Publications

Publications

2020

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Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
Jerber J, Seaton D, Cuomo A, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder M, Mountjoy E, Ghoussaini M, Lancaster M, Marioni J, Merkle F, Stegle O, Gaffney D, HipSci Consortium. Preprint DOI: 10.1101/2020.05.21.103820
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Stimulation strength controls the rate of initiation but not the molecular organization of TCR-induced signalling.
Ma CY, Marioni JC, Griffiths GM, Richard AC. eLife Volume 9 (2020) DOI: 10.7554/elife.53948
Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.
Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O. Nature communications Volume 11 (2020) p.1572 DOI: 10.1038/s41467-020-15098-y
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Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels.
Morgan MD, Patin E, Jagla B, Hasan M, Quintana-Murci L, Marioni JC. PLoS genetics Volume 16 (2020) p.e1008686 DOI: 10.1371/journal.pgen.1008686
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.
Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O. Nature communications Volume 11 (2020) p.810 DOI: 10.1038/s41467-020-14457-z

2019

Multi-omics profiling of mouse gastrulation at single-cell resolution.
Argelaguet R, Clark SJ, Mohammed H, Stapel LC, Krueger C, Kapourani CA, Imaz-Rosshandler I, Lohoff T, Xiang Y, Hanna CW, Smallwood S, Ibarra-Soria X, Buettner F, Sanguinetti G, Xie W, Krueger F, Göttgens B, Rugg-Gunn PJ, Kelsey G, Dean W, Nichols J, Stegle O, Marioni JC, Reik W. Nature Volume 576 (2019) p.487-491 DOI: 10.1038/s41586-019-1825-8
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Investigating higher order interactions in single cell data with scHOT
Ghazanfar S, Lin Y, Su X, Lin DM, Patrick E, Han ZG, Marioni JC, Yang JYH. Preprint DOI: 10.1101/841593
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MOFA+: a probabilistic framework for comprehensive integration of structured single-cell data
Argelaguet R, Arnol D, Bredikhin D, Deloro Y, Velten B, Marioni JC, Stegle O. Preprint DOI: 10.1101/837104
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Resolving the fibrotic niche of human liver cirrhosis at single-cell level.
Ramachandran P, Dobie R, Wilson-Kanamori JR, Dora EF, Henderson BEP, Luu NT, Portman JR, Matchett KP, Brice M, Marwick JA, Taylor RS, Efremova M, Vento-Tormo R, Carragher NO, Kendall TJ, Fallowfield JA, Harrison EM, Mole DJ, Wigmore SJ, Newsome PN, Weston CJ, Iredale JP, Tacke F, Pollard JW, Ponting CP, Marioni JC, Teichmann SA, Henderson NC. Nature Volume 575 (2019) p.512-518 DOI: 10.1038/s41586-019-1631-3
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CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets
Fleming SJ, Marioni JC, Babadi M. Preprint DOI: 10.1101/791699
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Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data.
Eling N, Richard AC, Richardson S, Marioni JC, Vallejos CA. Cell systems Volume 9 (2019) p.401-413 DOI: 10.1016/j.cels.2019.08.003
Author Correction: Challenges in measuring and understanding biological noise.
Eling N, Morgan MD, Marioni JC. Nature reviews. Genetics Volume 20 (2019) p.562 DOI: 10.1038/s41576-019-0142-2
Challenges in measuring and understanding biological noise.
Eling N, Morgan MD, Marioni JC. Nature reviews. Genetics Volume 20 (2019) p.536-548 DOI: 10.1038/s41576-019-0130-6
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12 Grand Challenges in Single-Cell Data Science
Laehnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Beerenwinkel N, Campbell KR, Mahfouz A, Pinello L, Skums P, Stamatakis A, Stephan-Otto Attolini C, Aparicio S, Baaijens J, Balvert M, de Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Jessurun Lobo T, Keizer EM, Khatri I, Kiełbasa SM, Korbel JO, Kozlov AM, Kuo T, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowski Ł, Reinders M, de Ridder J, Saliba A, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Preprint DOI: 10.7287/peerj.preprints.27885v3
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A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans.
