selected publications
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academic article
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Shi WLiao YTong LWu P-YPhan JHHassazadeh HRTong WWang MD. Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction.
Scientific Reports.
10:17925.
2020
Full text if available -
Sidwell TLiao YGarnham ALVasanthakumar AGloury RBlume JTeh PPChisanga DThelemann Cde Labastida Rivera FEngwerda CRCorcoran LKometani KKurosaki TSmyth GKShi WKallies A. Attenuation of TCR-induced transcription by Bach2 controls regulatory T cell differentiation and homeostasis.
Nature Communications.
11:1-17.
2020
Full text if available -
Utzschneider DTGabriel SSChisanga DGloury RGubser PMVasanthakumar AShi WKallies A. Early precursor T cells establish and propagate T cell exhaustion in chronic infection.
Nature Immunology.
21:1256-1266.
2020
Full text if available -
Vasanthakumar AChisanga DBlume JGloury RBritt KHenstridge DCZhan YTorres SVLiene SCollins NCao ESidwell TLi CSpallanzani RGLiao YBeavis PAGebhardt TTrevaskis NNutt SLZajac JDDavey RAFebbraio MAMathis DShi WKallies A. Sex-specific adipose tissue imprinting of regulatory T cells.
Nature.
579:581-585.
2020
Full text if available -
Fedele PLLiao YGong J-NYao Yvan Delft MFLow MSYTai LHerold MJJackson JTTeh CETan TO’Reilly LATellier JGrigoriadis GHuang DCSShi WNutt SLWillis SN. The transcription factor IRF4 represses proapoptotic BMF and BIM to licence multiple myeloma survival.
Leukemia.
2020
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Shields BJSlape CIVo NJackson JTPliego-Zamora ARanasinghe HShi WCurtis DJMcCormack MP. The NUP98-HOXD13 fusion oncogene induces thymocyte self-renewal via Lmo2/Lyl1.
Leukemia.
33:1868-1880.
2019
Full text if available -
Choi JBaldwin TMWong MBolden JEFairfax KALucas ECCole RBiben CMorgan CRamsay KANg APKauppi MCorcoran LMShi WWilson NWilson MJAlexander WSHilton DJde Graaf CA. Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans.
Nucleic Acids Research.
47:D780-D785.
2019
Full text if available -
Low MSYBrodie EJFedele PLLiao YGrigoriadis GStrasser AKallies AWillis SNTellier JShi WGabriel SO'Donnell KPitt CNutt SLTarlinton D. IRF4 Activity Is Required in Established Plasma Cells to Regulate Gene Transcription and Mitochondrial Homeostasis.
Cell Reports.
29:2634-2645.e5.
2019
Full text if available -
Mielke LALiao YClemens EBFirth MADuckworth BHuang QAlmeida FFChopin MKoay H-FBell CAHediyeh-Zadeh SPark SLRaghu DChoi JPutoczki TLHodgkin PDFranks AEMackay LKGodfrey DDavis MJXue H-HBryant VLKedzierska KShi WBelz GT. TCF-1 limits the formation of Tc17 cells via repression of the MAF-RORγt axis.
Journal of Experimental Medicine.
216:1682-1699.
2019
Full text if available -
Murphy CMuscat AAshley DMukaro VWest LLiao YChisanga DShi WCollins IBaron-Hay SPatil SLindeman GKhasraw M. Tailored NEOadjuvant epirubicin, cyclophosphamide and Nanoparticle Albumin-Bound paclitaxel for breast cancer: The phase II NEONAB trial—Clinical outcomes and molecular determinants of response.
PLoS ONE.
14.
2019
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Liao YSmyth GKShi W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads.
Nucleic Acids Research.
47.
2019
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Ly ALiao YPietrzak HIoannidis LJSidwell TGloury RDoerflinger MTriglia TQin RZGroom JRBelz GTGood-Jacobson KLShi WKallies AHansen DS. Transcription Factor T-bet in B Cells Modulates Germinal Center Polarization and Antibody Affinity Maturation in Response to Malaria.
