnage, M. E. (2017) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.244 · Cited by 192 · see citing works

Drug Discovery Paradigms: Phenotypic-Based Drug Discovery

Talevi, A., & Bellera, C. L. (2022) · Computer-aided drug discovery and design · doi:10.1007/978-3-030-95895-4_2 · Cited by 2 · see citing works

Phenotypic approaches to small-molecule discovery in chemical biology

Wagner, B. K., & Dey, M. (2021) · Cell chemical biology · doi:10.1016/j.chembiol.2021.02.018

The Resurrection of Phenotypic Drug Discovery

Childers, W. E., Elokely, K. M., & Abou-Gharbia, M. A. (2020) · ACS Medicinal Chemistry Letters · doi:10.1021/acsmedchemlett.0c00006 · Cited by 45 · see citing works