Saraiva LR, Riveros-McKay F, Mezzavilla M, Abou-Moussa EH, Arayata CJ, Makhlouf M, Trimmer C, Ibarra-Soria X, Khan M, Van Gerven L, Jorissen M, Gibbs M, O'Flynn C, McGrane S, Mombaerts P, Marioni JC, Mainland JD, Logan DW. Science advances Volume 5 (2019) p.eaax0396 DOI: 10.1126/sciadv.aax0396
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Epstein-Barr virus reprograms human B lymphocytes immediately in the prelatent phase of infection.
Mrozek-Gorska P, Buschle A, Pich D, Schwarzmayr T, Fechtner R, Scialdone A, Hammerschmidt W. Proceedings of the National Academy of Sciences of the United States of America Volume 116 (2019) p.16046-16055 DOI: 10.1073/pnas.1901314116
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Roraregulates activated T helper cells during inflammation
Haim-Vilmovsky L, Walker JA, Henriksson J, Miao Z, Natan E, Kar G, Clare S, Barlow JL, Charidemou E, Mamanova L, Chen X, Proserpio V, Pramanik J, Woodhouse S, Protasio AV, Efremova M, Berriman M, Dougan G, Fisher J, Marioni JC, McKenzie AN, Teichmann SA. Preprint DOI: 10.1101/709998
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A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division
Stojic L, Lun ATL, Mascalchi P, Ernst C, Redmond AM, Mangei J, Barr AR, Bousgouni V, Bakal C, Marioni JC, Odom DT, Gergely F. Preprint DOI: 10.1101/709030
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IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response.
Chen HC, Eling N, Martinez-Jimenez CP, O'Brien LM, Carbonaro V, Marioni JC, Odom DT, de la Roche M. EMBO reports Volume 20 (2019) p.e47379 DOI: 10.15252/embr.201847379
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Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
Cuomo AS, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, Vallier L, Marioni JC, Chhatriwala M, Stegle O, HipSci Consortium. Preprint DOI: 10.1101/630996
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Identification of a regeneration-organizing cell in the Xenopus tail.
Aztekin C, Hiscock TW, Marioni JC, Gurdon JB, Simons BD, Jullien J. Science (New York, N.Y.) Volume 364 (2019) p.653-658 DOI: 10.1126/science.aav9996
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EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.
Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T, participants in the 1st Human Cell Atlas Jamboree, Marioni JC. Genome biology Volume 20 (2019) p.63 DOI: 10.1186/s13059-019-1662-y
Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis.
Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT. Nature communications Volume 10 (2019) p.1251 DOI: 10.1038/s41467-019-09182-1
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A single-cell molecular map of mouse gastrulation and early organogenesis.
Pijuan-Sala B, Griffiths JA, Guibentif C, Hiscock TW, Jawaid W, Calero-Nieto FJ, Mulas C, Ibarra-Soria X, Tyser RCV, Ho DLL, Reik W, Srinivas S, Simons BD, Nichols J, Marioni JC, Göttgens B. Nature Volume 566 (2019) p.490-495 DOI: 10.1038/s41586-019-0933-9
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Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation.
Dhar R, Missarova AM, Lehner B, Carey LB. eLife Volume 8 (2019) DOI: 10.7554/elife.38904
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Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification: Supplementary Figures
Argelaguet R, Mohammed H, Clark S, Stapel C, Krueger C, Kapourani CA, Xiang Y, Hanna C, Smallwood S, Ibarra Soria X, Buettner F, Sanguinetti G, Krueger F, Xie W, Rugg-Gunn P, Kelsey G, Dean W, Nichols J, Stegle O, Marioni JC, Reik W. Preprint DOI: 10.1101/519207
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Wnt3a disrupts GR-TEAD4-PPARγ2 positive circuits and cytoskeletal rearrangement in a β-catenin-dependent manner during early adipogenesis.
Park B, Chang S, Lee GJ, Kang B, Kim JK, Park H. Cell death & disease Volume 10 (2019) p.16 DOI: 10.1038/s41419-018-1249-7
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Interspecific variation of olfactory preferences in flies, mice, and humans.
Manoel D, Makhlouf M, Scialdone A, Saraiva LR. Chemical senses Volume 44 (2019) p.7-9 DOI: 10.1093/chemse/bjy074
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Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution.
Messmer T, von Meyenn F, Savino A, Santos F, Mohammed H, Lun ATL, Marioni JC, Reik W. Cell reports Volume 26 (2019) p.815-824.e4 DOI: 10.1016/j.celrep.2018.12.099