Cell Reports.
29:2257-2269.e6.
2019
Full text if available -
Neumann CBlume JRoy UTeh PPVasanthakumar ABeller ALiao YHeinrich FArenzana TLHackney JAEidenschenk CGálvez EJCStehle CHeinz GAMaschmeyer PSidwell THu YAmsen DRomagnani CChang HDKruglov AMashreghi MFShi WStrowig TRutz SKallies AScheffold A. c-Maf-dependent Treg cell control of intestinal TH17 cells and IgA establishes host–microbiota homeostasis.
Nature Immunology.
20:471-481.
2019
Full text if available -
Avery DTKane ANguyen TLau ANguyen ALenthall HPayne KShi WBrigden HFrench EBier JHermes JRZahra DSewell WAButt DElliott MBoztug KMeyts IChoo SHsu PWong MBerglund LJGray PO’Sullivan MCole THolland SMMa CSBurkhart CCorcoran LMPhan TGBrink RUzel GDeenick EKTangye SG. Germline-activating mutations in PIK3CD compromise B cell development and function.
Journal of Experimental Medicine.
215:2073-2095.
2018
Full text if available -
Almeida FFTognarelli SMarçais AKueh AJFriede MELiao YWillis SNLuong KFaure FMercier FEGalluso JFirth MNarni-Mancinelli ERais BScadden DTSpallotta FWeil SGiannattasio AKalensee FZöller THuntington NDSchleicher UChiocchetti AGUgolini SHerold MJShi WKoch JSteinle AVivier EWalzer TBelz GTUllrich E. A point mutation in the Ncr1 signal peptide impairs the development of innate lymphoid cell subsets.
OncoImmunology.
7.
2018
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Davenport AJCross RSWatson KALiao YShi WPrince HMBeavis PATrapani JAKershaw MHRitchie DSDarcy PKNeeson PJJenkins MR. Chimeric antigen receptor T cells form nonclassical and potent immune synapses driving rapid cytotoxicity.
Proceedings of the National Academy of Sciences of USA.
115:E2068-E2076.
2018
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Lee AYEwing ADEllrott KHu YHoulahan KEBare JCEspiritu SMGHuang VDang KChong ZCaloian CYamaguchi TNKellen MRChen KNorman TCFriend SHGuinney JStolovitzky GHaussler DMargolin AAStuart JMBoutros PCBarnes BDBirol IChen XChiu RCox AJDing LFritz MHYGrigoriev AHach FKawash JKKorbel JOKruglyak SLiao YMcPherson ANip KMRausch TSahinalp SCSarrafi ISaunders CTSchulz-Trieglaff OShaw RShi WSmith SDSong LWang DYe K. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.
Genome Biology: biology for the post-genomic era.
19:1-15.
2018
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Fedele PLWillis SNLiao YLow MSRautela JSegal DHGong JNHuntington NDShi WHuang DCSGrigoriadis GTellier JNutt SL. IMiDs prime myeloma cells for daratumumab-mediated cytotoxicity through loss of Ikaros and Aiolos.
Blood.
132:2166-2178.
2018
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Trezise SKarnowski AFedele PLMithraprabhu SLiao YD’costa KKueh AJHardy MPOwczarek CMHerold MJSpencer AShi WWillis SNNutt SLCorcoran LM. Mining the plasma cell transcriptome for novel cell surface proteins.
International Journal of Molecular Sciences.
19.
2018
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Marsman CLafouresse FLiao YBaldwin TMMielke LAHu YMack MHertzog PJde Graaf CAShi WGroom JR. Plasmacytoid dendritic cell heterogeneity is defined by CXCL10 expression following TLR7 stimulation.
Immunology and Cell Biology.
96:1083-1094.
