Terry Speed - Publications

Affiliations: 
Statistics University of California, Berkeley, Berkeley, CA 

172 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Jacob L, Gagnon-Bartsch JA, Speed TP. Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed Biostatistics. 17: 16-28. DOI: 10.1093/biostatistics/kxv026  0.96
2015 Huang KT, Mikeska T, Li J, Takano EA, Millar EK, Graham PH, Boyle SE, Campbell IG, Speed TP, Dobrovic A, Fox SB. 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. Bmc Cancer. 15: 669. PMID 26452468 DOI: 10.1186/s12885-015-1676-0  0.96
2015 Peixoto L, Risso D, Poplawski SG, Wimmer ME, Speed TP, Wood MA, Abel T. How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets. Nucleic Acids Research. 43: 7664-74. PMID 26202970 DOI: 10.1093/nar/gkv736  0.96
2015 De Livera AM, Sysi-Aho M, Jacob L, Gagnon-Bartsch JA, Castillo S, Simpson JA, Speed TP. Statistical methods for handling unwanted variation in metabolomics data. Analytical Chemistry. 87: 3606-15. PMID 25692814 DOI: 10.1021/ac502439y  0.96
2015 Freytag S, Gagnon-Bartsch J, Speed TP, Bahlo M. Systematic noise degrades gene co-expression signals but can be corrected Bmc Bioinformatics. 16. DOI: 10.1186/s12859-015-0745-3  0.96
2015 Maksimovic J, Gagnon-Bartsch JA, Speed TP, Oshlack A. Removing unwanted variation in a differential methylation analysis of Illumina Human Methylation 450 array data Nucleic Acids Research. 43. DOI: 10.1093/nar/gkv526  0.96
2014 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, et al. Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8(+) T cell differentiation. Immunity. 41: 853-65. PMID 25517617 DOI: 10.1016/j.immuni.2014.11.001  0.96
2014 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, ... ... Speed TP, et al. Signatures of tumour immunity distinguish Asian and non-Asian gastric adenocarcinomas. Gut. PMID 25385008 DOI: 10.1136/gutjnl-2014-308252  0.96
2014 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, ... ... Speed TP, et al. Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data. Genome Biology. 15: 470. PMID 25270265 DOI: 10.1186/s13059-014-0470-7  0.96
2014 Risso D, Ngai J, Speed TP, Dudoit S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nature Biotechnology. 32: 896-902. PMID 25150836 DOI: 10.1038/nbt.2931  0.96
2014 Kim SY, Jacob L, Speed TP. Combining calls from multiple somatic mutation-callers Bmc Bioinformatics. 15. PMID 24885750 DOI: 10.1186/1471-2105-15-154  0.96
2014 Gandolfo LC, Bahlo M, Speed TP. Dating rare mutations from small samples with dense marker data Genetics. 197: 1315-1327. PMID 24879464 DOI: 10.1534/genetics.114.164616  0.96
2014 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. 81: 847-59. PMID 24559675 DOI: 10.1016/j.neuron.2014.01.001  0.96
2014 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. A positive feedback between p53 and miR-34 miRNAs mediates tumor suppression. Genes & Development. 28: 438-50. PMID 24532687 DOI: 10.1101/gad.233585.113  0.96
2014 Chandrananda D, Thorne NP, Ganesamoorthy D, Bruno DL, Benjamini Y, Speed TP, Slater HR, Bahlo M. Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery. Plos One. 9: e86993. PMID 24489824 DOI: 10.1371/journal.pone.0086993  0.96
2013 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, et al. G protein-linked signaling pathways in bipolar and major depressive disorders. Frontiers in Genetics. 4: 297. PMID 24391664 DOI: 10.3389/fgene.2013.00297  0.96
2013 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, et al. A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis. Elife. 2: e00822. PMID 24137534 DOI: 10.7554/eLife.00822  0.96
2013 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 Neglected Tropical Diseases. 7: e2403. PMID 24040428 DOI: 10.1371/journal.pntd.0002403  0.96
2013 De Livera AM, Olshansky M, Speed TP. Statistical analysis of metabolomics data Methods in Molecular Biology. 1055: 291-307. PMID 23963918 DOI: 10.1007/978-1-62703-577-4-20  0.96
2013 Kim SY, Speed TP. Comparing somatic mutation-callers: Beyond Venn diagrams Bmc Bioinformatics. 14. PMID 23758877 DOI: 10.1186/1471-2105-14-189  0.96
2013 Greening DW, Kapp EA, Ji H, Speed TP, Simpson RJ. Colon tumour secretopeptidome: insights into endogenous proteolytic cleavage events in the colon tumour microenvironment. Biochimica Et Biophysica Acta. 1834: 2396-407. PMID 23684732 DOI: 10.1016/j.bbapap.2013.05.006  0.96
2013 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. 27: 2105-7. PMID 23588714 DOI: 10.1038/leu.2013.116  0.96
2013 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 Journal of Immunology. 190: 4585-4594. PMID 23536629 DOI: 10.4049/jimmunol.1300099  0.96
2013 Purdom E, Restall C, Busuttil RA, Schluter H, Boussioutas A, Thompson EW, Anderson RL, Speed TP, Haviv I. Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts. Genetics Research. 95: 14-29. PMID 23497823 DOI: 10.1017/S0016672313000013  0.96
2013 Zhang Y, Mayba O, Pfeiffer A, Shi H, Tepperman JM, Speed TP, Quail PH. 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 Plos Genetics. 9. PMID 23382695 DOI: 10.1371/journal.pgen.1003244  0.96