2018

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SRPK1 maintains acute myeloid leukemia through effects on isoform usage of epigenetic regulators including BRD4.
Tzelepis K, De Braekeleer E, Aspris D, Barbieri I, Vijayabaskar MS, Liu WH, Gozdecka M, Metzakopian E, Toop HD, Dudek M, Robson SC, Hermida-Prado F, Yang YH, Babaei-Jadidi R, Garyfallos DA, Ponstingl H, Dias JML, Gallipoli P, Seiler M, Buonamici S, Vick B, Bannister AJ, Rad R, Prinjha RK, Marioni JC, Huntly B, Batson J, Morris JC, Pina C, Bradley A, Jeremias I, Bates DO, Yusa K, Kouzarides T, Vassiliou GS. Nature communications Volume 9 (2018) p.5378 DOI: 10.1038/s41467-018-07620-0
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Altered composition of the γδ T cell pool in lymph nodes during ageing enhances tumour growth
Chen H, Eling N, Martinez-Jimenez CP, O’Brien LM, Marioni JC, Odom DT, la Roche Md. Preprint DOI: 10.1101/480327
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Alterations in sperm long RNA contribute to the epigenetic inheritance of the effects of postnatal trauma.
Gapp K, van Steenwyk G, Germain PL, Matsushima W, Rudolph KLM, Manuella F, Roszkowski M, Vernaz G, Ghosh T, Pelczar P, Mansuy IM, Miska EA. Molecular psychiatry (2018) DOI: 10.1038/s41380-018-0271-6
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Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias.
Laumer CE, Gruber-Vodicka H, Hadfield MG, Pearse VB, Riesgo A, Marioni JC, Giribet G. eLife Volume 7 (2018) DOI: 10.7554/elife.36278
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COMRADES determines in vivo RNA structures and interactions.
Ziv O, Gabryelska MM, Lun ATL, Gebert LFR, Sheu-Gruttadauria J, Meredith LW, Liu ZY, Kwok CK, Qin CF, MacRae IJ, Goodfellow I, Marioni JC, Kudla G, Miska EA. Nature methods Volume 15 (2018) p.785-788 DOI: 10.1038/s41592-018-0121-0
Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data.
Eling N, Richard AC, Richardson S, Marioni JC, Vallejos CA. Cell systems Volume 7 (2018) p.284-294.e12 DOI: 10.1016/j.cels.2018.06.011
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Terminal uridylyltransferases target RNA viruses as part of the innate immune system.
Le Pen J, Jiang H, Di Domenico T, Kneuss E, Kosałka J, Leung C, Morgan M, Much C, Rudolph KLM, Enright AJ, O'Carroll D, Wang D, Miska EA. Nature structural & molecular biology Volume 25 (2018) p.778-786 DOI: 10.1038/s41594-018-0106-9
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CTCF maintains regulatory homeostasis of cancer pathways.
Aitken SJ, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C, Marioni JC, Odom DT. Genome biology Volume 19 (2018) p.106 DOI: 10.1186/s13059-018-1484-3
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T cell cytolytic capacity is independent of initial stimulation strength.
Richard AC, Lun ATL, Lau WWY, Göttgens B, Marioni JC, Griffiths GM. Nature immunology Volume 19 (2018) p.849-858 DOI: 10.1038/s41590-018-0160-9
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Detection and removal of barcode swapping in single-cell RNA-seq data.
Griffiths JA, Richard AC, Bach K, Lun ATL, Marioni JC. Nature communications Volume 9 (2018) p.2667 DOI: 10.1038/s41467-018-05083-x
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Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.
Stojic L, Lun ATL, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT. Nucleic acids research Volume 46 (2018) p.5950-5966 DOI: 10.1093/nar/gky437
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CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.
Morgan MD, Marioni JC. Genome biology Volume 19 (2018) p.81 DOI: 10.1186/s13059-018-1461-x
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Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis
Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT. Preprint DOI: 10.1101/350868
Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.
Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T, Marioni JC, Buettner F, Huber W, Stegle O. Molecular systems biology Volume 14 (2018) p.e8124 DOI: 10.15252/msb.20178124
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SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.
Do DV, Strauss B, Cukuroglu E, Macaulay I, Wee KB, Hu TX, Igor RLM, Lee C, Harrison A, Butler R, Dietmann S, Jernej U, Marioni J, Smith CWJ, Göke J, Surani MA. Cell discovery Volume 4 (2018) p.33 DOI: 10.1038/s41421-018-0032-3
Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body.
Achim K, Eling N, Vergara HM, Bertucci PY, Musser J, Vopalensky P, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. Molecular biology and evolution Volume 35 (2018) p.1047-1062 DOI: 10.1093/molbev/msx336
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Using single-cell genomics to understand developmental processes and cell fate decisions.
Griffiths JA, Scialdone A, Marioni JC. Molecular systems biology Volume 14 (2018) p.e8046 DOI: 10.15252/msb.20178046
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Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Lun ATL, Riesenfeld S, Andrews T, Gomes T, Marioni JC, The Phuong Dao, participants in the 1st Human Cell Atlas Jamboree. Preprint DOI: 10.1101/234872
Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Nature biotechnology Volume 36 (2018) p.421-427 DOI: 10.1038/nbt.4091
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scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.
Clark SJ, Argelaguet R, Kapourani CA, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W. Nature communications Volume 9 (2018) p.781 DOI: 10.1038/s41467-018-03149-4
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Spatiotemporal patterning of EpCAM is important for murine embryonic endo- and mesodermal differentiation.
Sarrach S, Huang Y, Niedermeyer S, Hachmeister M, Fischer L, Gille S, Pan M, Mack B, Kranz G, Libl D, Merl-Pham J, Hauck SM, Paoluzzi Tomada E, Kieslinger M, Jeremias I, Scialdone A, Gires O. Scientific reports Volume 8 (2018) p.1801 DOI: 10.1038/s41598-018-20131-8
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Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.
Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A, Jörg DJ, Tyser RCV, Calero-Nieto FJ, Mulas C, Nichols J, Vallier L, Srinivas S, Simons BD, Göttgens B, Marioni JC. Nature cell biology Volume 20 (2018) p.127-134 DOI: 10.1038/s41556-017-0013-z

