Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 84

1.

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.

2.

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 Apr 2. doi: 10.1038/nbt.4091. [Epub ahead of print]

PMID:
29608177
3.

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
4.

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.

5.

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 Jan 24. doi: 10.1093/molbev/msx336. [Epub ahead of print]

PMID:
29373712
6.

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.

PMID:
29311656
7.

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.

8.

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.

9.

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.

PMID:
29186120
10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

PMID:
28813177
16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

PMID:
28504682
21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.
36.

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. 2015 Oct 1;17(4):471-85. doi: 10.1016/j.stem.2015.09.011.

37.

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 Biol. 2015 Sep 21;16:201. doi: 10.1186/s13059-015-0749-3.

38.

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. 2015 Sep 4;10(9):e0137367. doi: 10.1371/journal.pone.0137367. eCollection 2015.

39.

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. 2015 Sep 1;85:54-61. doi: 10.1016/j.ymeth.2015.06.021. Epub 2015 Jul 2.

40.

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.

Sci Rep. 2015 Jun 25;5:11487. doi: 10.1038/srep11487.

41.

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.

Vallejos CA, Marioni JC, Richardson S.

PLoS Comput Biol. 2015 Jun 24;11(6):e1004333. doi: 10.1371/journal.pcbi.1004333. eCollection 2015 Jun.

42.

The technology and biology of single-cell RNA sequencing.

Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA.

Mol Cell. 2015 May 21;58(4):610-20. doi: 10.1016/j.molcel.2015.04.005. Review.

43.

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.

Nat Biotechnol. 2015 May;33(5):503-9. doi: 10.1038/nbt.3209. Epub 2015 Apr 13.

PMID:
25867922
44.

Computational and analytical challenges in single-cell transcriptomics.

Stegle O, Teichmann SA, Marioni JC.

Nat Rev Genet. 2015 Mar;16(3):133-45. doi: 10.1038/nrg3833. Epub 2015 Jan 28. Review.

PMID:
25628217
45.

Testing the mean matrix in high-dimensional transposable data.

Touloumis A, Tavaré S, Marioni JC.

Biometrics. 2015 Mar;71(1):157-166. doi: 10.1111/biom.12257. Epub 2015 Jan 23.

PMID:
25615804
46.

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.

Nat Biotechnol. 2015 Feb;33(2):155-60. doi: 10.1038/nbt.3102. Epub 2015 Jan 19.

PMID:
25599176
47.

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 Rep. 2014 Dec 24;9(6):1990-2000. doi: 10.1016/j.celrep.2014.11.034. Epub 2014 Dec 12.

48.

Single Cell Genomics meeting in Stockholm: from single cells to cell types.

Scialdone A, Achim K, Marioni JC.

Genome Biol. 2014 Oct 18;15(10):496. doi: 10.1186/s13059-014-0496-x.

49.

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 Res. 2015 Jan 1;75(1):194-202. doi: 10.1158/0008-5472.CAN-13-3131. Epub 2014 Nov 18.

50.

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. 2014 Oct 3;3:e02626. doi: 10.7554/eLife.02626.

Supplemental Content

Loading ...
Support Center