2013 Pham K, Shimoni R, Ludford-Menting MJ, Nowell CJ, Lobachevsky P, Bomzon Z, Gu M, Speed TP, McGlade CJ, Russell SM. Divergent lymphocyte signalling revealed by a powerful new tool for analysis of time-lapse microscopy. Immunology and Cell Biology. 91: 70-81. PMID 23032369 DOI: 10.1038/icb.2012.49  0.96
2013 Binz N, Ali Rahman IS, Chinnery HR, McKeone R, Simpson KM, Speed TP, Lai CM, Rakoczy PE. Effect of vascular endothelial growth factor upregulation on retinal gene expression in the Kimba mouse Clinical and Experimental Ophthalmology. 41: 251-262. PMID 22788671 DOI: 10.1111/j.1442-9071.2012.02845.x  0.96
2013 Speed T, Pitman J, Rice J. A brief history of the statistics department of the University of California at Berkeley Strength in Numbers: the Rising of Academic Statistics Departments in the U. S.. 317-338. DOI: 10.1007/978-1-4614-3649-2_23  0.96
2012 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. Analytical Chemistry. 84: 10768-76. PMID 23150939 DOI: 10.1021/ac302748b  0.96
2012 Couvillion MT, Bounova G, Purdom E, Speed TP, Collins K. A Tetrahymena Piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus. Molecular Cell. 48: 509-20. PMID 23084833 DOI: 10.1016/j.molcel.2012.09.010  0.96
2012 Zuccala ES, Gout AM, Dekiwadia C, Marapana DS, Angrisano F, Turnbull L, Riglar DT, Rogers KL, Whitchurch CB, Ralph SA, Speed TP, Baum J. Subcompartmentalisation of proteins in the rhoptries correlates with ordered events of erythrocyte invasion by the blood stage malaria parasite. Plos One. 7: e46160. PMID 23049965 DOI: 10.1371/journal.pone.0046160  0.96
2012 Hill SM, Lu Y, Molina J, Heiser LM, Spellman PT, Speed TP, Gray JW, Mills GB, Mukherjee S. Bayesian inference of signaling network topology in a cancer cell line. Bioinformatics (Oxford, England). 28: 2804-10. PMID 22923301 DOI: 10.1093/bioinformatics/bts514  0.96
2012 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. A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters. Plos One. 7: e43245. PMID 22905239 DOI: 10.1371/journal.pone.0043245  0.96
2012 Robinson MD, Strbenac D, Stirzaker C, Statham AL, Song J, Speed TP, Clark SJ. Copy-number-aware differential analysis of quantitative DNA sequencing data. Genome Research. 22: 2489-96. PMID 22879430 DOI: 10.1101/gr.139055.112  0.96
2012 Kerr JB, Hutt KJ, Cook M, Speed TP, Strasser A, Findlay JK, Scott CL. Cisplatin-induced primordial follicle oocyte killing and loss of fertility are not prevented by imatinib. Nature Medicine. 18: 1170-2; author reply. PMID 22869179 DOI: 10.1038/nm.2889  0.96
2012 Kuo T, Lew MJ, Mayba O, Harris CA, Speed TP, Wang JC. Genome-wide analysis of glucocorticoid receptor-binding sites in myotubes identifies gene networks modulating insulin signaling. Proceedings of the National Academy of Sciences of the United States of America. 109: 11160-5. PMID 22733784 DOI: 10.1073/pnas.1111334109  0.96
2012 Mueller I, Schoepflin S, Smith TA, Benton KL, Bretscher MT, Lin E, Kiniboro B, Zimmerman PA, Speed TP, Siba P, Felger I. Force of infection is key to understanding the epidemiology of Plasmodium falciparum malaria in Papua New Guinean children. Proceedings of the National Academy of Sciences of the United States of America. 109: 10030-5. PMID 22665809 DOI: 10.1073/pnas.1200841109  0.96
2012 Zhang N, Xu Y, O'Hely M, Speed TP, Scharfe C, Wang W. SRMA: an R package for resequencing array data analysis. Bioinformatics (Oxford, England). 28: 1928-30. PMID 22581181 DOI: 10.1093/bioinformatics/bts286  0.96
2012 Feng ZP, Chandrashekaran IR, Low A, Speed TP, Nicholson SE, Norton RS. The N-terminal domains of SOCS proteins: a conserved region in the disordered N-termini of SOCS4 and 5. Proteins. 80: 946-57. PMID 22423360 DOI: 10.1002/prot.23252  0.96
2012 Benjamini Y, Speed TP. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Research. 40: e72. PMID 22323520 DOI: 10.1093/nar/gks001  0.96
2012 Leitman DC, Paruthiyil S, Yuan C, Herber CB, Olshansky M, Tagliaferri M, Cohen I, Speed TP. Tissue-specific regulation of genes by estrogen receptors. Seminars in Reproductive Medicine. 30: 14-22. PMID 22271290 DOI: 10.1055/s-0031-1299593  0.96
2012 Wilkins EJ, Rubio JP, Kotschet KE, Cowie TF, Boon WC, O'Hely M, Burfoot R, Wang W, Sue CM, Speed TP, Stankovitch J, Horne MK. A DNA resequencing array for genes involved in Parkinson's disease. Parkinsonism & Related Disorders. 18: 386-90. PMID 22243833 DOI: 10.1016/j.parkreldis.2011.12.012  0.96
2012 Gagnon-Bartsch JA, Speed TP. Using control genes to correct for unwanted variation in microarray data Biostatistics. 13: 539-552. PMID 22101192 DOI: 10.1093/biostatistics/kxr034  0.96
2012 Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, Bayani N, Hu Z, Billig JI, Dueregger A, Lewis S, ... ... Speed TP, et al. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 109: 2724-9. PMID 22003129 DOI: 10.1073/pnas.1018854108  0.96
2011 Speed T. Mathematics. A correlation for the 21st century. Science (New York, N.Y.). 334: 1502-3. PMID 22174235 DOI: 10.1126/science.1215894  0.96
2011 Saunier EF, Vivar OI, Rubenstein A, Zhao X, Olshansky M, Baggett S, Staub RE, Tagliaferri M, Cohen I, Speed TP, Baxter JD, Leitman DC. Estrogenic plant extracts reverse weight gain and fat accumulation without causing mammary gland or uterine proliferation. Plos One. 6: e28333. PMID 22163294 DOI: 10.1371/journal.pone.0028333  0.96