2017

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Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis
Stojic L, Lun A, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT. Preprint DOI: 10.1101/234930
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Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing.
Bach K, Pensa S, Grzelak M, Hadfield J, Adams DJ, Marioni JC, Khaled WT. Nature communications Volume 8 (2017) p.2128 DOI: 10.1038/s41467-017-02001-5
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The Human Cell Atlas.
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, Human Cell Atlas Meeting Participants. eLife Volume 6 (2017) DOI: 10.7554/elife.27041
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Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.
Shahbazi MN, Scialdone A, Skorupska N, Weberling A, Recher G, Zhu M, Jedrusik A, Devito LG, Noli L, Macaulay IC, Buecker C, Khalaf Y, Ilic D, Voet T, Marioni JC, Zernicka-Goetz M. Nature Volume 552 (2017) p.239-243 DOI: 10.1038/nature24675
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Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.
Griffiths JA, Scialdone A, Marioni JC. BMC genomics Volume 18 (2017) p.904 DOI: 10.1186/s12864-017-4253-x
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Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.
Welby E, Lakowski J, Di Foggia V, Budinger D, Gonzalez-Cordero A, Lun ATL, Epstein M, Patel A, Cuevas E, Kruczek K, Naeem A, Minneci F, Hubank M, Jones DT, Marioni JC, Ali RR, Sowden JC. Stem cell reports Volume 9 (2017) p.1898-1915 DOI: 10.1016/j.stemcr.2017.10.018
f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC, Stegle O. Genome biology Volume 18 (2017) p.212 DOI: 10.1186/s13059-017-1334-8
Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.
Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P. Nature communications Volume 8 (2017) p.1092 DOI: 10.1038/s41467-017-01037-x
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Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data.
Lun ATL, Calero-Nieto FJ, Haim-Vilmovsky L, Göttgens B, Marioni JC. Genome research Volume 27 (2017) p.1795-1806 DOI: 10.1101/gr.222877.117
How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.
Marioni JC, Arendt D. Annual review of cell and developmental biology Volume 33 (2017) p.537-553 DOI: 10.1146/annurev-cellbio-100616-060818
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Detection and removal of barcode swapping in single-cell RNA-seq data
Griffiths JA, Richard AC, Bach K, Lun AT, Marioni JC. Preprint DOI: 10.1101/177048
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Impact of Alternative Splicing on the Human Proteome.
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Cell reports Volume 20 (2017) p.1229-1241 DOI: 10.1016/j.celrep.2017.07.025
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Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.
Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I, Mulas C, Chandra T, Voet T, Dean W, Nichols J, Marioni JC, Reik W. Cell reports Volume 20 (2017) p.1215-1228 DOI: 10.1016/j.celrep.2017.07.009
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Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues
Achim K, Eling N, Martinez Vergara H, Bertucci PY, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. Preprint DOI: 10.1101/167742
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Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours
Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Preprint DOI: 10.1101/165118
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Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data.
Lun ATL, Marioni JC. Biostatistics (Oxford, England) Volume 18 (2017) p.451-464 DOI: 10.1093/biostatistics/kxw055
Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.
Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. Nature communications Volume 8 (2017) p.36 DOI: 10.1038/s41467-017-00052-2
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Testing for differential abundance in mass cytometry data.
Lun ATL, Richard AC, Marioni JC. Nature methods Volume 14 (2017) p.707-709 DOI: 10.1038/nmeth.4295
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Normalizing single-cell RNA sequencing data: challenges and opportunities.
Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC. Nature methods Volume 14 (2017) p.565-571 DOI: 10.1038/nmeth.4292
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The Profile and Dynamics of RNA Modifications in Animals.
van Delft P, Akay A, Huber SM, Bueschl C, Rudolph KLM, Di Domenico T, Schuhmacher R, Miska EA, Balasubramanian S. Chembiochem : a European journal of chemical biology Volume 18 (2017) p.979-984 DOI: 10.1002/cbic.201700093
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Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.
Huang Y, Kim JK, Do DV, Lee C, Penfold CA, Zylicz JJ, Marioni JC, Hackett JA, Surani MA. eLife Volume 6 (2017) DOI: 10.7554/elife.22345
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Adipocyte Accumulation in the Bone Marrow during Obesity and Aging Impairs Stem Cell-Based Hematopoietic and Bone Regeneration.
Ambrosi TH, Scialdone A, Graja A, Gohlke S, Jank AM, Bocian C, Woelk L, Fan H, Logan DW, Schürmann A, Saraiva LR, Schulz TJ. Cell stem cell Volume 20 (2017) p.771-784.e6 DOI: 10.1016/j.stem.2017.02.009
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Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression
Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Triglia ET, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. Preprint DOI: 10.1101/117267
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Complex multi-enhancer contacts captured by genome architecture mapping.
Beagrie RA, Scialdone A, Schueler M, Kraemer DC, Chotalia M, Xie SQ, Barbieri M, de Santiago I, Lavitas LM, Branco MR, Fraser J, Dostie J, Game L, Dillon N, Edwards PA, Nicodemi M, Pombo A. Nature Volume 543 (2017) p.519-524 DOI: 10.1038/nature21411
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Aging increases cell-to-cell transcriptional variability upon immune stimulation.
Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT. Science (New York, N.Y.) Volume 355 (2017) p.1433-1436 DOI: 10.1126/science.aah4115

