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Items: 1 to 20 of 217

1.

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]

PMID:
30084929
2.

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.

3.

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.

PMID:
29942092
4.

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.

5.

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.

6.

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.

7.

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.

PMID:
29182143
8.

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.

9.

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.

10.

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.

11.

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.

PMID:
28082412
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.

13.

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.

14.

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.

15.

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.

PMID:
27134182
16.

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.

17.

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.

PMID:
26786119
18.

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.

19.

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.

20.

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.

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