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Eleven grand challenges in single-cell data science

Laehnemann,David
; 
Koester,Johannes
; 
Szczurek,Ewa
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McCarthy,Davis J.
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Hicks,Stephanie C.
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Robinson,Mark D.
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Vallejos,Catalina A.
; 
Campbell,Kieran R.
; 
Beerenwinkel,Niko
; 
Mahfouz,Ahmed
... show 10 more
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.
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Publisher Copyright: © 2020 The Author(s).
Date
2020-02-07
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Tilburg University Research Output Collection
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WHOLE-GENOME AMPLIFICATION, RNA-SEQUENCING DATA, TUMOR MICROENVIRONMENT, GENE-EXPRESSION, MAXIMUM-LIKELIHOOD, CHROMATIN ACCESSIBILITY, SPATIAL RECONSTRUCTION, ANALYSIS REVEALS, WIDE EXPRESSION, TREE INFERENCE
Citation
Laehnemann, D, Koester, J, Szczurek, E, McCarthy, D J, Hicks, S C, Robinson, M D, Vallejos, C A, Campbell, K R, Beerenwinkel, N, Mahfouz, A, Pinello, L, Skums, P, Stamatakis, A, Attolini, C S-O, Aparicio, S, Baaijens, J, Balvert, M, de Barbanson, B, Cappuccio, A, Corleone, G, Dutilh, B E, Florescu, M, Guryev, V, Holmer, R, Jahn, K, Lobo, T J, Keizer, E M, Khatri, I, Kielbasa, S M, Korbel, J O, Kozlov, A M, Kuo, T-H, Lelieveldt, B P F, Mandoiu, I I, Marioni, J C, Marschall, T, Moelder, F, Niknejad, A, Raczkowski, L, Reinders, M, de Ridder, J, Saliba, A-E, Somarakis, A, Stegle, O, Theis, F J, Yang, H, Zelikovsky, A, McHardy, A C, Raphael, B J, Shah, S P & Schonhuth, A 2020, 'Eleven grand challenges in single-cell data science', Genome biology, vol. 21, no. 1, 31, pp. 31. https://doi.org/10.1186/s13059-020-1926-6
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https://hdl.handle.net/20.500.14602/73333
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