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

Bray, Mark-Anthony, Singh, Shantanu, Han, Han, Davis, Chadwick T, Borgeson, Blake, Hartland, Cathy, Kost-Alimova, Maria, Gustafsdottir, Sigrun M +2 more·2016·Nature Protocols

Cited by (999)

Items 101–200 of 999

  1. Guided by evolution: from biology oriented synthesis to pseudo natural products
    Gregor S. Cremosnik, Jie Liu, Herbert Waldmann · 2020 · Natural Product Reports
  2. Cell Painting predicts impact of lung cancer variants
    Juan C. Caicedo, John Arévalo, Federica Piccioni, Mark-Anthony Bray, Cathy L. Hartland, Xiaoyun Wu, Angela N. Brooks, Alice H. Berger, Jesse S. Boehm, Anne Elizabeth Carpenter et al. · 2022 · Molecular Biology of the Cell
  3. Image‐Based Morphological Profiling Identifies a Lysosomotropic, Iron‐Sequestering Autophagy Inhibitor
    Luca Laraia, Guillaume Garivet, Daniel J. Foley, Nadine Kaiser, Sebastian Müller, Sarah Zinken, Thomas Pinkert, Julian Wilke, Dale Corkery, Axel Pahl et al. · 2019 · Angewandte Chemie International Edition
  4. Morphological Profiling Identifies a Common Mode of Action for Small Molecules with Different Targets
    Tabea Schneidewind, Alexandra Brause, Axel Pahl, Annina Burhop, Tom Mejuch, Sonja Sievers, Herbert Waldmann, Slava Ziegler · 2020 · ChemBioChem
  5. High-Throughput Routes to Biomaterials Discovery
    Mohammad Soheilmoghaddam, Madeleine Rumble, Justin John Cooper-White · 2021 · Chemical Reviews
  6. Tales of 1,008 small molecules: phenomic profiling through live-cell imaging in a panel of reporter cell lines
    Michael J. Cox, Steffen Jaensch, Jelle Van de Waeter, Laure Cougnaud, Daan Seynaeve, Soulaiman Benalla, Seong Joo Koo, Ilse Van den Wyngaert, Jean‐Marc Neefs, Dmitry Malkov et al. · 2020 · Scientific Reports
  7. Senescence-associated morphological profiles (SAMPs): an image-based phenotypic profiling method for evaluating the inter and intra model heterogeneity of senescence
    Wallis, Ryan, Milligan, Deborah, Hughes, Bethany, Mizen, Hannah, López-Domínguez, José Alberto, Eduputa, Ugochim, Tyler, Eleanor J., Serrano, Manuel, Bishop, Cleo L. · 2022 · Aging
  8. CLOOME: contrastive learning unlocks bioimaging databases for queries with chemical structures
    Ana Sanchez-Fernandez, Elisabeth Rumetshofer, Sepp Hochreiter, Günter Klambauer · 2023 · Nature Communications
  9. Next generation diversity-oriented synthesis: a paradigm shift from chemical diversity to biological diversity
    Ivan Pavlinov, Erica M. Gerlach, Leslie N. Aldrich · 2018 · Organic & Biomolecular Chemistry
  10. Systematic Chemogenetic Library Assembly
    Stephen M. Canham, Yuan Wang, Allen Cornett, Douglas S. Auld, Daniel K. Baeschlin, Maude Patoor, Philip R. Skaanderup, Ayako Honda, Luis Llamas, Greg Wendel et al. · 2020 · Cell chemical biology
  11. Systematic exploration of cell morphological phenotypes associated with a transcriptomic query
    Isar Nassiri, Matthew N. McCall · 2018 · Nucleic Acids Research
  12. High-content phenotypic and pathway profiling to advance drug discovery in diseases of unmet need
    Hughes, Rebecca E., Elliott, Richard J.R., Dawson, John C., Carragher, Neil O. · 2021 · Cell Chemical Biology
  13. Synergistic Effects of Stereochemistry and Appendages on the Performance Diversity of a Collection of Synthetic Compounds
    Bruno N. Melillo, Jochen Zoller, Bruce K. Hua, Oscar Verho, Jannik C. Borghs, Shawn D. Nelson, Micah Maetani, Mathias J. Wawer, Paul A. Clemons, Stuart L. Schreiber · 2018 · Journal of the American Chemical Society
  14. Examining multiple cellular pathways at once using multiplex hextuple luciferase assaying
