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Items: 1 to 20 of 152

1.

Murine Oncostatin M acts via Leukemia Inhibitory Factor Receptor to phosphorylate STAT3 but not STAT1, an effect that protects bone mass.

Walker EC, Johnson RW, Hu Y, Brennan HJ, Poulton IJ, Zhang JG, Jenkins BJ, Smyth GK, Nicola NA, Sims NA.

J Biol Chem. 2016 Aug 18. pii: jbc.M116.748483. [Epub ahead of print]

2.

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.

F1000Res. 2016 Jun 20;5:1438. doi: 10.12688/f1000research.8987.1. eCollection 2016.

3.

Haemopedia: An Expression Atlas of Murine Hematopoietic Cells.

de Graaf CA, Choi J, Baldwin TM, Bolden JE, Fairfax KA, Robinson AJ, Biben C, Morgan C, Ramsay K, Ng AP, Kauppi M, Kruse EA, Sargeant TJ, Seidenman N, D'Amico A, D'Ombrain MC, Lucas EC, Koernig S, Baz Morelli A, Wilson MJ, Dower SK, Williams B, Heazlewood SY, Hu Y, Nilsson SK, Wu L, Smyth GK, Alexander WS, Hilton DJ.

Stem Cell Reports. 2016 Aug 3. pii: S2213-6711(16)30131-X. doi: 10.1016/j.stemcr.2016.07.007. [Epub ahead of print]

4.

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.

Law CW, Alhamdoosh M, Su S, Smyth GK, Ritchie ME.

F1000Res. 2016 Jun 17;5:1408. doi: 10.12688/f1000research.9005.1. eCollection 2016.

5.

RANK ligand as a potential target for breast cancer prevention in BRCA1-mutation carriers.

Nolan E, Vaillant F, Branstetter D, Pal B, Giner G, Whitehead L, Lok SW, Mann GB; Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), Rohrbach K, Huang LY, Soriano R, Smyth GK, Dougall WC, Visvader JE, Lindeman GJ.

Nat Med. 2016 Aug;22(8):933-9. doi: 10.1038/nm.4118. Epub 2016 Jun 20.

PMID:
27322743
6.

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

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

Cell Rep. 2016 Apr 13. pii: S2211-1247(16)30355-2. doi: 10.1016/j.celrep.2016.03.066. [Epub ahead of print]

7.

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.

PMID:
27053337
8.

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
9.

A molecular threshold for effector CD8(+) T cell differentiation controlled by transcription factors Blimp-1 and T-bet.

Xin A, Masson F, Liao Y, Preston S, Guan T, Gloury R, Olshansky M, Lin JX, Li P, Speed TP, Smyth GK, Ernst M, Leonard WJ, Pellegrini M, Kaech SM, Nutt SL, Shi W, Belz GT, Kallies A.

Nat Immunol. 2016 Apr;17(4):422-32. doi: 10.1038/ni.3410. Epub 2016 Mar 7.

PMID:
26950239
10.

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 11];4:1080. doi: 10.12688/f1000research.7016.2. eCollection 2015.

11.

Blimp-1 controls plasma cell function through the regulation of immunoglobulin secretion and the unfolded protein response.

Tellier J, Shi W, Minnich M, Liao Y, Crawford S, Smyth GK, Kallies A, Busslinger M, Nutt SL.

Nat Immunol. 2016 Mar;17(3):323-30. doi: 10.1038/ni.3348. Epub 2016 Jan 18.

PMID:
26779600
12.

Acute myeloid leukemia requires Hhex to enable PRC2-mediated epigenetic repression of Cdkn2a.

Shields BJ, Jackson JT, Metcalf D, Shi W, Huang Q, Garnham AL, Glaser SP, Beck D, Pimanda JE, Bogue CW, Smyth GK, Alexander WS, McCormack MP.

Genes Dev. 2016 Jan 1;30(1):78-91. doi: 10.1101/gad.268425.115.

13.

TRAF2 regulates TNF and NF-κB signalling to suppress apoptosis and skin inflammation independently of Sphingosine kinase 1.

Etemadi N, Chopin M, Anderton H, Tanzer MC, Rickard JA, Abeysekera W, Hall C, Spall SK, Wang B, Xiong Y, Hla T, Pitson SM, Bonder CS, Wong WW, Ernst M, Smyth GK, Vaux DL, Nutt SL, Nachbur U, Silke J.

Elife. 2015 Dec 23;4. pii: e10592. doi: 10.7554/eLife.10592.

14.

Complementarity and redundancy of IL-22-producing innate lymphoid cells.

Rankin LC, Girard-Madoux MJ, Seillet C, Mielke LA, Kerdiles Y, Fenis A, Wieduwild E, Putoczki T, Mondot S, Lantz O, Demon D, Papenfuss AT, Smyth GK, Lamkanfi M, Carotta S, Renauld JC, Shi W, Carpentier S, Soos T, Arendt C, Ugolini S, Huntington ND, Belz GT, Vivier E.

Nat Immunol. 2016 Feb;17(2):179-86. doi: 10.1038/ni.3332. Epub 2015 Nov 30.

15.

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.

16.

An aspartyl protease defines a novel pathway for export of Toxoplasma proteins into the host cell.

Coffey MJ, Sleebs BE, Uboldi AD, Garnham A, Franco M, Marino ND, Panas MW, Ferguson DJ, Enciso M, O'Neill MT, Lopaticki S, Stewart RJ, Dewson G, Smyth GK, Smith BJ, Masters SL, Boothroyd JC, Boddey JA, Tonkin CJ.

Elife. 2015 Nov 18;4. pii: e10809. doi: 10.7554/eLife.10809.

17.

GM3 ganglioside and phosphatidylethanolamine-containing lipids are adipose tissue markers of insulin resistance in obese women.

Wentworth JM, Naselli G, Ngui K, Smyth GK, Liu R, O'Brien PE, Bruce C, Weir J, Cinel M, Meikle PJ, Harrison LC.

Int J Obes (Lond). 2016 Apr;40(4):706-13. doi: 10.1038/ijo.2015.223. Epub 2015 Oct 26.

PMID:
26499445
18.

Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells.

Shi W, Man K, Smyth GK, Nutt SL, Kallies A.

Genom Data. 2014 Nov 1;2:396-8. doi: 10.1016/j.gdata.2014.10.019. eCollection 2014 Dec.

19.

Transcriptional profiling of the postnatal brain of the Ts1Cje mouse model of Down syndrome.

Tan KL, Ling KH, Hewitt CA, Cheah PS, Simpson K, Gordon L, Pritchard MA, Smyth GK, Thomas T, Scott HS.

Genom Data. 2014 Oct 2;2:314-7. doi: 10.1016/j.gdata.2014.09.009. eCollection 2014 Dec.

20.

Differential Gene Expression Profiling of Orbital Adipose Tissue in Thyroid Orbitopathy.

Khong JJ, Wang LY, Smyth GK, McNab AA, Hardy TG, Selva D, Llamas B, Jung CH, Sharma S, Burdon KP, Ebeling PR, Craig JE.

Invest Ophthalmol Vis Sci. 2015 Oct;56(11):6438-47. doi: 10.1167/iovs.15-17185.

PMID:
26444724
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