CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness by Michael D. Morgan, John C. Marioni

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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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A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor [version 2; referees: 1 approved, 4 approved with reservations] by Aaron T.L. Lun, Davis J. McCarthy, 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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Functional comparison of innate immune signaling pathways in primates. by Luis B Barreiro, John C Marioni, Ran Blekhman, Matthew Stephens, Yoav Gilad

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Stimulation strength controls the rate of initiation but not the molecular organisation of TCR-induced signalling by Claire Y Ma, John C Marioni, Gillian M Griffiths, Arianne C Richard

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f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq by Florian Buettner, Naruemon Pratanwanich, Davis J. McCarthy, John C. Marioni, Oliver Stegle

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A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. by Athma A Pai, Jordana T Bell, John C Marioni, Jonathan K Pritchard, Yoav Gilad

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Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis by Christina Ernst, Nils Eling, Celia P. Martinez-Jimenez, John C. Marioni, Duncan T. Odom

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Correction: Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression by Jong Kyoung Kim, Aleksandra A. Kolodziejczyk, Tomislav Ilicic, Sarah A. Teichmann, John C. Marioni

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Detection and removal of barcode swapping in single-cell RNA-seq data by Jonathan A. Griffiths, Arianne C. Richard, Karsten Bach, Aaron T. L. Lun, 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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MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data by Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C. Marioni, Oliver Stegle

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Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing by Karsten Bach, Sara Pensa, Marta Grzelak, James Hadfield, David J. Adams, John C. Marioni, Walid T. Khaled

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Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens by Joannah R. Fergusson, Michael D. Morgan, Melanie Bruchard, Leonie Huitema, Leonie Huitema, Balthasar A. Heesters, Vincent van Unen, Jan Piet van Hamburg, Jan Piet van Hamburg, Nicole N. van der Wel, Daisy Picavet, Frits Koning, Sander W. Tas, Sander W. Tas, Mark S. Anderson, John C. Marioni, John C. Marioni, John C. Marioni, Georg A. Holländer, Hergen Spits

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CTCF maintains regulatory homeostasis of cancer pathways by Sarah J. Aitken, Ximena Ibarra-Soria, Elissavet Kentepozidou, Paul Flicek, Christine Feig, John C. Marioni, Duncan T. Odom

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