{"entity": "publication", "iuid": "3aeeee4fb27a43709020cd494838b201", "timestamp": "2026-09-28T11:19:32.711Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3aeeee4fb27a43709020cd494838b201.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3aeeee4fb27a43709020cd494838b201"}}, "title": "Defining and benchmarking open problems in single-cell analysis.", "authors": [{"family": "Luecken", "given": "Malte D", "initials": "MD", "orcid": "0000-0001-7464-7921", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/573854d96a9e4e21a3b96135c11c6efc.json"}}, {"family": "Gigante", "given": "Scott", "initials": "S", "orcid": "0000-0002-4544-2764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8ce3b76c8572484f9beaca36b35f448b.json"}}, {"family": "Burkhardt", "given": "Daniel B", "initials": "DB"}, {"family": "Cannoodt", "given": "Robrecht", "initials": "R"}, {"family": "Strobl", "given": "Daniel C", "initials": "DC"}, {"family": "Markov", "given": "Nikolay S", "initials": "NS"}, {"family": "Zappia", "given": "Luke", "initials": "L", "orcid": "0000-0001-7744-8565", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c1898aec5d94601878a2c3e88615c12.json"}}, {"family": "Palla", "given": "Giovanni", "initials": "G", "orcid": "0000-0002-8004-4462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e87add202a7b4520be57b5beaa24155c.json"}}, {"family": "Lewis", "given": "Wesley", "initials": "W"}, {"family": "Dimitrov", "given": "Daniel", "initials": "D"}, {"family": "Vinyard", "given": "Michael E", "initials": "ME"}, {"family": "Magruder", "given": "D S", "initials": "DS"}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Dann", "given": "Emma", "initials": "E", "orcid": "0000-0002-7400-7438", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a47e97c1382f4236ad8db31d548dce88.json"}}, {"family": "Qin", "given": "Qian", "initials": "Q", "orcid": "0000-0002-2119-6263", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/456b5063f5c14149986901df36edfc74.json"}}, {"family": "Otto", "given": "Dominik J", "initials": "DJ", "orcid": "0000-0002-6116-053X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb02bef5250244f7b7b27b75f2e1e267.json"}}, {"family": "Klein", "given": "Michal", "initials": "M"}, {"family": "Botvinnik", "given": "Olga Borisovna", "initials": "OB"}, {"family": "Deconinck", "given": "Louise", "initials": "L"}, {"family": "Waldrant", "given": "Kai", "initials": "K", "orcid": "0009-0003-8555-1361", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f43c84fd1b194a3b8d8bf82c288d8211.json"}}, {"family": "Open Problems Jamboree Members", "given": "", "initials": ""}, {"family": "Bloom", "given": "Jonathan M", "initials": "JM"}, {"family": "Pisco", "given": "Angela Oliveira", "initials": "AO"}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J"}, {"family": "Wulsin", "given": "Drausin", "initials": "D"}, {"family": "Pinello", "given": "Luca", "initials": "L", "orcid": "0000-0003-1109-3823", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1389786b0bcd42d9914854d752db406e.json"}}, {"family": "Saeys", "given": "Yvan", "initials": "Y", "orcid": "0000-0002-0415-1506", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93cfad61779e41b09cf3ab23af28bc83.json"}}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8969d033a36f40aab191ad1b3960114d.json"}}, {"family": "Krishnaswamy", "given": "Smita", "initials": "S", "orcid": "0000-0001-5823-1985", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4316839a64104ae6ada666b579d11e53.json"}}], "type": "journal article", "published": "2024-04-04", "journal": {"title": "Res Sq", "issn": "2693-5015", "issn-l": null}, "abstract": "With the growing number of single-cell analysis tools, benchmarks are increasingly important to guide analysis and method development. However, a lack of standardisation and extensibility in current benchmarks limits their usability, longevity, and relevance to the community. We present Open Problems, a living, extensible, community-guided benchmarking platform including 10 current single-cell tasks that we envision will raise standards for the selection, evaluation, and development of methods in single-cell analysis.", "doi": "10.21203/rs.3.rs-4181617/v1", "pmid": "38645152", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11030530"}, {"db": "pii", "key": "rs.3.rs-4181617"}], "notes": [], "created": "2026-09-23T13:47:19.336Z", "modified": "2026-09-23T13:47:19.463Z"}