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Plate IV.87 · Publications

Defining and benchmarking open problems in single-cell analysis

Article in Nature Biotechnology, July 2025.

Open accessSpatial, Omics Data

  1. Malte D. Luecken
  2. Scott Gigante
  3. Daniel B. Burkhardt
  4. Robrecht Cannoodt
  5. Daniel C. Strobl
  6. Nikolay S. Markov
  7. Luke Zappia
  8. Giovanni Palla
  9. Wesley Lewis
  10. Daniel Dimitrov
  11. Michael E. Vinyard
  12. D. S. Magruder
  13. Michaela F. Mueller
  14. Alma Andersson
  15. Emma Dann
  16. Qian Qin
  17. Dominik J. Otto
  18. Michal Klein
  19. Olga Borisovna Botvinnik
  20. Louise Deconinck
  21. Kai Waldrant
  22. Sai Nirmayi Yasa
  23. Artur Szałata
  24. Andrew Benz
  25. Zhijian Li
  26. Open Problems Jamboree Members
  27. Bastian Rieck
  28. Constantin Ahlmann-Eltze
  29. Eduardo da Veiga Beltrame
  30. Carmen Bravo González-Blas
  31. Ann T. Chen
  32. Benjamin DeMeo
  33. Can Ergen
  34. Swann Floc’hlay
  35. Adam Gayoso
  36. Stephanie Hicks
  37. Yuge Ji
  38. Vitalii Kleshchevnikov
  39. Gioele La Manno
  40. Maximilian G. Lombardo
  41. Romain Lopez
  42. Dario Righelli
  43. Hirak Sarkar
  44. Valentine Svensson
  45. Alexander Tong
  46. Galen Xing
  47. Chenling Xu
  48. Jonathan M. Bloom
  49. Angela Oliveira Pisco
  50. Julio Saez-Rodriguez
  51. Drausin Wulsin
  52. Luca Pinello
  53. Yvan Saeys
  54. Fabian J. Theis
  55. Smita Krishnaswamy

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.

Versions2

  1. PublishedNature Biotechnology10.1038/s41587-025-02694-w
  2. PreprintResearch Square10.21203/rs.3.rs-4181617/v1

Cite

@article{luecken2025defining,
  title = {{Defining and benchmarking open problems in single-cell analysis}},
  author = {Luecken, Malte D. and Gigante, Scott and Burkhardt, Daniel B. and Cannoodt, Robrecht and Strobl, Daniel C. and Markov, Nikolay S. and Zappia, Luke and Palla, Giovanni and Lewis, Wesley and Dimitrov, Daniel and Vinyard, Michael E. and Magruder, D. S. and Mueller, Michaela F. and Andersson, Alma and Dann, Emma and Qin, Qian and Otto, Dominik J. and Klein, Michal and Botvinnik, Olga Borisovna and Deconinck, Louise and Waldrant, Kai and Yasa, Sai Nirmayi and Szałata, Artur and Benz, Andrew and Li, Zhijian and Open Problems Jamboree Members and Rieck, Bastian and Ahlmann-Eltze, Constantin and da Veiga Beltrame, Eduardo and Bravo González-Blas, Carmen and Chen, Ann T. and DeMeo, Benjamin and Ergen, Can and Floc’hlay, Swann and Gayoso, Adam and Hicks, Stephanie and Ji, Yuge and Kleshchevnikov, Vitalii and La Manno, Gioele and Lombardo, Maximilian G. and Lopez, Romain and Righelli, Dario and Sarkar, Hirak and Svensson, Valentine and Tong, Alexander and Xing, Galen and Xu, Chenling and Bloom, Jonathan M. and Pisco, Angela Oliveira and Saez-Rodriguez, Julio and Wulsin, Drausin and Pinello, Luca and Saeys, Yvan and Theis, Fabian J. and Krishnaswamy, Smita},
  journal = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  year = {2025},
  month = jul,
  doi = {10.1038/s41587-025-02694-w},
  url = {https://doi.org/10.1038/s41587-025-02694-w},
  pmid = {40595413}
}
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