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Items: 1 to 50 of 103

1.

Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens.

Fergusson JR, Morgan MD, Bruchard M, Huitema L, Heesters BA, van Unen V, van Hamburg JP, van der Wel NN, Picavet D, Koning F, Tas SW, Anderson MS, Marioni JC, Holländer GA, Spits H.

Front Immunol. 2019 Jan 14;9:2902. doi: 10.3389/fimmu.2018.02902. eCollection 2018.

2.

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 Rep. 2019 Jan 22;26(4):815-824.e4. doi: 10.1016/j.celrep.2018.12.099.

3.

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.

Nat Commun. 2018 Dec 19;9(1):5378. doi: 10.1038/s41467-018-07620-0.

4.

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. 2018 Oct 30;7. pii: e36278. doi: 10.7554/eLife.36278.

5.

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.

Nat Methods. 2018 Oct;15(10):785-788. doi: 10.1038/s41592-018-0121-0. Epub 2018 Sep 10.

PMID:
30202058
6.

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 Syst. 2018 Sep 26;7(3):284-294.e12. doi: 10.1016/j.cels.2018.06.011. Epub 2018 Aug 29.

7.

CTCF maintains regulatory homeostasis of cancer pathways.

Aitken SJ, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C, Marioni JC, Odom DT.

Genome Biol. 2018 Aug 7;19(1):106. doi: 10.1186/s13059-018-1484-3.

8.

T cell cytolytic capacity is independent of initial stimulation strength.

Richard AC, Lun ATL, Lau WWY, Göttgens B, Marioni JC, Griffiths GM.

Nat Immunol. 2018 Aug;19(8):849-858. doi: 10.1038/s41590-018-0160-9. Epub 2018 Jul 16.

9.

Detection and removal of barcode swapping in single-cell RNA-seq data.

Griffiths JA, Richard AC, Bach K, Lun ATL, Marioni JC.

Nat Commun. 2018 Jul 10;9(1):2667. doi: 10.1038/s41467-018-05083-x.

10.

CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.

Morgan MD, Marioni JC.

Genome Biol. 2018 Jun 26;19(1):81. doi: 10.1186/s13059-018-1461-x.

11.

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 Discov. 2018 Jun 19;4:33. doi: 10.1038/s41421-018-0032-3. eCollection 2018.

12.

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.

Mol Syst Biol. 2018 Jun 20;14(6):e8124. doi: 10.15252/msb.20178124.

13.

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 Res. 2018 Jul 6;46(12):5950-5966. doi: 10.1093/nar/gky437.

14.

Using single-cell genomics to understand developmental processes and cell fate decisions.

Griffiths JA, Scialdone A, Marioni JC.

Mol Syst Biol. 2018 Apr 16;14(4):e8046. doi: 10.15252/msb.20178046. Review.

15.

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.

Haghverdi L, Lun ATL, Morgan MD, Marioni JC.

Nat Biotechnol. 2018 Jun;36(5):421-427. doi: 10.1038/nbt.4091. Epub 2018 Apr 2.

16.

Erratum: 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. 2018 Feb 28;555(7694):126. doi: 10.1038/nature25995.

PMID:
29493594
17.

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.

Nat Commun. 2018 Feb 22;9(1):781. doi: 10.1038/s41467-018-03149-4.

18.

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.

Mol Biol Evol. 2018 May 1;35(5):1047-1062. doi: 10.1093/molbev/msx336.

19.

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.

Nat Cell Biol. 2018 Feb;20(2):127-134. doi: 10.1038/s41556-017-0013-z. Epub 2018 Jan 8.

20.

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.

Nat Commun. 2017 Dec 11;8(1):2128. doi: 10.1038/s41467-017-02001-5.

21.

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. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

22.

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. 2017 Dec 14;552(7684):239-243. doi: 10.1038/nature24675. Epub 2017 Nov 29. Erratum in: Nature. 2018 Feb 28;555(7694):126.

23.

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.

Griffiths JA, Scialdone A, Marioni JC.

BMC Genomics. 2017 Nov 25;18(1):904. doi: 10.1186/s12864-017-4253-x.

24.

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. 2017 Dec 12;9(6):1898-1915. doi: 10.1016/j.stemcr.2017.10.018. Epub 2017 Nov 16.

25.

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.

Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC, Stegle O.

Genome Biol. 2017 Nov 7;18(1):212. doi: 10.1186/s13059-017-1334-8.

26.

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.

Nat Commun. 2017 Oct 23;8(1):1092. doi: 10.1038/s41467-017-01037-x.

