{"entity": "researcher", "timestamp": "2026-08-11T08:15:44.012Z", "family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "affiliations": ["Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, 751 24, Uppsala, Sweden"], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e"}}, "publications": [{"entity": "publication", "iuid": "f8ff8e625f5d45218a355407b7607936", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8ff8e625f5d45218a355407b7607936.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8ff8e625f5d45218a355407b7607936"}}, "title": "Co-exposure to PFAS and hydroxylated PCBs is associated with increased odds of multiple sclerosis", "authors": [{"family": "Vaivade", "given": "Aina", "initials": "A"}, {"family": "Sreenivasan", "given": "Akshai Parakkal", "initials": "AP", "orcid": "0000-0002-7293-6487", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b2f62a3bda9471d9227a6924b8adf7c.json"}}, {"family": "Erngren", "given": "Ida", "initials": "I", "orcid": "0000-0001-7867-9525", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8a16aaaf5194acba6b8649690a101d8.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Emami Khoonsari", "given": "Payam", "initials": "P"}, {"family": "Siljebo", "given": "Jakob", "initials": "J"}, {"family": "Al-Grety", "given": "Asma", "initials": "A"}, {"family": "Carlsson", "given": "Henrik", "initials": "H", "orcid": "0000-0001-5558-6641", "researcher": {"href": "https://publications.scilifelab.se/researcher/de9581804a0b4b22991b34ebe89e9017.json"}}, {"family": "\u00c5kerfeldt", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Hedstr\u00f6m", "given": "Anna Karin", "initials": "AK", "orcid": "0000-0002-6612-4749", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4a1c4b315cd4a09b8f98a87b6cd2fba.json"}}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Alfredsson", "given": "Lars", "initials": "L", "orcid": "0000-0003-1688-6697", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df230614a8a448e8607e03480169658.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Burman", "given": "Joachim", "initials": "J", "orcid": "0000-0002-7045-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b9b82661abc49baaeac34bfcfc45321.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K", "orcid": "0000-0002-0680-1410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae376585168459681f5e2cae0c75b96.json"}}], "type": "journal-article", "published": "2026-01-00", "journal": {"title": "Environment International", "issn": "0160-4120", "issn-l": "0160-4120", "volume": "207", "issue": null, "pages": "109993"}, "abstract": "Persistent organic pollutants often co-occur in human exposure environments, yet their combined effects on disease risk remain poorly understood. This study examined associations between serum concentrations of 14 per- and polyfluorinated substances (PFAS) and three hydroxylated polychlorinated biphenyls (OH-PCBs) and the onset of multiple sclerosis (MS), utilizing data from the Swedish population-based Epidemiological Investigation of Multiple Sclerosis (EIMS) cohort, comprising 907 MS cases and 907 matched controls. We employed single-substance logistic regression and quantile g-computation to evaluate cumulative and individual compound associations. We considered linear and non-linear risk patterns while adjusting for lifestyle factors and MS-associated HLA alleles. Our analysis revealed non-linear associations for several individual compounds, particularly perfluorooctane sulfonic acid (PFOS), perfluorononanoic acid, 2,2',3,4',5,5',6-heptachloro-4-biphenylol (4-OH-CB187), and 2,2',4,4',5,5'-, Hexachloro-3-biphenylol (3-OH-CB153), with increased odds of MS. Interaction analyses further indicated that the association between PFOS and MS odds was modified by the presence of the HLA-B*44:02 allele, known for its protective effect on MS risk. Mixture modeling highlighted that combined exposures to PFAS and OH-PCBs significantly increased MS odds, even when associations for individual compounds were weak or absent. These findings emphasize the complexity of associations between environmental contaminants, lifestyle and genetic risk factors, and the odds of MS. They underscore the importance of addressing co-exposure in environmental health research and call for further studies to elucidate underlying biological