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Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements.

Peters TJ, French HJ, Bradford ST, Pidsley R, Stirzaker C, Varinli H, Nair S, Qu W, Song J, Giles KA, Statham AL, Speirs H, Speed TP, Clark SJ.

Bioinformatics. 2018 Aug 1. doi: 10.1093/bioinformatics/bty675. [Epub ahead of print]


The healthy ageing gene expression signature for Alzheimer's disease diagnosis: a random sampling perspective.

Jacob L, Speed TP.

Genome Biol. 2018 Jul 25;19(1):97. doi: 10.1186/s13059-018-1481-6.


Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis.

Savas P, Virassamy B, Ye C, Salim A, Mintoff CP, Caramia F, Salgado R, Byrne DJ, Teo ZL, Dushyanthen S, Byrne A, Wein L, Luen SJ, Poliness C, Nightingale SS, Skandarajah AS, Gyorki DE, Thornton CM, Beavis PA, Fox SB; Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), Darcy PK, Speed TP, Mackay LK, Neeson PJ, Loi S.

Nat Med. 2018 Jul;24(7):986-993. doi: 10.1038/s41591-018-0078-7. Epub 2018 Jun 25.


Accurate RNA Sequencing From Formalin-Fixed Cancer Tissue To Represent High-Quality Transcriptome From Frozen Tissue.

Li J, Fu C, Speed TP, Wang W, Symmans WF.

JCO Precis Oncol. 2018;2018. doi: 10.1200/PO.17.00091. Epub 2018 Jan 26.


Correction to: A statistical framework for analyzing deep mutational scanning data.

Rubin AF, Gelman H, Lucas N, Bajjalieh SM, Papenfuss AT, Speed TP, Fowler DM.

Genome Biol. 2018 Feb 7;19(1):17. doi: 10.1186/s13059-018-1391-7.


RLE plots: Visualizing unwanted variation in high dimensional data.

Gandolfo LC, Speed TP.

PLoS One. 2018 Feb 5;13(2):e0191629. doi: 10.1371/journal.pone.0191629. eCollection 2018.


Joint Modeling of Mixed Plasmodium Species Infections Using a Bivariate Poisson Lognormal Model.

Colborn KL, Mueller I, Speed TP.

Am J Trop Med Hyg. 2018 Jan;98(1):71-76. doi: 10.4269/ajtmh.17-0523.


GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.

Cameron DL, Schröder J, Penington JS, Do H, Molania R, Dobrovic A, Speed TP, Papenfuss AT.

Genome Res. 2017 Dec;27(12):2050-2060. doi: 10.1101/gr.222109.117. Epub 2017 Nov 2.


A statistical framework for analyzing deep mutational scanning data.

Rubin AF, Gelman H, Lucas N, Bajjalieh SM, Papenfuss AT, Speed TP, Fowler DM.

Genome Biol. 2017 Aug 7;18(1):150. doi: 10.1186/s13059-017-1272-5. Erratum in: Genome Biol. 2018 Feb 7;19(1):17.


Correction: The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE".

Savas P, Teo ZL, Lefevre C, Flensburg C, Caramia F, Alsop K, Mansour M, Francis PA, Thorne HA, Silva MJ, Kanu N, Dietzen M, Rowan A, Kschischo M, Fox S, Bowtell DD, Dawson SJ, Speed TP, Swanton C, Loi S.

PLoS Med. 2017 Apr 21;14(4):e1002302. doi: 10.1371/journal.pmed.1002302. eCollection 2017 Apr.


Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells.

Choi YJ, Lin CP, Risso D, Chen S, Kim TA, Tan MH, Li JB, Wu Y, Chen C, Xuan Z, Macfarlan T, Peng W, Lloyd KC, Kim SY, Speed TP, He L.

Science. 2017 Feb 10;355(6325). pii: eaag1927. doi: 10.1126/science.aag1927. Epub 2017 Jan 12.


The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE".

Savas P, Teo ZL, Lefevre C, Flensburg C, Caramia F, Alsop K, Mansour M, Francis PA, Thorne HA, Silva MJ, Kanu N, Dietzen M, Rowan A, Kschischo M, Fox S, Bowtell DD, Dawson SJ, Speed TP, Swanton C, Loi S.

PLoS Med. 2016 Dec 27;13(12):e1002204. doi: 10.1371/journal.pmed.1002204. eCollection 2016 Dec. Erratum in: PLoS Med. 2017 Apr 21;14 (4):e1002302.


Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex.

Gerstner JR, Koberstein JN, Watson AJ, Zapero N, Risso D, Speed TP, Frank MG, Peixoto L.

BMC Genomics. 2016 Oct 25;17(Suppl 8):727.


Contextual fear conditioning induces differential alternative splicing.

Poplawski SG, Peixoto L, Porcari GS, Wimmer ME, McNally AG, Mizuno K, Giese KP, Chatterjee S, Koberstein JN, Risso D, Speed TP, Abel T.

Neurobiol Learn Mem. 2016 Oct;134 Pt B:221-35. doi: 10.1016/j.nlm.2016.07.018. Epub 2016 Jul 20.


Corrigendum to 'MicroRNAs in CD4+ T cell subsets are markers of disease risk and T cell dysfunction in individuals at risk for type 1 diabetes' [J. Autoimmun. 68C (2016) 52-61].

Zhang Y, Feng ZP, Naselli G, Bell F, Wettenhall J, Auyeung P, Ellis JA, Ponsonby AL, Speed TP, Chong MM, Harrison LC.

J Autoimmun. 2016 Sep;73:130. doi: 10.1016/j.jaut.2016.04.002. Epub 2016 Apr 25. No abstract available.


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.


MicroRNAs in CD4(+) T cell subsets are markers of disease risk and T cell dysfunction in individuals at risk for type 1 diabetes.

Zhang Y, Feng ZP, Naselli G, Bell F, Wettenhall J, Auyeung P, Ellis JA, Ponsonby AL, Speed TP, Chong MM, Harrison LC.

J Autoimmun. 2016 Apr;68:52-61. doi: 10.1016/j.jaut.2015.12.006. Epub 2016 Jan 11.


Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour.

Huang KT, Mikeska T, Li J, Takano EA, Millar EK, Graham PH, Boyle SE, Campbell IG, Speed TP, Dobrovic A, Fox SB.

BMC Cancer. 2015 Oct 9;15:669. doi: 10.1186/s12885-015-1676-0.


Systematic noise degrades gene co-expression signals but can be corrected.

Freytag S, Gagnon-Bartsch J, Speed TP, Bahlo M.

BMC Bioinformatics. 2015 Sep 24;16:309. doi: 10.1186/s12859-015-0745-3.


Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed.

Jacob L, Gagnon-Bartsch JA, Speed TP.

Biostatistics. 2016 Jan;17(1):16-28. doi: 10.1093/biostatistics/kxv026. Epub 2015 Aug 17.


How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets.

Peixoto L, Risso D, Poplawski SG, Wimmer ME, Speed TP, Wood MA, Abel T.

Nucleic Acids Res. 2015 Sep 18;43(16):7664-74. doi: 10.1093/nar/gkv736. Epub 2015 Jul 21.


Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data.

Maksimovic J, Gagnon-Bartsch JA, Speed TP, Oshlack A.

Nucleic Acids Res. 2015 Sep 18;43(16):e106. doi: 10.1093/nar/gkv526. Epub 2015 May 18.


Statistical methods for handling unwanted variation in metabolomics data.

De Livera AM, Sysi-Aho M, Jacob L, Gagnon-Bartsch JA, Castillo S, Simpson JA, Speed TP.

Anal Chem. 2015 Apr 7;87(7):3606-15. doi: 10.1021/ac502439y. Epub 2015 Mar 6.


Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8(+) T cell differentiation.

Russ BE, Olshanksy M, Smallwood HS, Li J, Denton AE, Prier JE, Stock AT, Croom HA, Cullen JG, Nguyen ML, Rowe S, Olson MR, Finkelstein DB, Kelso A, Thomas PG, Speed TP, Rao S, Turner SJ.

Immunity. 2014 Nov 20;41(5):853-65. doi: 10.1016/j.immuni.2014.11.001. Epub 2014 Nov 6. Erratum in: Immunity. 2014 Dec 18;41(6):1064.


Signatures of tumour immunity distinguish Asian and non-Asian gastric adenocarcinomas.

Lin SJ, Gagnon-Bartsch JA, Tan IB, Earle S, Ruff L, Pettinger K, Ylstra B, van Grieken N, Rha SY, Chung HC, Lee JS, Cheong JH, Noh SH, Aoyama T, Miyagi Y, Tsuburaya A, Yoshikawa T, Ajani JA, Boussioutas A, Yeoh KG, Yong WP, So J, Lee J, Kang WK, Kim S, Kameda Y, Arai T, Zur Hausen A, Speed TP, Grabsch HI, Tan P.

