The scverse project provides a computational ecosystem for single-cell omics data analysis

Isaac Virshup^#¹, Danila Bredikhin^#^{2

3

4}, Lukas Heumos^#^{1

5

6}, Giovanni Palla^#^{7

8}, Gregor Sturm^#⁹, Adam Gayoso^#¹⁰, Ilia Kats¹¹, Mikaela Koutrouli¹²; Scverse Community; Bonnie Berger^{13

14

15}, Dana Pe'er^{16

17}, Aviv Regev¹⁸, Sarah A Teichmann^{19

20}, Francesca Finotello^{21

22}, F Alexander Wolf^{7

23}, Nir Yosef^{10

24

25

26}, Oliver Stegle^{27

11

19

28}, Fabian J Theis^{7

8

19

29}

Collaborators, Affiliations

Collaborators

Affiliations

¹ Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany. steering-council@scverse.org.
² European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany. steering-council@scverse.org.
³ Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany. steering-council@scverse.org.
⁴ Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany. steering-council@scverse.org.
⁵ Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive; Helmholtz Zentrum Munich, Member of the German Center for Lung Research (DZL), Munich, Germany. steering-council@scverse.org.
⁶ School of Life Sciences, Technical University of Munich, Munich, Germany. steering-council@scverse.org.
⁷ Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
⁸ School of Life Sciences, Technical University of Munich, Munich, Germany.
⁹ Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria.
¹⁰ Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
¹¹ Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
¹² Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
¹³ Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁴ Harvard-MIT Health Sciences and Technology Program, Cambridge, MA, USA.
¹⁵ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
¹⁶ Computational and Systems Biology Program, Sloan Kettering Institute, New York, NY, USA.
¹⁷ Howard Hughes Medical Institute, Chevy Chase, MD, USA.
¹⁸ Genentech Research and Early Development, Genentech Inc, South San Francisco, CA, USA.
¹⁹ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
²⁰ Cavendish Laboratory, University of Cambridge, Cambridge, UK.
²¹ Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria.
²² Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria.
²³ Lamin Labs, Munich, Germany.
²⁴ Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.
²⁵ Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
²⁶ Chan Zuckerberg Biohub, San Francisco, CA, USA.
²⁷ European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
²⁸ Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
²⁹ School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.

^# Contributed equally.

PMID: 37037904
DOI: 10.1038/s41587-023-01733-8

The scverse project provides a computational ecosystem for single-cell omics data analysis

Isaac Virshup et al. Nat Biotechnol. 2023 May.

. 2023 May;41(5):604-606.

doi: 10.1038/s41587-023-01733-8.

Authors

Collaborators

Affiliations

¹ Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany. steering-council@scverse.org.
² European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany. steering-council@scverse.org.
³ Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany. steering-council@scverse.org.
⁴ Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany. steering-council@scverse.org.
⁵ Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive; Helmholtz Zentrum Munich, Member of the German Center for Lung Research (DZL), Munich, Germany. steering-council@scverse.org.
⁶ School of Life Sciences, Technical University of Munich, Munich, Germany. steering-council@scverse.org.
⁷ Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
⁸ School of Life Sciences, Technical University of Munich, Munich, Germany.
⁹ Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria.
¹⁰ Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
¹¹ Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
¹² Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
¹³ Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁴ Harvard-MIT Health Sciences and Technology Program, Cambridge, MA, USA.
¹⁵ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
¹⁶ Computational and Systems Biology Program, Sloan Kettering Institute, New York, NY, USA.
¹⁷ Howard Hughes Medical Institute, Chevy Chase, MD, USA.
¹⁸ Genentech Research and Early Development, Genentech Inc, South San Francisco, CA, USA.
¹⁹ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
²⁰ Cavendish Laboratory, University of Cambridge, Cambridge, UK.
²¹ Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria.
²² Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria.
²³ Lamin Labs, Munich, Germany.
²⁴ Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.
²⁵ Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
²⁶ Chan Zuckerberg Biohub, San Francisco, CA, USA.
²⁷ European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
²⁸ Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
²⁹ School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.

^# Contributed equally.

PMID: 37037904
DOI: 10.1038/s41587-023-01733-8

No abstract available

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References

1. Zappia, L. & Theis, F. J. Genome Biol. 22, 301 (2021).
1. Wolf, F. A., Angerer, P. & Theis, F. J. Genome Biol. 19, 15 (2018).
1. Gayoso, A. et al. Nat. Biotechnol. 40, 163–166 (2022). - DOI - PubMed
1. Bredikhin, D., Kats, I. & Stegle, O. Genome Biol. 23, 42 (2022).
1. Liu, Z. & Zhang, Z. Science 376, 695–696 (2022). - DOI - PubMed

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The scverse project provides a computational ecosystem for single-cell omics data analysis

Collaborators

Affiliations

The scverse project provides a computational ecosystem for single-cell omics data analysis

Authors

Collaborators

Affiliations

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources