Genome Biology (Feb 2020)
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,
- Alicja Rączkowska,
- 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
Affiliations
- David Lähnemann
- Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen
- Johannes Köster
- Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen
- Ewa Szczurek
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw
- Davis J. McCarthy
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research
- Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins University
- Mark D. Robinson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zürich
- Catalina A. Vallejos
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital
- Kieran R. Campbell
- Department of Statistics, University of British Columbia
- Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich
- Ahmed Mahfouz
- Leiden Computational Biology Center, Leiden University Medical Center
- Luca Pinello
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute
- Pavel Skums
- Department of Computer Science, Georgia State University
- Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies
- Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology
- Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Agency
- Jasmijn Baaijens
- Life Sciences and Health, Centrum Wiskunde & Informatica
- Marleen Balvert
- Life Sciences and Health, Centrum Wiskunde & Informatica
- Buys de Barbanson
- Center for Molecular Medicine, University Medical Center Utrecht
- Antonio Cappuccio
- Institute for Advanced Study, University of Amsterdam
- Giacomo Corleone
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London
- Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University
- Maria Florescu
- Center for Molecular Medicine, University Medical Center Utrecht
- Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen
- Rens Holmer
- Bioinformatics Group, Wageningen University
- Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zurich
- Thamar Jessurun Lobo
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen
- Emma M. Keizer
- Biometris, Wageningen University & Research
- Indu Khatri
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center
- Szymon M. Kielbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center
- Jan O. Korbel
- Genome Biology Unit, European Molecular Biology Laboratory
- Alexey M. Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies
- Tzu-Hao Kuo
- Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research
- Boudewijn P.F. Lelieveldt
- PRB lab, Delft University of Technology
- Ion I. Mandoiu
- Computer Science & Engineering Department, University of Connecticut
- John C. Marioni
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge
- Tobias Marschall
- Center for Bioinformatics, Saarland University
- Felix Mölder
- Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen
- Amir Niknejad
- Computation molecular design, Zuse Institute Berlin
- Alicja Rączkowska
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw
- Marcel Reinders
- Leiden Computational Biology Center, Leiden University Medical Center
- Jeroen de Ridder
- Center for Molecular Medicine, University Medical Center Utrecht
- Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research
- Antonios Somarakis
- Division of Image Processing, Department of Radiology, Leiden University Medical Center
- Oliver Stegle
- Genome Biology Unit, European Molecular Biology Laboratory
- Fabian J. Theis
- Institute of Computational Biology, Helmholtz Zentrum München–German Research Center for Environmental Health
- Huan Yang
- Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research–LACDR–Leiden University
- Alex Zelikovsky
- Department of Computer Science, Georgia State University
- Alice C. McHardy
- Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research
- Benjamin J. Raphael
- Department of Computer Science, Princeton University
- Sohrab P. Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center
- Alexander Schönhuth
- Life Sciences and Health, Centrum Wiskunde & Informatica
- DOI
- https://doi.org/10.1186/s13059-020-1926-6
- Journal volume & issue
-
Vol. 21,
no. 1
pp. 1 – 35
Abstract
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.