2016

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Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis.
Ernst C, Pike J, Aitken SJ, Long HK, Eling N, Stojic L, Ward MC, Connor F, Rayner TF, Lukk M, Klose RJ, Kutter C, Odom DT. eLife Volume 5 (2016) DOI: 10.7554/elife.20235
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Sirtuin 1 stimulates the proliferation and the expression of glycolysis genes in pancreatic neoplastic lesions.
Pinho AV, Mawson A, Gill A, Arshi M, Warmerdam M, Giry-Laterriere M, Eling N, Lie T, Kuster E, Camargo S, Biankin AV, Wu J, Rooman I. Oncotarget Volume 7 (2016) p.74768-74778 DOI: 10.18632/oncotarget.11013
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Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data
Lun ATL, Marioni JC. Preprint DOI: 10.1101/073973
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A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.
Lun AT, McCarthy DJ, Marioni JC. F1000Research Volume 5 (2016) p.2122 DOI: 10.12688/f1000research.9501.2
Resolving early mesoderm diversification through single-cell expression profiling.
Scialdone A, Tanaka Y, Jawaid W, Moignard V, Wilson NK, Macaulay IC, Marioni JC, Göttgens B. Nature Volume 535 (2016) p.289-293 DOI: 10.1038/nature18633
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HDTD: analyzing multi-tissue gene expression data.
Touloumis A, Marioni JC, Tavaré S. Bioinformatics (Oxford, England) Volume 32 (2016) p.2193-2195 DOI: 10.1093/bioinformatics/btw224
Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.
Rudolph KL, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C, Odom DT. PLoS genetics Volume 12 (2016) p.e1006024 DOI: 10.1371/journal.pgen.1006024
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Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
Lun AT, Bach K, Marioni JC. Genome biology Volume 17 (2016) p.75 DOI: 10.1186/s13059-016-0947-7
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Structure and evolutionary history of a large family of NLR proteins in the zebrafish.
Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni JC, Soylemez O, Kondrashov F, Leptin M. Open biology Volume 6 (2016) p.160009 DOI: 10.1098/rsob.160009
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Beyond comparisons of means: understanding changes in gene expression at the single-cell level.
Vallejos CA, Richardson S, Marioni JC. Genome biology Volume 17 (2016) p.70 DOI: 10.1186/s13059-016-0930-3
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Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.
Goolam M, Scialdone A, Graham SJL, Macaulay IC, Jedrusik A, Hupalowska A, Voet T, Marioni JC, Zernicka-Goetz M. Cell Volume 165 (2016) p.61-74 DOI: 10.1016/j.cell.2016.01.047
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Classification of low quality cells from single-cell RNA-seq data.
Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA. Genome biology Volume 17 (2016) p.29 DOI: 10.1186/s13059-016-0888-1
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Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC. Nature communications Volume 7 (2016) p.10415 DOI: 10.1038/ncomms10415
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Beyond comparisons of means: understanding changes in gene expression at the single-cell level
Vallejos CA, Richardson S, Marioni JC. Preprint DOI: 10.1101/035949

2015

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Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq.