    Alejandro Sarrion‐Perdigones, Lyra Chang, Yezabel Gonzalez, Tatiana Gallego‐Flores, Damian W. Young, Koen J. T. Venken · 2019 · Nature Communications
  15. The frontier of live tissue imaging across space and time
    Qiang Huang, Aliesha Garrett, Shree Bose, Stephanie J. Blocker, Anne C. Rios, Hans C. Clevers, Xiling Shen · 2021 · Cell stem cell
  16. Bioactive Compound Collections: From Design to Target Identification
    Luca Laraia, Lucas Robke, Herbert Waldmann · 2018 · Chem
  17. Deep learning large-scale drug discovery and repurposing
    Min Yu, Weiming Li, Yunru Yu, Yu Zhao, Lizhi Xiao, Volker Martin Lauschke, Yi-Yu Cheng, Xingcai Zhang, Yì Wáng · 2024 · Nature Computational Science
  18. Connectivity Mapping: Methods and Applications
    Alexandra B. Keenan, Megan L. Wojciechowicz, Zichen Wang, Kathleen M. Jagodnik, Sherry L. Jenkins, Alexander Lachmann, Avi Ma’ayan · 2019 · Annual Review of Biomedical Data Science
  19. Comparison of Cellular Morphological Descriptors and Molecular Fingerprints for the Prediction of Cytotoxicity- and Proliferation-Related Assays
    Srijit Seal, Hongbin Yang, Luis Vollmers, Andreas Bender · 2021 · Chemical Research in Toxicology
  20. Morphological profiling by means of the Cell Painting assay enables identification of tubulin-targeting compounds
    Mohammad Akbarzadeh, Ilka Deipenwisch, Beate Schoelermann, Axel Pahl, Sonja Sievers, Slava Ziegler, Herbert Waldmann · 2021 · Cell chemical biology
  21. High-dimensional phenotyping to define the genetic basis of cellular morphology
    Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A. Cimini, Ajay Nadig, Emily R. Peirent, Dhara Liyanage, Gregory P. Way, Erin Weisbart, Aparna Nathan et al. · 2024 · Nature Communications
  22. TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41
    Carey, Kimberly L., Paulus, Geraldine L.C., Wang, Lingfei, Balce, Dale R., Luo, Jessica W., Bergman, Phil, Ferder, Ianina C., Kong, Lingjia, Renaud, Nicole, Singh, Shantanu et al. · 2020 · Cell Reports
  23. Developing context appropriate toxicity testing approaches using new alternative methods (NAMs)
    Melvin E. Andersen · 2019 · ALTEX
  24. Using chemical and biological data to predict drug toxicity
    Anika Liu, Srijit Seal, Hongbin Yang, Andreas Bender · 2023 · SLAS DISCOVERY
  25. Artificial intelligence (AI) in drug design and discovery: A comprehensive review
    Ajmal Rashid Bhat, Sumeer Ahmed · 2025 · In Silico Research in Biomedicine
  26. CD146 controls the quality of clinical grade mesenchymal stem cells from human dental pulp
    Lan Ma, Zhiqing Huang, Di Wu, Xiaoxing Kou, Xueli Mao, Songtao Shi · 2021 · Stem Cell Research & Therapy
  27. Self-supervision advances morphological profiling by unlocking powerful image representations
    Vladislav Kim, Nikolaos Adaloglou, M. Osterland, Flavio M. Morelli, Marah Halawa, Tim König, D. Gnutt, P. A. Marin Zapata · 2024 · bioRxiv
  28. The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices
    Oana M. Enache, David L. Lahr, Ted Natoli, Lev Litichevskiy, David Wadden, Corey Flynn, Joshua Gould, Jacob K. Asiedu, Rajiv Narayan, Aravind Subramanian · 2018 · Bioinformatics
  29. Design, Synthesis, and Biological Evaluation of Chemically and Biologically Diverse Pyrroquinoline Pseudo Natural Products
    Jie Liu, Gregor S. Cremosnik, Felix Otte, Axel Pahl, Sonja Sievers, Carsten Strohmann B, Herbert Waldmann · 2020 · Angewandte Chemie International Edition
  30. Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic
    Yuen Ler Chow, Shantanu Singh, Anne Elizabeth Carpenter, Gregory P. Way · 2022 · PLoS Computational Biology