2011 Shen P, Wang W, Krishnakumar S, Palm C, Chi AK, Enns GM, Davis RW, Speed TP, Mindrinos MN, Scharfe C. High-quality DNA sequence capture of 524 disease candidate genes. Proceedings of the National Academy of Sciences of the United States of America. 108: 6549-54. PMID 21467225 DOI: 10.1073/pnas.1018981108  0.96
2011 Lee EF, Clarke OB, Evangelista M, Feng Z, Speed TP, Tchoubrieva EB, Strasser A, Kalinna BH, Colman PM, Fairlie WD. Discovery and molecular characterization of a Bcl-2-regulated cell death pathway in schistosomes. Proceedings of the National Academy of Sciences of the United States of America. 108: 6999-7003. PMID 21444803 DOI: 10.1073/pnas.1100652108  0.96
2011 Wang XV, Verhaak RG, Purdom E, Spellman PT, Speed TP. Unifying gene expression measures from multiple platforms using factor analysis. Plos One. 6: e17691. PMID 21436879 DOI: 10.1371/journal.pone.0017691  0.96
2011 White S, Ohnesorg T, Notini A, Roeszler K, Hewitt J, Daggag H, Smith C, Turbitt E, Gustin S, van den Bergen J, Miles D, Western P, Arboleda V, Schumacher V, Gordon L, ... ... Speed T, et al. Copy number variation in patients with disorders of sex development due to 46,XY gonadal dysgenesis. Plos One. 6: e17793. PMID 21408189 DOI: 10.1371/journal.pone.0017793  0.96
2011 Lopaticki S, Maier AG, Thompson J, Wilson DW, Tham WH, Triglia T, Gout A, Speed TP, Beeson JG, Healer J, Cowman AF. Reticulocyte and erythrocyte binding-like proteins function cooperatively in invasion of human erythrocytes by malaria parasites. Infection and Immunity. 79: 1107-17. PMID 21149582 DOI: 10.1128/IAI.01021-10  0.96
2011 Wang W, Shen P, Thiyagarajan S, Lin S, Palm C, Horvath R, Klopstock T, Cutler D, Pique L, Schrijver I, Davis RW, Mindrinos M, Speed TP, Scharfe C. Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing. Nucleic Acids Research. 39: 44-58. PMID 20843780 DOI: 10.1093/nar/gkq750  0.96
2011 Speed T. Too much or too little scepticism? Significance. 8: 35-35. DOI: 10.1111/j.1740-9713.2011.00477.x  0.96
2011 Robinson MD, Stirzaker C, Statham AL, Coolen MW, Song JZ, Nair SS, Strbenac D, Speed TP, Clark SJ. Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation (Genome Research (2010), 20 (1719-1729)) Genome Research. 21: 146.  0.96
2010 Robinson MD, Statham AL, Speed TP, Clark SJ. Protocol matters: which methylome are you actually studying? Epigenomics. 2: 587-98. PMID 21566704 DOI: 10.2217/epi.10.36  0.96
2010 Yu CY, Mayba O, Lee JV, Tran J, Harris C, Speed TP, Wang JC. Genome-wide analysis of glucocorticoid receptor binding regions in adipocytes reveal gene network involved in triglyceride homeostasis. Plos One. 5: e15188. PMID 21187916 DOI: 10.1371/journal.pone.0015188  0.96
2010 Tan IK, Mackin L, Wang N, Papenfuss AT, Elso CM, Ashton MP, Quirk F, Phipson B, Bahlo M, Speed TP, Smyth GK, Morahan G, Brodnicki TC. A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility. Genome Research. 20: 1629-38. PMID 21051460 DOI: 10.1101/gr.101881.109  0.96
2010 Robinson MD, Stirzaker C, Statham AL, Coolen MW, Song JZ, Nair SS, Strbenac D, Speed TP, Clark SJ. Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Research. 20: 1719-29. PMID 21045081 DOI: 10.1101/gr.110601.110  0.96
2010 Leitman DC, Paruthiyil S, Vivar OI, Saunier EF, Herber CB, Cohen I, Tagliaferri M, Speed TP. Regulation of specific target genes and biological responses by estrogen receptor subtype agonists. Current Opinion in Pharmacology. 10: 629-36. PMID 20951642 DOI: 10.1016/j.coph.2010.09.009  0.96
2010 Speca DJ, Chihara D, Ashique AM, Bowers MS, Pierce-Shimomura JT, Lee J, Rabbee N, Speed TP, Gularte RJ, Chitwood J, Medrano JF, Liao M, Sonner JM, Eger EI, Peterson AS, et al. Conserved role of unc-79 in ethanol responses in lightweight mutant mice. Plos Genetics. 6. PMID 20714347 DOI: 10.1371/journal.pgen.1001057  0.96
2010 Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, Wang N, Parvin B, Fontenay G, Speed T, Garbe J, et al. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Molecular Cancer Research : McR. 8: 961-74. PMID 20605923 DOI: 10.1158/1541-7786.MCR-09-0528  0.96
2010 Loi S, Haibe-Kains B, Majjaj S, Lallemand F, Durbecq V, Larsimont D, Gonzalez-Angulo AM, Pusztai L, Symmans WF, Bardelli A, Ellis P, Tutt AN, Gillett CE, Hennessy BT, Mills GB, ... ... Speed TP, et al. PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 107: 10208-13. PMID 20479250 DOI: 10.1073/pnas.0907011107  0.96
2010 Bengtsson H, Neuvial P, Speed TP. TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays Bmc Bioinformatics. 11. PMID 20462408 DOI: 10.1186/1471-2105-11-245  0.96
2010 Carmichael CL, Wilkins EJ, Bengtsson H, Horwitz MS, Speed TP, Vincent PC, Young G, Hahn CN, Escher R, Scott HS. Poor prognosis in familial acute myeloid leukaemia with combined biallelic CEBPA mutations and downstream events affecting the ATM, FLT3 and CDX2 genes. British Journal of Haematology. 150: 382-5. PMID 20456351 DOI: 10.1111/j.1365-2141.2010.08204.x  0.96
2010 Vivar OI, Zhao X, Saunier EF, Griffin C, Mayba OS, Tagliaferri M, Cohen I, Speed TP, Leitman DC. Estrogen receptor beta binds to and regulates three distinct classes of target genes. The Journal of Biological Chemistry. 285: 22059-66. PMID 20404318 DOI: 10.1074/jbc.M110.114116  0.96
