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Items: 1 to 20 of 143

1.

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

Lun AT, Smyth GK.

F1000Res. 2015 Oct 16;4:1080. doi: 10.12688/f1000research.7016.1. eCollection 2015.

2.

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 Jan 18. doi: 10.1038/ni.3348. [Epub ahead of print]

PMID:
26779600
3.

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.

PMID:
26728554
4.

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, Abeysekra 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. [Epub ahead of print]

5.

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.

PMID:
26595889
6.

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

Lun AT, Smyth GK.

Nucleic Acids Res. 2015 Nov 17. pii: gkv1191. [Epub ahead of print]

7.

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

Coffey MJ, Sleebs BE, Uboldi AD, Garnham AL, 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. [Epub ahead of print]

8.

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). 2015 Oct 26. doi: 10.1038/ijo.2015.223. [Epub ahead of print]

PMID:
26499445
9.

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.

10.

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.

11.

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
12.

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.

13.

Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits.

Pal B, Chen Y, Bert A, Hu Y, Sheridan JM, Beck T, Shi W, Satterley K, Jamieson P, Goodall GJ, Lindeman GJ, Smyth GK, Visvader JE.

Breast Cancer Res. 2015 Jun 18;17:85. doi: 10.1186/s13058-015-0585-0.

14.

Distinctive pro-inflammatory gene signatures induced in articular chondrocytes by oncostatin M and IL-6 are regulated by Suppressor of Cytokine Signaling-3.

Liu X, Liu R, Croker BA, Lawlor KE, Smyth GK, Wicks IP.

Osteoarthritis Cartilage. 2015 Oct;23(10):1743-54. doi: 10.1016/j.joca.2015.05.011. Epub 2015 Jun 2.

PMID:
26045176
15.

Early lineage priming by trisomy of erg leads to myeloproliferation in a down syndrome model.

Ng AP, Hu Y, Metcalf D, Hyland CD, Ierino H, Phipson B, Wu D, Baldwin TM, Kauppi M, Kiu H, Di Rago L, Hilton DJ, Smyth GK, Alexander WS.

PLoS Genet. 2015 May 14;11(5):e1005211. doi: 10.1371/journal.pgen.1005211. eCollection 2015 May.

16.

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses.

Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME, Asselin-Labat ML, Smyth GK, Ritchie ME.

Nucleic Acids Res. 2015 Sep 3;43(15):e97. doi: 10.1093/nar/gkv412. Epub 2015 Apr 29.

17.

MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo.

Sheikh BN, Downer NL, Phipson B, Vanyai HK, Kueh AJ, McCarthy DJ, Smyth GK, Thomas T, Voss AK.

Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):5437-42. doi: 10.1073/pnas.1422872112. Epub 2015 Apr 14.

18.

Erratum: The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue-resident regulatory T cells.

Vasanthakumar A, Moro K, Xin A, Liao Y, Gloury R, Kawamoto S, Fagarasan S, Mielke LA, Afshar-Sterle S, Masters SL, Nakae S, Saito H, Wentworth JM, Li P, Liao W, Leonard WJ, Smyth GK, Shi W, Nutt SL, Koyasu S, Kallies A.

Nat Immunol. 2015 May;16(5):544. doi: 10.1038/ni0515-544d. No abstract available.

PMID:
25898200
19.

Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells.

Shi W, Liao Y, Willis SN, Taubenheim N, Inouye M, Tarlinton DM, Smyth GK, Hodgkin PD, Nutt SL, Corcoran LM.

Nat Immunol. 2015 Jun;16(6):663-73. doi: 10.1038/ni.3154. Epub 2015 Apr 20.

PMID:
25894659
20.

A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1.

Sheridan JM, Ritchie ME, Best SA, Jiang K, Beck TJ, Vaillant F, Liu K, Dickins RA, Smyth GK, Lindeman GJ, Visvader JE.

BMC Cancer. 2015 Apr 3;15:221. doi: 10.1186/s12885-015-1187-z.

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