Eleven grand challenges in single-cell data science
Genome biology, vol. 21, pp. 31
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.
Authors 51
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Düsseldorf University Hospital · Essen University Hospital · Helmholtz Centre for Infection Research · Heinrich Heine University Düsseldorf · University of Duisburg-Essen
Affiliation as printed
Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
Department of Paediatric Oncology, Haematology and Immunology, Medical Faculty, Heinrich Heine University, University Hospital, Düsseldorf, Germany
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Harvard University · Dana-Farber Cancer Institute · Essen University Hospital · University of Duisburg-Essen
Affiliation as printed
Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
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Affiliation as printed
Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland
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The University of Melbourne · St Vincents Institute of Medical Research
Affiliation as printed
Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Australia
Melbourne Integrative Genomics, School of BioSciences-School of Mathematics & Statistics, Faculty of Science, University of Melbourne, Melbourne, Australia
Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, Australia
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Affiliation as printed
Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
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SIB Swiss Institute of Bioinformatics · University of Zurich
Affiliation as printed
Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
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Western General Hospital · The Alan Turing Institute · Institute of Genetics and Cancer · MRC Human Genetics Unit · University of Edinburgh
Affiliation as printed
MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
The Alan Turing Institute, British Library, London, UK
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BC Cancer Agency · University of British Columbia
Affiliation as printed
Data Science Institute, University of British Columbia, Vancouver, Canada
Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
Department of Statistics, University of British Columbia, Vancouver, Canada
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SIB Swiss Institute of Bioinformatics · ETH Zurich
Affiliation as printed
Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Leiden University Medical Center · Delft University of Technology
Affiliation as printed
Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
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Broad Institute · Harvard University · Massachusetts General Hospital
Affiliation as printed
Broad Institute of Harvard and MIT, Cambridge, MA, USA
Department of Pathology, Harvard Medical School, Boston, USA
Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Charlestown, USA
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Affiliation as printed
Department of Computer Science, Georgia State University, Atlanta, USA
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Karlsruhe Institute of Technology · Heidelberg Institute for Theoretical Studies
Affiliation as printed
Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Institute for Research in Biomedicine · Barcelona Institute of Science and Technology
Affiliation as printed
Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
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BC Cancer Agency · University of British Columbia
Affiliation as printed
Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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Centrum Wiskunde & Informatica
Affiliation as printed
Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
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Centrum Wiskunde & Informatica · Utrecht University
Affiliation as printed
Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
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University Medical Center Utrecht · Oncode Institute · Hubrecht Institute for Developmental Biology and Stem Cell Research
Affiliation as printed
Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
Oncode Institute, Utrecht, The Netherlands
Quantitative biology, Hubrecht Institute, Utrecht, The Netherlands
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Affiliation as printed
Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands
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Affiliation as printed
Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
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Utrecht University · Radboud University Medical Center
Affiliation as printed
Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
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University Medical Center Utrecht · Oncode Institute · Hubrecht Institute for Developmental Biology and Stem Cell Research
Affiliation as printed
Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
Oncode Institute, Utrecht, The Netherlands
Quantitative biology, Hubrecht Institute, Utrecht, The Netherlands
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University Medical Center Groningen · University of Groningen
Affiliation as printed
European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
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SIB Swiss Institute of Bioinformatics · ETH Zurich
Affiliation as printed
Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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University Medical Center Groningen · University of Groningen
Affiliation as printed
European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Wageningen University & Research
Affiliation as printed
Biometris, Wageningen University & Research, Wageningen, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
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European Molecular Biology Laboratory
Affiliation as printed
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Heidelberg Institute for Theoretical Studies
Affiliation as printed
Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
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Helmholtz Centre for Infection Research
Affiliation as printed
Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Boudewijn P. F. Lelieveldt Aachen Division of Image Processing Department of Radiology, Leiden University Medical Center
Leiden University · Leiden University Medical Center · Delft University of Technology
Affiliation as printed
Division of Image Processing, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
PRB lab, Delft University of Technology, Delft, The Netherlands
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Affiliation as printed
Computer Science & Engineering Department, University of Connecticut, Storrs, USA
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European Bioinformatics Institute · University of Cambridge · Cancer Research UK · Wellcome Sanger Institute
Affiliation as printed
Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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Max Planck Institute for Informatics · Saarland University
Affiliation as printed
Center for Bioinformatics, Saarland University, Saarbrücken, Germany
Max Planck Institute for Informatics, Saarbrücken, Germany
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Essen University Hospital · University of Duisburg-Essen
Affiliation as printed
Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Affiliation as printed
Computation molecular design, Zuse Institute Berlin, Berlin, Germany
Mathematics Department, Mount Saint Vincent, New York, USA
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Affiliation as printed
Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland
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Leiden University Medical Center · Delft University of Technology
Affiliation as printed
Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
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University Medical Center Utrecht · Oncode Institute
Affiliation as printed
Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
Oncode Institute, Utrecht, The Netherlands
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Helmholtz Institute for RNA-based Infection Research
Affiliation as printed
Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
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Antonios Somarakis Aachen Division of Image Processing Department of Radiology, Leiden University Medical Center
Leiden University · Leiden University Medical Center
Affiliation as printed
Division of Image Processing, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
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European Bioinformatics Institute · German Cancer Research Center · European Molecular Biology Laboratory
Affiliation as printed
Division of Computational Genomics and Systems Genetics, German Cancer Research Center-DKFZ, Heidelberg, Germany
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Helmholtz Munich · Institute of Computational Biology
Affiliation as printed
Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
Institute of Computational Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
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Affiliation as printed
Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research-LACDR-Leiden University, Leiden, The Netherlands
Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research–LACDR–Leiden University, Leiden, The Netherlands
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Sechenov University · Georgia State University
Affiliation as printed
Department of Computer Science, Georgia State University, Atlanta, USA
The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
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Helmholtz Centre for Infection Research
Affiliation as printed
Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Affiliation as printed
Department of Computer Science, Princeton University, Princeton, USA
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Memorial Sloan Kettering Cancer Center
Affiliation as printed
Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
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Alexander Schönhuth corresponding
Centrum Wiskunde & Informatica · Utrecht University
Affiliation as printed
Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands. as@cwi.nl
Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands. as@cwi.nl
Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
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