2010 Ramakrishna M, Williams LH, Boyle SE, Bearfoot JL, Sridhar A, Speed TP, Gorringe KL, Campbell IG. Identification of candidate growth promoting genes in ovarian cancer through integrated copy number and expression analysis. Plos One. 5: e9983. PMID 20386695 DOI: 10.1371/journal.pone.0009983  0.96
2010 Atkinson EJ, McDonnell SK, Witte JS, Crawford DC, Fan Y, Fridley B, Li D, Li L, Rodin A, Sadee W, Speed T, Weiss ST, Yang J, Yerges L, Schaid DJ. Conference Scene: Lessons learned from the 5th Statistical Analysis Workshop of the Pharmacogenetics Research Network. Pharmacogenomics. 11: 297-303. PMID 20235785 DOI: 10.2217/pgs.10.5  0.96
2010 Coolen MW, Stirzaker C, Song JZ, Statham AL, Kassir Z, Moreno CS, Young AN, Varma V, Speed TP, Cowley M, Lacaze P, Kaplan W, Robinson MD, Clark SJ. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nature Cell Biology. 12: 235-46. PMID 20173741 DOI: 10.1038/ncb2023  0.96
2010 Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O'Kelly M, Tamayo P, Weir BA, ... ... Speed TP, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 17: 98-110. PMID 20129251 DOI: 10.1016/j.ccr.2009.12.020  0.96
2010 Levy N, Paruthiyil S, Zhao X, Vivar OI, Saunier EF, Griffin C, Tagliaferri M, Cohen I, Speed TP, Leitman DC. Unliganded estrogen receptor-beta regulation of genes is inhibited by tamoxifen. Molecular and Cellular Endocrinology. 315: 201-7. PMID 19744542 DOI: 10.1016/j.mce.2009.08.030  0.96
2010 Speed T. The unreasonable effectiveness of statistics in genome science Significance. 7: 133-133. DOI: 10.1111/j.1740-9713.2010.00441.x  0.96
2010 Mukherjee S, Speed TP, Hill SM. Model Averaging for Biological Networks with Prior Information Medical Biostatistics For Complex Diseases. 347-372. DOI: 10.1002/9783527630332.ch17  0.96
2009 Irizarry RA, Wang C, Zhou Y, Speed TP. Gene set enrichment analysis made simple. Statistical Methods in Medical Research. 18: 565-75. PMID 20048385 DOI: 10.1177/0962280209351908  0.96
2009 Ge Y, Sealfon SC, Speed TP. Multiple testing and its applications to microarrays. Statistical Methods in Medical Research. 18: 543-63. PMID 20048384 DOI: 10.1177/0962280209351899  0.96
2009 Speed T, Zhao H. Microarrays. Statistical Methods in Medical Research. 18: 531-2. PMID 20048382 DOI: 10.1177/0962280209352042  0.96
2009 Krane DE, Bahn V, Balding D, Barlow B, Cash H, Desportes BL, D'Eustachio P, Devlin K, Doom TE, Dror I, Ford S, Funk C, Gilder J, Hampikian G, Inman K, ... ... Speed T, et al. Time for DNA disclosure. Science (New York, N.Y.). 326: 1631-2. PMID 20019271 DOI: 10.1126/science.326.5960.1631  0.96
2009 Sui Y, Zhao X, Speed TP, Wu Z. Background adjustment for DNA microarrays using a database of microarray experiments. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1501-15. PMID 19958080 DOI: 10.1089/cmb.2009.0063  0.96
2009 Powell JA, Thomas D, Barry EF, Kok CH, McClure BJ, Tsykin A, To LB, Brown A, Lewis ID, Herbert K, Goodall GJ, Speed TP, Asou N, Jacob B, Osato M, et al. Expression profiling of a hemopoietic cell survival transcriptome implicates osteopontin as a functional prognostic factor in AML. Blood. 114: 4859-70. PMID 19805619 DOI: 10.1182/blood-2009-02-204818  0.96
2009 Paruthiyil S, Cvoro A, Zhao X, Wu Z, Sui Y, Staub RE, Baggett S, Herber CB, Griffin C, Tagliaferri M, Harris HA, Cohen I, Bjeldanes LF, Speed TP, Schaufele F, et al. Drug and cell type-specific regulation of genes with different classes of estrogen receptor beta-selective agonists. Plos One. 4: e6271. PMID 19609440 DOI: 10.1371/journal.pone.0006271  0.96
2009 Bengtsson H, Wirapati P, Speed TP. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6 Bioinformatics. 25: 2149-2156. PMID 19535535 DOI: 10.1093/bioinformatics/btp371  0.96
2009 Robinson MD, Speed TP. Differential splicing using whole-transcript microarrays Bmc Bioinformatics. 10. PMID 19463149 DOI: 10.1186/1471-2105-10-156  0.96
2009 Tonkin CJ, Carret CK, Duraisingh MT, Voss TS, Ralph SA, Hommel M, Duffy MF, Silva LM, Scherf A, Ivens A, Speed TP, Beeson JG, Cowman AF. Sir2 paralogues cooperate to regulate virulence genes and antigenic variation in Plasmodium falciparum. Plos Biology. 7: e84. PMID 19402747 DOI: 10.1371/journal.pbio.1000084  0.96
2009 Bengtsson H, Ray A, Spellman P, Speed TP. A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods Bioinformatics. 25: 861-867. PMID 19193730 DOI: 10.1093/bioinformatics/btp074  0.96
2009 Chandran D, Tai YC, Hather G, Dewdney J, Denoux C, Burgess DG, Ausubel FM, Speed TP, Wildermuth MC. Temporal global expression data reveal known and novel salicylate-impacted processes and regulators mediating powdery mildew growth and reproduction on Arabidopsis. Plant Physiology. 149: 1435-51. PMID 19176722 DOI: 10.1104/pp.108.132985  0.96
2009 Pask AJ, Papenfuss AT, Ager EI, McColl KA, Speed TP, Renfree MB. Analysis of the platypus genome suggests a transposon origin for mammalian imprinting Genome Biology. 10: R1. PMID 19121219  0.96
2009 Ball LJ, Levy N, Zhao X, Griffin C, Tagliaferri M, Cohen I, Ricke WA, Speed TP, Firestone GL, Leitman DC. Cell type- and estrogen receptor-subtype specific regulation of selective estrogen receptor modulator regulatory elements. Molecular and Cellular Endocrinology. 299: 204-11. PMID 19059307 DOI: 10.1016/j.mce.2008.10.050  0.96
