EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays by Stathis Megas, Valentina Lorenzi, John C. Marioni

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Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data by Jonathan A. Griffiths, Antonio Scialdone, John C. Marioni

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BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. by Catalina A Vallejos, John C Marioni, Sylvia Richardson

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Using single‐cell genomics to understand developmental processes and cell fate decisions by Jonathan A Griffiths, Antonio Scialdone, John C Marioni

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BASiCS workflow: a step-by-step analysis of expression variability using single cell RNA sequencing data [version 2; peer review: 1 approved, 2 approved with reservations] by Catalina A. Vallejos, Nils Eling, Alan O'Callaghan, John C. Marioni

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CellRegMap: a statistical framework for mapping context‐specific regulatory variants using scRNA‐seq by Anna S E Cuomo, Tobias Heinen, Danai Vagiaki, Danilo Horta, John C Marioni, Oliver Stegle

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Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels. by Michael D Morgan, Etienne Patin, Bernd Jagla, Milena Hasan, Lluís Quintana-Murci, John C Marioni

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Time-resolved single-cell RNAseq profiling identifies a novel Fabp5+ subpopulation of inflammatory myeloid cells with delayed cytotoxic profile in chronic spinal cord injury by Regan Hamel, Luca Peruzzotti-Jametti, Katherine Ridley, Veronica Testa, Bryan Yu, David Rowitch, John C. Marioni, Stefano Pluchino

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Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets by Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle

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Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States. by Konrad L M Rudolph, Bianca M Schmitt, Diego Villar, Robert J White, John C Marioni, Claudia Kutter, Duncan T Odom

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The dynamic genetic determinants of increased transcriptional divergence in spermatids by Jasper Panten, Tobias Heinen, Christina Ernst, Nils Eling, Rebecca E. Wagner, Maja Satorius, John C. Marioni, Oliver Stegle, Duncan T. Odom

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Impact of Alternative Splicing on the Human Proteome by Yansheng Liu, Mar Gonzàlez-Porta, Sergio Santos, Alvis Brazma, John C. Marioni, Ruedi Aebersold, Ashok R. Venkitaraman, Vihandha O. Wickramasinghe

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scSNV-seq: high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics by Sarah E. Cooper, Matthew A. Coelho, Magdalena E. Strauss, Aleksander M. Gontarczyk, Qianxin Wu, Mathew J. Garnett, John C. Marioni, Andrew R. Bassett

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Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition by Yun Huang, Jong Kyoung Kim, Dang Vinh Do, Caroline Lee, Christopher A Penfold, Jan J Zylicz, John C Marioni, Jamie A Hackett, M Azim Surani

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Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation by Ran Wang, Xianfa Yang, Jiehui Chen, Lin Zhang, Jonathan A. Griffiths, Guizhong Cui, Yingying Chen, Yun Qian, Guangdun Peng, Jinsong Li, Liantang Wang, John C. Marioni, Patrick P. L. Tam, Naihe Jing

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Ageing compromises mouse thymus function and remodels epithelial cell differentiation by Jeanette Baran-Gale, Michael D Morgan, Stefano Maio, Fatima Dhalla, Irene Calvo-Asensio, Mary E Deadman, Adam E Handel, Ashley Maynard, Steven Chen, Foad Green, Rene V Sit, Norma F Neff, Spyros Darmanis, Weilun Tan, Andy P May, John C Marioni, Chris P Ponting, Georg A Holländer

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Mapping Rora expression in resting and activated CD4+ T cells. by Liora Haim-Vilmovsky, Johan Henriksson, Jennifer A Walker, Zhichao Miao, Eviatar Natan, Gozde Kar, Simon Clare, Jillian L Barlow, Evelina Charidemou, Lira Mamanova, Xi Chen, Valentina Proserpio, Jhuma Pramanik, Steven Woodhouse, Anna V Protasio, Mirjana Efremova, Julian L Griffin, Matt Berriman, Gordon Dougan, Jasmin Fisher, John C Marioni, Andrew N J McKenzie, Sarah A Teichmann

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Eleven grand challenges in single-cell data science by 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

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