2018
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Jackson JTShields BJShi WDi Rago LMetcalf DNicola NAMcCormack MP. Hhex Regulates Hematopoietic Stem Cell Self-Renewal and Stress Hematopoiesis via Repression of Cdkn2a.
Stem Cells.
35:1948-1957.
2017
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Kueh AJPal MTai LLiao YSmyth GKShi WHerold MJ. An update on using CRISPR/Cas9 in the one-cell stage mouse embryo for generating complex mutant alleles.
Cell Death and Differentiation.
24:1821-1822.
2017
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Dias SD'Amico ACretney ELiao YTellier JBruggeman CAlmeida FFLeahy JBelz GTSmyth GKShi WNutt SL. Effector Regulatory T Cell Differentiation and Immune Homeostasis Depend on the Transcription Factor Myb.
Immunity.
46:78-91.
2017
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Willis SNTellier JLiao YTrezise SLight AO'Donnell KGarrett-Sinha LAShi WTarlinton DMNutt SL. Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB.
Nature Communications.
8.
2017
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Vasanthakumar ALiao YTeh PPascutti MFOja AEGarnham ALGloury RTempany JCSidwell TCuadrado ETuijnenburg PKuijpers TWLalaoui NMielke LABryant VLHodgkin PDSilke JSmyth GKNolte MAShi WKallies A. The TNF Receptor Superfamily-NF-κB Axis Is Critical to Maintain Effector Regulatory T Cells in Lymphoid and Non-lymphoid Tissues.
Cell Reports.
20:2906-2920.
2017
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Man KGabriel SSLiao YGloury RPreston SHenstridge DCPellegrini MZehn DBerberich-Siebelt FFebbraio MAShi WKallies A. Transcription Factor IRF4 Promotes CD8+ T Cell Exhaustion and Limits the Development of Memory-like T Cells during Chronic Infection.
Immunity.
47:1129-1141.e5.
2017
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Delconte RBKolesnik TBDagley LFRautela JShi WPutz EMStannard KZhang J-GTeh CFirth MUshiki TAndoniou CEDegli-Esposti MASharp PPSanvitale CEInfusini GLiau NPDLinossi EMBurns CJCarotta SGray DHDSeillet CHutchinson DSBelz GTWebb AIAlexander WSLi SSBullock ANBabon JJSmyth MJNicholson SEHuntington ND. CIS is a potent checkpoint in NK cell–mediated tumor immunity.
Nature Immunology.
17:816-824.
2016
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Viant CRankin LCGirard-Madoux MJHSeillet CShi WSmyth MJBartholin LWalzer THuntington NDVivier EBelz GT. Transforming growth factor–β and Notch ligands act as opposing environmental cues in regulating the plasticity of type 3 innate lymphoid cells.
Science Signaling.
9:ra46-ra46.
2016
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Xin AMasson FLiao YPreston SGuan TGloury ROlshansky MLin J-XLi PSpeed TPSmyth GKErnst MLeonard WJPellegrini MKaech SMNutt SLShi WBelz GTKallies A. A molecular threshold for effector CD8(+) T cell differentiation controlled by transcription factors Blimp-1 and T-bet.
Nature Immunology.
17:422-432.
2016
Full text if available -
Shields BJJackson JTMetcalf DShi WHuang QGarnham ALGlaser SPBeck DPimanda JEBogue CWSmyth GKAlexander WSMcCormack MP. Acute myeloid leukemia requires Hhex to enable PRC2-mediated epigenetic repression ofCdkn2a.
Genes and Development.
30:78-91.
2016
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Tellier JShi WMinnich MLiao YCrawford SSmyth GKKallies ABusslinger MNutt SL. Blimp-1 controls plasma cell function through the regulation of immunoglobulin secretion and the unfolded protein response.
Nature Immunology.
17:323-330.
2016
Full text if available -
Rankin LCGirard-Madoux MJHSeillet CMielke LAKerdiles YFenis AWieduwild EPutoczki TMondot SLantz ODemon DPapenfuss ATSmyth GKLamkanfi MCarotta SRenauld J-CShi WCarpentier SSoos TArendt CUgolini SHuntington NDBelz GTVivier E. Complementarity and redundancy of IL-22-producing innate lymphoid cells.