Gut. 2015 Nov;64(11):1721-31. doi: 10.1136/gutjnl-2014-308252. Epub 2014 Nov 10.


Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data.

Lönnstedt IM, Caramia F, Li J, Fumagalli D, Salgado R, Rowan A, Salm M, Kanu N, Savas P, Horswell S, Gade S, Loibl S, Neven P, Sotiriou C, Swanton C, Loi S, Speed TP.

Genome Biol. 2014 Oct 1;15(9):470. doi: 10.1186/s13059-014-0470-7.


Normalization of RNA-seq data using factor analysis of control genes or samples.

Risso D, Ngai J, Speed TP, Dudoit S.

Nat Biotechnol. 2014 Sep;32(9):896-902. doi: 10.1038/nbt.2931. Epub 2014 Aug 24.


Combining calls from multiple somatic mutation-callers.

Kim SY, Jacob L, Speed TP.

BMC Bioinformatics. 2014 May 21;15:154. doi: 10.1186/1471-2105-15-154.


Dating rare mutations from small samples with dense marker data.

Gandolfo LC, Bahlo M, Speed TP.

Genetics. 2014 Aug;197(4):1315-27. doi: 10.1534/genetics.114.164616. Epub 2014 May 30.


Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron.

Ferreira T, Wilson SR, Choi YG, Risso D, Dudoit S, Speed TP, Ngai J.

Neuron. 2014 Feb 19;81(4):847-59. doi: 10.1016/j.neuron.2014.01.001.


A positive feedback between p53 and miR-34 miRNAs mediates tumor suppression.

Okada N, Lin CP, Ribeiro MC, Biton A, Lai G, He X, Bu P, Vogel H, Jablons DM, Keller AC, Wilkinson JE, He B, Speed TP, He L.

Genes Dev. 2014 Mar 1;28(5):438-50. doi: 10.1101/gad.233585.113. Epub 2014 Feb 14.


Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery.

Chandrananda D, Thorne NP, Ganesamoorthy D, Bruno DL, Benjamini Y, Speed TP, Slater HR, Bahlo M.

PLoS One. 2014 Jan 29;9(1):e86993. doi: 10.1371/journal.pone.0086993. eCollection 2014.


G protein-linked signaling pathways in bipolar and major depressive disorders.

Tomita H, Ziegler ME, Kim HB, Evans SJ, Choudary PV, Li JZ, Meng F, Dai M, Myers RM, Neal CR, Speed TP, Barchas JD, Schatzberg AF, Watson SJ, Akil H, Jones EG, Bunney WE, Vawter MP.

Front Genet. 2013 Dec 23;4:297. doi: 10.3389/fgene.2013.00297. eCollection 2013.


A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis.

Olive V, Sabio E, Bennett MJ, De Jong CS, Biton A, McGann JC, Greaney SK, Sodir NM, Zhou AY, Balakrishnan A, Foth M, Luftig MA, Goga A, Speed TP, Xuan Z, Evan GI, Wan Y, Minella AC, He L.

Elife. 2013 Oct 15;2:e00822. doi: 10.7554/eLife.00822.


A high force of plasmodium vivax blood-stage infection drives the rapid acquisition of immunity in papua new guinean children.

Koepfli C, Colborn KL, Kiniboro B, Lin E, Speed TP, Siba PM, Felger I, Mueller I.

PLoS Negl Trop Dis. 2013 Sep 5;7(9):e2403. doi: 10.1371/journal.pntd.0002403. eCollection 2013.


Statistical analysis of metabolomics data.

De Livera AM, Olshansky M, Speed TP.

Methods Mol Biol. 2013;1055:291-307. doi: 10.1007/978-1-62703-577-4_20.


Comparing somatic mutation-callers: beyond Venn diagrams.

Kim SY, Speed TP.

BMC Bioinformatics. 2013 Jun 10;14:189. doi: 10.1186/1471-2105-14-189.


Colon tumour secretopeptidome: insights into endogenous proteolytic cleavage events in the colon tumour microenvironment.

Greening DW, Kapp EA, Ji H, Speed TP, Simpson RJ.

Biochim Biophys Acta. 2013 Nov;1834(11):2396-407. doi: 10.1016/j.bbapap.2013.05.006. Epub 2013 May 15.


