12 Grand challenges in single-cell data science

Abstract: The recent upswing of microfluidics and combinatorial indexing strategies, further enhanced by very low sequencing costs, have turned single cell sequencing into an empowering technology; analyzing thousands—or even millions—of cells per experimental run is becoming a routine assignment in laboratories worldwide. As a consequence, we are witnessing a data revolution in single cell biology. Although some issues are similar in spirit to those experienced in bulk sequencing, many of the emerging data science problems are unique to single cell analysis; together, they give rise to the new realm of 'Single Cell Data Science'. Here, we outline twelve challenges that will be central in bringing this new field forward. For each challenge, the current state of the art in terms of prior work is reviewed, and open problems are formulated, with an emphasis on the research goals that motivate them. This compendium is meant to serve as a guideline for established researchers, newcomers and students alike, highlighting interesting and rewarding problems in 'Single Cell Data Science' for the coming years.

David Laehnemann, Johannes Köster​, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, et al. 12 Grand challenges in single-cell data science. PeerJ Preprints, 2019.
@article { bib:2019_singlecellchallenges_preprint,
author = { David Laehnemann and Johannes K{\"o}ster​ and Ewa Szczurek and Davis J McCarthy and Stephanie C Hicks and Mark D Robinson and Catalina A Vallejos and Niko Beerenwinkel and Kieran R Campbell and Ahmed Mahfouz and Luca Pinello and Pavel Skums and Alexandros Stamatakis and Camille Stephan-Otto Attolini and Samuel Aparicio and Jasmijn Baaijens and Marleen Balvert and Buys de Barbanson and Antonio Cappuccio and Giacomo Corleone and Bas Dutilh and Maria Florescu and Victor Guryev and Rens Holmer and Katharin Jahn and Thamar Jessurun Lobo and Emma M Keizer and Indu Khatri and Szymon M Kiełbasa and Jan O Korbel and Alexey M Kozlov and Tzu-Hao Kuo and Boudewijn Lelieveldt and Ion I Mandoiu and John C Marioni and Tobias Marschall and Felix M{\"o}lder and Amir Niknejad and Łukasz Rączkowski and Marcel Reinders and Jeroen de Ridder and Antoine-Emmanuel Saliba and Antonis Somarakis and Oliver Stegle and Fabian J Theis and Huan Yang and Alex Zelikovsky and Alice C McHardy and Benjamin J Raphael and Sohrab P Shah and Alexander Sch{\"o}nhuth​ },
title = { 12 Grand challenges in single-cell data science },
year = { 2019 },
doi = { 10.7287/peerj.preprints.27885v2 },
Single cell data science challenges screenshot