{"entity": "researcher", "timestamp": "2026-10-05T21:05:12.563Z", "family": "Tanoli", "given": "Ziaurrehman", "initials": "Z", "orcid": "0000-0003-2435-9862", "affiliations": ["Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/313c5ea401cf4c178d088e587d9f288f.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/313c5ea401cf4c178d088e587d9f288f"}}, "publications": [{"entity": "publication", "iuid": "fd6b36b9b7954640a91eda229981e7a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd6b36b9b7954640a91eda229981e7a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd6b36b9b7954640a91eda229981e7a4"}}, "title": "Computational drug repurposing: approaches, evaluation of in silico resources and case studies.", "authors": [{"family": "Tanoli", "given": "Ziaurrehman", "initials": "Z", "orcid": "0000-0003-2435-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/313c5ea401cf4c178d088e587d9f288f.json"}}, {"family": "Fern\u00e1ndez-Torras", "given": "Adri\u00e0", "initials": "A"}, {"family": "\u00d6zcan", "given": "Umut Onur", "initials": "UO", "orcid": "0000-0002-7317-1682", "researcher": {"href": "https://publications.scilifelab.se/researcher/263b2b77f07a473db81d4e1bf628bbaf.json"}}, {"family": "Kushnir", "given": "Aleksandr", "initials": "A"}, {"family": "Nader", "given": "Kristen Michelle", "initials": "KM", "orcid": "0009-0002-1068-0831", "researcher": {"href": "https://publications.scilifelab.se/researcher/28b9535c8a1a41fcb2b50677151dc92c.json"}}, {"family": "Gadiya", "given": "Yojana", "initials": "Y", "orcid": "0000-0002-7683-0452", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda537ad863640fbbe1b3e85e05092bb.json"}}, {"family": "Fiorenza", "given": "Laura", "initials": "L"}, {"family": "Ianevski", "given": "Aleksandr", "initials": "A", "orcid": "0000-0002-7780-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/438e80f3668b41c08d75618faabb285d.json"}}, {"family": "V\u00e4h\u00e4-Koskela", "given": "Markus", "initials": "M", "orcid": "0000-0001-7764-7820", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5c55c58b0f64591878356ab8c1a3ff4.json"}}, {"family": "Miihkinen", "given": "Mitro", "initials": "M", "orcid": "0000-0001-6822-3647", "researcher": {"href": "https://publications.scilifelab.se/researcher/782f144499194829a67e53d90af357bd.json"}}, {"family": "Seemab", "given": "Umair", "initials": "U"}, {"family": "Leinonen", "given": "Henri", "initials": "H", "orcid": "0000-0002-0388-832X", "researcher": {"href": "https://publications.scilifelab.se/researcher/08beef151ecb47978cc70e49d428d039.json"}}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Tampere", "given": "Marianna", "initials": "M"}, {"family": "Kalman", "given": "Adelinn", "initials": "A"}, {"family": "Ballante", "given": "Flavio", "initials": "F", "orcid": "0000-0002-4831-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/20429d2a46f4479a9c262875794a3a9d.json"}}, {"family": "Benfenati", "given": "Emilio", "initials": "E"}, {"family": "Saunders", "given": "Gary", "initials": "G"}, {"family": "Potdar", "given": "Swapnil", "initials": "S"}, {"family": "G\u00f3mez Garc\u00eda", "given": "Ismael", "initials": "I"}, {"family": "Garc\u00eda-Serna", "given": "Ricard", "initials": "R"}, {"family": "Talarico", "given": "Carmine", "initials": "C"}, {"family": "Beccari", "given": "Andrea Rosario", "initials": "AR", "orcid": "0000-0001-6830-2695", "researcher": {"href": "https://publications.scilifelab.se/researcher/a834a85c9dfd4cd69fe9578b05bfdb92.json"}}, {"family": "Schaal", "given": "Wesley", "initials": "W"}, {"family": "Polo", "given": "Andrea", "initials": "A"}, {"family": "Costantini", "given": "Susan", "initials": "S"}, {"family": "Cabri", "given": "Enrico", "initials": "E"}, {"family": "Jacobs", "given": "Marc", "initials": "M", "orcid": "0000-0003-4153-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/2057ce10fc4a40c28d6c99ddbca2da22.json"}}, {"family": "Saarela", "given": "Jani", "initials": "J"}, {"family": "Budillon", "given": "Alfredo", "initials": "A", "orcid": "0000-0002-6330-6053", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aa51cfd215b44aaa4fd2c262c84c13a.