The people behind Open Problems.
A community of maintainers, scientific advisors, per-task contributors and alumni spanning more than 50 institutions, sustained by the organizations that fund our compute and engineering.
Core team & advisors.
The maintainers and founders who steward the platform, and the senior researchers who guide its scientific direction.
Core team
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Daniel BurkhardtCellarityfoundercore -
Malte D. LückenHelmholtz Munichfoundercore -
Scott GiganteCellarityfoundercore -
Robrecht CannoodtEdarocore -
Luke ZappiaData Intuitivecore -
Julia NaasHelmholtz Munichcore
Scientific advisors
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Fabian J. TheisHelmholtz Munichadvisor - SKSmita KrishnaswamyYale Universityadvisor
Alumni
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Angela Oliveira PiscoCZIadvisor - JBJonathan BloomMITadvisor
Everyone who built the benchmarks.
Authors credited across every task release, collected automatically from the benchmark data. Each card lists the tasks they contributed to.
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Alejandro GranadosauthorPredict Modality -
Alex TongauthorPredict Modality -
Alma AnderssonauthormaintainerSpatial Decomposition -
Andrew BenzauthorPerturbation Prediction -
Artur SzałataauthorPerturbation Prediction -
Bastian RieckauthorPredict Modality -
Ben DeMeoauthorDimensionality Reduction for Visualisation -
Can ErgencontributorSpatial Decomposition - Daniel BurkhardtauthorPerturbation Prediction
- Daniel BurkhardtauthorcontributorPredict ModalitySpatial Decomposition
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Daniel DimitrovmaintainerauthorCell-Cell Communication -
Daniel StroblauthorBatch integrationBatch Integration -
Dongyuan SongauthorSpatially Variable Genes -
Giovanni PallaauthormaintainerSpatial Decomposition - GYGuanao YanauthorSpatially Variable Genes
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Hirak SarkarauthorSpatial Decomposition -
Jalil NourisacontributorPerturbation Prediction -
Jean YangauthorSpatial Simulators -
Jingyi Jessica LiauthorSpatially Variable Genes -
Juan A. Cordero VarelacontributorDimensionality Reduction for Visualisation -
Kai WaldrantcontributorBatch integrationBatch IntegrationDenoisingDimensionality Reduction for VisualisationPredict Modality -
Kaiwen DengcontributorPredict Modality -
Louise DeconinckauthorPredict Modality -
Luca PinelloauthorSpatially Variable Genes - Luke ZappiamaintainerauthorDimensionality Reduction for Visualisation
- Malte LueckenauthorBatch integrationBatch IntegrationPerturbation Prediction
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Mengbo WangcontributorPerturbation Prediction -
Michael VinyardauthorDimensionality Reduction for Visualisation -
Michaela MuellermaintainerauthorBatch integrationBatch Integration -
Michal KleinauthorDimensionality Reduction for Visualisation -
Nikolay MarkovauthormaintainerLabel Projection -
Rico MeinlcontributorPerturbation Prediction - Robrecht CannoodtcontributorauthormaintainerBatch integrationBatch IntegrationCell-Cell CommunicationDenoisingDimensionality Reduction for VisualisationFoundation ModelsLabel ProjectionPerturbation PredictionPredict ModalitySpatial SimulatorsSpatially Variable Genes
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Sai Nirmayi YasacontributorDimensionality Reduction for VisualisationSpatial DecompositionSpatial SimulatorsSpatially Variable Genes - Scott GigantecontributorauthormaintainerBatch integrationBatch IntegrationCell-Cell CommunicationDenoisingDimensionality Reduction for VisualisationLabel ProjectionSpatial Decomposition
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Tianyu LiucontributorPerturbation Prediction -
Tin M. TunjiccontributorPerturbation Prediction -
Vishnuvasan RaghuramancontributorCell-Cell Communication -
Vitalii KleshchevnikovauthorSpatial Decomposition -
Wesley LewisauthormaintainerDenoising -
Xiaoqi LiangauthorSpatial Simulators -
Yue CaoauthormaintainerSpatial Simulators -
Zain M. PatelauthorSpatially Variable Genes -
Zhijian LiauthormaintainerSpatially Variable Genes
Sponsors & partners.
Open Problems is sustained by organizations funding compute, engineering and scientific leadership.
Funds the cloud benchmarking infrastructure and core maintainer time through the Essential Open Source Software for Science program.
Acts as the project's fiscal host, providing nonprofit financial and administrative support.
Hosts the Institute of Computational Biology and several core team members.
Builds and maintains the engineering tooling behind the platform.
Provides managed compute for reproducible benchmark runs at scale.
Supports the Nextflow pipelines that orchestrate every benchmark.
Interested in supporting the platform?
We partner with funders and infrastructure providers who want to accelerate open, reproducible single-cell science.
Cite the project.
If you use Open Problems, please cite the platform paper. To reference a specific competition or dataset, cite the corresponding work.
Defining and benchmarking open problems in single-cell analysis
Malte D. Luecken, Scott Gigante, Daniel B. Burkhardt et al.
@article{luecken2025openproblems,
title = {Defining and benchmarking open problems in single-cell analysis},
author = {Malte D. Luecken and Scott Gigante and Daniel B. Burkhardt and others},
year = {2025},
doi = {10.1038/s41587-025-02694-w}
} A sandbox for prediction and integration of DNA, RNA, and proteins in single cells
Malte Luecken, Daniel Burkhardt, Robrecht Cannoodt et al.
@inproceedings{luecken2021neurips,
title = {A sandbox for prediction and integration of DNA, RNA, and proteins in single cells},
author = {Malte Luecken and Daniel Burkhardt and Robrecht Cannoodt and Christopher Lance and Aditi Agrawal and Hananeh Aliee and Ann Chen and Louise Deconinck and Angela Detweiler and Alejandro Granados and Shelly Huynh and Laura Isacco},
year = {2021}
} Multimodal single cell data integration challenge: results and lessons learned
Christopher Lance, Malte D. Luecken, Daniel B. Burkhardt et al.
@article{lance2022multimodal,
title = {Multimodal single cell data integration challenge: results and lessons learned},
author = {Christopher Lance and Malte D. Luecken and Daniel B. Burkhardt and Robrecht Cannoodt and Pia Rautenstrauch and Anna Laddach and Aidyn Ubingazhibov and Zhi-Jie Cao and Kaiwen Deng and Sumeer Khan and Qiao Liu and Nikolay Russkikh},
year = {2022},
doi = {10.1101/2022.04.11.487796}
}