Nature Immunology.
17:179-186.
2016
Full text if available -
Seillet CMielke LAAmann-Zalcenstein DBSu SGao JAlmeida FFShi WRitchie MENaik SHHuntington NDCarotta SBelz GT. Deciphering the innate lymphoid cell transcriptional program.
Cell Reports.
17:436-447.
2016
Full text if available -
Gloury RZotos DZuidscherwoude MMasson FLiao YHasbold JCorcoran LMHodgkin PDBelz GTShi WNutt SLTarlinton DMKallies A. Dynamic changes in Id3 and E-protein activity orchestrate germinal center and plasma cell development.
Journal of Experimental Medicine.
213:1095-1111.
2016
Full text if available -
Mackay LKMinnich MKragten NAMLiao YNota BSeillet CZaid AMan KPreston SFreestone DBraun AWynne-Jones EBehr FMStark RPellicci DGGodfrey DIBelz GTPellegrini MGebhardt TBusslinger MShi WCarbone FRVan Lier RAWKallies AVan Gisbergen KPJM. Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes.
Science.
352:459-463.
2016
Full text if available -
Delconte RBShi WSathe PUshiki TSeillet CMinnich MKolesnik TBRankin LCMielke LAZhang J-GBusslinger MSmyth MJHutchinson DSNutt SLNicholson SEAlexander WSCorcoran LMVivier EBelz GTCarotta SHuntington ND. The helix-loop-helix protein Id2 governs NK cell fate by tuning their sensitivity to interleukin-15.
Immunity.
44:103-115.
2016
Full text if available -
Ritchie MEPhipson BWu DHu YLaw CWShi WSmyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies.
Nucleic Acids Research.
43:e47-e47.
2015
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Jackson JTNasa CShi WHuntington NDBogue CWAlexander WSMcCormack MP. A crucial role for the homeodomain transcription factor Hhex in lymphopoiesis.
Blood.
125:803-814.
2015
Full text if available -
Froldi FSzuperak MWeng C-FShi WPapenfuss ATCheng LY. The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells.
Genes and Development.
29:129-143.
2015
Full text if available -
Kraakman MJKammoun HLAllen TLDeswaerte VHenstridge DCEstevez EMatthews VBNeill BWhite DAMurphy AJPeijs LYang CRisis SBruce CRDu X-JBobik ALee-Young RSKingwell BAVasanthakumar AShi WKallies ALancaster GIRose-John SFebbraio MA. Blocking IL-6 trans-signaling prevents high-fat diet-induced adipose tissue macrophage recruitment but does not improve insulin resistance.
Cell Metabolism.
21:403-416.
2015
Full text if available -
Pal BChen YBert AHu YSheridan JMBeck TShi WSatterley KJamieson PGoodall GJLindeman GJSmyth GKVisvader JE. Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits.
Breast Cancer Research.
17.
2015
Full text if available -
Vasanthakumar AMoro KXin ALiao YGloury RKawamoto SFagarasan SMielke LAAfshar-Sterle SMasters SLNakae SSaito HWentworth JMLi PLiao WLeonard WJSmyth GKShi WNutt SLKoyasu SKallies A. The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue–resident regulatory T cells.
Nature Immunology.
16:276-285.
2015
Full text if available -
Shi WLiao YWillis SNTaubenheim NInouye MTarlinton DMSmyth GKHodgkin PDNutt SLCorcoran LM. Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells.
Nature Immunology.
16:663-673.
2015
Full text if available -
Shi WMan KSmyth GKNutt SLKallies A. Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells.
Genomics Data.
2:396-398.
2014
Full text if available -
Holmes MLHuntington NDThong RPLBrady JHayakawa YAndoniou CEFleming PShi WSmyth GKDegli‐Esposti MABelz GTKallies ACarotta SSmyth MJNutt SL. Peripheral natural killer cell maturation depends on the transcription factor Aiolos.