mechanisms.", "doi": "10.1016/j.envint.2025.109993", "pmid": "41411973", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0160-4120(25)00744-5"}], "notes": [], "created": "2026-02-10T09:53:14.232Z", "modified": "2026-03-24T09:16:23.730Z"}, {"entity": "publication", "iuid": "8e45f7b6f0c546ee93553d78ecbf4c23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e45f7b6f0c546ee93553d78ecbf4c23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e45f7b6f0c546ee93553d78ecbf4c23"}}, "title": "Morphological cell profiling for drug repurposing against SARS-CoV-2 infection", "authors": [{"family": "Asp", "given": "Elin", "initials": "E", "orcid": "0009-0006-6794-0779", "researcher": {"href": "https://publications.scilifelab.se/researcher/38e711145de94b0ba2e0a1891747a134.json"}}, {"family": "Rietdijk", "given": "Jonne", "initials": "J"}, {"family": "Tampere", "given": "Marianna", "initials": "M", "orcid": "0000-0001-5744-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c6c86cb20394d17abebb40db23407c8.json"}}, {"family": "Axelsson", "given": "Hanna", "initials": "H", "orcid": "0000-0003-2365-1749", "researcher": {"href": "https://publications.scilifelab.se/researcher/63b88c4d11c443f39121c6d93fcff1f0.json"}}, {"family": "Njenda", "given": "Duncan", "initials": "D", "orcid": "0000-0001-8276-9726", "researcher": {"href": "https://publications.scilifelab.se/researcher/c14c27f4d60549da9949c97ed66a15b5.json"}}, {"family": "Potdar", "given": "Swapnil", "initials": "S", "orcid": "0000-0002-2778-6918", "researcher": {"href": "https://publications.scilifelab.se/researcher/f298f1f4f73048ab9266e9f5a0ab83da.json"}}, {"family": "Kalman", "given": "Adelinn", "initials": "A"}, {"family": "Georgieva", "given": "Polina", "initials": "P", "orcid": "0000-0001-8326-4738", "researcher": {"href": "https://publications.scilifelab.se/researcher/394f19ff3cff4b1c94d0a9a92e976b73.json"}}, {"family": "Lapins", "given": "Maris", "initials": "M"}, {"family": "Ballante", "given": "Flavio", "initials": "F", "orcid": "0000-0002-4831-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/20429d2a46f4479a9c262875794a3a9d.json"}}, {"family": "Soler", "given": "Alicia", "initials": "A"}, {"family": "de Kort", "given": "Martin", "initials": "M", "orcid": "0000-0002-7264-5436", "researcher": {"href": "https://publications.scilifelab.se/researcher/016a2e73e1254b84aeb5898e8a026f1b.json"}}, {"family": "Aittokallio", "given": "Tero", "initials": "T", "orcid": "0000-0002-0886-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/47e0db692d16440ea6779948c188713a.json"}}, {"family": "Zaliani", "given": "Andrea", "initials": "A"}, {"family": "Kuzikov", "given": "Maria", "initials": "M"}, {"family": "Gribbon", "given": "Philip", "initials": "P"}, {"family": "Lo", "given": "Donald", "initials": "D"}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications.scilifelab.se/researcher/28ad5f6a1a064e52aca72780adc4bb96.json"}}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B", "orcid": "0000-0001-8658-5967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4645bc97a8024c548111802101b83571.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", "orcid": "0000-0001-5501-466X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0461a910ec4b4faa8668bb4044e76f61.json"}}], "type": "posted-content", "published": "2025-08-28", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.08.28.672794", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-25T11:34:50.011Z", "modified": "2025-12-18T19:09:56.756Z"}, {"entity": "publication", "iuid": "ab9b4fd3312a411fa7600da6cc9fc651", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651"}}, "title": "Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling.", "authors": [{"family": "Wenson", "given": "Leonie", "initials": "L", "orcid": "0000-0002-1864-1258", "researcher": {"href": "https://publications.scilifelab.se/researcher/989e0534adbd426386cec5526c5e9668.json"}}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Erbilgin", "given": "Y\u00fccel", "initials": "Y"}, {"family": "Salman", "given": "Bar\u0131\u015f", "initials": "B", "orcid": "0000-0002-7657-8576", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb919f7fcc794c8898fe800056d42f38.json"}}, {"family": "Sundqvist", "given": "Anders", "initials": "A"}, {"family": "Schaal", "given": "Wesley", "initials": "W", "orcid": "0000-0001-6770-0878", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab184845a24f4effb22ec2b338ab8960.json"}}, {"family": "Sandbaumh\u00fcter", "given": "Friederike