Publications

1. 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 Deciphering clonality in aneuploid tumors using SNP array and sequencing data. Genome Biol. 2014 Oct 1;15(9):470. [Epub ahead of print] PMID:25270265
2. Risso D, Ngai J, Speed TP, Dudoit S.  Normalization of RNA-seq data using factor analysis of control genes or samples. Nat Biotechnol. 2014 Sep;32(9):896-902. PMID: 25150836
3. Kim SY, Jacob L, Speed TP. Combining calls from multiple somatic mutation-callers. BMC Bioinformatics. 2014 May 21;15:154. doi: 10.1186/1471-2105-15-154 PMID: 24885750
4. Gandolfo LC, Bahlo M, Speed TP. Dating Rare Mutations from Small Samples with Dense Marker Data. Genetics. 2014 May 30;197(4):1315-1327.  PMID: 24879464
5. Ferreira T, Wilson SR, Choi YG, Risso D, Dudoit S, Speed TP, Ngai J Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron. Neuron. 2014 Feb 19;81(4):847-59. doi: 10.1016/j.neuron.2014.01.001. PMID: 24559675
6. Koepfli C, Colborn KL, Kiniboro B, Lin E, Speed TP, Siba PM, Felger I, Mueller I. A high force of plasmodium vivax blood-stage infection drives the rapid acquisition of immunity in papua new guinean children. PLoS Negl Trop Dis. 2013 Sep 5;7(9):e2403.  PMID: 24040428
7. Greening DW, Kapp EA, Ji H, Speed TP, Simpson RJ.Colon tumour secretopeptidome: insights into endogenous proteolytic cleavage events in the colon tumour microenvironment. Biochim Biophys Acta. 2013 Nov;1834(11):2396-407.  PMID: 23684732
8. 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. Distribution of genomic breakpoints in chronic myeloid leukemia: analysis of 308 patients. Leukemia. 2013 Oct;27(10):2105-7.  PMID: 23588714
9. Masson F, Minnich M, Olshansky M, Bilic I, Mount AM, Kallies A, Speed TP, Busslinger M, Nutt SL, Belz GT. Id2-mediated inhibition of E2A represses memory CD8+ T cell differentiation. J Immunol. 2013 190(9):4585-94. PMID: 23536629
10. De Livera AM, Dias DA, De Souza D, Rupasinghe T, Pyke J, Tull D, Roessner U, McConville M, Speed TP Normalizing and integrating metabolomics data. Anal Chem. 2012 Dec 18;84(24):10768-76. PMID: 23150939