2009 Mukherjee S, Pelech S, Neve RM, Kuo WL, Ziyad S, Spellman PT, Gray JW, Speed TP. Sparse combinatorial inference with an application in cancer biology. Bioinformatics (Oxford, England). 25: 265-71. PMID 19038985 DOI: 10.1093/bioinformatics/btn611  0.96
2009 Tai YC, Speed TP. On gene ranking using replicated microarray time course data. Biometrics. 65: 40-51. PMID 18537947 DOI: 10.1111/j.1541-0420.2008.01057.x  0.96
2009 Loi S, Sotiriou C, Haibe-Kains B, Lallemand F, Conus NM, Piccart MJ, Speed TP, McArthur GA. Gene expression profiling identifies activated growth factor signaling in poor prognosis (Luminal-B) estrogen receptor positive breast cancer Bmc Medical Genomics. 2. DOI: 10.1186/1755-8794-2-37  0.96
2008 Mukherjee S, Speed TP. Network inference using informative priors Proceedings of the National Academy of Sciences of the United States of America. 105: 14313-14318. PMID 18799736 DOI: 10.1073/pnas.0802272105  0.96
2008 Michaud J, Simpson KM, Escher R, Buchet-Poyau K, Beissbarth T, Carmichael C, Ritchie ME, Schütz F, Cannon P, Liu M, Shen X, Ito Y, Raskind WH, Horwitz MS, Osato M, ... ... Speed TP, et al. Integrative analysis of RUNX1 downstream pathways and target genes. Bmc Genomics. 9: 363. PMID 18671852 DOI: 10.1186/1471-2164-9-363  0.96
2008 Rubio JP, Stankovich J, Field J, Tubridy N, Marriott M, Chapman C, Bahlo M, Perera D, Johnson LJ, Tait BD, Varney MD, Speed TP, Taylor BV, Foote SJ, Butzkueven H, et al. Replication of KIAA0350, IL2RA, RPL5 and CD58 as multiple sclerosis susceptibility genes in Australians Genes and Immunity. 9: 624-630. PMID 18650830 DOI: 10.1038/gene.2008.59  0.96
2008 Purdom E, Simpson KM, Robinson MD, Conboy JG, Lapuk AV, Speed TP. FIRMA: A method for detection of alternative splicing from exon array data Bioinformatics. 24: 1707-1714. PMID 18573797 DOI: 10.1093/bioinformatics/btn284  0.96
2008 Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, ... ... Speed TP, et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. Plos Biology. 6: e27. PMID 18271625 DOI: 10.1371/journal.pbio.0060027  0.96
2008 Bengtsson H, Irizarry R, Carvalho B, Speed TP. Estimation and assessment of raw copy numbers at the single locus level Bioinformatics. 24: 759-767. PMID 18204055 DOI: 10.1093/bioinformatics/btn016  0.96
2008 Burfoot RK, Jensen CJ, Field J, Stankovich J, Varney MD, Johnson LJ, Butzkueven H, Booth D, Bahlo M, Tait BD, Taylor BV, Speed TP, Heard R, Stewart GJ, Foote SJ, et al. SNP mapping and candidate gene sequencing in the class I region of the HLA complex: searching for multiple sclerosis susceptibility genes in Tasmanians. Tissue Antigens. 71: 42-50. PMID 17971048 DOI: 10.1111/j.1399-0039.2007.00962.x  0.96
2008 Levy N, Tatomer D, Herber CB, Zhao X, Tang H, Sargeant T, Ball LJ, Summers J, Speed TP, Leitman DC. Differential regulation of native estrogen receptor-regulatory elements by estradiol, tamoxifen, and raloxifene. Molecular Endocrinology (Baltimore, Md.). 22: 287-303. PMID 17962382 DOI: 10.1210/me.2007-0340  0.96
2008 Guipponi M, Toh MY, Tan J, Park D, Hanson K, Ballana E, Kwong D, Cannon PZ, Wu Q, Gout A, Delorenzi M, Speed TP, Smith RJ, Dahl HH, Petersen M, et al. An integrated genetic and functional analysis of the role of type II transmembrane serine proteases (TMPRSSs) in hearing loss. Human Mutation. 29: 130-41. PMID 17918732 DOI: 10.1002/humu.20617  0.96
2008 Hallgrímsdóttir IB, Speed TP. The power of two-locus affected sib-pair linkage analysis to detect interacting disease loci Genetic Epidemiology. 32: 84-88. PMID 17654608 DOI: 10.1002/gepi.20254  0.96
2008 Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Hou CC, Ogawa N, Inwood W, Sementchenko V, Beaton A, ... ... Speed TP, et al. Correction: Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm (PLoS Biology (2008) 6,2 (e27) DOI: 10.1371/journal.pbio.0060027) Plos Biology. 6: 1600. DOI: 10.1371/journal.pbio.0060190  0.96
2008 Zhang NR, Wildermuth MC, Speed TP. Transcription factor binding site prediction with multivariate gene expression data Annals of Applied Statistics. 2: 332-365. DOI: 10.1214/07-AOAS142  0.96
2008 Brettschneider J, Collin F, Bolstad B, Speed T. Rejoinder Technometrics. 50: 279-283. DOI: 10.1198/004017008000000389  0.96
2008 Brettschneider J, Bolstad B, Collin F, Speed T. Quality assessment for short oligonucleotide microarray data Technometrics. 50: 241-264. DOI: 10.1198/004017008000000334  0.96
2008 Speed T. Journal of Computational Biology: Preface Journal of Computational Biology. 15: 653. DOI: 10.1089/cmb.2008.P001  0.96
2008 Speed TP, Zhao H. Chromosome Maps Handbook of Statistical Genetics: Third Edition. 1: 1-39. DOI: 10.1002/9780470061619.ch1  0.96
2008 Ge Y, Sealfon SC, Speed TP. Some step-down procedures controlling the false discovery rate under dependence Statistica Sinica. 18: 881-904.  0.96
2007 Szpara ML, Vranizan K, Tai YC, Goodman CS, Speed TP, Ngai J. Analysis of gene expression during neurite outgrowth and regeneration. Bmc Neuroscience. 8: 100. PMID 18036227 DOI: 10.1186/1471-2202-8-100  0.96
2007 Robinson MD, Speed TP. A comparison of affymetrix gene expression arrays Bmc Bioinformatics. 8. PMID 18005448 DOI: 10.1186/1471-2105-8-449  0.96
