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Eleven grand challenges in single-cell data science

  • David Lähnemann
  • , Johannes Köster
  • , Ewa Szczurek
  • , Davis J McCarthy
  • , Stephanie C Hicks
  • , Mark D Robinson
  • , Catalina A Vallejos
  • , Kieran R Campbell
  • , Niko Beerenwinkel
  • , Ahmed Mahfouz
  • , Luca Pinello
  • , Pavel Skums
  • , Alexandros Stamatakis
  • , Camille Stephan-Otto Attolini
  • , Samuel Aparicio
  • , Jasmijn Baaijens
  • , Marleen Balvert
  • , Buys de Barbanson
  • , Antonio Cappuccio
  • , Giacomo Corleone
    • Bas E Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M Keizer, Indu Khatri, Szymon M Kielbasa, Jan O Korbel, Alexey M Kozlov, Tzu-Hao Kuo, Boudewijn P F Lelieveldt, Ion I Mandoiu, John C Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J Theis, Huan Yang, Alex Zelikovsky, Alice C McHardy, Benjamin J Raphael, Sohrab P Shah, Alexander Schönhuth
  • Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
  • Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA.
  • Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland.
  • Melbourne Integrative Genomics, School of BioSciences-School of Mathematics & Statistics, Faculty of Science, University of Melbourne, Melbourne, Australia.
  • Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
  • Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland.
  • The Alan Turing Institute, British Library, London, UK.
  • Data Science Institute, University of British Columbia, Vancouver, Canada.
  • SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
  • Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands.
  • Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Department of Computer Science, Georgia State University, Atlanta, USA.
  • Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.
  • Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain.
  • Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
  • Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands.
  • Quantitative biology, Hubrecht Institute, Utrecht, The Netherlands.
  • Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands.
  • Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK.
  • European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
  • Wageningen University & Research
  • Leiden University Medical Center
  • Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands.
  • Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
  • Division of Image Processing, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands.
  • Computer Science & Engineering Department, University of Connecticut, Storrs, USA.
  • European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
  • Max Planck Institute for Informatics, Saarbrücken, Germany.
  • Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
  • Mathematics Department, Mount Saint Vincent, New York, USA.
  • Oncode Institute, Utrecht, The Netherlands.
  • Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany.
  • Division of Computational Genomics and Systems Genetics, German Cancer Research Center-DKFZ, Heidelberg, Germany.
  • Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
  • Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research-LACDR-Leiden University, Leiden, The Netherlands.
  • The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
  • Department of Computer Science, Princeton University, Princeton, USA.
  • Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA.
  • extern

Research output: Contribution to journal › Review article › peer-review

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.

Original languageEnglish
Article number31
Number of pages35
JournalGenome Biology
Volume21
Issue number1
DOIs
Publication statusPublished - 7 Feb 2020

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