{"entity": "researcher", "timestamp": "2026-08-20T20:33:04.891Z", "family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2"}}, "publications": [{"entity": "publication", "iuid": "e177577e72f9469d9f12a233faf0b7dc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e177577e72f9469d9f12a233faf0b7dc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e177577e72f9469d9f12a233faf0b7dc"}}, "title": "The time dimension matters: Improving mode of action classification with live-cell imaging", "authors": [{"family": "Forsgren", "given": "Edvin", "initials": "E", "orcid": "0000-0002-1898-4453", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e981f1564556453499272c9e539cfd39.json"}}, {"family": "Rietdijk", "given": "Jonne", "initials": "J", "orcid": "0000-0003-3799-6684", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8ddf53fb09464533af556a7226b4aa59.json"}}, {"family": "Holmberg", "given": "David", "initials": "D", "orcid": "0000-0001-7204-0026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3a9ed06b6fd4d148bc29629a0fd55a5.json"}}, {"family": "Juneblad", "given": "Julia", "initials": "J", "orcid": "0009-0005-5122-4762", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1863932c2ce649938d454b15f3eb77b1.json"}}, {"family": "Migliori", "given": "Bianca", "initials": "B", "orcid": "0000-0002-6333-314X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/46b4720c0d64431292e7cd99fc011f97.json"}}, {"family": "Johansson", "given": "Martin M", "initials": "MM", "orcid": "0000-0002-3733-8975", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2855ed29e434d8e9cb64c882492438c.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Trygg", "given": "Johan", "initials": "J", "orcid": "0000-0003-3799-6094", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e227e1e1bb84083b9534f4124830f6d.json"}}, {"family": "Lovell", "given": "Gillian", "initials": "G", "orcid": "0009-0004-5180-9704", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/23c69adcd63c4a10a532ef14af15bb2f.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Jonsson", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0001-8357-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13ef98fdf5154e7394768a61a276adac.json"}}], "type": "journal-article", "published": "2026-06-00", "journal": {"title": "Artificial Intelligence in the Life Sciences", "issn": "2667-3185", "volume": "9", "pages": "100152", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ailsci.2025.100152", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T06:41:39.157Z", "modified": "2026-08-20T06:41:39.564Z"}, {"entity": "publication", "iuid": "3d32f06fdbb54a10b4ad781dfcdff80d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d32f06fdbb54a10b4ad781dfcdff80d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d32f06fdbb54a10b4ad781dfcdff80d"}}, "title": "The time dimension matters: Improving mode of action classification with live-cell imaging", "authors": [{"family": "Forsgren", "given": "Edvin", "initials": "E", "orcid": "0000-0002-1898-4453", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e981f1564556453499272c9e539cfd39.json"}}, {"family": "Rietdijk", "given": "Jonne", "initials": "J", "orcid": "0000-0003-3799-6684", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8ddf53fb09464533af556a7226b4aa59.json"}}, {"family": "Holmberg", "given": "David", "initials": "D", "orcid": "0000-0001-7204-0026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3a9ed06b6fd4d148bc29629a0fd55a5.json"}}, {"family": "Juneblad", "given": "Julia", "initials": "J", "orcid": "0009-0005-5122-4762", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1863932c2ce649938d454b15f3eb77b1.json"}}, {"family": "Migliori", "given": "Bianca", "initials": "B", "orcid": "0000-0002-6333-314X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/46b4720c0d64431292e7cd99fc011f97.json"}}, {"family": "Johansson", "given": "Martin M", "initials": "MM", "orcid": "0000-0002-3733-8975", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2855ed29e434d8e9cb64c882492438c.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Trygg", "given": "Johan", "initials": "J", "orcid": "0000-0003-3799-6094", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e227e1e1bb84083b9534f4124830f6d.json"}}, {"family": "Lovell", "given": "Gillian", "initials": "G", "orcid": "0009-0004-5180-9704", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/23c69adcd63c4a10a532ef14af15bb2f.