ArticleNature biotechnology2025
Defining and benchmarking open problems in single-cell analysis.
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Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
0numbers the graph read from it
0cells of the map it votes in
30citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- scDiagnostics: systematic assessment of cell type annotation in single-cell transcriptomics data.Briefings in bioinformatics · 2026Article
- Mapping ovarian cellular and molecular landscape across the lifespan of women: a scoping review.Human reproduction update · 2026Article
- Integration of artificial intelligence and multi-omics for precision medicine.Functional & integrative genomics · 2026Review
- Review
- Foundation models in omics research: a comprehensive survey.Briefings in bioinformatics · 2026Review
- Bridging annotated microscopy imaging data and analysis method development for scientific discovery.Patterns (New York, N.Y.) · 2026Review
- From gene correlations to cell clusters: COTAN improved scRNA-seq analysis.NAR genomics and bioinformatics · 2026Article
- Article
- Interpretation, extrapolation and perturbation of single cells.Nature reviews. Genetics · 2026Review
- Turep: Detecting cross-cancer tumor-reactive T cells in single-cell and spatial transcriptomics data.bioRxiv : the preprint server for biology · 2026Article
- crocketa: an automated Snakemake framework for integrated single-cell transcriptome and immune-repertoire analysis.BMC genomics · 2026Article
- Representation learning of single-cell RNA-seq data.RNA (New York, N.Y.) · 2026Review
- Illuminating cell states by a comprehensive and interpretable single cell foundation model.Nature communications · 2026Article
- ABaCo: addressing heterogeneity challenges in metagenomic data integration with adversarial generative models.Nucleic acids research · 2026Article
- Stochastic gradient descent estimation of generalized matrix factorization models with application to single-cell RNA sequencing data.Biostatistics (Oxford, England) · 2026Article
- Stack: In-Context Learning of Single-Cell Biology.bioRxiv : the preprint server for biology · 2026Article
- Revealing a coherent cell-state landscape across single-cell datasets with CONCORD.Nature biotechnology · 2026Article
- Toward trustworthy virtual cells: a roadmap for perturbation-resolved, context-aware, and experimentally validated cell models.Frontiers in cell and developmental biology · 2026Review
- AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential.NPJ digital medicine · 2025Review
- FADVI: disentangled representation learning for robust integration of single-cell and spatial omics data.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
- Update of
Authors and funding
34 authors.
Malte D Luecken *Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.ORCID http://orcid.org/0000-0001-7464-7921
Scott Gigante *Immunai, New York, USA.ORCID http://orcid.org/0000-0002-4544-2764
Daniel B Burkhardt *NVIDIA, Santa Clara, CA, USA.
Robrecht Cannoodt *Data Intuitive, Lebbeke, Belgium.ORCID http://orcid.org/0000-0003-3641-729X
Daniel C StroblInstitute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.
Nikolay S MarkovDivision of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
Luke ZappiaInstitute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.ORCID http://orcid.org/0000-0001-7744-8565
Giovanni PallaInstitute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.ORCID http://orcid.org/0000-0002-8004-4462
Wesley LewisInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
Daniel DimitrovFaculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany.
Michael E VinyardDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
D S MagruderDepartment of Computer Science, Yale University, New Haven, CT, USA.
Michaela F MuellerInstitute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.
Alma AnderssonGenentech Inc, South San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-4773-9975
Emma DannWellcome Sanger Institute, Cambridge, UK.ORCID http://orcid.org/0000-0002-7400-7438
Qian QinBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-2119-6263
Dominik J OttoBasic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-6116-053X
Michal KleinApple, Paris, France.
Olga Borisovna BotvinnikData Sciences Platform, Chan Zuckerberg Biohub, San Francisco, CA, USA.
Louise DeconinckData Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium.ORCID http://orcid.org/0000-0001-8100-6823
Kai WaldrantData Intuitive, Lebbeke, Belgium.ORCID http://orcid.org/0009-0003-8555-1361
Sai Nirmayi YasaData Intuitive, Lebbeke, Belgium.
Artur SzałataInstitute of Computational Biology, Helmholtz Munich, Neuherberg, Germany.ORCID http://orcid.org/0000-0001-8413-234X
Andrew BenzCellarity, Inc, Somerville, MA, USA.
Zhijian LiBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-1523-1333
Open Problems Jamboree Members
Jonathan M BloomDepartment of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
Angela Oliveira PiscoData Sciences Platform, Chan Zuckerberg Biohub, San Francisco, CA, USA.
Julio Saez-RodriguezFaculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany.
Drausin WulsinImmunai, New York, USA.
Luca PinelloMolecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0003-1109-3823
Yvan SaeysData Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium.ORCID http://orcid.org/0000-0002-0415-1506
Fabian J TheisInstitute of Computational Biology, Helmholtz Munich, Neuherberg, Germany. fabian.theis@helmholtz-munich.de.ORCID http://orcid.org/0000-0002-2419-1943
Smita KrishnaswamyInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA. smita.krishnaswamy@yale.edu.ORCID http://orcid.org/0000-0001-5823-1985
Funding
EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020) 860329 Marie-Curie ITN "STRATEGY-CKD"European Commission (EC) 101054957Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders) 1SF3822NU.S. Department of Health & Human Services | National Institutes of Health (NIH) T15U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) 1F31CA257625
Abstract
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.