| Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection S Seal, J Carreras-Puigvert, MA Trapotsi, H Yang, O Spjuth, A Bender Communications Biology 5 (1), 858, 2022 | 40 | 2022 |
| Computational analyses of mechanism of action (MoA): data, methods and integration MA Trapotsi, L Hosseini-Gerami, A Bender RSC Chemical Biology 3 (2), 170-200, 2022 | 36 | 2022 |
| Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions MA Trapotsi, LH Mervin, AM Afzal, N Sturm, O Engkvist, IP Barrett, ... Journal of Chemical Information and Modeling 61 (3), 1444-1456, 2021 | 31 | 2021 |
| Cell morphological profiling enables high-throughput screening for PROteolysis TArgeting Chimera (PROTAC) phenotypic signature MA Trapotsi, E Mouchet, G Williams, T Monteverde, K Juhani, R Turkki, ... ACS Chemical Biology 17 (7), 1733-1744, 2022 | 28 | 2022 |
| Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data S Seal, H Yang, MA Trapotsi, S Singh, J Carreras-Puigvert, O Spjuth, ... Journal of Cheminformatics 15 (1), 56, 2023 | 17 | 2023 |
| Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty LH Mervin, MA Trapotsi, AM Afzal, IP Barrett, A Bender, O Engkvist Journal of Cheminformatics 13, 1-17, 2021 | 12 | 2021 |
| Bioinformatic Approaches in the Understanding of Mechanism of Action (MoA) MA Trapotsi, I Barrett, O Engkvist, A Bender Target Discovery and Validation: Methods and Strategies for Drug Discovery …, 2019 | 5 | 2019 |
| Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus J van Lopik, A Alizada, MA Trapotsi, GJ Hannon, S Bornelöv, ... Nature Communications 14 (1), 7337, 2023 | 3 | 2023 |
| Multitask bioactivity predictions using structural chemical and cell morphology information MA Trapotsi, I Barrett, L Mervin, AM Afzal, N Sturm, O Engkvist, A Bender | 3 | 2020 |
| Development and evaluation of ADME models using proprietary and opensource data MA Trapotsi | 3 | 2018 |
| Evaluation and optimization of sequence-based gene regulatory deep learning models AM Rafi, D Nogina, D Penzar, D Lee, D Lee, N Kim, S Kim, D Kim, Y Shin, ... bioRxiv, 2023 | 2 | 2023 |
| Merging Bioactivity Predictions from Cell Morphology and Chemical Fingerprint Models by Leveraging Similarity to Training Data S Seal, H Yang, MA Trapotsi, S Singh, J Carreras-Puigvert, O Spjuth, ... bioRxiv, 2022.08. 11.503624, 2022 | 1 | 2022 |
| FlaHMM: unistrand flamenco-like piRNA cluster prediction in Drosophila species using hidden Markov models MA Trapotsi, J van Lopik, GJ Hannon, BC Nicholson, S Bornelöv bioRxiv, 2024.05. 14.592433, 2024 | | 2024 |
| A Decade in a Systematic Review: The Evolution and Impact of Cell Painting S Seal, MA Trapotsi, O Spjuth, S Singh, J Carreras-Puigvert, N Greene, ... bioRxiv, 2024.05. 04.592531, 2024 | | 2024 |
| PKSmart: An Open-Source Computational Model to Predict in vivo Pharmacokinetics of Small Molecules S Seal, M Trapotsi, V Subramanian, O Spjuth, N Greene, A Bender bioRxiv, 2024.02. 02.578658, 2024 | | 2024 |
| Unistrand piRNA clusters are an evolutionary conserved mechanism to suppress endogenous retroviruses across the Drosophila genus J van Lopik, MA Trapotsi, GJ Hannon, S Bornelov, B Czech Nicholson bioRxiv, 2023.02. 27.530199, 2023 | | 2023 |
| In silico Prediction and Biological Validation of Novel Angiogenesis Modulators from Traditional Chinese Medicine Y Zhu, H Yang, L HAN, LH Mervin, L Hosseini-Gerami, P Li, P Wright, ... Frontiers in Pharmacology 14, 171, 2023 | | 2023 |
| Using Heterogeneous Information Sources for Understanding and Predicting Biological Effects of Compounds MA Trapotsi | | 2022 |
