Defining and Benchmarking Open Problems in Single-Cell Analysis (2025)
A community-driven benchmark platform for evaluating and advancing single-cell analysis methods.
Luecken, M. D.*, Gigante, S.*, Burkhardt, D. B.*, Cannoodt, R.*, Strobl, D. C., Markov, N. S., Zappia, L., Palla, G., Lewis, W., Dimitrov, D., Vinyard, M. E., Magruder, D. S., Mueller, M. F., Andersson, A., Dann, E., Qin, Q., Otto, D. J., Klein, M., Botvinnik, O. B., Deconinck, L., Waldrant, K., Yasa, S. N., Szałata, A., Benz, A., Li, Z., Open Problems Jamboree Members, Bloom, J. M., Pisco, A. O., Saez-Rodriguez, J., Wulsin, D., Pinello, L., Saeys, Y., Theis, F. J., & Krishnaswamy, S. (2025).
Defining and benchmarking open problems in single-cell analysis. Nature Biotechnology, Correspondence.
Abstract:
Single-cell genomics has revolutionized biological research by enabling high-resolution insights into cellular heterogeneity. The rapid growth of tools—over 1,700 algorithms to date—calls for robust evaluation frameworks. In response, we introduce Open Problems, a community-driven platform defining and benchmarking 12 essential analysis tasks in single-cell research. This living benchmark aims to guide best practices, improve reproducibility, and stimulate methodological development by applying a standardized evaluation framework across the field.
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