Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus
van Lopik, Jasper, Alizada, Azad, Trapotsi, Maria-Anna, Hannon, Gregory J., Bornelöv, Susanne, Czech Nicholson, Benjamin
Published in Nature communications (13.11.2023)
Published in Nature communications (13.11.2023)
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Journal Article
Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data
Seal, Srijit, Yang, Hongbin, Trapotsi, Maria-Anna, Singh, Satvik, Carreras-Puigvert, Jordi, Spjuth, Ola, Bender, Andreas
Published in Journal of cheminformatics (02.06.2023)
Published in Journal of cheminformatics (02.06.2023)
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Journal Article
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty
Mervin, Lewis H., Trapotsi, Maria-Anna, Afzal, Avid M., Barrett, Ian P., Bender, Andreas, Engkvist, Ola
Published in Journal of cheminformatics (19.08.2021)
Published in Journal of cheminformatics (19.08.2021)
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Journal Article
In silico prediction and biological assessment of novel angiogenesis modulators from traditional Chinese medicine
Zhu, Yingli, Yang, Hongbin, Han, Liwen, Mervin, Lewis H, Hosseini-Gerami, Layla, Li, Peihai, Wright, Peter, Trapotsi, Maria-Anna, Liu, Kechun, Fan, Tai-Ping, Bender, Andreas
Published in Frontiers in pharmacology (03.02.2023)
Published in Frontiers in pharmacology (03.02.2023)
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Journal Article
Computational analyses of mechanism of action (MoA): data, methods and integration
Trapotsi, Maria-Anna, Hosseini-Gerami, Layla, Bender, Andreas
Published in RSC chemical biology (09.02.2022)
Published in RSC chemical biology (09.02.2022)
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Journal Article
Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions
Trapotsi, Maria-Anna, Mervin, Lewis H, Afzal, Avid M, Sturm, Noé, Engkvist, Ola, Barrett, Ian P, Bender, Andreas
Published in Journal of chemical information and modeling (22.03.2021)
Published in Journal of chemical information and modeling (22.03.2021)
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Journal Article
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., Müllers, Erik, Barrett, Ian, Engkvist, Ola, Bender, Andreas, Moreau, Kevin
Published in ACS chemical biology (15.07.2022)
Published in ACS chemical biology (15.07.2022)
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Journal Article
Bioinformatic Approaches in the Understanding of Mechanism of Action (MoA)
Published in Target Discovery and Validation
(2020)
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Book Chapter
A community effort to optimize sequence-based deep learning models of gene regulation
Rafi, Abdul Muntakim, Nogina, Daria, Penzar, Dmitry, Lee, Dohoon, Lee, Danyeong, Kim, Nayeon, Kim, Sangyeup, Kim, Dohyeon, Shin, Yeojin, Kwak, Il-Youp, Meshcheryakov, Georgy, Lando, Andrey, Zinkevich, Arsenii, Kim, Byeong-Chan, Lee, Juhyun, Kang, Taein, Vaishnav, Eeshit Dhaval, Yadollahpour, Payman, Kim, Sun, Albrecht, Jake, Regev, Aviv, Gong, Wuming, Kulakovskiy, Ivan V, Meyer, Pablo, de Boer, Carl G
Published in Nature biotechnology (11.10.2024)
Published in Nature biotechnology (11.10.2024)
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Journal Article
A Decade in a Systematic Review: The Evolution and Impact of Cell Painting
Seal, Srijit, Trapotsi, Maria-Anna, Spjuth, Ola, Singh, Shantanu, Carreras-Puigvert, Jordi, Greene, Nigel, Bender, Andreas, Carpenter, Anne E
Year of Publication 04.05.2024
Year of Publication 04.05.2024
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Journal Article
A Decade in a Systematic Review: The Evolution and Impact of Cell Painting
Seal, Srijit, Trapotsi, Maria-Anna, Spjuth, Ola, Singh, Shantanu, Carreras-Puigvert, Jordi, Greene, Nigel, Bender, Andreas, Carpenter, Anne E
Published in bioRxiv (07.05.2024)
Published in bioRxiv (07.05.2024)
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Journal Article
A Decade in a Systematic Review: The Evolution and Impact of Cell Painting
Seal, Srijit, Trapotsi, Maria-Anna, Spjuth, Ola, Singh, Shantanu, Carreras-Puigvert, Jordi, Greene, Nigel, Bender, Andreas, Carpenter, Anne E
Published in ArXiv.org (04.05.2024)
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Published in ArXiv.org (04.05.2024)
Journal Article
Merging Bioactivity Predictions from Cell Morphology and Chemical Fingerprint Models by Leveraging Similarity to Training Data
Seal, Srijit, Yang, Hongbin, Maria-Anna Trapotsi, Singh, Satvik, Carreras-Puigvert, Jordi, Spjuth, Ola, Bender, Andreas
Published in bioRxiv (10.01.2023)
Published in bioRxiv (10.01.2023)
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