Saraiva LR, Ibarra-Soria X, Khan M, Omura M, Scialdone A, Mombaerts P, Marioni JC, Logan DW. Scientific reports Volume 5 (2015) p.18178 DOI: 10.1038/srep18178
Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC. Nature communications Volume 6 (2015) p.8687 DOI: 10.1038/ncomms9687
Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.
Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P, Marioni JC, Teichmann SA. Cell stem cell Volume 17 (2015) p.471-485 DOI: 10.1016/j.stem.2015.09.011
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Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength.
Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR. Genome biology Volume 16 (2015) p.201 DOI: 10.1186/s13059-015-0749-3
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Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.
Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT. PloS one Volume 10 (2015) p.e0137367 DOI: 10.1371/journal.pone.0137367
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Structure and evolutionary history of a large family of NLR proteins in the zebrafish
Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni J, Soylemez O, Kondrashov F, Leptin M. Preprint DOI: 10.1101/022061
Computational assignment of cell-cycle stage from single-cell transcriptome data.
Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F. Methods (San Diego, Calif.) Volume 85 (2015) p.54-61 DOI: 10.1016/j.ymeth.2015.06.021
Molecular and neuronal homology between the olfactory systems of zebrafish and mouse.
Saraiva LR, Ahuja G, Ivandic I, Syed AS, Marioni JC, Korsching SI, Logan DW. Scientific reports Volume 5 (2015) p.11487 DOI: 10.1038/srep11487
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
Vallejos CA, Marioni JC, Richardson S. PLoS computational biology Volume 11 (2015) p.e1004333 DOI: 10.1371/journal.pcbi.1004333
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Identification of artesunate as a specific activator of ferroptosis in pancreatic cancer cells.
Eling N, Reuter L, Hazin J, Hamacher-Brady A, Brady NR. Oncoscience Volume 2 (2015) p.517-532 DOI: 10.18632/oncoscience.160
The technology and biology of single-cell RNA sequencing.
Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA. Molecular cell Volume 58 (2015) p.610-620 DOI: 10.1016/j.molcel.2015.04.005
High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.
Achim K, Pettit JB, Saraiva LR, Gavriouchkina D, Larsson T, Arendt D, Marioni JC. Nature biotechnology Volume 33 (2015) p.503-509 DOI: 10.1038/nbt.3209
How plants manage food reserves at night: quantitative models and open questions.
Scialdone A, Howard M. Frontiers in plant science Volume 6 (2015) p.204 DOI: 10.3389/fpls.2015.00204
Computational and analytical challenges in single-cell transcriptomics.
Stegle O, Teichmann SA, Marioni JC. Nature reviews. Genetics Volume 16 (2015) p.133-145 DOI: 10.1038/nrg3833
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Testing the mean matrix in high-dimensional transposable data.
Touloumis A, Tavaré S, Marioni JC. Biometrics Volume 71 (2015) p.157-166 DOI: 10.1111/biom.12257
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O. Nature biotechnology Volume 33 (2015) p.155-160 DOI: 10.1038/nbt.3102
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Emerging Drug Target In Pancreatic Cancer: Placing Sirtuin 1 on the Canvas.
Giry-Laterriere M, Pinho AV, Eling N, Chantrill L, Rooman I. Current cancer drug targets Volume 15 (2015) p.463-468 DOI: 10.2174/1568009615666150512102957