2007 Georlette D, Ahn S, MacAlpine DM, Cheung E, Lewis PW, Beall EL, Bell SP, Speed T, Manak JR, Botchan MR. Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb MuvB/dREAM complex in proliferating cells. Genes & Development. 21: 2880-96. PMID 17978103 DOI: 10.1101/gad.1600107  0.96
2007 Robinson MD, De Souza DP, Keen WW, Saunders EC, McConville MJ, Speed TP, Likić VA. A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments Bmc Bioinformatics. 8. PMID 17963529 DOI: 10.1186/1471-2105-8-419  0.96
2007 McCoubrie JE, Miller SK, Sargeant T, Good RT, Hodder AN, Speed TP, De Koning-Ward TF, Crabb BS. Evidence for a common role for the serine-type Plasmodium falciparum serine repeat antigen proteases: Implications for vaccine and drug design Infection and Immunity. 75: 5565-5574. PMID 17893128 DOI: 10.1128/IAI.00405-07  0.96
2007 Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, ... ... Speed TP, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 447: 167-77. PMID 17495919 DOI: 10.1038/nature05805  0.96
2007 Belov K, Sanderson CE, Deakin JE, Wong ES, Assange D, McColl KA, Gout A, de Bono B, Barrow AD, Speed TP, Trowsdale J, Papenfuss AT. Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system. Genome Research. 17: 982-91. PMID 17495011 DOI: 10.1101/gr.6121807  0.96
2007 Qin X, Ahn S, Speed TP, Rubin GM. Global analyses of mRNA translational control during early Drosophila embryogenesis. Genome Biology. 8: R63. PMID 17448252 DOI: 10.1186/gb-2007-8-4-r63  0.96
2007 Levy N, Zhao X, Tang H, Jaffe RB, Speed TP, Leitman DC. Multiple transcription factor elements collaborate with estrogen receptor α to activate an inducible estrogen response element in the NKG2E gene Endocrinology. 148: 3449-3450. PMID 17395694 DOI: 10.1210/en.2006-1632  0.96
2007 Rubio JP, Bahlo M, Stankovich J, Burfoot RK, Johnson LJ, Huxtable S, Butzkueven H, Lin L, Taylor BV, Speed TP, Kilpatrick TJ, Mignot E, Foote SJ. Analysis of extended HLA haplotypes in multiple sclerosis and narcolepsy families confirms a predisposing effect for the class I region in Tasmanian MS patients. Immunogenetics. 59: 177-86. PMID 17256150 DOI: 10.1007/s00251-006-0183-5  0.96
2007 Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics (Oxford, England). 8: 485-99. PMID 17189563 DOI: 10.1093/biostatistics/kxl042  0.96
2007 Sliwerska E, Meng F, Speed TP, Jones EG, Bunney WE, Akil H, Watson SJ, Burmeister M. SNPs on chips: the hidden genetic code in expression arrays. Biological Psychiatry. 61: 13-6. PMID 16690034 DOI: 10.1016/j.biopsych.2006.01.023  0.96
2007 Ge Y, Sealfon SC, Tseng CH, Speed TP. A Holm-type procedure controlling the false discovery rate Statistics and Probability Letters. 77: 1756-1762. DOI: 10.1016/j.spl.2007.04.019  0.96
2007 Speed T. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4453: v-vi.  0.96
2006 Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, Speed T, Spellman PT, DeVries S, Lapuk A, Wang NJ, et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell. 10: 515-27. PMID 17157791 DOI: 10.1016/j.ccr.2006.10.008  0.96
2006 Deakin JE, Papenfuss AT, Belov K, Cross JG, Coggill P, Palmer S, Sims S, Speed TP, Beck S, Graves JA. Evolution and comparative analysis of the MHC Class III inflammatory region. Bmc Genomics. 7: 281. PMID 17081307 DOI: 10.1186/1471-2164-7-281  0.96
2006 Dugas JC, Tai YC, Speed TP, Ngai J, Barres BA. Functional genomic analysis of oligodendrocyte differentiation. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 26: 10967-83. PMID 17065439 DOI: 10.1523/JNEUROSCI.2572-06.2006  0.96
2006 Wormald S, Hilton DJ, Smyth GK, Speed TP. Proximal genomic localization of STAT1 binding and regulated transcriptional activity. Bmc Genomics. 7: 254. PMID 17032459 DOI: 10.1186/1471-2164-7-254  0.96
2006 Lin E, Pappenfuss T, Tan RB, Senyschyn D, Bahlo M, Speed TP, Foote SJ. Mapping of the Plasmodium chabaudi resistance locus char2. Infection and Immunity. 74: 5814-9. PMID 16988259 DOI: 10.1128/IAI.01690-05  0.96
2006 Baum J, Papenfuss AT, Baum B, Speed TP, Cowman AF. Regulation of apicomplexan actin-based motility Nature Reviews Microbiology. 4: 621-628. PMID 16845432 DOI: 10.1038/nrmicro1465  0.96
2006 Vawter MP, Tomita H, Meng F, Bolstad B, Li J, Evans S, Choudary P, Atz M, Shao L, Neal C, Walsh DM, Burmeister M, Speed T, Myers R, Jones EG, et al. Mitochondrial-related gene expression changes are sensitive to agonal-pH state: implications for brain disorders. Molecular Psychiatry. 11: 615, 663-79. PMID 16636682 DOI: 10.1038/sj.mp.4001830  0.96
2006 Gilson PR, Nebl T, Vukcevic D, Moritz RL, Sargeant T, Speed TP, Schofield L, Crabb BS. Identification and stoichiometry of glycosylphosphatidylinositol-anchored membrane proteins of the human malaria parasite Plasmodium falciparum Molecular and Cellular Proteomics. 5: 1286-1299. PMID 16603573 DOI: 10.1074/mcp.M600035-MCP200  0.96
2006 Armstrong NJ, Brodnicki TC, Speed TP. Mind the gap: Analysis of marker-assisted breeding strategies for inbred mouse strains Mammalian Genome. 17: 273-287. PMID 16596449 DOI: 10.1007/s00335-005-0123-y  0.96
2006 Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP. Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature. 440: 242-5. PMID 16525476 DOI: 10.1038/nature04559  0.96