A", "initials": "FA"}, {"family": "Jansson", "given": "Erik T", "initials": "ET"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}, {"family": "Davidsson", "given": "Anton", "initials": "A"}, {"family": "Stenerl\u00f6w", "given": "Bo", "initials": "B", "orcid": "0000-0001-8878-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/22437ff9315d43089232926973feb0d2.json"}}, {"family": "Espinoza", "given": "Jaime A", "initials": "JA", "orcid": "0000-0002-0731-2715", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cdf2cd80f5b4f87adf6d936b6390ee8.json"}}, {"family": "Lindstr\u00f6m", "given": "Mikael", "initials": "M", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O", "orcid": "0000-0003-2883-1925", "researcher": {"href": "https://publications.scilifelab.se/researcher/68df823efa304c0b9962684ac1515808.json"}}], "type": "journal article", "published": "2025-08-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": "7130"}, "abstract": "The ability to analyze whether DNA contains lesions is essential in identifying mutagenic substances. Currently, the detection of single-stranded DNA breaks (SSBs) lacks precision. To address this limitation, we develop a method for sequence-templated erroneous end-labelling sequencing (STEEL-seq), which enables the mapping of SSBs. The method requires a highly error-prone DNA polymerase, so we engineer a chimeric DNA polymerase, Sloppymerase, capable of replicating DNA in the absence of one nucleotide. Following the omission of a specific nucleotide (e.g., dATP) from the reaction mixture, Sloppymerase introduces mismatches directly downstream of SSBs at positions where deoxyadenosine should occur. This mismatch pattern, coupled with the retention of sequence information flanking these sites, ensures that the identified hits are bona fide SSBs. STEEL-seq is compatible with a variety of sequencing technologies, as demonstrated using Sanger, Illumina, PacBio, and Nanopore systems. Using STEEL-seq, we determine the SSB/base pair frequency in the human genome to range between 0.7 and 3.8 \u00d7 10-6 with an enrichment in active promoter regions.", "doi": "10.1038/s41467-025-62512-4", "pmid": "40759655", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12322144"}, {"db": "pii", "key": "10.1038/s41467-025-62512-4"}], "notes": [], "created": "2025-08-19T13:16:23.958Z", "modified": "2025-11-28T10:45:45.544Z"}, {"entity": "publication", "iuid": "b5fbc4b85dea4d92ba07db4892a0f3f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5fbc4b85dea4d92ba07db4892a0f3f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5fbc4b85dea4d92ba07db4892a0f3f5"}}, "title": "Integrating Cell Painting and Thermal Proteome Profiling for Inference of Targets and Mechanism of Action", "authors": [{"family": "Johansson", "given": "Camilla", "initials": "C", "orcid": "0000-0002-2685-5715", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fb85fc7f3e44ad1ae5ab810d7d177d0.json"}}, {"family": "Johansson", "given": "Martin", "initials": "M", "orcid": "0000-0002-3733-8975", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1fdb7ed5e7047f3963ada15a0f8d48e.json"}}, {"family": "Carreras Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications.scilifelab.se/researcher/28ad5f6a1a064e52aca72780adc4bb96.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Jansson", "given": "Erik T", "initials": "ET", "orcid": "0000-0002-0675-3412", "researcher": {"href": "https://publications.scilifelab.se/researcher/b896baf96b99439b941fcb6b5c53802e.json"}}], "type": "posted-content", "published": "2025-06-02", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.05.30.657006", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2025-12-03T08:44:57.191Z", "modified": "2025-12-19T07:57:28.071Z"}, {"entity": "publication", "iuid": "e2d13bad5737495b893d34596e3fee25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2d13bad5737495b893d34596e3fee25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2d13bad5737495b893d34596e3fee25"}}, "title": "Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis.", "authors": [{"family": "Sreenivasan", "given": "Akshai Parakkal", "initials": "AP"}, {"family": "Vaivade", "given": "Aina", "initials": "A"}, {"family": "Noui", "given": "Yassine", "initials": "Y", "orcid": "0000-0002-0513-7546", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e4b7066daf4084b24fdbbac41e3c9e.json"}}, {"family": "Khoonsari", "given": "Payam