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

doi:10.1186/s13059-020-1926-6

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Eleven grand challenges in single-cell data science

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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, …

Genome Biology

2020

DOI: https://doi.org/10.1186/s13059-020-1926-6

Appears in Data-Centric Engineering

Abstract

Animals

Data Science

Humans

RNA-Seq

Single-Cell Analysis

human

Review

animal

procedures

single cell analysis

Genomics

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. © 2020 The Author(s).

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Title: Eleven grand challenges in single-cell data science
Creators - without role: David Lähnemann - Düsseldorf University Hospital
Johannes Köster - Dana-Farber Cancer Institute
Ewa Szczurek - University of Warsaw
Davis J. McCarthy - St Vincents Institute of Medical Research
Stephanie C. Hicks - Johns Hopkins University
Mark D. Robinson - SIB Swiss Institute of Bioinformatics
Catalina A. Vallejos - Institute of Genetics and Cancer
Kieran R. Campbell - BC Cancer Agency
Niko Beerenwinkel - ETH Zurich
Ahmed Mahfouz - Leiden University Medical Center
Luca Pinello - Center for Cancer Research
Pavel Skums - Georgia State University
Alexandros Stamatakis - Heidelberg Institute for Theoretical Studies
Camille Stephan-Otto Attolini
Samuel Aparicio - BC Cancer Agency
Jasmijn Baaijens - Centrum Wiskunde & Informatica
Marleen Balvert - Centrum Wiskunde & Informatica
Buys de Barbanson
Antonio Cappuccio - Netherlands Institute for Advanced Study in the Humanities and Social Sciences
Giacomo Corleone - Imperial College London
Bas E. Dutilh - Radboud University Medical Center
Maria Florescu - Hubrecht Institute for Developmental Biology and Stem Cell Research
Victor Guryev - University Medical Center Groningen
Rens Holmer - Wageningen University & Research
Katharina Jahn - SIB Swiss Institute of Bioinformatics
Thamar Jessurun Lobo - University of Groningen
Emma M. Keizer - Wageningen University & Research
Indu Khatri - Leiden University Medical Center
Szymon M. Kielbasa
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 I. Mandoiu - University of Connecticut
John C. Marioni - Cancer Research UK Cambridge Center
Tobias Marschall - Saarland University
Felix Mölder - University of Duisburg-Essen
Amir Niknejad - Zuse Institute Berlin
Lukasz Raczkowski
Marcel Reinders - Delft University of Technology
Jeroen de Ridder
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 - Centre for Human Drug Research
Alex Zelikovsky - Georgia State University
Alice C. McHardy - Helmholtz Centre for Infection Research
Benjamin J. Raphael - Princeton University
Sohrab P. Shah - Memorial Sloan Kettering Cancer Center
Alexander Schönhuth - Utrecht University
Publication Details: Genome Biology
Publisher: BioMed Central Ltd.
Grant note: AC was supported by an IAS Fellowship for external researchers at the University of Amsterdam. ACM was supported by the Helmholtz Incubator (Sparse2Big ZT-I-0007). AMK and ASt were supported by the Klaus Tschira Foundation. AZ was supported by the National Science Foundation (NSF: DBI-1564899, CCF-1619110) and the National Institutes of Health (NIH: 1R01EB025022-01). BdB was supported by the Oncode Institute (220-H72009 – KWF/2016-1/10158). BED was supported by the Netherlands Organisation for Scientific Research (NWO: Vidi grant 864.14.004). BJR was supported by the NSF (CCF-1053753), the NIH (R01HG007069), and the Chan Zuckerberg Initiative (CZI) Donor-Advised Fund (DAF) (2018-182608), an advised fund of the Silicon Valley Community Foundation. CAV was supported by the University of Edinburgh (Chancellor’s Fellowship) and by The Alan Turing Institute (EPSRC grant EP/N510129/1). DJM was supported by the National Health and Medical Research Council of Australia (GNT1112681 and GNT1162829). DL was supported by the Katharina Hardt Stiftung and the Deutsche Krebshilfe (national Network Genomic Medicine Lung Cancer, nNGM). FJT was supported by the German Research Foundation (DFG: Collaborative Research Centre 1243, Subproject A17), the Helmholtz Incubator (Sparse2big ZT-I-0007), the BMBF (01IS18036A, 01IS18053A, and 01ZX1711A), and the CZI DAF (182835). GC was supported by Marie Sklodowska-Curie grant (agreement no. 642691, Epipredict). IIM was supported by the NSF (award 1564936). JCM was supported by core funding from the European Molecular Biology Laboratory (EMBL) and core support from Cancer Research UK (CRUK: C9545/A29580). JdR was supported by the NWO (Vidi grant 639.072.715). JK was supported by the NWO (Veni grant 016.173.076). JOK was supported by core funding from the EMBL. KJ was supported by SystemsX.ch (RTD Grant 2013/150). KRC was funded by postdoctoral fellowships from the Canadian Institutes of Health Research (CIHR), the Canadian Statistical Sciences Institute (CANSSI), and the UBC Data Science Institute. LP was supported by the NIH – National Human Genome Research Institute (NHGRI) Career Development Award (R00HG008399), the Genomic Innovator Award (R35HG010717), and the CZI DAF (2018-182734). MB was supported by the NWO (Vidi grant 639.072.309 and Vidi grant 864.14.004). MDR was supported by the Swiss National Science Foundation (310030 175841, CRSII5 177208) and the CZI DAF (2018-182828) and acknowledges support from the University Research Priority Program Evolution in Action at the University of Zurich. NB was supported by the ERC (Synergy Grant 609883). OS was supported by core funding from the EMBL. PS was supported by the NIH (1R01EB025022). SA was supported by BC Cancer Foundation, CIHR, Canadian Cancer Society (CCS) Research Institute (CCSRI), Terry Fox Research Institute (TFRI), and CRUK. SCH was supported by the NIH – NHGRI (R00HG009007) and by the CZI DAF (182891, 193161, 356-01). SPS was supported by a Susan G. Komen scholar award, the Nicholls Biondi Endowed Chair in Computational Oncology, Cycle for Survival Benefitting Memorial Sloan Kettering Cancer Center, the TFRI, and the CCS. THK was supported by the Award of a Research Fellowships for the Promotion of Scientific Cooperation at the Helmholtz-Centre for Infection Research.
Identifiers: 9921216509548
Academic Unit: Data-centric engineering
Language: English
Resource Type: Journal article
Date published: 2020

Eleven grand challenges in single-cell data science

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