2014

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Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.
Peat JR, Dean W, Clark SJ, Krueger F, Smallwood SA, Ficz G, Kim JK, Marioni JC, Hore TA, Reik W. Cell reports Volume 9 (2014) p.1990-2000 DOI: 10.1016/j.celrep.2014.11.034
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Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone.
Piccirillo SG, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis NJ, Howarth KD, Collins VP, Venkitaraman AR, Curtis C, Marioni JC, Tavaré S, Watts C. Cancer research Volume 75 (2015) p.194-202 DOI: 10.1158/0008-5472.can-13-3131
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Single Cell Genomics meeting in Stockholm: from single cells to cell types.
Scialdone A, Achim K, Marioni JC. Genome biology Volume 15 (2014) p.496 DOI: 10.1186/s13059-014-0496-x
Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.
Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD. eLife Volume 3 (2014) p.e02626 DOI: 10.7554/elife.02626
RNA-Seq gene profiling--a systematic empirical comparison.
Fonseca NA, Marioni J, Brazma A. PloS one Volume 9 (2014) p.e107026 DOI: 10.1371/journal.pone.0107026
Identifying cell types from spatially referenced single-cell expression datasets.
Pettit JB, Tomer R, Achim K, Richardson S, Azizi L, Marioni J. PLoS computational biology Volume 10 (2014) p.e1003824 DOI: 10.1371/journal.pcbi.1003824
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High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.
Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ, Talianidis I, Odom DT, Marioni JC, Kutter C. Genome research Volume 24 (2014) p.1797-1807 DOI: 10.1101/gr.176784.114
Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.
Uslu VV, Petretich M, Ruf S, Langenfeld K, Fonseca NA, Marioni JC, Spitz F. Nature genetics Volume 46 (2014) p.753-758 DOI: 10.1038/ng.2971
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Random monoallelic gene expression increases upon embryonic stem cell differentiation.
Eckersley-Maslin MA, Thybert D, Bergmann JH, Marioni JC, Flicek P, Spector DL. Developmental cell Volume 28 (2014) p.351-365 DOI: 10.1016/j.devcel.2014.01.017
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NFκB and STAT3 synergistically activate the expression of FAT10, a gene counteracting the tumor suppressor p53.
Choi Y, Kim JK, Yoo JY. Molecular oncology Volume 8 (2014) p.642-655 DOI: 10.1016/j.molonc.2014.01.007

