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Items: 35

1.

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 Biol. 2019 Mar 22;20(1):63. doi: 10.1186/s13059-019-1662-y.

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.

Transcription Factor PU.1 Promotes Conventional Dendritic Cell Identity and Function via Induction of Transcriptional Regulator DC-SCRIPT.

Chopin M, Lun AT, Zhan Y, Schreuder J, Coughlan H, D'Amico A, Mielke LA, Almeida FF, Kueh AJ, Dickins RA, Belz GT, Naik SH, Lew AM, Bouillet P, Herold MJ, Smyth GK, Corcoran LM, Nutt SL.

Immunity. 2019 Jan 15;50(1):77-90.e5. doi: 10.1016/j.immuni.2018.11.010. Epub 2019 Jan 2.

PMID:
30611612
4.

Transcription-factor-mediated supervision of global genome architecture maintains B cell identity.

Johanson TM, Lun ATL, Coughlan HD, Tan T, Smyth GK, Nutt SL, Allan RS.

Nat Immunol. 2018 Nov;19(11):1257-1264. doi: 10.1038/s41590-018-0234-8. Epub 2018 Oct 15.

PMID:
30323344
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.

6.

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.

7.

iSEE: Interactive SummarizedExperiment Explorer.

Rue-Albrecht K, Marini F, Soneson C, Lun ATL.

F1000Res. 2018 Jun 14;7:741. doi: 10.12688/f1000research.14966.1. eCollection 2018.

8.

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.

9.

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development.

Johanson TM, Coughlan HD, Lun ATL, Bediaga NG, Naselli G, Garnham AL, Harrison LC, Smyth GK, Allan RS.

PLoS Genet. 2018 Jun 8;14(6):e1007431. doi: 10.1371/journal.pgen.1007431. eCollection 2018 Jun.

10.

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.

11.

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types.

Lun ATL, Pagès H, Smith ML.

PLoS Comput Biol. 2018 May 3;14(5):e1006135. doi: 10.1371/journal.pcbi.1006135. eCollection 2018 May.

12.

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.

13.

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.

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.

No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data.

Lun ATL, Smyth GK.

Stat Appl Genet Mol Biol. 2017 Apr 25;16(2):83-93. doi: 10.1515/sagmb-2017-0010.

PMID:
28599403
16.

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.

17.

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.

18.

A non-canonical function of Ezh2 preserves immune homeostasis.

Vasanthakumar A, Xu D, Lun AT, Kueh AJ, van Gisbergen KP, Iannarella N, Li X, Yu L, Wang D, Williams BR, Lee SC, Majewski IJ, Godfrey DI, Smyth GK, Alexander WS, Herold MJ, Kallies A, Nutt SL, Allan RS.

EMBO Rep. 2017 Apr;18(4):619-631. doi: 10.15252/embr.201643237. Epub 2017 Feb 21.

19.

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.

McCarthy DJ, Campbell KR, Lun AT, Wills QF.

Bioinformatics. 2017 Apr 15;33(8):1179-1186. doi: 10.1093/bioinformatics/btw777.

20.

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.

21.

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.

Chen Y, Lun AT, Smyth GK.

Version 2. F1000Res. 2016 Jun 20 [revised 2016 Jan 1];5:1438. doi: 10.12688/f1000research.8987.2. eCollection 2016.

22.

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments.

Lun AT, Perry M, Ing-Simmons E.

Version 2. F1000Res. 2016 May 20 [revised 2016 Jan 1];5:950. doi: 10.12688/f1000research.8759.2. eCollection 2016.

23.

RUNX2 Mediates Plasmacytoid Dendritic Cell Egress from the Bone Marrow and Controls Viral Immunity.

Chopin M, Preston SP, Lun ATL, Tellier J, Smyth GK, Pellegrini M, Belz GT, Corcoran LM, Visvader JE, Wu L, Nutt SL.

Cell Rep. 2016 Apr 26;15(4):866-878. doi: 10.1016/j.celrep.2016.03.066. Epub 2016 Apr 14.

24.

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.

25.

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.

Taberlay PC, Achinger-Kawecka J, Lun AT, Buske FA, Sabir K, Gould CM, Zotenko E, Bert SA, Giles KA, Bauer DC, Smyth GK, Stirzaker C, O'Donoghue SI, Clark SJ.

Genome Res. 2016 Jun;26(6):719-31. doi: 10.1101/gr.201517.115. Epub 2016 Apr 6.

26.

It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR.

Lun AT, Chen Y, Smyth GK.

Methods Mol Biol. 2016;1418:391-416. doi: 10.1007/978-1-4939-3578-9_19.

PMID:
27008025
27.

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data.

Lun AT, Smyth GK.

Version 2. F1000Res. 2015 Oct 16 [revised 2016 Jan 1];4:1080. doi: 10.12688/f1000research.7016.2. eCollection 2015.

28.

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows.

Lun AT, Smyth GK.

Nucleic Acids Res. 2016 Mar 18;44(5):e45. doi: 10.1093/nar/gkv1191. Epub 2015 Nov 17.

29.

Transcriptome and H3K27 tri-methylation profiling of Ezh2-deficient lung epithelium.

Holik AZ, Galvis LA, Lun AT, Ritchie ME, Asselin-Labat ML.

Genom Data. 2015 Jul 16;5:346-51. doi: 10.1016/j.gdata.2015.07.006. eCollection 2015 Sep.

30.

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data.

Lun AT, Smyth GK.

BMC Bioinformatics. 2015 Aug 19;16:258. doi: 10.1186/s12859-015-0683-0.

31.

Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung.

Galvis LA, Holik AZ, Short KM, Pasquet J, Lun AT, Blewitt ME, Smyth IM, Ritchie ME, Asselin-Labat ML.

Development. 2015 Apr 15;142(8):1458-69. doi: 10.1242/dev.122077. Epub 2015 Mar 19.

32.

EGF-mediated induction of Mcl-1 at the switch to lactation is essential for alveolar cell survival.

Fu NY, Rios AC, Pal B, Soetanto R, Lun AT, Liu K, Beck T, Best SA, Vaillant F, Bouillet P, Strasser A, Preiss T, Smyth GK, Lindeman GJ, Visvader JE.

Nat Cell Biol. 2015 Apr;17(4):365-75. doi: 10.1038/ncb3117. Epub 2015 Mar 2.

PMID:
25730472
33.

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly.

Lun AT, Smyth GK.

Nucleic Acids Res. 2014 Jun;42(11):e95. doi: 10.1093/nar/gku351. Epub 2014 May 22.

34.

Mass trees: a new phylogenetic approach and algorithm to chart evolutionary history with mass spectrometry.

Lun AT, Swaminathan K, Wong JW, Downard KM.

Anal Chem. 2013 Jun 4;85(11):5475-82. doi: 10.1021/ac4005875. Epub 2013 May 21.

PMID:
23647083
35.

FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry.

Lun AT, Wong JW, Downard KM.

BMC Bioinformatics. 2012 Aug 20;13:208. doi: 10.1186/1471-2105-13-208.

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