2006 Sargeant TJ, Marti M, Caler E, Carlton JM, Simpson K, Speed TP, Cowman AF. Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites Genome Biology. 7. PMID 16507167 DOI: 10.1186/gb-2006-7-2-r12  0.96
2006 Wormald S, Zhang JG, Krebs DL, Mielke LA, Silver J, Alexander WS, Speed TP, Nicola NA, Hilton DJ. The comparative roles of suppressor of cytokine signaling-1 and -3 in the inhibition and desensitization of cytokine signaling. The Journal of Biological Chemistry. 281: 11135-43. PMID 16473883 DOI: 10.1074/jbc.M509595200  0.96
2006 Speca DJ, Rabbee N, Chihara D, Speed TP, Peterson AS. A genetic screen for behavioral mutations that perturb dopaminergic homeostasis in mice Genes, Brain and Behavior. 5: 19-28. PMID 16436185 DOI: 10.1111/j.1601-183X.2005.00127.x  0.96
2006 Belov K, Deakin JE, Papenfuss AT, Baker ML, Melman SD, Siddle HV, Gouin N, Goode DL, Sargeant TJ, Robinson MD, Wakefield MJ, Mahony S, Cross JG, Benos PV, Samollow PB, ... Speed TP, et al. Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. Plos Biology. 4: e46. PMID 16435885 DOI: 10.1371/journal.pbio.0040046  0.96
2006 Stankovich J, Cox CJ, Tan RB, Montgomery DS, Huxtable SJ, Rubio JP, Ehm MG, Johnson L, Butzkueven H, Kilpatrick TJ, Speed TP, Roses AD, Bahlo M, Foote SJ. On the utility of data from the International HapMap Project for Australian association studies. Human Genetics. 119: 220-2. PMID 16404587 DOI: 10.1007/s00439-005-0120-y  0.96
2006 Bahlo M, Stankovich J, Speed TP, Rubio JP, Burfoot RK, Foote SJ. Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data. Human Genetics. 119: 38-50. PMID 16362347 DOI: 10.1007/s00439-005-0114-9  0.96
2006 Binz N, Graham CE, Simpson K, Lai YKY, Shen WY, Lai CM, Speed TP, Rakoczy PE. Long-term effect of therapeutic laser photocoagulation on gene expression in the eye Faseb Journal. 20: 383-385. PMID 16354724 DOI: 10.1096/fj.05-3890fje  0.96
2006 Armstrong NJ, McPeek MS, Speed TP. Incorporating interference into linkage analysis for experimental crosses. Biostatistics (Oxford, England). 7: 374-86. PMID 16354713 DOI: 10.1093/biostatistics/kxj012  0.96
2006 Rabbee N, Speed TP. A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics (Oxford, England). 22: 7-12. PMID 16267090 DOI: 10.1093/bioinformatics/bti741  0.96
2006 Tai YC, Speed TP. A multivariate empirical Bayes statistic for replicated microarray time course data Annals of Statistics. 34: 2387-2412. DOI: 10.1214/009053606000000759  0.96
2005 Likić VA, Gooley PR, Speed TP, Strehler EE. A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics Protein Science. 14: 2955-2963. PMID 16322577 DOI: 10.1110/ps.051681605  0.96
2005 Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Research. 33: e175. PMID 16284200 DOI: 10.1093/nar/gni179  0.96
2005 Sakthianandeswaren A, Elso CM, Simpson K, Curtis JM, Kumar B, Speed TP, Handman E, Foote SJ. The wound repair response controls outcome to cutaneous leishmaniasis. Proceedings of the National Academy of Sciences of the United States of America. 102: 15551-6. PMID 16223880 DOI: 10.1073/pnas.0505630102  0.96
2005 Zhao X, Huang H, Speed TP. Finding short DNA motifs using permuted Markov models Journal of Computational Biology. 12: 894-906. PMID 16108724 DOI: 10.1089/cmb.2005.12.894  0.96
2005 Booth DR, Arthur AT, Teutsch SM, Bye C, Rubio J, Armati PJ, Pollard JD, Heard RN, Stewart GJ. Gene expression and genotyping studies implicate the interleukin 7 receptor in the pathogenesis of primary progressive multiple sclerosis. Journal of Molecular Medicine (Berlin, Germany). 83: 822-30. PMID 16075257 DOI: 10.1007/s00109-005-0684-y  0.96
2005 Foote SJ, Rubio JP, Bahlo M, Kilpatrick TJ, Speed TP, Stankovich J, Burfoot R, Butzkueven H, Johnson L, Wilkinson C, Taylor B, Sale M, van der Mei IA, Dickinson JL, Groom P. Multiple sclerosis: a haplotype association study. Novartis Foundation Symposium. 267: 31-9; discussion 39-. PMID 15999799  0.96
2005 Beissbarth T, Tye-Din JA, Smyth GK, Speed TP, Anderson RP. A systematic approach for comprehensive T-cell epitope discovery using peptide libraries. Bioinformatics (Oxford, England). 21: i29-37. PMID 15961469 DOI: 10.1093/bioinformatics/bti1013  0.96
2005 Wilkinson TN, Speed TP, Tregear GW, Bathgate RAD. Coevolution of the relaxin-like peptides and their receptors Annals of the New York Academy of Sciences. 1041: 534-539. PMID 15956757 DOI: 10.1196/annals.1282.080  0.96
2005 Wilkinson TN, Speed TP, Tregear GW, Bathgate RA. Evolution of the relaxin-like peptide family: from neuropeptide to reproduction. Annals of the New York Academy of Sciences. 1041: 530-3. PMID 15956756 DOI: 10.1196/annals.1282.079  0.96
2005 Baird PN, Foote SJ, Mackey DA, Craig J, Speed TP, Bureau A. Evidence for a novel glaucoma locus at chromosome 3p21-22. Human Genetics. 117: 249-57. PMID 15906098 DOI: 10.1007/s00439-005-1296-x  0.96
2005 Stankovich J, Bahlo M, Rubio JP, Wilkinson CR, Thomson R, Banks A, Ring M, Foote SJ, Speed TP. Identifying nineteenth century genealogical links from genotypes. Human Genetics. 117: 188-99. PMID 15883841 DOI: 10.1007/s00439-005-1279-y  0.96
2005 Simpson KM, Baum J, Good RT, Winzeler EA, Cowman AF, Speed TP. A comparison of match-only algorithms for the analysis of Plasmodium falciparum oligonucleotide arrays International Journal For Parasitology. 35: 523-531. PMID 15826644 DOI: 10.1016/j.ijpara.2005.02.010  0.96