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Jonsson", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0001-8357-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13ef98fdf5154e7394768a61a276adac.json"}}], "type": "posted-content", "published": "2025-04-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.04.22.649936", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:02:23.879Z", "modified": "2026-08-20T11:02:23.987Z"}, {"entity": "publication", "iuid": "f877e8b426a9495d9674c62ca38e1435", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f877e8b426a9495d9674c62ca38e1435.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f877e8b426a9495d9674c62ca38e1435"}}, "title": "Single-Cell Morphological Profiling Reveals Insights into Programmed Cell Death", "authors": [{"family": "Frey", "given": "Benjamin", "initials": "B", "orcid": "0009-0004-7649-8340", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b30c616976c44a1dbe45ee85ff5ba156.json"}}, {"family": "Holmberg", "given": "David", "initials": "D", "orcid": "0000-0001-7204-0026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3a9ed06b6fd4d148bc29629a0fd55a5.json"}}, {"family": "Bystr\u00f6m", "given": "Petter", "initials": "P", "orcid": "0009-0001-8093-6604", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a85c60661f34c6da8e0ab61ebe3cdbc.json"}}, {"family": "Bergman", "given": "Ebba", "initials": "E", "orcid": "0000-0003-0484-6022", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/23cb8b95d4bb42dda1189dcba13251e1.json"}}, {"family": "Georgiev", "given": "Polina", "initials": "P"}, {"family": "Johansson", "given": "Martin M", "initials": "MM", "orcid": "0000-0002-3733-8975", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2855ed29e434d8e9cb64c882492438c.json"}}, {"family": "Hennig", "given": "Patrick", "initials": "P"}, {"family": "Rietdijk", "given": "Jonne", "initials": "J", "orcid": "0000-0003-3799-6684", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8ddf53fb09464533af556a7226b4aa59.json"}}, {"family": "Ros\u00e9n", "given": "Dan", "initials": "D"}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}], "type": "posted-content", "published": "2025-01-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.01.15.633042", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:59:47.950Z", "modified": "2026-08-20T10:59:48.158Z"}, {"entity": "publication", "iuid": "934f69a0412044b4b32374cc6cd1ae49", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/934f69a0412044b4b32374cc6cd1ae49.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/934f69a0412044b4b32374cc6cd1ae49"}}, "title": "A Decade in a Systematic Review: The Evolution and Impact of Cell Painting.", "authors": [{"family": "Seal", "given": "Srijit", "initials": "S", "orcid": "0000-0003-2790-8679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf360510777949acaa72a940f13e17bf.json"}}, {"family": "Trapotsi", "given": "Maria-Anna", "initials": "MA", "orcid": "0000-0002-9177-4241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f90a4eeefb14159b4397b84a116e152.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Singh", "given": "Shantanu", "initials": "S", "orcid": "0000-0003-3150-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fab52cf5bb64d62878524fc2da36dd1.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Greene", "given": "Nigel", "initials": "N", "orcid": "0000-0003-0433-4596", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e97367503f749bc934ddb3f10a84891.json"}}, {"family": "Bender", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6683-7546", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fea25f8013a14bb587c85df858f74d55.json"}}, {"family": "Carpenter", "given": "Anne E", "initials": "AE", "orcid": "0000-0003-1555-8261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bda2a39a0ac4fd9a7d95298608afb74.json"}}], "type": "preprint", "published": "2024-05-07", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions. Here, we systematically review the substantial methodological advancements and applications of Cell Painting. Advancements include improvements in the Cell Painting protocol, assay adaptations for different types of perturbations and applications, and improved methodologies for feature extraction, quality control, and batch effect correction. Moreover, machine learning methods recently surpassed classical approaches in their ability to extract biologically useful information from Cell Painting images. Cell Painting data have been used alone or in combination with