ReviewGenome biology2020
Eleven grand challenges in single-cell data science.
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Review in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 762 papers.
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762citing papers in PubMed
–field-weighted citation impact
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Who cites it
762 citing papers in PubMed.
- Immunophenotyping by Single-Cell CITE-Seq.Methods in molecular biology (Clifton, N.J.) · 2027Article
- An imputation method for single-cell RNA sequencing data based on a parallel gated recurrent unit neural network.Quantitative biology (Beijing, China) · 2026Article
- A Method for Imputing scRNA-seq Data Based on Mobile Graph Convolutional Generative Adversarial Networks.Biochemical genetics · 2026Article
- Decoding Skeletal Biology Through Transcriptomics: Insights from Bulk, Single-Cell, Spatial, and Multi-Omics Approaches.International journal of molecular sciences · 2026Review
- Article
- Special Issue "Machine Learning and Bioinformatics in Human Health and Disease 2nd Edition".International journal of molecular sciences · 2026Article
- From Cluster to Claim: Calibrating Interpretation in Single-Cell Transcriptomics.Advanced genetics (Hoboken, N.J.) · 2026Article
- Dissecting immunosuppressive microenvironment in chemotherapy-resistant colorectal cancer through single-cell transcriptomic analysis.Translational oncology · 2026Article
- scDiagnostics: systematic assessment of cell type annotation in single-cell transcriptomics data.Briefings in bioinformatics · 2026Article
- Article
- Monocarboxylate Transporter 2 (MCT2) Reduction Is Associated with Increased Lung Tumor Growth and Alterations in the Immune Microenvironment in a Subcutaneous Tumor Model.International journal of molecular sciences · 2026Article
- Integration of artificial intelligence and multi-omics for precision medicine.Functional & integrative genomics · 2026Review
- Integrating machine learning and multi-omics analysis to identify and validate key genes associated with periodontitis.Acta odontologica Scandinavica · 2026Article
- Multi-regional transcriptomics reveals robust consensus subtypes beyond tumor heterogeneity of breast cancer.Translational oncology · 2026Article
- SKIM: A fast sketching strategy integrated with model's dynamic-feedback for large-scale single-cell transcriptomic analysis.PLoS computational biology · 2026Article
- Article
- Article
- Article
- ATACompass enables cross-species cell identity mapping for scATAC-seq without gene annotations.Cell reports methods · 2026Article
- Is adenosine signalling entering the precision medicine era? From receptor pharmacology to patient stratification.Purinergic signalling · 2026Review
702 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
51 authors.
David LähnemannAlgorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
Johannes KösterAlgorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
Ewa SzczurekInstitute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland.
Davis J McCarthyBioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Australia.
Stephanie C HicksDepartment of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
Mark D RobinsonInstitute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland.ORCID http://orcid.org/0000-0002-3048-5518
Catalina A VallejosMRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.
Kieran R CampbellDepartment of Statistics, University of British Columbia, Vancouver, Canada.
Niko BeerenwinkelDepartment of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Ahmed MahfouzLeiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands.
Luca PinelloMolecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Charlestown, USA.
Pavel SkumsDepartment of Computer Science, Georgia State University, Atlanta, USA.
Alexandros StamatakisComputational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
Camille Stephan-Otto AttoliniInstitute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain.
Samuel AparicioDepartment of Molecular Oncology, BC Cancer Agency, Vancouver, Canada.
Jasmijn BaaijensLife Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands.
Marleen BalvertLife Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands.
Buys de BarbansonCenter for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.
Antonio CappuccioInstitute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands.
Giacomo CorleoneDepartment of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK.
Bas E DutilhTheoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands.
Maria FlorescuCenter for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.
Victor GuryevEuropean Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
Rens HolmerBioinformatics Group, Wageningen University, Wageningen, The Netherlands.
Katharina JahnDepartment of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Thamar Jessurun LoboEuropean Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
Emma M KeizerBiometris, Wageningen University & Research, Wageningen, The Netherlands.
Indu KhatriDepartment of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.
Szymon M KielbasaDepartment of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands.
Jan O KorbelGenome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Alexey M KozlovComputational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
Tzu-Hao KuoComputational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Boudewijn P F LelieveldtPRB lab, Delft University of Technology, Delft, The Netherlands.
Ion I MandoiuComputer Science & Engineering Department, University of Connecticut, Storrs, USA.
John C MarioniCancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK.
Tobias MarschallCenter for Bioinformatics, Saarland University, Saarbrücken, Germany.
Felix MölderAlgorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
Amir NiknejadComputation molecular design, Zuse Institute Berlin, Berlin, Germany.
Alicja RączkowskaInstitute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland.
Marcel ReindersLeiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands.
Jeroen de RidderCenter for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.
Antoine-Emmanuel SalibaHelmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany.
Antonios SomarakisDivision of Image Processing, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands.
Oliver StegleGenome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Fabian J TheisInstitute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Huan YangDivision of Drug Discovery and Safety, Leiden Academic Center for Drug Research-LACDR-Leiden University, Leiden, The Netherlands.
Alex ZelikovskyDepartment of Computer Science, Georgia State University, Atlanta, USA.
Alice C McHardyComputational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Benjamin J RaphaelDepartment of Computer Science, Princeton University, Princeton, USA.
Sohrab P ShahComputational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA.
Alexander SchönhuthLife Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands. as@cwi.nl.
Funding
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Hongbiao Carl Lekaye · 1985 to 2026
$347.4MMultiscale exploration of the functional non-coding genomeR35HG010717 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI PINELLO, LUCA · 2019 to 2023
$2.6MComputational Characterization of Genetic HeterogeneityR01HG007069 · NHGRI · PRINCETON UNIVERSITY · PI RAPHAEL, BENJAMIN · 2013 to 2015
$1.1MQUBBD: VIRAL EVOLUTION AND SPREAD OF INFECTIOUS DISEASE IN COMPLEX NETWORK: BIG DATA ANALYSIS AND MODELINGR01EB025022 · NIBIB · GEORGIA STATE UNIVERSITY · PI SKUMS, PAVEL, VANNBERG, FREDRIK · 2017 to 2019
$891kDiscovering disease-causal variants by linking genetic and epigenetic variationR00HG008399 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI PINELLO, LUCA · 2017 to 2019
$747kStatistical Methods for the Normalization and Quantification of Single-Cell RNA-Sequencing DataR00HG009007 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI HICKS, STEPHANIE CARINNE · 2018 to 2020
$725kCancer Research UK 22231Cancer Research UK C9545/A29580NCI NIH HHS P30 CA008748NHGRI NIH HHS R00 HG008399NHGRI NIH HHS R00 HG009007NHGRI NIH HHS R01 HG007069NHGRI NIH HHS R35 HG010717NIBIB NIH HHS R01 EB025022
Abstract
The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands-or even millions-of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.
Indexed as
AnimalsData ScienceGenomicsHumansRNA-SeqSingle-Cell Analysis
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