Distribution of genomic breakpoints in chronic myeloid leukemia: analysis of 308 patients.

Ross DM, O'Hely M, Bartley PA, Dang P, Score J, Goyne JM, Sobrinho-Simoes M, Cross NC, Melo JV, Speed TP, Hughes TP, Morley AA.

Leukemia. 2013 Oct;27(10):2105-7. doi: 10.1038/leu.2013.116. Epub 2013 Apr 16. No abstract available.


Id2-mediated inhibition of E2A represses memory CD8+ T cell differentiation.

Masson F, Minnich M, Olshansky M, Bilic I, Mount AM, Kallies A, Speed TP, Busslinger M, Nutt SL, Belz GT.

J Immunol. 2013 May 1;190(9):4585-94. doi: 10.4049/jimmunol.1300099. Epub 2013 Mar 27.


Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts.

Purdom E, Restall C, Busuttil RA, Schluter H, Boussioutas A, Thompson EW, Anderson RL, Speed TP, Haviv I.

Genet Res (Camb). 2013 Feb;95(1):14-29. doi: 10.1017/S0016672313000013. Epub 2013 Mar 18.


A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis.

Zhang Y, Mayba O, Pfeiffer A, Shi H, Tepperman JM, Speed TP, Quail PH.

PLoS Genet. 2013;9(1):e1003244. doi: 10.1371/journal.pgen.1003244. Epub 2013 Jan 31.


Normalizing and integrating metabolomics data.

De Livera AM, Dias DA, De Souza D, Rupasinghe T, Pyke J, Tull D, Roessner U, McConville M, Speed TP.

Anal Chem. 2012 Dec 18;84(24):10768-76. doi: 10.1021/ac302748b. Epub 2012 Nov 29.


A Tetrahymena Piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus.

Couvillion MT, Bounova G, Purdom E, Speed TP, Collins K.

Mol Cell. 2012 Nov 30;48(4):509-20. doi: 10.1016/j.molcel.2012.09.010. Epub 2012 Oct 18.


Subcompartmentalisation of proteins in the rhoptries correlates with ordered events of erythrocyte invasion by the blood stage malaria parasite.

Zuccala ES, Gout AM, Dekiwadia C, Marapana DS, Angrisano F, Turnbull L, Riglar DT, Rogers KL, Whitchurch CB, Ralph SA, Speed TP, Baum J.

PLoS One. 2012;7(9):e46160. doi: 10.1371/journal.pone.0046160. Epub 2012 Sep 25.


Divergent lymphocyte signalling revealed by a powerful new tool for analysis of time-lapse microscopy.

Pham K, Shimoni R, Ludford-Menting MJ, Nowell CJ, Lobachevsky P, Bomzon Z, Gu M, Speed TP, McGlade CJ, Russell SM.

Immunol Cell Biol. 2013 Jan;91(1):70-81. doi: 10.1038/icb.2012.49. Epub 2012 Oct 2.


Bayesian inference of signaling network topology in a cancer cell line.

Hill SM, Lu Y, Molina J, Heiser LM, Spellman PT, Speed TP, Gray JW, Mills GB, Mukherjee S.

Bioinformatics. 2012 Nov 1;28(21):2804-10. doi: 10.1093/bioinformatics/bts514. Epub 2012 Aug 24.


A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters.

Celik N, Webb CT, Leyton DL, Holt KE, Heinz E, Gorrell R, Kwok T, Naderer T, Strugnell RA, Speed TP, Teasdale RD, Likić VA, Lithgow T.

PLoS One. 2012;7(8):e43245. doi: 10.1371/journal.pone.0043245. Epub 2012 Aug 14.


Copy-number-aware differential analysis of quantitative DNA sequencing data.

Robinson MD, Strbenac D, Stirzaker C, Statham AL, Song J, Speed TP, Clark SJ.

Genome Res. 2012 Dec;22(12):2489-96. doi: 10.1101/gr.139055.112. Epub 2012 Aug 9.


Cisplatin-induced primordial follicle oocyte killing and loss of fertility are not prevented by imatinib.

Kerr JB, Hutt KJ, Cook M, Speed TP, Strasser A, Findlay JK, Scott CL.

Nat Med. 2012 Aug;18(8):1170-2; author reply 1172-4. doi: 10.1038/nm.2889. No abstract available.

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