Evidence map›Paper›PMID 38645152›Full record

ArticleResearch square2024

Defining and benchmarking open problems in single-cell analysis.

Malte D Luecken, Scott Gigante, Daniel B Burkhardt, Robrecht Cannoodt, Daniel C Strobl, Nikolay S Markov, Luke Zappia, Giovanni Palla, Wesley Lewis, Daniel Dimitrov and 19 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

29 authors.

Malte D LueckenInstitute of computational Biology, Helmholtz Munich, Neuherberg, Germany.ORCID 0000-0001-7464-7921
Scott GiganteImmunai, New York, USA.ORCID 0000-0002-4544-2764
Daniel B BurkhardtCellarity, Inc. Somerville, USA.
Robrecht CannoodtData Intuitive, Lebbeke, Belgium.
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.
Luke ZappiaInstitute of computational Biology, Helmholtz Munich, Neuherberg, Germany.ORCID 0000-0001-7744-8565
Giovanni PallaInstitute of computational Biology, Helmholtz Munich, Neuherberg, Germany.ORCID 0000-0002-8004-4462
Wesley LewisInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA.
Daniel DimitrovHeidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, 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.
Alma AnderssonGenentech Inc.
Emma DannWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID 0000-0002-7400-7438
Qian QinBroad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID 0000-0002-2119-6263
Dominik J OttoBasic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA.ORCID 0000-0002-6116-053X
Michal KleinApple.
Olga Borisovna BotvinnikData Sciences Platform, Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158.
Louise DeconinckData Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium.
Kai WaldrantData Intuitive, Lebbeke, Belgium.ORCID 0009-0003-8555-1361
Open Problems Jamboree Members
Jonathan M BloomMassachusetts Institute of Technology.
Angela Oliveira PiscoData Sciences Platform, Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158.
Julio Saez-RodriguezHeidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany.
Drausin WulsinImmunai, New York, USA.
Luca PinelloMolecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.ORCID 0000-0003-1109-3823
Yvan SaeysData Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium.ORCID 0000-0002-0415-1506
Fabian J TheisInstitute of computational Biology, Helmholtz Munich, Neuherberg, Germany.ORCID 0000-0002-2419-1943
Smita KrishnaswamyInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA.ORCID 0000-0001-5823-1985

Funding

Cancer Genomics:Integrative and Scalable Solutions in R / BioconductorU24CA180996 · NCI · ROSWELL PARK CANCER INSTITUTE CORP · PI MORGAN, MARTIN T, WALDRON, LEVI · 2014 to 2023
$6.9M
Multiscale exploration of the functional non-coding genomeR35HG010717 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI PINELLO, LUCA · 2019 to 2023
$2.6M
Determining the role of LSD1 in multiple myeloma through a multi-omics approach at single cell resolutionF31CA257625 · NCI · HARVARD UNIVERSITY · PI VINYARD, MICHAEL EDWARD · 2021 to 2024
$168k
NCI NIH HHS F31 CA257625NCI NIH HHS U24 CA180996NHGRI NIH HHS R35 HG010717Wellcome Trust
6 · The paper itself

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.

Identifiers

PMID38645152
PMCPMC11030530

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.