Emami", "initials": "PE", "orcid": "0000-0002-4137-5517", "researcher": {"href": "https://publications.scilifelab.se/researcher/23c186a5ec4f46479fe0db63caa77ed2.json"}}, {"family": "Burman", "given": "Joachim", "initials": "J"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K"}], "type": "journal article", "published": "2025-04-24", "journal": {"title": "NPJ Digit Med", "issn": "2398-6352", "volume": "8", "issue": "1", "pages": "224", "issn-l": null}, "abstract": "Accurate assessment of progression and disease course in multiple sclerosis (MS) is vital for timely and appropriate clinical intervention. The gradual transition from relapsing-remitting MS (RRMS) to secondary progressive MS (SPMS) is often diagnosed retrospectively with a typical delay of three years. To address this diagnostic delay, we developed a predictive model that uses electronic health records to distinguish between RRMS and SPMS at each individual visit. To enable reliable predictions, conformal prediction was implemented at the individual patient level with a confidence of 93%. Our model accurately predicted the change in diagnosis from RRMS to SPMS for patients who transitioned during the study period. Additionally, we identified new patients who, with high probability, are in the transition phase but have not yet received a clinical diagnosis. Our methodology aids in monitoring MS progression and proactively identifying transitioning patients. An anonymized model is available at https://msp-tracker.serve.scilifelab.se/ .", "doi": "10.1038/s41746-025-01616-z", "pmid": "40275055", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41746-025-01616-z"}], "notes": [], "created": "2025-04-25T09:40:03.092Z", "modified": "2025-04-25T09:40:06.333Z"}, {"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": "fcaf83e14171434292e517ec5c5af2a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcaf83e14171434292e517ec5c5af2a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcaf83e14171434292e517ec5c5af2a8"}}, "title": "Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening.", "authors": [{"family": "Vaivade", "given": "Aina", "initials": "A"}, {"family": "Erngren", "given": "Ida", "initials": "I", "orcid": "0000-0001-7867-9525", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8a16aaaf5194acba6b8649690a101d8.json"}}, {"family": "Carlsson", "given": "Henrik", "initials": "H", "orcid": "0000-0001-5558-6641", "researcher": {"href": "https://publications.scilifelab.se/researcher/de9581804a0b4b22991b34ebe89e9017.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Emami Khoonsari", "given": "Payam", "initials": "P"}, {"family": "Noui", "given": "Yassine", "initials": "Y", "orcid": "0000-0002-0513-7546", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e4b7066daf4084b24fdbbac41e3c9e.json"}}, {"family": "Al-Grety", "given": "Asma", "initials": "A"}, {"family": "\u00c5kerfeldt", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Gallo", "given": "Valentina", "initials": "V"}, {"family": "Larsson", "given": "Anders Olof", "initials": "AO"}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Hedstr\u00f6m", "given": "Anna Karin", "initials": "AK", "orcid": "0000-0002-6612-4749", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4a1c4b315cd4a09b8f98a87b6cd2fba.json"}}, {"family": "Alfredsson", "given": "Lars", "initials": "L", "orcid": "0000-0003-1688-6697", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df230614a8a448e8607e03480169658.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Burman", "given": "Joachim", "initials": "J", "orcid": "0000-0002-7045-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b9b82661abc49baaeac34bfcfc45321.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K", "orcid": "0000-0002-0680-1410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ae376585168459681f5e2cae0c75b96.json"}}], "type": "journal article", "published": "2025-02-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2014", "issn-l": "2041-1723"}, "abstract": "Exposure to per- and polyfluorinated substances (PFAS) and hydroxylated polychlorinated biphenyls (OH-PCBs) is associated with adverse human health effects, including immunosuppression. It is unknown if these substances can affect the course of autoimmune diseases. This study was based on 907 individuals with multiple sclerosis (MS) and 907 matched controls, where the MS cases were followed longitudinally using the Swedish MS register. We demonstrate sex- and disease-specific differences in serum PFAS concentrations between individuals with MS and controls. Moreover, two OH-PCBs (4-OH-CB187 and 3-OH-CB153) are associated with an increased risk of developing multiple sclerosis, regardless of sex and immigration status. With a clinical follow-up time of up to 18 years, an increase in serum concentrations of perfluorooctanoic acid (PFOA), perfluorooctane sulfonic acid (PFOS), and perfluorodecanoic acid (PFDA) decreases the risk of confirmed disability worsening in both sexes, as well as perfluoroheptanesulfonic acid (PFHpS) and perfluorononanoic acid (PFNA), only in males with MS. These results show previously unknown associations between OH-PCBs and the risk of developing MS, as well as the inverse associations between PFAS exposure and the risk of disability worsening in MS.", "doi": "10.1038/s41467-025-57172-3", "pmid": "40016224", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-57172-3"}], "notes": [], "created": "2025-03-01T11:13:17.025Z", "modified": "2025-03-24T08:20:33.179Z"}, {"entity": "publication", "iuid": "79a9f40ca8e84b22978cef973223751e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79a9f40ca8e84b22978cef973223751e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79a9f40ca8e84b22978cef973223751e"}}, "title": "High-content morphological profiling by Cell Painting in 3D spheroids", "authors": [{"family": "Ringers", "given": "Christa", "initials": "C", "orcid": "0000-0002-0807-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/1870bfae83214898acf048b2ecbd81ba.json"}}, {"family": "Holmberg", "given": "David", "initials": "D", "orcid": "0000-0001-7204-0026", "researcher": {"href": "https://publications.scilifelab.se/researcher/56fa719ef91e45c4bdb4171fa4a40338.json"}}, {"family": "Flobak", "given": "\u00c5smund", "initials": "\u00c5", "orcid": "0000-0002-3357-425X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dbad688aeb44d039f3bc7e51f75b2bf.json"}}, {"family": "Georgieva", "given": "Polina", "initials": "P", "orcid": "0000-0001-8326-4738", "researcher": {"href": "https://publications.scilifelab.se/researcher/394f19ff3cff4b1c94d0a9a92e976b73.json"}}, {"family": "Jarvius", "given": "Malin", "initials": "M", "orcid": "0000-0002-1565-6155", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6b510afc21748adb6b432173c3fdab2.json"}}, {"family": "Johansson", "given": "Martin", "initials": "M", "orcid": "0000-0002-3733-8975", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1fdb7ed5e7047f3963ada15a0f8d48e.json"}}, {"family": "Larsson", "given": "Anders", "initials": "A", "orcid": "0000-0002-2096-8102", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4a4e2ec44f1446e98ee05ff0f45e484.json"}}, {"family": "Ros\u00e9n", "given": "Dan", "initials": "D"}, {"family": "Seashore\u2013Ludlow", "given": "Brinton", "initials": "B", "orcid": "0000-0001-8658-5967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4645bc97a8024c548111802101b83571.json"}}, {"family": "Visnes", "given": "Torkild", "initials": "T", "orcid": "0000-0003-1047-988X", "researcher": {"href": "https://publications.scilifelab.se/researcher/599a0da924424d098adc248b67fabf05.json"}}, {"family": "Carreras Puigvert", "given": "Jordi", "initials": "J", "orcid": "0000-0002-7671-3707", "researcher": {"href": "https://publications.scilifelab.se/researcher/28ad5f6a1a064e52aca72780adc4bb96.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}], "type": "posted-content", "published": "2025-02-08", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.02.05.636642", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [], "notes": [], "created": "2025-04-15T11:55:48.934Z", "modified": "2025-12-18T19:20:13.620Z"}, {"entity": "publication", "iuid": "058e4ab4248b4f38bf463af3cb986da6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/058e4ab4248b4f38bf463af3cb986da6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/058e4ab4248b4f38bf463af3cb986da6"}}, "title": "A method for Boolean analysis of protein interactions at a molecular