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Eleven grand challenges in single-cell data science

by Köster, Johannes , Jahn, Katharina , Khatri, Indu , Baaijens, Jasmijn , McHardy, Alice C. , Campbell, Kieran R. , Mahfouz, Ahmed , Dutilh, Bas E. , Lähnemann, David , Corleone, Giacomo , Marioni, John C. , Lelieveldt, Boudewijn P.F. , Aparicio, Samuel , Cappuccio, Antonio , Marschall, Tobias , Kozlov, Alexey M. , Kuo, Tzu-Hao , Somarakis, Antonios , Theis, Fabian J. , Rączkowska, Alicja , Niknejad, Amir , Szczurek, Ewa , Attolini, Camille Stephan-Otto , Ridder, Jeroen de , Stamatakis, Alexandros , Holmer, Rens , Barbanson, Buys de , Vallejos, Catalina A. , Korbel, Jan O. , Mandoiu, Ion I. , Beerenwinkel, Niko , Schönhuth, Alexander , Robinson, Mark D. , Shah, Sohrab P. , Zelikovsky, Alex , Kielbasa, Szymon M. , Balvert, Marleen , Pinello, Luca , Lobo, Thamar Jessurun , McCarthy, Davis J. , Stegle, Oliver , Guryev, Victor , Florescu, Maria , Reinders, Marcel , Saliba, Antoine-Emmanuel , Keizer, Emma M. , Skums, Pavel , Raphael, Benjamin J. , Hicks, Stephanie C. , Yang, Huan , Mölder, Felix

in Animal Genetics and Genomics / Animals / Bioinformatics / Biomedical and Life Sciences / Data science / Data Science - methods / Evolutionary Biology / fields / genome / Genomics - methods / Human Genetics / Humans / Life Sciences / Microbial Genetics and Genomics / microfluidic technology / Microfluidics / Plant Genetics and Genomics / Review / RNA-Seq - methods / Single-Cell Analysis - methods / students / wills

2020

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2020

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2020

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Journal Article

Eleven grand challenges in single-cell data science

Köster, Johannes,

Jahn, Katharina,

Khatri, Indu,

Baaijens, Jasmijn,

McHardy, Alice C.,

Campbell, Kieran R.,

Mahfouz, Ahmed,

Dutilh, Bas E.,

Lähnemann, David,

Corleone, Giacomo,

Marioni, John C.,

Lelieveldt, Boudewijn P.F.,

Aparicio, Samuel,

Cappuccio, Antonio,

Marschall, Tobias,

Kozlov, Alexey M.,

Kuo, Tzu-Hao,

Somarakis, Antonios,

Theis, Fabian J.,

Rączkowska, Alicja,

Niknejad, Amir,

Szczurek, Ewa,

Attolini, Camille Stephan-Otto,

Ridder, Jeroen de,

Stamatakis, Alexandros,

Holmer, Rens,

Barbanson, Buys de,

Vallejos, Catalina A.,

Korbel, Jan O.,

Mandoiu, Ion I.,

Beerenwinkel, Niko,

Schönhuth, Alexander,

Robinson, Mark D.,

Shah, Sohrab P.,

Zelikovsky, Alex,

Kielbasa, Szymon M.,

Balvert, Marleen,

Pinello, Luca,

Lobo, Thamar Jessurun,

McCarthy, Davis J.,

Stegle, Oliver,

Guryev, Victor,

Florescu, Maria,

Reinders, Marcel,

Saliba, Antoine-Emmanuel,

Keizer, Emma M.,

Skums, Pavel,

Raphael, Benjamin J.,

Hicks, Stephanie C.,

Yang, Huan,

Mölder, Felix

2020

Overview

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

BioMed Central,Springer Nature B.V,BMC

Subject

Animal Genetics and Genomics

/ Animals

/ Bioinformatics

/ Biomedical and Life Sciences

/ Data science

/ Data Science - methods

/ Evolutionary Biology