other - omics data to decipher the mechanism of action of a compound, its toxicity profile, and many other biological effects. Overall, key methodological advances have expanded Cell Painting's ability to capture cellular responses to various perturbations. Future advances will likely lie in advancing computational and experimental techniques, developing new publicly available datasets, and integrating them with other high-content data types.", "doi": "10.1101/2024.05.04.592531", "pmid": "38766203", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11100607"}, {"db": "pii", "key": "2024.05.04.592531"}], "notes": [], "created": "2026-08-20T10:54:50.205Z", "modified": "2026-08-20T10:54:50.323Z"}, {"entity": "publication", "iuid": "bc1a8965388d4dcab37b9050baee86f9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bc1a8965388d4dcab37b9050baee86f9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bc1a8965388d4dcab37b9050baee86f9"}}, "title": "From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability.", "authors": [{"family": "Seal", "given": "Srijit", "initials": "S", "orcid": "0000-0003-2790-8679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf360510777949acaa72a940f13e17bf.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Singh", "given": "Shantanu", "initials": "S", "orcid": "0000-0003-3150-3025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fab52cf5bb64d62878524fc2da36dd1.json"}}, {"family": "Carpenter", "given": "Anne E", "initials": "AE", "orcid": "0000-0003-1555-8261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bda2a39a0ac4fd9a7d95298608afb74.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Bender", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6683-7546", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fea25f8013a14bb587c85df858f74d55.json"}}], "type": "journal article", "published": "2024-03-01", "journal": {"title": "Mol. Biol. Cell", "issn": "1939-4586", "volume": "35", "issue": "3", "pages": "mr2", "issn-l": "1059-1524"}, "abstract": "Cell Painting assays generate morphological profiles that are versatile descriptors of biological systems and have been used to predict in vitro and in vivo drug effects. However, Cell Painting features extracted from classical software such as CellProfiler are based on statistical calculations and often not readily biologically interpretable. In this study, we propose a new feature space, which we call BioMorph, that maps these Cell Painting features with readouts from comprehensive Cell Health assays. We validated that the resulting BioMorph space effectively connected compounds not only with the morphological features associated with their bioactivity but with deeper insights into phenotypic characteristics and cellular processes associated with the given bioactivity. The BioMorph space revealed the mechanism of action for individual compounds, including dual-acting compounds such as emetine, an inhibitor of both protein synthesis and DNA replication. Overall, BioMorph space offers a biologically relevant way to interpret the cell morphological features derived using software such as CellProfiler and to generate hypotheses for experimental validation.", "doi": "10.1091/mbc.E23-08-0298", "pmid": "38170589", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10916876"}], "notes": [], "created": "2026-08-20T09:38:45.160Z", "modified": "2026-08-20T09:38:45.255Z"}, {"entity": "publication", "iuid": "d231ebae020f4ea2a3a8b143ad8583c1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d231ebae020f4ea2a3a8b143ad8583c1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d231ebae020f4ea2a3a8b143ad8583c1"}}, "title": "From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability", "authors": [{"family": "Seal", "given": "Srijit", "initials": "S", "orcid": "0000-0003-2790-8679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf360510777949acaa72a940f13e17bf.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Carpenter", "given": "Anne E", "initials": "AE", "orcid": "0000-0003-1555-8261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bda2a39a0ac4fd9a7d95298608afb74.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Bender", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6683-7546", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fea25f8013a14bb587c85df858f74d55.json"}}], "type": "posted-content", "published": "2023-07-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.07.14.549031", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:47:10.362Z", "modified": "2026-08-20T10:47:10.444Z"}, {"entity": "publication", "iuid": "ce40cc04a01842b485fd371f05a29141", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ce40cc04a01842b485fd371f05a29141.