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Xhaard", "given": "Henri", "initials": "H"}, {"family": "Quintana", "given": "Jordi", "initials": "J"}, {"family": "Mestres", "given": "Jordi", "initials": "J", "orcid": "0000-0002-5202-4501", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b0fe21b221a4723bff492055fa6061b.json"}}, {"family": "Gribbon", "given": "Philip", "initials": "P"}, {"family": "Ussi", "given": "Anton E", "initials": "AE"}, {"family": "Lo", "given": "Donald C", "initials": "DC"}, {"family": "de Kort", "given": "Martin", "initials": "M", "orcid": "0000-0002-7264-5436", "researcher": {"href": "https://publications.scilifelab.se/researcher/016a2e73e1254b84aeb5898e8a026f1b.json"}}, {"family": "Wennerberg", "given": "Krister", "initials": "K", "orcid": "0000-0002-1352-4220", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a447e220e144c63a907f9c824ccc9da.json"}}, {"family": "Fratelli", "given": "Maddalena", "initials": "M", "orcid": "0000-0002-1769-3427", "researcher": {"href": "https://publications.scilifelab.se/researcher/a159ec26402b411dac5d5081a64f36cb.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Aittokallio", "given": "Tero", "initials": "T", "orcid": "0000-0002-0886-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/47e0db692d16440ea6779948c188713a.json"}}], "type": "journal article", "published": "2025-03-18", "journal": {"title": "Nat Rev Drug Discov", "issn": "1474-1784", "issn-l": "1474-1776"}, "abstract": "Repurposing of existing drugs for new indications has attracted substantial attention owing to its potential to accelerate drug development and reduce costs. Hundreds of computational resources such as databases and predictive platforms have been developed that can be applied for drug repurposing, making it challenging to select the right resource for a specific drug repurposing project. With the aim of helping to address this challenge, here we overview computational approaches to drug repurposing based on a comprehensive survey of available in silico resources using a purpose-built drug repurposing ontology that classifies the resources into hierarchical categories and provides application-specific information. We also present an expert evaluation of selected resources and three drug repurposing case studies implemented within the Horizon Europe REMEDi4ALL project to demonstrate the practical use of the resources. This comprehensive Review with expert evaluations and case studies provides guidelines and recommendations on the best use of various in silico resources for drug repurposing and establishes a basis for a sustainable and extendable drug repurposing web catalogue.", "doi": "10.1038/s41573-025-01164-x", "pmid": "40102635", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41573-025-01164-x"}], "notes": [], "created": "2025-06-04T12:37:06.655Z", "modified": "2025-10-17T13:04:26.771Z"}, {"entity": "publication", "iuid": "a8e768d017534882926ec31cc6be13df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8e768d017534882926ec31cc6be13df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8e768d017534882926ec31cc6be13df"}}, "title": "From library to landscape: integrative annotation workflows for compound libraries in drug repurposing", "authors": [{"family": "Reinshagen", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-8080-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/8414f1d0ee0144c88a72beb83f38e21c.json"}}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Gadiya", "given": "Yojana", "initials": "Y", "orcid": "0000-0002-7683-0452", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda537ad863640fbbe1b3e85e05092bb.json"}}, {"family": "Gustavsson", "given": "Anna Lena", "initials": "AL"}, {"family": "Tanoli", "given": "Ziaurrehman", "initials": "Z", "orcid": "0000-0003-2435-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/313c5ea401cf4c178d088e587d9f288f.json"}}, {"family": "Aittokallio", "given": "Tero", "initials": "T", "orcid": "0000-0002-0886-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/47e0db692d16440ea6779948c188713a.json"}}, {"family": "Huchting", "given": "Johanna", "initials": "J"}, {"family": "Jenmalm-Jensen", "given": "Annika", "initials": "A"}, {"family": "Gribbon", "given": "Philip", "initials": "P"}, {"family": "Zaliani", "given": "Andrea", "initials": "A"}, {"family": "Ballante", "given": "Flavio", "initials": "F", "orcid": "0000-0002-4831-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/20429d2a46f4479a9c262875794a3a9d.json"}}], "type": "journal-article", "published": "2025-01-18", "journal": {"title": "Database (Oxford)", "issn": "1758-0463", "issn-l": "1758-0463", "volume": "2025", "issue": null, "pages": null}, "abstract": "In the rapidly advancing landscape of drug discovery and repurposing, efficient access and integration of chemical and bioactivity data from public repositories have become essential. To address this need, we developed two complementary annotation pipelines (KNIME- and Python-based) that automate the extraction and