  31. New approach methods to assess developmental and adult neurotoxicity for regulatory use: a PARC work package 5 project
    Tal, Tamara, Myhre, Oddvar, Fritsche, Ellen, Rüegg, Joëlle, Craenen, Kai, Aiello-Holden, Kiara, Agrillo, Caroline, Babin, Patrick J., Escher, Beate I., Dirven, Hubert et al. · 2024 · Frontiers in Toxicology
  32. High-resolution genome-wide mapping of chromosome-arm-scale truncations induced by CRISPR–Cas9 editing
    Nathan H. Lazar, Safiye Çelik, Lu Chen, Marta M. Fay, Jonathan C. Irish, James Jensen, Conor A. Tillinghast, John Urbanik, William P. Bone, Genevieve H. L. Roberts et al. · 2024 · Nature Genetics
  33. Cell and small animal models for phenotypic drug discovery
    Mihaly Szabo, Sara Svensson Akusjärvi, Ankur Saxena, Jianping Liu, Gayathri Chandrasekar, Satish Srinivas Kitambi · 2017 · Drug Design Development and Therapy
  34. Morphological subprofile analysis for bioactivity annotation of small molecules
    Axel Pahl, Beate Schölermann, Philipp Lampe, Marion Rusch, Mark Dow, Christian Hedberg, Adam S. Nelson, Sonja Sievers, Herbert Waldmann, Slava Ziegler · 2023 · Cell chemical biology
  35. Artificial intelligence for high content imaging in drug discovery
    Jordi Carreras Puigvert, Ola Spjuth · 2024 · Current Opinion in Structural Biology
  36. Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations
    Mojca Mattiazzi Ušaj, Clarence Hue Lok Yeung, Helena Friesen, Charles M. Boone, Brenda Andrews · 2021 · Cell Systems
  37. Metabolic and phenotypic changes induced by PFAS exposure in two human hepatocyte cell models
    Andi Alijagić, Lisanna Sinisalu, Daniel Duberg, Oleksandr Kotlyar, Nikolai N. Scherbak, Magnus Engwall, Matej Orešič, Tuulia Hyötyläinen · 2024 · Environment International
  38. Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology
    Oren Z. Kraus, Kian Kenyon-Dean, Saber Saberian, Maryam Fallah, Peter McLean, Jess Leung, Vasudev Sharma, Ayla Khan, Jia Balakrishnan, Safiye Çelik et al. · 2024 · IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings - IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings
  39. Cell Morphological Profiling Enables High-Throughput Screening for PROteolysis TArgeting Chimera (PROTAC) Phenotypic Signature
    Trapotsi, Maria-Anna, Mouchet, Elizabeth, Williams, Guy, Monteverde, Tiziana, Juhani, Karolina, Turkki, Riku, Miljković, Filip, Martinsson, Anton, Mervin, Lewis, Pryde, Kenneth R. et al. · 2022 · ACS Chemical Biology
  40. Harnessing the power of artificial intelligence to advance cell therapy
    Sara Capponi, Kyle G. Daniels · 2023 · Immunological Reviews
  41. Natural Product Synthesis in the 21st Century: Beyond the Mountain Top
    Ryan A. Shenvi · 2024 · ACS Central Science
  42. Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence
    Duran-Frigola, Miquel, Cigler, Marko, Winter, Georg E. · 2023 · Journal of the American Chemical Society
  43. Cell Painting-based bioactivity prediction boosts high-throughput screening hit-rates and compound diversity
    Johan Fredin Haslum, Charles-Hugues Lardeau, Johan Karlsson, Riku Turkki, Karl‐Johan Leuchowius, Kevin Smith, Erik Müllers · 2024 · Nature Communications
  44. Morphological profiling for drug discovery in the era of deep learning
    Qiaosi Tang, Ranjala Ratnayake, Gustavo de Miranda Seabra, Zhe Jiang, Ruogu Fang, Lina Cui, Yousong Ding, Tamer Kahveci, Jiang Bian, Chenglong Li et al. · 2024 · Briefings in Bioinformatics
  45. Cell size homeostasis is maintained by CDK4-dependent activation of p38 MAPK
    Ceryl Tan, Miriam Bracha Ginzberg, Rachel Webster, Seshu Iyengar, Shixuan Liu, David J. Papadopoli, John B. Concannon, Yuan Wang, Douglas S. Auld, Jeremy L. Jenkins et al. · 2021 · Developmental Cell