The EMBO Journal.
33:2721-2734.
2014
Full text if available -
Potts KSSargeant TJMarkham JFShi WBiben CJosefsson ECWhitehead LWRogers KLLiakhovitskaia ASmyth GKKile BTMedvinsky AAlexander WSHilton DJTaoudi S. A lineage of diploid platelet-forming cells precedes polyploid megakaryocyte formation in the mouse embryo.
Blood.
124:2725-2729.
2014
Full text if available -
Li SŁabaj PPZumbo PSykacek PShi WShi LPhan JWu P-YWang MWang CThierry-Mieg DThierry-Mieg JKreil DPMason CE. Detecting and correcting systematic variation in large-scale RNA sequencing data.
Nature Biotechnology.
32:888-895.
2014
Full text if available -
Chevrier SEmslie DShi WKratina TWellard CKarnowski AErikci ESmyth GKChowdhury KTarlinton DCorcoran LM. The BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity.
Journal of Experimental Medicine.
211:827-840.
2014
Full text if available -
Willis SNGood-Jacobson KLCurtis JLight ATellier JShi WSmyth GKTarlinton DMBelz GTCorcoran LMKallies ANutt SL. Transcription Factor IRF4 Regulates Germinal Center Cell Formation through a B Cell–Intrinsic Mechanism.
Journal of Immunology.
192:3200-3206.
2014
Full text if available -
Su ZLabaj PPLi SThierry-Mieg JThierry-Mieg DShi WWang CSchroth GPSetterquist RAThompson JFJones WDXiao WXu WJensen RVKelly RXu JConesa AFurlanello CGao HHong HJafari NLetovsky SLiao YLu FOakeley EJPeng ZPraul CASantoyo-Lopez JScherer AShi TSmyth GKStaedtler FSykacek PTan X-XThompson EAVandesompele JWang MDWang JWolfinger RDZavadil JAuerbach SSBao WBinder HBlomquist TBrilliant MHBushel PRCain WCatalano JGChang C-WChen TChen GChen RChierici MChu T-MClevert D-ADeng YDerti ADevanarayan VDong ZDopazo JDu TFang HFang YFasold MFernandez AFischer MFurio-Tari PFuscoe JCCaiment FGaj SGandara JGao HGe WGondo YGong BGong MGong ZGreen BGuo CGuo LGuo L-WHadfield JHellemans JHochreiter SJia MJian MJohnson CDKay SKleinjans JLababidi SLevy SLi Q-ZLi LLi LLi PLi YLi HLi JLi SLin SMLopez FJLu XLuo HMa XMeehan JMegherbi DBMei NMu BNing BPandey APerez-Florido JPerkins RGPeters RPhan JHPirooznia MQian FQing TRainbow LRocca-Serra PSambourg LSansone S-ASchwartz SShah RShen JSmith TMStegle OStralis-Pavese NStupka ESuzuki YSzkotnicki LTTinning MTu Bvan Deft JVela-Boza AVenturini EWalker SJWan LWang WWang JWang JWieben EDWilley JCWu P-YXuan JYang YYe ZYin YYu YYuan Y-CZhang JZhang KKZhang WZhang WZhang YZhao CZheng YZhou YZumbo PTong WKreil DPMason CEShi L. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
Nature Biotechnology.
32:903-914.
2014
Full text if available -
Munro SALund SPPine PSBinder HClevert DAConesa ADopazo JFasold MHochreiter SHong HJafari NKreil DPŁabaj PPLi SLiao YLin SMMeehan JMason CESantoyo-Lopez JSetterquist RAShi LShi WSmyth GKStralis-Pavese NSu ZTong WWang CWang JXu JYe ZYang YYu YSalit M. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.
Nature Communications.
5.
2014
Full text if available -
Liao YSmyth GKShi W. FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
Bioinformatics.