integration of curated chemical and bioactivity data from public repositories. These pipelines support any user-provided compound library, enabling reproducible workflows that integrate data from heterogeneous sources such as ChEMBL and PubChem. As part of the REMEDi4ALL project, with the aim of establishing a European platform for drug repurposing, we validated our framework using a harmonized subset of the Specs repurposing collection, which includes >5000 compounds available at the partner institutes. We also developed two interactive dashboards that support multilayered analyses and visualization by integrating chemical properties, bioactivity profiles, and relational data. Our results demonstrate that this framework streamlines the collection of harmonized data and facilitates analyses that are critical for drug repurposing efforts, while remaining versatile for broader applications in drug discovery. Moreover, the analysis of the annotations reveals that the Specs subset includes chemical scaffolds representative of a significant portion of approved drugs and compounds undergoing clinical evaluation, underscoring its potential as a rich source of drug repurposing candidates. Both pipeline protocols are publicly available online, and the dashboards are open access.", "doi": "10.1093/database/baaf081", "pmid": "41364066", "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12687465"}, {"db": "pii", "key": "8374761"}], "notes": [], "created": "2026-03-17T12:54:07.801Z", "modified": "2026-03-17T13:00:51.224Z"}, {"entity": "publication", "iuid": "0b22f005027a427ca5d7a0dad0e905e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b22f005027a427ca5d7a0dad0e905e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b22f005027a427ca5d7a0dad0e905e7"}}, "title": "Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data.", "authors": [{"family": "Potdar", "given": "Swapnil", "initials": "S", "orcid": "0000-0002-2778-6918", "researcher": {"href": "https://publications.scilifelab.se/researcher/f298f1f4f73048ab9266e9f5a0ab83da.json"}}, {"family": "Ianevski", "given": "Filipp", "initials": "F"}, {"family": "Ianevski", "given": "Aleksandr", "initials": "A"}, {"family": "Tanoli", "given": "Ziaurrehman", "initials": "Z", "orcid": "0000-0003-2435-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/313c5ea401cf4c178d088e587d9f288f.json"}}, {"family": "Wennerberg", "given": "Krister", "initials": "K"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Aittokallio", "given": "Tero", "initials": "T", "orcid": "0000-0002-0886-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/47e0db692d16440ea6779948c188713a.json"}}, {"family": "Saarela", "given": "Jani", "initials": "J", "orcid": "0000-0001-7306-7175", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5febb7d8bc04ecb9664e3be19f4bb37.json"}}], "type": "journal article", "published": "2023-07-05", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "51", "issue": "W1", "pages": "W57-W61", "issn-l": "0305-1048"}, "abstract": "Functional precision medicine (fPM) offers an exciting, simplified approach to finding the right applications for existing molecules and enhancing therapeutic potential. Integrative and robust tools ensuring high accuracy and reliability of the results are critical. In response to this need, we previously developed Breeze, a drug screening data analysis pipeline, designed to facilitate quality control, dose-response curve fitting, and data visualization in a user-friendly manner. Here, we describe the latest version of Breeze (release 2.0), which implements an array of advanced data exploration capabilities, providing users with comprehensive post-analysis and interactive visualization options that are essential for minimizing false positive/negative outcomes and ensuring accurate interpretation of drug sensitivity and resistance data. The Breeze 2.0 web-tool also enables integrative analysis and cross-comparison of user-uploaded data with publicly available drug response datasets. The updated version incorporates new drug quantification metrics, supports analysis of both multi-dose and single-dose drug screening data and introduces a redesigned, intuitive user interface. With these enhancements, Breeze 2.0 is anticipated to substantially broaden its potential applications in diverse domains of fPM.", "doi": "10.1093/nar/gkad390", "pmid": "37178002", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10320147"}, {"db": "pii", "key": "7161532"}], "notes": [], "created": "2023-10-18T18:48:30.305Z", "modified": "2025-10-17T13:04:27.648Z"}]}