  46. Reference compounds for characterizing cellular injury in high-content cellular morphology assays
    Jayme L. Dahlin, Bruce K. Hua, Beth E. Zucconi, Shawn D. Nelson, Shantanu Singh, Anne Elizabeth Carpenter, Jonathan H. Shrimp, Evelyne Lima‐Fernandes, Mathias J. Wawer, Lawrence P. W. Chung et al. · 2023 · Nature Communications
  47. nELISA: a high-throughput, high-plex platform enables quantitative profiling of the inflammatory secretome
    Milad Dagher, Grant Ongo, Nathaniel Robichaud, Jinglin Kong, Woojong Rho, Ivan Teahulos, Arya Tavakoli, Samantha Bovaird, Shahem Merjaneh, Andrew Tan et al. · 2025 · Nature Methods
  48. Marine dissolved organic matter: a vast and unexplored molecular space
    Teresa S. Catalá, Spencer L. Shorte, Thorsten Dittmar · 2021 · Applied Microbiology and Biotechnology
  49. Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery
    Michael F. Cuccarese, Berton A. Earnshaw, Katie Heiser, Ben Fogelson, Chadwick T. Davis, Peter McLean, Hannah B. Gordon, Kathleen-Rose Skelly, Fiona L. Weathersby, Vlad Rodic et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  50. Combining Automated Organoid Workflows with Artificial Intelligence‐Based Analyses: Opportunities to Build a New Generation of Interdisciplinary High‐Throughput Screens for Parkinson's Disease and Beyond
    Henrik Renner, Hans Robert Schöler, Jan M. Bruder · 2021 · Movement Disorders
  51. DynaMorph: self-supervised learning of morphodynamic states of live cells
    Zhenqin Wu, Bryant B. Chhun, Galina Popova, Syuan-Ming Guo, Chang N. Kim, Li-Hao Yeh, Tomasz Jan Nowakowski, James Zou, Shalin B. Mehta · 2022 · Molecular Biology of the Cell
  52. Artificial intelligence integration in the drug lifecycle and in regulatory science: policy implications, challenges and opportunities
    Wahiba Oualikene-Gonin, Marie‐Christine Jaulent, Jean-Pierre Thierry, Sofia Oliveira‐Martins, Laëtitia Belgodère, Patrick Maison, Joël Ankri, The Scientific Advisory Board of ANSM · 2024 · Frontiers in Pharmacology
  53. A Scaffold‐Diversity Synthesis of Biologically Intriguing Cyclic Sulfonamides
    Stefan Zimmermann, Mohammad Akbarzadeh, Felix Otte, Carsten Strohmann B, Muthukumar G. Sankar, Slava Ziegler, Axel Pahl, Sonja Sievers, Kamal Kumar · 2019 · Chemistry - A European Journal
  54. High content phenotypic screening identifies serotonin receptor modulators with selective activity upon breast cancer cell cycle and cytokine signaling pathways
    Scott J. Warchal, John C. Dawson, Emelie Shepherd, Alison F. Munro, Rebecca E. Hughes, Ashraff Makda, Neil O. Carragher · 2019 · Bioorganic & Medicinal Chemistry
  55. Unbiased single-cell morphology with self-supervised vision transformers
    Michael Doron, Théo Moutakanni, Zitong Chen, Nikita Moshkov, Mathilde Caron, Hugo Touvron, Piotr Bojanowski, Wolfgang M. Pernice, Juan C. Caicedo · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Squid: Simplifying Quantitative Imaging Platform Development and Deployment
    Hongquan Li, Deepak Krishnamurthy, Ethan Li, Pranav Vyas, Nibha Akireddy, Chew Chai, Manu Prakash · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  57. Comparison of Approaches for Determining Bioactivity Hits from High-Dimensional Profiling Data
    Johanna Nyffeler, Derik E. Haggard, Clinton M. Willis, R. Woodrow Setzer, Richard Judson, Katie Paul Friedman, Logan J. Everett, Joshua Harrill · 2020 · SLAS DISCOVERY
  58. Expanding the antibacterial selectivity of polyether ionophore antibiotics through diversity-focused semisynthesis
