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Defining and benchmarking open problems in single-cell analysis.

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Title: Defining and benchmarking open problems in single-cell analysis.
Authors: Luecken MD; Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.; Institute of Lung Health & Immunity, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany., Gigante S; Immunai, New York, USA., Burkhardt DB; NVIDIA, Santa Clara, CA, USA., Cannoodt R; Data Intuitive, Lebbeke, Belgium.; Data Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium.; Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium., Strobl DC; Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.; Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany.; TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany., Markov NS; Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA., Zappia L; Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.; Data Intuitive, Lebbeke, Belgium.; Department of Mathematics, School of Computing, Information and Technology, Technical University of Munich, Munich, Germany., Palla G; Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.; TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany., Lewis W; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA., Dimitrov D; Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany., Vinyard ME; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA., Magruder DS; Department of Computer Science, Yale University, New Haven, CT, USA., Mueller MF; Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.; Institute of Lung Health & Immunity, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany.; TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany., Andersson A; Genentech Inc, South San Francisco, CA, USA.; Gene Technology, Royal Institute of Technology (KTH), Stockholm, Sweden.; Science for Life Laboratory (SciLifeLab), Solna, Sweden., Dann E; Wellcome Sanger Institute, Cambridge, UK., Qin Q; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Otto DJ; Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.; Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.; Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA., Klein M; Apple, Paris, France., Botvinnik OB; Data Sciences Platform, Chan Zuckerberg Biohub, San Francisco, CA, USA.; Bridge Bio Pharma, Palo Alto, CA, USA., Deconinck L; Data Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium.; Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium., Waldrant K; Data Intuitive, Lebbeke, Belgium., Yasa SN; Data Intuitive, Lebbeke, Belgium., Szałata A; Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.; Department of Mathematics, School of Computing, Information and Technology, Technical University of Munich, Munich, Germany., Benz A; Cellarity, Inc, Somerville, MA, USA., Li Z; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA., Bloom JM; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA., Pisco AO; Data Sciences Platform, Chan Zuckerberg Biohub, San Francisco, CA, USA.; Insitro, South San Francisco, USA., Saez-Rodriguez J; Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany., Wulsin D; Immunai, New York, USA., Pinello L; Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA., Saeys Y; Data Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium.; Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium.; VIB Center for AI & Computational Biology (VIB.AI), Ghent, Belgium., Theis FJ; Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany. fabian.theis@helmholtz-munich.de.; Department of Mathematics, School of Computing, Information and Technology, Technical University of Munich, Munich, Germany. fabian.theis@helmholtz-munich.de.; Cellular Genetics Programme, Wellcome Sanger Institute, Hinxton, UK. fabian.theis@helmholtz-munich.de., Krishnaswamy S; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA. smita.krishnaswamy@yale.edu.; Department of Computer Science, Yale University, New Haven, CT, USA. smita.krishnaswamy@yale.edu.; Department of Genetics, Yale University, New Haven, CT, USA. smita.krishnaswamy@yale.edu.
Corporate Authors: Open Problems Jamboree Members
Source: Nature biotechnology [Nat Biotechnol] 2025 Jul; Vol. 43 (7), pp. 1035-1040.
Publication Type: Letter
Journal Info: Publisher: Nature America Publishing Country of Publication: United States NLM ID: 9604648 Publication Model: Print Cited Medium: Internet ISSN: 1546-1696 (Electronic) Linking ISSN: 10870156 NLM ISO Abbreviation: Nat Biotechnol Subsets: MEDLINE; In Process
Database: MEDLINE Ultimate
FullText Text:
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PubType: Editorial & Opinion
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Data Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium.; Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium.; VIB Center for AI & Computational Biology (VIB.AI), Ghent, Belgium.<br /><searchLink fieldCode="AU" term="%22Theis+FJ%22">Theis FJ</searchLink>; Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany. fabian.theis@helmholtz-munich.de.; Department of Mathematics, School of Computing, Information and Technology, Technical University of Munich, Munich, Germany. fabian.theis@helmholtz-munich.de.; Cellular Genetics Programme, Wellcome Sanger Institute, Hinxton, UK. fabian.theis@helmholtz-munich.de.<br /><searchLink fieldCode="AU" term="%22Krishnaswamy+S%22">Krishnaswamy S</searchLink>; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA. smita.krishnaswamy@yale.edu.; Department of Computer Science, Yale University, New Haven, CT, USA. smita.krishnaswamy@yale.edu.; 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