level.", "authors": [{"family": "Raykova", "given": "Doroteya", "initials": "D", "orcid": "0000-0001-6452-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a81c40491e349178167f148f2351875.json"}}, {"family": "Kermpatsou", "given": "Despoina", "initials": "D", "orcid": "0000-0001-5872-4472", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfafe1fe67374c25ac5111ecd42c2fd4.json"}}, {"family": "Malmqvist", "given": "Tony", "initials": "T", "orcid": "0000-0003-0609-2009", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee835b51354e4cb5aff5dfbf43964dc8.json"}}, {"family": "Harrison", "given": "Philip J", "initials": "PJ"}, {"family": "Sander", "given": "Marie Rubin", "initials": "MR", "orcid": "0000-0002-9783-5682", "researcher": {"href": "https://publications.scilifelab.se/researcher/68a774625f6948d693bf4ad09eaba273.json"}}, {"family": "Stiller", "given": "Christiane", "initials": "C", "orcid": "0000-0002-6552-8426", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f8bb525e1094fbfbfb71dbbff62cbc7.json"}}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Leino", "given": "Mattias", "initials": "M"}, {"family": "Ricardo", "given": "Sara", "initials": "S", "orcid": "0000-0003-4091-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5599dd22d9e44a5af16850baf14e10e.json"}}, {"family": "Klemm", "given": "Anna", "initials": "A", "orcid": "0000-0002-3466-1320", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ae78afb2a424b0ab70d49871f361d13.json"}}, {"family": "David", "given": "Leonor", "initials": "L", "orcid": "0000-0003-4207-9258", "researcher": {"href": "https://publications.scilifelab.se/researcher/510030f8783044e8b644277783308bf6.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Vemuri", "given": "Kalyani", "initials": "K", "orcid": "0000-0003-2544-5412", "researcher": {"href": "https://publications.scilifelab.se/researcher/b74c149757644aa5a0997af9ca583a45.json"}}, {"family": "Dimberg", "given": "Anna", "initials": "A", "orcid": "0000-0003-4422-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/c53166298a214331866c8cbf3bb9a3b9.json"}}, {"family": "Sundqvist", "given": "Anders", "initials": "A"}, {"family": "Norlin", "given": "Maria", "initials": "M", "orcid": "0000-0003-4348-6269", "researcher": {"href": "https://publications.scilifelab.se/researcher/a10ffe5af28b4398b8d19743f7927e34.json"}}, {"family": "Klaesson", "given": "Axel", "initials": "A"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O", "orcid": "0000-0003-2883-1925", "researcher": {"href": "https://publications.scilifelab.se/researcher/68df823efa304c0b9962684ac1515808.json"}}], "type": "journal article", "published": "2022-08-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "4755", "issn-l": "2041-1723"}, "abstract": "Determining the levels of protein-protein interactions is essential for the analysis of signaling within the cell, characterization of mutation effects, protein function and activation in health and disease, among others. Herein, we describe MolBoolean - a method to detect interactions between endogenous proteins in various subcellular compartments, utilizing antibody-DNA conjugates for identification and signal amplification. In contrast to proximity ligation assays, MolBoolean simultaneously indicates the relative abundances of protein A and B not interacting with each other, as well as the pool of A and B proteins that are proximal enough to be considered an AB complex. MolBoolean is applicable both in fixed cells and tissue sections. The specific and quantifiable data that the method generates provide opportunities for both diagnostic use and medical research.", "doi": "10.1038/s41467-022-32395-w", "pmid": "35963857", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-32395-w"}, {"db": "pmc", "key": "PMC9375095"}], "notes": [], "created": "2022-08-30T09:04:56.787Z", "modified": "2022-08-30T09:04:57.234Z"}, {"entity": "publication", "iuid": "25767f6b12324baf8a7d77f9fc6f6c61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25767f6b12324baf8a7d77f9fc6f6c61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25767f6b12324baf8a7d77f9fc6f6c61"}}, "title": "Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening.", "authors": [{"family": "Schaal", "given": "Wesley", "initials": "W"}, {"family": "Ameur", "given": "Adam", "initials": "A"}, {"family": "Olsson-Str\u00f6mberg", "given": "Ulla", "initials": "U"}, {"family": "Hermanson", "given": "Monica", "initials": "M"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}], "type": "journal article", "published": "2022-07-15", "journal": {"title": "Cancer Inform", "issn": "1176-9351", "volume": "21", "pages": "11769351221110872", "issn-l": null}, "abstract": "The aim of this project was to implement long-read sequencing for BCR-ABL1 TKI resistance mutation screening in a clinical setting for patients undergoing treatment for chronic myeloid leukemia.