27.

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 Res. 2017 Nov;27(11):1795-1806. doi: 10.1101/gr.222877.117. Epub 2017 Oct 13.

28.

How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.

Marioni JC, Arendt D.

Annu Rev Cell Dev Biol. 2017 Oct 6;33:537-553. doi: 10.1146/annurev-cellbio-100616-060818. Epub 2017 Aug 16. Review.

PMID:
28813177
29.

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 Rep. 2017 Aug 1;20(5):1229-1241. doi: 10.1016/j.celrep.2017.07.025.

30.

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 Rep. 2017 Aug 1;20(5):1215-1228. doi: 10.1016/j.celrep.2017.07.009.

31.

On the mechanism of Candida tropicalis biofilm reduction by the combined action of naturally-occurring anthraquinones and blue light.

Marioni J, Bresolí-Obach R, Agut M, Comini LR, Cabrera JL, Paraje MG, Nonell S, Núñez Montoya SC.

PLoS One. 2017 Jul 19;12(7):e0181517. doi: 10.1371/journal.pone.0181517. eCollection 2017.

32.

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.

Nat Commun. 2017 Jun 26;8(1):36. doi: 10.1038/s41467-017-00052-2.

33.

Normalizing single-cell RNA sequencing data: challenges and opportunities.

Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC.

Nat Methods. 2017 Jun;14(6):565-571. doi: 10.1038/nmeth.4292. Epub 2017 May 15.

34.

Testing for differential abundance in mass cytometry data.

Lun ATL, Richard AC, Marioni JC.

Nat Methods. 2017 Jul;14(7):707-709. doi: 10.1038/nmeth.4295. Epub 2017 May 15.

35.

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. 2017 Mar 31;355(6332):1433-1436. doi: 10.1126/science.aah4115.

36.

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data.

Lun ATL, Marioni JC.

Biostatistics. 2017 Jul 1;18(3):451-464. doi: 10.1093/biostatistics/kxw055.

37.

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. 2017 Mar 21;6. pii: e22345. doi: 10.7554/eLife.22345.

38.

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

Lun AT, McCarthy DJ, Marioni JC.

Version 2. F1000Res. 2016 Aug 31 [revised 2016 Jan 1];5:2122. eCollection 2016.

39.

The anthraquinones rubiadin and its 1-methyl ether isolated from Heterophyllaea pustulata reduces Candida tropicalis biofilms formation.

Marioni J, da Silva MA, Cabrera JL, Montoya SC, Paraje MG.

Phytomedicine. 2016 Nov 15;23(12):1321-1328. doi: 10.1016/j.phymed.2016.07.008. Epub 2016 Jul 20.

PMID:
27765351
40.

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. 2016 Jul 14;535(7611):289-293. doi: 10.1038/nature18633. Epub 2016 Jul 6.

41.

HDTD: analyzing multi-tissue gene expression data.

Touloumis A, Marioni JC, Tavaré S.

Bioinformatics. 2016 Jul 15;32(14):2193-5. doi: 10.1093/bioinformatics/btw224. Epub 2016 Jun 7.

42.

Reduction of Candida tropicalis biofilm by photoactivation of a Heterophyllaea pustulata extract.

Marioni J, Arce JE, Cabrera JL, Paraje MG, Núñez Montoya SC.

Pharm Biol. 2016 Dec;54(12):2791-2801. Epub 2016 Jun 3.

PMID:
27256704
43.

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 Biol. 2016 Apr;6(4):160009. doi: 10.1098/rsob.160009. Epub 2016 Apr 27.

44.

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 Genet. 2016 May 11;12(5):e1006024. doi: 10.1371/journal.pgen.1006024. eCollection 2016 May.

45.

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

Lun AT, Bach K, Marioni JC.

Genome Biol. 2016 Apr 27;17:75. doi: 10.1186/s13059-016-0947-7.

46.

Beyond comparisons of means: understanding changes in gene expression at the single-cell level.

Vallejos CA, Richardson S, Marioni JC.

Genome Biol. 2016 Apr 15;17:70. doi: 10.1186/s13059-016-0930-3.

47.

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. 2016 Mar 24;165(1):61-74. doi: 10.1016/j.cell.2016.01.047.

48.

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 Biol. 2016 Feb 17;17:29. doi: 10.1186/s13059-016-0888-1.

49.

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.

Nat Commun. 2016 Jan 11;7:10415. doi: 10.1038/ncomms10415. No abstract available.

50.

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.

Sci Rep. 2015 Dec 16;5:18178. doi: 10.1038/srep18178.

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