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ce40cc04a01842b485fd371f05a29141"}}, "title": "Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection.", "authors": [{"family": "Seal", "given": "Srijit", "initials": "S", "orcid": "0000-0003-2790-8679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf360510777949acaa72a940f13e17bf.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Trapotsi", "given": "Maria-Anna", "initials": "MA"}, {"family": "Yang", "given": "Hongbin", "initials": "H"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Bender", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6683-7546", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fea25f8013a14bb587c85df858f74d55.json"}}], "type": "journal article", "published": "2022-08-23", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "858", "issn-l": "2399-3642"}, "abstract": "Mitochondrial toxicity is an important safety endpoint in drug discovery. Models based solely on chemical structure for predicting mitochondrial toxicity are currently limited in accuracy and applicability domain to the chemical space of the training compounds. In this work, we aimed to utilize both -omics and chemical data to push beyond the state-of-the-art. We combined Cell Painting and Gene Expression data with chemical structural information from Morgan fingerprints for 382 chemical perturbants tested in the Tox21 mitochondrial membrane depolarization assay. We observed that mitochondrial toxicants differ from non-toxic compounds in morphological space and identified compound clusters having similar mechanisms of mitochondrial toxicity, thereby indicating that morphological space provides biological insights related to mechanisms of action of this endpoint. We further showed that models combining Cell Painting, Gene Expression features and Morgan fingerprints improved model performance on an external test set of 244 compounds by 60% (in terms of F1 score) and improved extrapolation to new chemical space. The performance of our combined models was comparable with dedicated in vitro assays for mitochondrial toxicity. Our results suggest that combining chemical descriptors with biological readouts enhances the detection of mitochondrial toxicants, with practical implications in drug discovery.", "doi": "10.1038/s42003-022-03763-5", "pmid": "35999457", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9399120"}, {"db": "pii", "key": "10.1038/s42003-022-03763-5"}], "notes": [], "created": "2026-08-20T09:25:11.982Z", "modified": "2026-08-20T09:25:12.044Z"}, {"entity": "publication", "iuid": "d4048b84014049d6a37daf6c6b694bb6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d4048b84014049d6a37daf6c6b694bb6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d4048b84014049d6a37daf6c6b694bb6"}}, "title": "Merging Bioactivity Predictions from Cell Morphology and Chemical Fingerprint Models Using Similarity to Training Data", "authors": [{"family": "Seal", "given": "Srijit", "initials": "S", "orcid": "0000-0003-2790-8679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf360510777949acaa72a940f13e17bf.json"}}, {"family": "Yang", "given": "Hongbin", "initials": "H", "orcid": "0000-0001-6740-1632", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be7b76ff277f4f8596a2394c676a4785.json"}}, {"family": "Trapotsi", "given": "Maria Anna", "initials": "MA", "orcid": "0000-0002-9177-4241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f90a4eeefb14159b4397b84a116e152.json"}}, {"family": "Singh", "given": "Satvik", "initials": "S", "orcid": "0000-0002-2971-4256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2a4a927dac9423ba8d4f7153463dd40.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Bender", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6683-7546", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fea25f8013a14bb587c85df858f74d55.json"}}], "type": "posted-content", "published": "2022-08-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.08.11.503624", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:12:56.598Z", "modified": "2026-08-20T10:12:56.725Z"}, {"entity": "publication", "iuid": "5e3ee38a74aa4edc86dbdc132d558486", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5e3ee38a74aa4edc86dbdc132d558486.