\n\nProcesses were established for registering and transferring samples from the clinic to an academic sequencing facility for long-read sequencing. An automated analysis pipeline for detecting mutations was established, and an information system was implemented comprising features for data management, analysis and visualization. Clinical validation was performed by identifying BCR-ABL1 TKI resistance mutations by Sanger and long-read sequencing in parallel. The developed software is available as open source via GitHub at https://github.com/pharmbio/clamp.\n\nThe information system enabled traceable transfer of samples from the clinic to the sequencing facility, robust and automated analysis of the long-read sequence data, and communication of results from sequence analysis in a reporting format that could be easily interpreted and acted upon by clinical experts. In a validation study, all 17 resistance mutations found by Sanger sequencing were also detected by long-read sequencing. An additional 16 mutations were found only by long-read sequencing, all of them with frequencies below the limit of detection for Sanger sequencing. The clonal distributions of co-existing mutations were automatically resolved through the long-read data analysis. After the implementation and validation, the clinical laboratory switched their routine protocol from using Sanger to long-read sequencing for this application.\n\nLong-read sequencing delivers results with higher sensitivity compared to Sanger sequencing and enables earlier detection of emerging TKI resistance mutations. The developed processes, analysis workflow, and software components lower barriers for adoption and could be extended to other applications.", "doi": "10.1177/11769351221110872", "pmid": "35860345", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1177_11769351221110872"}, {"db": "pmc", "key": "PMC9290162"}], "notes": [], "created": "2022-09-05T07:28:19.500Z", "modified": "2022-09-05T07:28:19.543Z"}, {"entity": "publication", "iuid": "147a11e9aff7495293bd505f345a38a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/147a11e9aff7495293bd505f345a38a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/147a11e9aff7495293bd505f345a38a1"}}, "title": "SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines.", "authors": [{"family": "Lampa", "given": "Samuel", "initials": "S", "orcid": "0000-0001-6740-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4be992e2eed49c8ba1aaa0a4319ec24.json"}}, {"family": "Dahl\u00f6", "given": "Martin", "initials": "M", "orcid": "0000-0001-5447-9465", "researcher": {"href": "https://publications.scilifelab.se/researcher/32395b4dcca540a7a997b88ed20c9252.json"}}, {"family": "Alvarsson", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-8682-7206", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8eb231a432647ee89b22e3e0dbbc651.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}], "type": "journal article", "published": "2019-05-01", "journal": {"volume": "8", "issn": "2047-217X", "issue": "5", "pages": null, "title": "Gigascience", "issn-l": "2047-217X"}, "abstract": "The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines, assist with job automation, and aid reproducibility of analyses. Many contemporary workflow tools are specialized or not designed for highly complex workflows, such as with nested loops, dynamic scheduling, and parametrization, which is common in, e.g., machine learning.\n\nSciPipe is a workflow programming library implemented in the programming language Go, for managing complex and dynamic pipelines in bioinformatics, cheminformatics, and other fields. SciPipe helps in particular with workflow constructs common in machine learning, such as extensive branching, parameter sweeps, and dynamic scheduling and parametrization of downstream tasks. SciPipe builds on flow-based programming principles to support agile development of workflows based on a library of self-contained, reusable components. It supports running subsets of workflows for improved iterative development and provides a data-centric audit logging feature that saves a full audit trace for every output file of a workflow, which can be converted to other formats such as HTML, TeX, and PDF on demand. The utility of SciPipe is demonstrated with a machine learning pipeline, a genomics, and a transcriptomics pipeline.