    Shaoquan Lin, Han Liu, Esben B. Svenningsen, Malene Wollesen, Kristian M. Jacobsen, Frederikke D. Andersen, Jaime Moyano-Villameriel, Christine N. Pedersen, Peter Nørby, Thomas Tørring et al. · 2020 · Nature Chemistry
  59. Multi-parametric functional imaging of cell cultures and tissues with a CMOS microelectrode array
    Jeffrey Abbott, Avik Mukherjee, Wenxuan Wu, Tianyang Ye, Han Sae Jung, Kevin M. Cheung, Rona S. Gertner, Markus Basan, Donhee Ham, Hongkun Park · 2022 · Lab on a Chip
  60. Key aspects of modern GPCR drug discovery
    Philip Addis, Utsav Bali, Frank Baron, Adrian P. Campbell, Steven P. D. Harborne, Liz Jagger, Gavin Milne, Martin J. Pearce, Elizabeth M. Rosethorne, Rupert Satchell et al. · 2023 · SLAS DISCOVERY
  61. COSMOS: a platform for real-time morphology-based, label-free cell sorting using deep learning
    Mahyar Salek, Nianzhen Li, Hou-Pu Chou, Kiran Saini, Andreja Jovic, Kevin B. Jacobs, Chassidy Johnson, Vivian Lu, Esther J. Lee, Christina C. Chang et al. · 2023 · Communications Biology
  62. Efficient production of protocatechuic acid using systems engineering of Escherichia coli
    Ming Wang, Haomiao Wang, Cong Gao, Wanqing Wei, Jia Liu, Xiulai Chen, Guipeng Hu, Wei Song, Jing Wu, Fan Zhang et al. · 2024 · Metabolic Engineering
  63. Cocktail effects of tire wear particles leachates on diverse biological models: A multilevel analysis
    Jessy Le Du-Carrée, Clara Kempkens Palacios, Anna Rotander, Maria Larsson, Andi Alijagić, Oleksandr Kotlyar, Magnus Engwall, Viktor Sjöberg, Steffen H. Keiter, Rodrigo Almeda · 2024 · Journal of Hazardous Materials
  64. Perspectives on Drug Repurposing
    Alejandro Schcolnik‐Cabrera, Daniel Juárez-López, Alfonso Dueñas‐González · 2020 · Current Medicinal Chemistry
  65. In silico approaches in organ toxicity hazard assessment: Current status and future needs in predicting liver toxicity
    Arianna Bassan, Vinícius M. Alves, Alexander Amberg, Lennart T. Anger, Scott S. Auerbach, Lisa D. Beilke, Andreas Bender, M Cronin, Kevin P. Cross, Jui‐Hua Hsieh et al. · 2021 · Computational Toxicology
  66. Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler
    Samantha Laber, Sophie Strobel, Josep Maria Mercader, Hesam Dashti, Felipe R. C. dos Santos, Phil Kubitz, Maya Jackson, Alina Ainbinder, Julius Honecker, Saaket Agrawal et al. · 2023 · Cell Genomics
  67. Predicting cell morphological responses to perturbations using generative modeling
    Alessandro Palma, Fabian Joachim Theis, Mohammad Lotfollahi · 2025 · Nature Communications
  68. Modelling non-alcoholic fatty liver disease in human hepatocyte-like cells
    Marcus J. Lyall, Jessy Cartier, John P. Thomson, Kate Cameron, Jose Meseguer-Ripolles, Eoghan O’Duibhir, Dagmara Szkolnicka, Baltasar Lucendo‐Villarin, Yu Wang, Giovanny Rodriguez Blanco et al. · 2018 · Philosophical Transactions of the Royal Society B Biological Sciences
  69. Computational Methods for Single-Cell Imaging and Omics Data Integration
    Ebony Rose Watson, Atefeh Taherian Fard, Jessica C. Mar · 2022 · Frontiers in Molecular Biosciences
  70. Deep-learning analysis of micropattern-based organoids enables high-throughput drug screening of Huntington’s disease models
    Jakob Johannes Metzger, Carlota Pereda Serras, Arjun S. Adhikari, Tomomi Haremaki, Szilvia Galgoczi, Eric D. Siggia, Ali H. Brivanlou, Fred Etoc · 2022 · Cell Reports Methods
  71. Real-Time Biological Annotation of Synthetic Compounds
    Christopher J. Gerry, Bruce K. Hua, Mathias J. Wawer, Jonathan P. Knowles, Shawn D. Nelson, Oscar Verho, Sivaraman Dandapani, Bridget K. Wagner, Paul A. Clemons, Kevin I. Booker‐Milburn et al. · 2016 · Journal of the American Chemical Society