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5e3ee38a74aa4edc86dbdc132d558486"}}, "title": "Designing microplate layouts using artificial intelligence", "authors": [{"family": "Francisco Rodr\u00edguez", "given": "Mar\u00eda Andre\u00edna", "initials": "MA", "orcid": "0000-0001-8745-9858", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2bd8dd95fcff4a36bb25ec06d2e05bb3.json"}}, {"family": "Puigvert", "given": "Jordi Carreras", "initials": "JC", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}], "type": "posted-content", "published": "2022-04-01", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.03.31.486595", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:10:37.016Z", "modified": "2026-08-20T10:10:37.091Z"}, {"entity": "publication", "iuid": "a0ab7878639b4d79be7adafe2c6413e8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a0ab7878639b4d79be7adafe2c6413e8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a0ab7878639b4d79be7adafe2c6413e8"}}, "title": "Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects", "authors": [{"family": "Rietdijk", "given": "Jonne", "initials": "J", "orcid": "0000-0003-3799-6684", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8ddf53fb09464533af556a7226b4aa59.json"}}, {"family": "Aggarwal", "given": "Tanya", "initials": "T"}, {"family": "Georgieva", "given": "Polina", "initials": "P", "orcid": "0000-0001-8326-4738", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/38811419378d4c77bad0ab92f8209d40.json"}}, {"family": "Lapins", "given": "Maris", "initials": "M", "orcid": "0000-0002-0122-6680", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/229dd86a1de44e60bd2747cee36411c8.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}], "type": "posted-content", "published": "2022-02-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.02.10.479889", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:09:34.727Z", "modified": "2026-08-20T10:09:34.906Z"}, {"entity": "publication", "iuid": "d8c81c9739d146cfb69de5ea31b4b9de", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d8c81c9739d146cfb69de5ea31b4b9de.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d8c81c9739d146cfb69de5ea31b4b9de"}}, "title": "Integrating Cell Morphology with Gene Expression and Chemical Structure to Aid Mitochondrial Toxicity Detection", "authors": [{"family": "Seal", "given": "Srijit", "initials": "S", "orcid": "0000-0003-2790-8679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf360510777949acaa72a940f13e17bf.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Trapotsi", "given": "Maria Anna", "initials": "MA", "orcid": "0000-0002-9177-4241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f90a4eeefb14159b4397b84a116e152.json"}}, {"family": "Yang", "given": "Hongbin", "initials": "H", "orcid": "0000-0001-6740-1632", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be7b76ff277f4f8596a2394c676a4785.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Bender", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6683-7546", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fea25f8013a14bb587c85df858f74d55.json"}}], "type": "posted-content", "published": "2022-01-07", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.01.07.475326", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:08:01.956Z", "modified": "2026-08-20T10:08:02.084Z"}, {"entity": "publication", "iuid": "0825dfd004cd41a5a533fcb87bf4479b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0825dfd004cd41a5a533fcb87bf4479b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0825dfd004cd41a5a533fcb87bf4479b"}}, "title": "A phenomics approach for antiviral drug discovery.", "authors": [{"family": "Rietdijk", "given": "Jonne", "initials": "J"}, {"family": "Tampere", "given": "Marianna", "initials": "M"}, {"family": "Pettke", "given": "Aleksandra", "initials": "A"}, {"family": "Georgiev", "given": "Polina", "initials": "P"}, {"family": "Lapins", "given": "Maris", "initials": "M"}, {"family": "Warpman-Berglund", "given": "Ulrika", "initials": "U"}, {"family": "Spjuth", "given": "Ola", "initials": "O"}, {"family": "Puumalainen", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}], "type": "journal article", "published": "2021-08-02", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "19", "issue": "1", "pages": "156", "issn-l": "1741-7007"}, "abstract": "The emergence and continued global spread of the current COVID-19 pandemic has highlighted the need