\n\nSciPipe provides a solution for agile development of complex and dynamic pipelines, especially in machine learning, through a flexible application programming interface suitable for scientists used to programming or scripting.", "doi": "10.1093/gigascience/giz044", "pmid": "31029061", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "5480570"}, {"db": "pmc", "key": "PMC6486472"}, {"db": "figshare", "key": "10.6084/m9.figshare.3985674"}], "notes": [], "created": "2019-04-29T07:14:49.754Z", "modified": "2024-01-16T13:48:44.374Z"}, {"entity": "publication", "iuid": "fe38a9e085de4033b895eda33e1ecee9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe38a9e085de4033b895eda33e1ecee9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe38a9e085de4033b895eda33e1ecee9"}}, "title": "Deep Learning in Image Cytometry: A Review.", "authors": [{"family": "Gupta", "given": "Anindya", "initials": "A", "orcid": "0000-0003-3557-4947", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5ba336ef3ab4d819a2f367e0e4f988c.json"}}, {"family": "Harrison", "given": "Philip J", "initials": "PJ", "orcid": "0000-0003-4046-9017", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbabe660124f4d96bcc4f604f61e569e.json"}}, {"family": "Wieslander", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-6289-7285", "researcher": {"href": "https://publications.scilifelab.se/researcher/a271478f5e2c407f9e5f9aceb6b92e10.json"}}, {"family": "Pielawski", "given": "Nicolas", "initials": "N", "orcid": "0000-0001-8182-0091", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8bf24da074a451fa245ff20f07e4b48.json"}}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications.scilifelab.se/researcher/da3da754a0264d538a98d8a85874aec1.json"}}, {"family": "Partel", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-4482-3119", "researcher": {"href": "https://publications.scilifelab.se/researcher/cca1e7c3e70a4d45aacc3a46d14b9cbe.json"}}, {"family": "Solorzano", "given": "Leslie", "initials": "L", "orcid": "0000-0001-8658-6417", "researcher": {"href": "https://publications.scilifelab.se/researcher/24c62ca6579b4055a95d0dba53722939.json"}}, {"family": "Suveer", "given": "Amit", "initials": "A", "orcid": "0000-0002-7779-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2079df9478364042935868f40b69b113.json"}}, {"family": "Klemm", "given": "Anna H", "initials": "AH", "orcid": "0000-0002-3466-1320", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ae78afb2a424b0ab70d49871f361d13.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "Sintorn", "given": "Ida-Maria", "initials": "IM", "orcid": "0000-0002-8307-7411", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ff79494ec3842ffaa7448d2e3277f6b.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}], "type": "journal article", "published": "2019-04-00", "journal": {"title": "Cytometry A", "issn": "1552-4930", "issn-l": "1552-4922", "volume": "95", "issue": "4", "pages": "366-380"}, "abstract": "Artificial intelligence, deep convolutional neural networks, and deep learning are all niche terms that are increasingly appearing in scientific presentations as well as in the general media. In this review, we focus on deep learning and how it is applied to microscopy image data of cells and tissue samples. Starting with an analogy to neuroscience, we aim to give the reader an overview of the key concepts of neural networks, and an understanding of how deep learning differs from more classical approaches for extracting information from image data. We aim to increase the understanding of these methods, while highlighting considerations regarding input data requirements, computational resources, challenges, and limitations. We do not provide a full manual for applying these methods to your own data, but rather review previously published articles on deep learning in image cytometry, and guide the readers toward further reading on specific networks and methods, including new methods not yet applied to cytometry data. \u00a9 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.", "doi": "10.1002/cyto.a.23701", "pmid": "30565841", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6590257"}], "notes": [], "created": "2018-12-30T16:32:19.557Z", "modified": "2023-06-19T12:59:01.277Z"}]}