  72. High-Content Imaging to Phenotype Antimicrobial Effects on Individual Bacteria at Scale
    Sushmita Sridhar, Sally Forrest, Ben Warne, Mailis Maes, Stephen G. Baker, Gordon Dougan B, Josefin Bartholdson Scott · 2021 · mSystems
  73. A phenomics approach for antiviral drug discovery
    Jonne Rietdijk, Marianna Tampere, Aleksandra Pettke, Polina Georgieva, Maris Lapins, Ulrika Warpman Berglund, Ola Spjuth, Marjo-Riitta Puumalainen, Jordi Carreras Puigvert · 2021 · BMC Biology
  74. Chemiluminescent duplex analysis using phenoxy-1,2-dioxetane luminophores with color modulation
    Sara Gutkin, Rozan Tannous, Qais Z. Jaber, Micha Fridman, Doron Shabat · 2023 · Chemical Science
  75. Profiling cellular morphodynamics by spatiotemporal spectrum decomposition
    Xiao Ma, Onur Dağliyan, Klaus M. Hahn, Gaudenz M. Danuser · 2018 · PLoS Computational Biology
  76. A human pluripotent stem cell model for the analysis of metabolic dysfunction in hepatic steatosis
    Matthew C. Sinton, Jose Meseguer-Ripolles, Baltasar Lucendo‐Villarin, Sara Wernig-Zorc, John P. Thomson, Roderick N. Carter, Marcus J. Lyall, Paul D. Walker, Alpesh Thakker, Richard R. Meehan et al. · 2020 · iScience
  77. A genome-wide optical pooled screen reveals regulators of cellular antiviral responses
    Rebecca J. Carlson, Michael D Leiken, Alina Guna, Nir Hacohen, Paul C. Blainey · 2023 · Proceedings of the National Academy of Sciences
  78. CellDeathPred: a deep learning framework for ferroptosis and apoptosis prediction based on cell painting
    Kenji Schorpp, Alaa Bessadok, Aidin Biibosunov, Ina Rothenaigner, Stefanie Strasser, Tingying Peng, Kamyar Hadian · 2023 · Cell Death Discovery
  79. Towards generative digital twins in biomedical research
    Jiqing Wu, Viktor Hendrik Koelzer · 2024 · Computational and Structural Biotechnology Journal
  80. High-Content Phenotypic Profiling in Esophageal Adenocarcinoma Identifies Selectively Active Pharmacological Classes of Drugs for Repurposing and Chemical Starting Points for Novel Drug Discovery
    Rebecca E. Hughes, Richard J. R. Elliott, Alison F. Munro, Ashraff Makda, J. Robert O’Neill, Ted R. Hupp, Neil O. Carragher · 2020 · SLAS DISCOVERY
  81. Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses
    Marianna Tampere, Aleksandra Pettke, Cristiano Salata, Olov A. Wallner, Tobias Koolmeister, Armando Cázares‐Körner, Torkild Visnes, Maria C. Hesselman, Elena Kunold, Elisée Wiita et al. · 2020 · Viruses
  82. A large-scale benchmark for network inference from single-cell perturbation data
    Chevalley, Mathieu, Roohani, Yusuf H., Mehrjou, Arash, Leskovec, Jure, Schwab, Patrick · 2025 · Communications Biology
  83. Building the next generation of virtual cells to understand cellular biology
    Graham T. Johnson, Eran Agmon, Matthew Akamatsu, Emma K. Lundberg, Blair M. Lyons, Wei Ouyang, Omar A. Quintero, Megan M. Riel-Mehan, Susanne M. Rafelski, Rick Horwitz · 2023 · Biophysical Journal
  84. RxRx1: A Dataset for Evaluating Experimental Batch Correction Methods
    Maciej Sypetkowski, Morteza Rezanejad, Saber Saberian, Oren Z. Kraus, John Urbanik, James Taylor, Ben Mabey, Mason L. Victors, Jason Yosinski, Alborz Rezazadeh Sereshkeh et al. · 2023 · IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)
  85. Pooled multicolour tagging for visualizing subcellular protein dynamics
    Andreas Reicher, Jiří Reiniš, Maria Ciobanu, Pavel Růžička, Monika Malik, Marton I. Siklos, Viktoriia Kartysh, Tatjana Tomek, Anna Koren, André F. Rendeiro et al. · 2024 · Nature Cell Biology
  86. Nellie: automated organelle segmentation, tracking and hierarchical feature extraction in 2D/3D live-cell microscopy