for methods to identify novel or repurposed therapeutic drugs in a fast and effective way. Despite the availability of methods for the discovery of antiviral drugs, the majority tend to focus on the effects of such drugs on a given virus, its constituent proteins, or enzymatic activity, often neglecting the consequences on host cells. This may lead to partial assessment of the efficacy of the tested anti-viral compounds, as potential toxicity impacting the overall physiology of host cells may mask the effects of both viral infection and drug candidates. Here we present a method able to assess the general health of host cells based on morphological profiling, for untargeted phenotypic drug screening against viral infections.\n\nWe combine Cell Painting with antibody-based detection of viral infection in a single assay. We designed an image analysis pipeline for segmentation and classification of virus-infected and non-infected cells, followed by extraction of morphological properties. We show that this methodology can successfully capture virus-induced phenotypic signatures of MRC-5 human lung fibroblasts infected with human coronavirus 229E (CoV-229E). Moreover, we demonstrate that our method can be used in phenotypic drug screening using a panel of nine host- and virus-targeting antivirals. Treatment with effective antiviral compounds reversed the morphological profile of the host cells towards a non-infected state.\n\nThe phenomics approach presented here, which makes use of a modified Cell Painting protocol by incorporating an anti-virus antibody stain, can be used for the unbiased morphological profiling of virus infection on host cells. The method can identify antiviral reference compounds, as well as novel antivirals, demonstrating its suitability to be implemented as a strategy for antiviral drug repurposing and drug discovery.", "doi": "10.1186/s12915-021-01086-1", "pmid": "34334126", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8325993"}, {"db": "pii", "key": "10.1186/s12915-021-01086-1"}], "notes": [], "created": "2026-08-20T12:20:19.114Z", "modified": "2026-08-20T12:20:19.177Z"}, {"entity": "publication", "iuid": "849012b13e6d40bebf1e5edd27cc7d24", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/849012b13e6d40bebf1e5edd27cc7d24.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/849012b13e6d40bebf1e5edd27cc7d24"}}, "title": "An Open-Source Modular Framework for Automated Pipetting and Imaging Applications", "authors": [{"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Bowman", "given": "Richard", "initials": "R", "orcid": "0000-0002-1531-8199", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd8285f431ce4ff59d9b6b288cec6b9d.json"}}, {"family": "Wang", "given": "Haoran", "initials": "H"}, {"family": "Bumke", "given": "Kaspar E", "initials": "KE"}, {"family": "Collins", "given": "Joel T", "initials": "JT"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Diederich", "given": "Benedict", "initials": "B", "orcid": "0000-0003-0453-6286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25fb1523d3854ce59fdfe3841250ac3c.json"}}], "type": "posted-content", "published": "2021-06-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.06.24.449732", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:05:13.473Z", "modified": "2026-08-20T10:05:13.584Z"}, {"entity": "publication", "iuid": "36f8e2add74d43b4b4afbc4a66bfd420", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/36f8e2add74d43b4b4afbc4a66bfd420.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/36f8e2add74d43b4b4afbc4a66bfd420"}}, "title": "A phenomics approach for in vitro antiviral drug discovery", "authors": [{"family": "Rietdijk", "given": "Jonne", "initials": "J"}, {"family": "Tampere", "given": "Marianna", "initials": "M"}, {"family": "Pettke", "given": "Aleksandra", "initials": "A"}, {"family": "Georgieva", "given": "Polina", "initials": "P"}, {"family": "Lapins", "given": "Maris", "initials": "M"}, {"family": "Berglund", "given": "Ulrika Warpman", "initials": "UW"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Puumalainen", "given": "Marjo Riitta", "initials": "MR"}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}], "type": "posted-content", "published": "2021-01-13", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.01.13.423947", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:01:08.099Z", "modified": "2026-08-20T10:01:08.162Z"}, {"entity": "publication", "iuid": "476cb452a5ef4e1ea482d00c60f7f0e4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/476cb452a5ef4e1ea482d00c60f7f0e4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/476cb452a5ef4e1ea482d00c60f7f0e4"}}, "title": "Gefitinib