2005 Yap VB, Speed T. Rooting a phylogenetic tree with nonreversible substitution models. Bmc Evolutionary Biology. 5: 2. PMID 15629063 DOI: 10.1186/1471-2148-5-2  0.96
2005 Beißbarth T, Tye-Din JA, Smyth GK, Speed TP, Anderson RP. A systematic approach for comprehensive T-cell epitope discovery using peptide libraries Ismb 2005 Proceedings - 13th International Conference On Intelligent Systems For Molecular Biology. i29-i37.  0.96
2004 Rabbee N, Speca D, Armstrong NJ, Speed TP. Power calculations for selective genotyping in QTL mapping in backcross mice. Genetical Research. 84: 103-8. PMID 15678748 DOI: 10.1017/S0016672304007086  0.96
2004 Bolstad BM, Collin F, Simpson KM, Irizarry RA, Speed TP. Experimental Design and Low-Level Analysis of Microarray Data International Review of Neurobiology. 60: 25-58. PMID 15474586 DOI: 10.1016/S0074-7742(04)60002-X  0.96
2004 Moritz RL, Ji H, Schütz F, Connolly LM, Kapp EA, Speed TP, Simpson RJ. A proteome strategy for fractionating proteins and peptides using continuous free-flow electrophoresis coupled off-line to reversed-phase high-performance liquid chromatography Analytical Chemistry. 76: 4811-4824. PMID 15307793 DOI: 10.1021/ac049717l  0.96
2004 Bourgon R, Delorenzi M, Sargeant T, Hodder AN, Crabb BS, Speed TP. The serine repeat antigen (SERA) gene family phylogeny in plasmodium: The impact of GC content and reconciliation of gene and species trees Molecular Biology and Evolution. 21: 2161-2171. PMID 15306658 DOI: 10.1093/molbev/msh228  0.96
2004 Lin DM, Yang YH, Scolnick JA, Brunet LJ, Marsh H, Peng V, Okazaki Y, Hayashizaki Y, Speed TP, Ngai J. Spatial patterns of gene expression in the olfactory bulb. Proceedings of the National Academy of Sciences of the United States of America. 101: 12718-23. PMID 15304640 DOI: 10.1073/pnas.0404872101  0.96
2004 Beissbarth T, Hyde L, Smyth GK, Job C, Boon WM, Tan SS, Scott HS, Speed TP. Statistical modeling of sequencing errors in SAGE libraries. Bioinformatics (Oxford, England). 20: i31-9. PMID 15262778 DOI: 10.1093/bioinformatics/bth924  0.96
2004 Marciano PG, Brettschneider J, Manduchi E, Davis JE, Eastman S, Raghupathi R, Saatman KE, Speed TP, Stoeckert CJ, Eberwine JH, McIntosh TK. Neuron-specific mRNA complexity responses during hippocampal apoptosis after traumatic brain injury. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 24: 2866-76. PMID 15044525 DOI: 10.1523/JNEUROSCI.5051-03.2004  0.96
2004 Rubio JP, Bahlo M, Tubridy N, Stankovich J, Burfoot R, Butzkueven H, Chapman C, Johnson L, Marriott M, Mraz G, Tait B, Wilkinson C, Taylor B, Speed TP, Foote SJ, et al. Extended haplotype analysis in the HLA complex reveals an increased frequency of the HFE-C282Y mutation in individuals with multiple sclerosis. Human Genetics. 114: 573-80. PMID 15014978 DOI: 10.1007/s00439-004-1095-9  0.96
2004 Beißbarth T, Speed TP. GOstat: Find statistically overrepresented Gene Ontologies with a group of genes Bioinformatics. 20: 1464-1465. PMID 14962934 DOI: 10.1093/bioinformatics/bth088  0.96
2004 Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP. A benchmark for Affymetrix GeneChip expression measures. Bioinformatics (Oxford, England). 20: 323-31. PMID 14960458 DOI: 10.1093/bioinformatics/btg410  0.96
2004 Yap VB, Speed TP. Modeling DNA Base Substitution in Large Genomic Regions from Two Organisms Journal of Molecular Evolution. 58: 12-18. PMID 14743311 DOI: 10.1007/s00239-003-2520-8  0.96
2004 Li LM, Speed TP. Deconvolution of sparse positive spikes Journal of Computational and Graphical Statistics. 13: 853-870. DOI: 10.1198/106186004X13118  0.96
2004 Lawrence C, Auger I, Gupta M, Liu JS, Speed T, Thorne JL. Discussions on "A Bayesian approach to DNA sequence segmentation" Biometrics. 60: 581-588. DOI: 10.1111/j.0006-341X.2004.206_2.x  0.96
2003 Schütz F, Kapp EA, Simpson RJ, Speed TP. Deriving statistical models for predicting peptide tandem MS product ion intensities Biochemical Society Transactions. 31: 1479-1483. PMID 14641094  0.96
2003 Kapp EA, Schütz F, Reid GE, Eddes JS, Moritz RL, O'Hair RA, Speed TP, Simpson RJ. Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Analytical Chemistry. 75: 6251-64. PMID 14616009 DOI: 10.1021/ac034616t  0.96
2003 Smyth GK, Speed T. Normalization of cDNA microarray data. Methods (San Diego, Calif.). 31: 265-73. PMID 14597310 DOI: 10.1016/S1046-2023(03)00155-5  0.96
2003 Hodder AN, Drew DR, Epa VC, Delorenzi M, Bourgon R, Miller SK, Moritz RL, Frecklington DF, Simpson RJ, Speed TP, Pike RN, Crabb BS. Enzymic, phylogenetic, and structural characterization of the unusual papain-like protease domain of Plasmodium falciparum SERA5. The Journal of Biological Chemistry. 278: 48169-77. PMID 13679369 DOI: 10.1074/jbc.M306755200  0.96
2003 de Koning-Ward TF, O'Donnell RA, Drew DR, Thomson R, Speed TP, Crabb BS. A new rodent model to assess blood stage immunity to the Plasmodium falciparum antigen merozoite surface protein 119 reveals a protective role for invasion inhibitory antibodies. The Journal of Experimental Medicine. 198: 869-75. PMID 12963693 DOI: 10.1084/jem.20030085  0.96
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