30:923-930.
2014
Full text if available -
Corcoran LEmslie DKratina TShi WHirsch STaubenheim NChevrier S. Oct2 and Obf1 as Facilitators of B:T Cell Collaboration during a Humoral Immune Response.
Frontiers in Immunology.
5.
2014
Full text if available -
Liu GJCimmino LJude JGHu YWitkowski MTMcKenzie MDKartal-Kaess MBest SATuohey LLiao YShi WMullighan CGFarrar MANutt SLSmyth GKZuber JDickins RA. Pax5 loss imposes a reversible differentiation block in B-progenitor acute lymphoblastic leukemia.
Genes and Development.
28:1337-1350.
2014
Full text if available -
Dagley LFWhite CALiao YShi WSmyth GKOrian JMEmili APurcell AW. Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain.
Proteomics.
14:241-261.
2014
Full text if available -
Carotta SWillis SNHasbold JInouye MPang SHMEmslie DLight AChopin MShi WWang HMorse HCTarlinton DMCorcoran LMHodgkin PDNutt SL. The transcription factors IRF8 and PU.1 negatively regulate plasma cell differentiation.
Journal of Experimental Medicine.
211:2169-2181.
2014
Full text if available -
Law CWChen YShi WSmyth GK. voom: precision weights unlock linear model analysis tools for RNA-seq read counts.
Genome Biology: biology for the post-genomic era.
15:R29-R29.
2014
Full text if available -
Li DCai WGu RZhang YZhang HTang KXu PKatirai FShi WWang LHuang THuang B. Th17 cell plays a role in the pathogenesis of Hashimoto's thyroiditis in patients.
Clinical Immunology.
149:411-420.
2013
Full text if available -
Man KMiasari MShi WXin AHenstridge DCPreston SPellegrini MBelz GTSmyth GKFebbraio MANutt SLKallies A. The transcription factor IRF4 is essential for TCR affinity–mediated metabolic programming and clonal expansion of T cells.
Nature Immunology.
14:1155-1165.
2013
Full text if available -
McCormack MPShields BJJackson JTNasa CShi WSlater NJTremblay CSRabbitts THCurtis DJ. Requirement for Lyl1 in a model of Lmo2-driven early T-cell precursor ALL.
Blood.
122:2093-2103.
2013
Full text if available -
Bolden JEShi WJankowski KKan C-YCluse LMartin BPMacKenzie KLSmyth GKJohnstone RW. HDAC inhibitors induce tumor-cell-selective pro-apoptotic transcriptional responses.
Cell Death and Disease.
4:e519-e519.
2013
Full text if available -
Pal BBouras TShi WVaillant FSheridan JMFu NBreslin KJiang KRitchie MEYoung MLindeman GJSmyth GKVisvader JE. Global Changes in the mammary epigenome are induced by hormonal cues and coordinated by Ezh2.
Cell Reports.
3:411-426.
2013
Full text if available -
Liao YSmyth GKShi W. The Subread aligner: Fast, accurate and scalable read mapping by seed-and-vote.
Nucleic Acids Research.
41.
2013
Full text if available -
Tang JZCarmichael CLShi WMetcalf DNg APHyland CDJenkins NACopeland NGHowell VMZhao ZJSmyth GKKile BTAlexander WS. Transposon mutagenesis reveals cooperation of ETS family transcription factors with signaling pathways in erythro-megakaryocytic leukemia.
Proceedings of the National Academy of Sciences of USA.
110:6091-6096.
2013
Full text if available -
Asselin-Labat M-LSutherland KDVaillant FGyorki DEWu DHolroyd SBreslin KWard TShi WBath MLDeb SFox SBSmyth GKLindeman GJVisvader JE. Gata-3 Negatively Regulates the Tumor-Initiating Capacity of Mammary Luminal Progenitor Cells and Targets the Putative Tumor Suppressor Caspase-14.
Molecular and Cellular Biology.