and Afatinib Show Potential Efficacy for Fanconi Anemia-Related Head and Neck Cancer.", "authors": [{"family": "Montanuy", "given": "Helena", "initials": "H"}, {"family": "Mart\u00ednez-Barriocanal", "given": "\u00c1gueda", "initials": "\u00c1"}, {"family": "Antonio Casado", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0003-2479-1508", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1b8e3d25bcb4a40abbacff39173315d.json"}}, {"family": "Rovirosa", "given": "Lloren\u00e7", "initials": "L", "orcid": "0000-0003-2986-9001", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce88723f24d4ec79daaf137f5e78abb.json"}}, {"family": "Ram\u00edrez", "given": "Maria Jos\u00e9", "initials": "MJ", "orcid": "0000-0003-1417-7731", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f596124d88784e7d8cd4b38039a4db6b.json"}}, {"family": "Nieto", "given": "Roc\u00edo", "initials": "R"}, {"family": "Carrascoso-Rubio", "given": "Carlos", "initials": "C", "orcid": "0000-0002-6911-2946", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf9646728180480f8b05804386ef8414.json"}}, {"family": "Riera", "given": "Pau", "initials": "P", "orcid": "0000-0002-3074-3927", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/78b0e8ee70fb4d9fb1a8989208af6c57.json"}}, {"family": "Gonz\u00e1lez", "given": "Alan", "initials": "A"}, {"family": "Lerma", "given": "Enrique", "initials": "E"}, {"family": "Lasa", "given": "Adriana", "initials": "A", "orcid": "0000-0001-9957-9646", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21a4c5e794d144e6a20a422da51cfe33.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9c300823ae241eea419a01e4397fcc2.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T"}, {"family": "Bueren", "given": "Juan A", "initials": "JA"}, {"family": "Arango", "given": "Diego", "initials": "D"}, {"family": "Minguill\u00f3n", "given": "Jordi", "initials": "J"}, {"family": "Surrall\u00e9s", "given": "Jordi", "initials": "J"}], "type": "journal article", "published": "2020-06-15", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "volume": "26", "issue": "12", "pages": "3044-3057", "issn-l": "1078-0432"}, "abstract": "Fanconi anemia rare disease is characterized by bone marrow failure and a high predisposition to solid tumors, especially head and neck squamous cell carcinoma (HNSCC). Patients with Fanconi anemia with HNSCC are not eligible for conventional therapies due to high toxicity in healthy cells, predominantly hematotoxicity, and the only treatment currently available is surgical resection. In this work, we searched and validated two already approved drugs as new potential therapies for HNSCC in patients with Fanconi anemia.\n\nWe conducted a high-content screening of 3,802 drugs in a FANCA-deficient tumor cell line to identify nongenotoxic drugs with cytotoxic/cytostatic activity. The best candidates were further studied in vitro and in vivo for efficacy and safety.\n\nSeveral FDA/European Medicines Agency (EMA)-approved anticancer drugs showed cancer-specific lethality or cell growth inhibition in Fanconi anemia HNSCC cell lines. The two best candidates, gefitinib and afatinib, EGFR inhibitors approved for non-small cell lung cancer (NSCLC), displayed nontumor/tumor IC50 ratios of approximately 400 and approximately 100 times, respectively. Neither gefitinib nor afatinib activated the Fanconi anemia signaling pathway or induced chromosomal fragility in Fanconi anemia cell lines. Importantly, both drugs inhibited tumor growth in xenograft experiments in immunodeficient mice using two Fanconi anemia patient-derived HNSCCs. Finally, in vivo toxicity studies in Fanca-deficient mice showed that administration of gefitinib or afatinib was well-tolerated, displayed manageable side effects, no toxicity to bone marrow progenitors, and did not alter any hematologic parameters.\n\nOur data present a complete preclinical analysis and promising therapeutic line of the first FDA/EMA-approved anticancer drugs exerting cancer-specific toxicity for HNSCC in patients with Fanconi anemia.", "doi": "10.1158/1078-0432.CCR-19-1625", "pmid": "32005748", "labels": [], "xrefs": [{"db": "pii", "key": "1078-0432.CCR-19-1625"}], "notes": [], "created": "2026-08-20T12:12:10.338Z", "modified": "2026-08-20T12:12:10.627Z"}]}