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Eleven grand challenges in single-cell data science

Genome biology · 2020 · Vol. 21(1) · pp. 31–31

David Lähnemann✉(Düsseldorf University Hospital)Johannes Köster(Harvard University)Ewa Szczurek(University of Warsaw)Davis J. McCarthy(The University of Melbourne)Stephanie C. Hicks(Johns Hopkins University)Mark D. Robinson(SIB Swiss Institute of Bioinformatics)Catalina A. Vallejos(Turing Institute)Kieran R. Campbell(BC Cancer Agency)Niko Beerenwinkel(SIB Swiss Institute of Bioinformatics)Ahmed Mahfouz(Leiden University Medical Center)Luca Pinello(Broad Institute)Pavel Skums(Georgia State University)Alexandros Stamatakis(Karlsruhe Institute of Technology)Camille Stephan‐Otto Attolini(Institute for Research in Biomedicine)Samuel Aparício(BC Cancer Agency)Jasmijn A. Baaijens(Centrum Wiskunde & Informatica)Marleen Balvert(Centrum Wiskunde & Informatica)Buys de Barbanson(University Medical Center Utrecht)Antonio Cappuccio(Netherlands Institute for Advanced Study in the Humanities and Social Sciences)Giacomo Corleone(Imperial College London)Bas E. Dutilh(Radboud University Nijmegen)Maria Florescu(University Medical Center Utrecht)Victor Guryev(University Medical Center Groningen)Rens Holmer(Wageningen University & Research)Katharina Jahn(SIB Swiss Institute of Bioinformatics)Thamar Jessurun Lobo(University Medical Center Groningen)Emma M Keizer(Wageningen University & Research)Indu Khatri(Leiden University Medical Center)Szymon M. Kiełbasa(Leiden University Medical Center)Jan O. Korbel(European Molecular Biology Laboratory)Alexey M. Kozlov(Heidelberg Institute for Theoretical Studies)Tzu-Hao Kuo(Helmholtz Centre for Infection Research)Boudewijn P. F. Lelieveldt(Leiden University Medical Center)Ion Măndoiu(University of Connecticut)John C. Marioni(European Bioinformatics Institute)Tobias Marschall(Max Planck Institute for Informatics)Felix Mölder(University of Duisburg-Essen)Amir Niknejad(Mount Saint Vincent University)Alicja Rączkowska(University of Warsaw)Marcel Reinders(Leiden University Medical Center)Jeroen de Ridder(University Medical Center Utrecht)Antoine-Emmanuel Saliba(Helmholtz Institute for RNA-based Infection Research)Antonios Somarakis(Leiden University Medical Center)Oliver Stegle(European Bioinformatics Institute)Fabian J. Theis(Helmholtz Zentrum München)Huan Yang(Leiden University)Alex Zelikovsky(Sechenov University)Alice C. McHardy(Helmholtz Centre for Infection Research)Benjamin J. Raphael(Princeton University)Sohrab P. Shah(Memorial Sloan Kettering Cancer Center)Alexander Schönhuth(Centrum Wiskunde & Informatica)

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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.

Single-cell and spatial transcriptomics Cell Image Analysis Techniques Gene Regulatory Network AnalysisCompendiumData scienceBiologyField (mathematics)Computer scienceComputational biology