31:4609-4622.
2011
Full text if available -
Campbell DJZhang YKelly DJGilbert REMcCarthy DJShi WSmyth GK. Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart.
Clinical and Experimental Pharmacology and Physiology.
38:623-631.
2011
Full text if available -
Lahoud MHAhmet FKitsoulis SWan SSVremec DLee C-NPhipson BShi WSmyth GKLew AMKato YMueller SNDavey GMHeath WRShortman KCaminschi I. Targeting Antigen to Mouse Dendritic Cells via Clec9A Induces Potent CD4 T Cell Responses Biased toward a Follicular Helper Phenotype.
Journal of Immunology.
187:842-850.
2011
Full text if available -
Ritchie MEDunning MJSmith MLShi WLynch AG. BeadArray Expression Analysis Using Bioconductor.
PLoS Computational Biology.
7:e1002276-e1002276.
2011
Full text if available -
Cretney EXin AShi WMinnich MMasson FMiasari MBelz GTSmyth GKBusslinger MNutt SLKallies A. The transcription factors Blimp-1 and IRF4 jointly control the differentiation and function of effector regulatory T cells.
Nature Immunology.
12:304-313.
2011
Full text if available -
Shi WOshlack ASmyth GK. Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips.
Nucleic Acids Research.
38:e204-e204.
2010
Full text if available -
Shi Wde Graaf CAKinkel SAAchtman AHBaldwin TSchofield LScott HSHilton DJSmyth GK. Estimating the proportion of microarray probes expressed in an RNA sample.
Nucleic Acids Research.
38:2168-2176.
2010
Full text if available -
Shi WBanerjee ARitchie MEGerondakis SSmyth GK. Illumina WG-6 BeadChip strips should be normalized separately.
BMC Bioinformatics.
10:372-372.
2009
Full text if available -
Hou JShi WLi GZhou W. An effective non-parametric method for globally clustering genes from expression profiles.
Medical and Biological Engineering and Computing.
45:1175-1185.
2007
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Shi WZhou WXu D. Identifying cis-regulatory elements by statistical analysis and phylogenetic footprinting and analyzing their coexistence and related gene ontology.
Physiological Genomics.
31:374-384.
2007
Full text if available
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Shi WLiao YTong LWu P-YPhan JHHassazadeh HRTong WWang MD. Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction.
Scientific Reports.
10:17925.
2020
-
conference paper
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Masson FXin ALiao YPreston SGuan TGloury ROlshansky MLin J-XLi PSpeed TPSmyth GKErnst MLeonard WJPellegrini MKaech SNutt SLShi WBelz GTKallies A. A combinatorial threshold model for effector differentiation of CD8(+) T cells mediated by Blimp-1 and T-bet.
European Journal of Immunology.
5-5.
2016
-
Masson FXin ALiao YPreston SGuan TGloury ROlshansky MLin J-XLi PSpeed TPSmyth GKErnst MLeonard WJPellegrini MKaech SNutt SLShi WBelz GTKallies A. A combinatorial threshold model for effector differentiation of CD8(+) T cells mediated by Blimp-1 and T-bet.
European Journal of Immunology.
5-5.
2016
-
erratum
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Vasanthakumar AMoro KXin ALiao YGloury RKawamoto SFagarasan SMielke LAAfshar-Sterle SMasters SLNakae SSaito HWentworth JMLi PLiao WLeonard WJSmyth GKShi WNutt SLKoyasu SKallies A. Erratum: The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue–resident regulatory T cells.
Nature Immunology.
544-544.
2015
Full text if available
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Vasanthakumar AMoro KXin ALiao YGloury RKawamoto SFagarasan SMielke LAAfshar-Sterle SMasters SLNakae SSaito HWentworth JMLi PLiao WLeonard WJSmyth GKShi WNutt SLKoyasu SKallies A. Erratum: The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue–resident regulatory T cells.
Nature Immunology.
544-544.
2015