    Austin E.Y.T. Lefebvre, Gabriel Sturm, Ting‐Yu Lin, Emily H. Stoops, Magdalena Preciado López, Benjamin Kaufmann-Malaga, Kayley Hake · 2025 · Nature Methods
  87. The Cell Painting Assay as a Screening Tool for the Discovery of Bioactivities in New Chemical Matter
    Axel Pahl, Sonja Sievers · 2018 · Methods in molecular biology
  88. Capturing single-cell heterogeneity via data fusion improves image-based profiling
    Mohammad Hossein Rohban, Hamdah Shafqat Abbasi, Shantanu Singh, Anne Elizabeth Carpenter · 2019 · Nature Communications
  89. Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data
    Srijit Seal, Hongbin Yang, Maria‐Anna Trapotsi, Satvik Singh, Jordi Carreras Puigvert, Ola Spjuth, Andreas Bender · 2023 · Journal of Cheminformatics
  90. Functional annotation map of natural compounds in traditional Chinese medicines library: TCMs with myocardial protection as a case
    Xudong Xing, Mengru Sun, Zifan Guo, Yongjuan Zhao, Yu-Ru Cai, Ping Zhou, Huiying Wang, Wen Yuan Gao, Ping Li, Hua Qiang Yang · 2023 · Acta Pharmaceutica Sinica B
  91. How Not To Drown in Data: A Guide for Biomaterial Engineers
    Aliaksei S. Vasilevich, Aurélie Carlier, Jan de Boer, Shantanu Singh · 2017 · Trends in biotechnology
  92. The Convergence of Stem Cell Technologies and Phenotypic Drug Discovery
    Alexandra Friese, Andrei Ursu, Andreas Hochheimer, Hans Robert Schöler, Herbert Waldmann, Jan M. Bruder · 2019 · Cell chemical biology
  93. Virtual screening for small-molecule pathway regulators by image-profile matching
    Mohammad Hossein Rohban, Ashley M. Fuller, Ceryl Tan, Jonathan T. Goldstein, Deepsing Syangtan, Amos Gutnick, Ann Devine, Madhura P. Nijsure, Megan Rigby, Joshua R. Sacher et al. · 2022 · Cell Systems
  94. Applying Deep Neural Network Analysis to High-Content Image-Based Assays
    Yang, Samuel J., Lipnick, Scott L., Makhortova, Nina R., Venugopalan, Subhashini, Fan, Minjie, Armstrong, Zan, Schlaeger, Thorsten M., Deng, Liyong, Chung, Wendy K., O’Callaghan, Liadan et al. · 2019 · SLAS DISCOVERY
  95. High-dimension single-cell analysis applied to cancer
    Lili Wang, Kenneth J. Livak, Catherine J. Wu · 2017 · Molecular Aspects of Medicine
  96. A pooled Cell Painting CRISPR screening platform enables de novo inference of gene function by self-supervised deep learning
    Srinivasan Sivanandan, Bobby Leitmann, Eric Lubeck, Mohammad Muneeb Sultan, Panagiotis Stanitsas, Navpreet Ranu, Alexis Ewer, Jordan E. Mancuso, Zachary F. Phillips, Albert M. Kim et al. · 2025 · Nature Communications
  97. Helios: History and Anatomy of a Successful In-House Enterprise High-Throughput Screening and Profiling Data Analysis System
    Hanspeter Gubler, Nicholas Clare, Laurent Galafassi, Uwe Geissler, Michel Girod, Guy Herr · 2018 · SLAS DISCOVERY
  98. Combining experimental strategies for successful target deconvolution
    Isabel V. L. Wilkinson, Georg C. Terstappen, Angela J. Russell · 2020 · Drug Discovery Today
  99. Organocatalytic Asymmetric Multicomponent Cascade Reaction for the Synthesis of Contiguously Substituted Tetrahydronaphthols
    Yidong Liu, Joseph A. Izzo, David McLeod, Sebastijan Ričko, Esben B. Svenningsen, Thomas Bjørnskov Poulsen, Karl Anker Jørgensen · 2021 · Journal of the American Chemical Society
  100. High Skp2 expression is associated with a mesenchymal phenotype and increased tumorigenic potential of prostate cancer cells
    Šárka Šimečková, Zuzana Kahounová, Radek Fedr, Ján Remšík, Eva Slabáková, Tereza Suchánková, Jiřina Procházková, Jan Bouchal, Gvantsa Kharaishvili, Milan Král et al. · 2019 · Scientific Reports