2013

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A. Nucleic acids research Volume 42 (2014) p.D926-32 DOI: 10.1093/nar/gkt1270
Accounting for technical noise in single-cell RNA-seq experiments.
Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG. Nature methods Volume 10 (2013) p.1093-1095 DOI: 10.1038/nmeth.2645
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Organizing a PhD symposium--an inside view. Setting up a scientific meeting is challenging--a PhD symposium offers its own unique opportunities and pitfalls.
Schröder MS, Harnett D, Minke BA, Nair PS, Committee Member Consortium. EMBO reports Volume 14 (2013) p.856-860 DOI: 10.1038/embor.2013.147
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Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.
Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT. Cell Volume 154 (2013) p.530-540 DOI: 10.1016/j.cell.2013.07.007
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Peroxiredoxin-3 is overexpressed in prostate cancer and promotes cancer cell survival by protecting cells from oxidative stress.
Whitaker HC, Patel D, Howat WJ, Warren AY, Kay JD, Sangan T, Marioni JC, Mitchell J, Aldridge S, Luxton HJ, Massie C, Lynch AG, Neal DE. British journal of cancer Volume 109 (2013) p.983-993 DOI: 10.1038/bjc.2013.396
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Arabidopsis plants perform arithmetic division to prevent starvation at night.
Scialdone A, Mugford ST, Feike D, Skeffington A, Borrill P, Graf A, Smith AM, Howard M. eLife Volume 2 (2013) p.e00669 DOI: 10.7554/elife.00669
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Polymer models of chromatin organization.
Barbieri M, Scialdone A, Piccolo A, Chiariello AM, di Lanno C, Prisco A, Pombo A, Nicodemi M. Frontiers in genetics Volume 4 (2013) p.113 DOI: 10.3389/fgene.2013.00113
bioWeb3D: an online webGL 3D data visualisation tool.
Pettit JB, Marioni JC. BMC bioinformatics Volume 14 (2013) p.185 DOI: 10.1186/1471-2105-14-185
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Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.
Sottoriva A, Spiteri I, Piccirillo SG, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C, Tavaré S. Proceedings of the National Academy of Sciences of the United States of America Volume 110 (2013) p.4009-4014 DOI: 10.1073/pnas.1219747110
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Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.
Kim JK, Marioni JC. Genome biology Volume 14 (2013) p.R7 DOI: 10.1186/gb-2013-14-1-r7

2012

Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC. Bioinformatics (Oxford, England) Volume 28 (2012) p.3169-3177 DOI: 10.1093/bioinformatics/bts605
Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.
Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC. Genome research Volume 22 (2012) p.2376-2384 DOI: 10.1101/gr.142281.112
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Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.
Barreiro LB, Tailleux L, Pai AA, Gicquel B, Marioni JC, Gilad Y. Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.1204-1209 DOI: 10.1073/pnas.1115761109

2011

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Comparative RNA sequencing reveals substantial genetic variation in endangered primates.
Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y. Genome research Volume 22 (2012) p.602-610 DOI: 10.1101/gr.130468.111
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Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices.
Oh YM, Kim JK, Choi S, Yoo JY. Nucleic acids research Volume 40 (2012) p.e38 DOI: 10.1093/nar/gkr1252
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Probabilistic models for semisupervised discriminative motif discovery in DNA sequences.
Kim JK, Choi S. IEEE/ACM transactions on computational biology and bioinformatics Volume 8 (2011) p.1309-1317 DOI: 10.1109/tcbb.2010.84
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The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group. Bioinformatics (Oxford, England) Volume 27 (2011) p.2156-2158 DOI: 10.1093/bioinformatics/btr330
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Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma.
Goh XY, Rees JR, Paterson AL, Chin SF, Marioni JC, Save V, O'Donovan M, Eijk PP, Alderson D, Ylstra B, Caldas C, Fitzgerald RC. Gut Volume 60 (2011) p.1317-1326 DOI: 10.1136/gut.2010.234179
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A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.
Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y. PLoS genetics Volume 7 (2011) p.e1001316 DOI: 10.1371/journal.pgen.1001316
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Gene expression differences among primates are associated with changes in a histone epigenetic modification.
Cain CE, Blekhman R, Marioni JC, Gilad Y. Genetics Volume 187 (2011) p.1225-1234 DOI: 10.1534/genetics.110.126177

2010

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Functional comparison of innate immune signaling pathways in primates.
Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y. PLoS genetics Volume 6 (2010) p.e1001249 DOI: 10.1371/journal.pgen.1001249
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Genomic-scale capture and sequencing of endogenous DNA from feces.
Perry GH, Marioni JC, Melsted P, Gilad Y. Molecular ecology Volume 19 (2010) p.5332-5344 DOI: 10.1111/j.1365-294x.2010.04888.x
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Understanding mechanisms underlying human gene expression variation with RNA sequencing.
Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. Nature Volume 464 (2010) p.768-772 DOI: 10.1038/nature08872

2009

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Sex-specific and lineage-specific alternative splicing in primates.
Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y. Genome research Volume 20 (2010) p.180-189 DOI: 10.1101/gr.099226.109