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Items: 1 to 20 of 56

1.

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

L Lun AT, Bach K, Marioni JC.

Genome Biol. 2016 Apr 27;17(1):75. doi: 10.1186/s13059-016-0947-7.

2.

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(1):70. doi: 10.1186/s13059-016-0930-3.

3.

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.

Goolam M, Scialdone A, Graham SJ, 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.

4.

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(1):29. doi: 10.1186/s13059-016-0888-1.

5.

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.

6.

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.

7.

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

Kim JK, Kolodziejczyk AA, Illicic T, Teichmann SA, Marioni JC.

Nat Commun. 2015 Oct 22;6:8687. doi: 10.1038/ncomms9687.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

PMID:
26000846
15.

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
16.

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
17.

Testing the mean matrix in high-dimensional transposable data.

Touloumis A, Tavaré S, Marioni JC.

Biometrics. 2015 Mar;71(1):157-66. doi: 10.1111/biom.12257. Epub 2015 Jan 23.

PMID:
25615804
18.

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
19.

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.

20.

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.

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