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Results: 1 to 20 of 232

1.

Statistical Methods for Handling Unwanted Variation in Metabolomics Data.

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

Anal Chem. 2015 Mar 6. [Epub ahead of print]

PMID:
25692814
2.

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.

PMID:
25517617
3.

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. 2014 Nov 10. pii: gutjnl-2014-308252. doi: 10.1136/gutjnl-2014-308252. [Epub ahead of print]

4.

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.

5.

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
6.

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.

7.

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.

PMID:
24879464
8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

PMID:
23963918
15.

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.

16.

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.

PMID:
23684732
17.

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.

PMID:
23588714
18.

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.

19.

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.

PMID:
23497823
20.

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.

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