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Items: 1 to 20 of 210

1.

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.

PMID:
28784151
2.

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.

PMID:
28430777
3.

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
4.

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.

PMID:
28027312
5.

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.

PMID:
27801296
6.

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.

PMID:
27451143
7.

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
8.

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
9.

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
10.

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.

PMID:
26452468
11.

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.

PMID:
26403471
12.

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.

PMID:
26286812
13.

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.

PMID:
26202970
14.

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.

PMID:
25990733
15.

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.

PMID:
25692814
16.

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.

PMID:
25517617
17.

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.

PMID:
25385008
18.

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.

PMID:
25270265
19.

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.

PMID:
25150836
20.

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.

PMID:
24885750

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