Speednihbiosketch_dec_1_09

BIOGRAPHICAL SKETCH
eRA COMMONS USER NAME TERRYSPEED EDUCATION/TRAINING A. Positions and Honors
Positions and Employment
Tutor, Senior Tutor, Lecturer, Department of Mathematics, Monash University (Australia) Lecturer, Department of Probability and Statistics, University of Sheffield (U.K.) Associate Professor, Department of Mathematics, University of Western Australia Professor, Department of Mathematics, University of Western Australia Chair, Department of Mathematics, University of Western Australia Chief, Division of Mathematics and Statistics, Commonwealth Scientific and Industrial Research Organization, Canberra, Australia Chair, Department of Statistics, University of California, Berkeley Professor, Department of Statistics, University of California, Berkeley Senior Principal Research Fel ow, Bioinformatics Division, Walter & Eliza Hal Institute of Medical Research, Melbourne, Australia Other Experience and Professional Memberships
Associate editor of Journal of Computational Biology, Australian Journal of Statistics, Bernoul i
Member of NIH Genome Study Section (1995-98)
Honors and Awards
Fel ow, Institute of Mathematical Statistics (1984) Member, International Statistical Institute Fel ow, American Statistical Association (1989) Fel ow, American Association for the Advancement of Science Fel ow, Australian Academy of Sciences (2001) Awarded 2002 Pitman Medal (Statistical Society of Australia) Awarded 2003 Moyal Medal (Macquarie University) Australian Government Centenary Award Medal 2003 Joint recipient of 2004 Outstanding Applications Paper Award, American Statistical Association for the paper Irizarry et al. (2003) NHMRC Achievement Award for Excel ence in Health and Medical Research (2007) B. Recent peer-reviewed publications (in chronological order).
Rubio, J.P., Bahlo, M., Stankovich, J., Burfoot, R.K., Johnson, L.J., Huxtable, S., Butzkueven, H., Lin, L., Taylor, B.V., Speed,
T.P., Kilpatrick, T.J., Mignot, E., Foote, S.J. 2007. Analysis of extended HLA haplotypes in multiple sclerosis and narcolepsy
families confirms a predisposing ef ect for the class I region in Tasmanian MS patients. Immunogenetics. 59:177-86.
Mikkelsen, T.S., …, Speed, T.P., et al. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding
sequences. Nature. 447:167-177.
Belov, K., Sanderson, C.E., Deakin, J.E., Wong, E.S., Assange, D., McCol , K.A., Gout, A., de Bono, B., Barrow, A.D., Speed.
T.P., Trowsdale, J., Papenfuss, A.T. 2007. Characterization of the opossum immune genome provides insights into the evolution
of the mammalian immune system. Genome Res. Jul; 17:982-991
Qin, X., Ahn, S., Speed, T.P., Rubin, G.M. 2007. Global analyses of mRNA translational control during early Drosophila
embryogenesis. Genome Biol. 2007 Apr 22;8(4):R63
Levy, N., Zhao, X., Tang, H., Jaf e, R.B., Speed, T.P., Leitman, D.C. 2007. Multiple Transcription Factor Elements Col aborate with
ER{alpha} to Activate an Inducible Estrogen Response Element in the NKG2E gene. Endocrinology.2007 Jul;148(7):3449-58.
Hal grimsdot ir IB, Speed TP. (2007) The power of two-locus affected sib-pair linkage analysis to detect interacting disease loci.
Genet Epidemiol. 2008 Jan;32(1):84-8
Bret schneider, J., Col in, F., Bolstad, B. and Speed TP. (2007) Quality assessment for short oligonucleotide microarray data.
Technometrics: MS06-032R, 50(3):241-264
McCoubrie JE, Mil er SK, Sargeant T, Good RT, Hodder AN, Speed TP, de Koning-Ward TF, Crabb BS. (2007) Evidence for a
common role for the serine-type Plasmodium falciparum SERA proteases: Implications for vaccine and drug design. Infect Immun.
75(12):5565-74.
Robinson MD, De Souza DP, Wai Keen W, Saunders EC, McConvil e MJ, Speed TP, Likic VA. (2007) A dynamic programming
approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments. BMC Bioinformatics.
Oct 29;8(1):419.
Robinson MD, Speed TP (2007) A comparison of Af ymetrix gene expression arrays. BMC Bioinformatics, Nov 15; 8(1):449.
Ge, Y., Sealfon, S.C., Tseng, C-H and Speed TP. (2007) A Holm-type procedure control ing the false discovery rate. Statistics and
Probability Letters, 77(18): 1756-1762.
Georlette D, Ahn S, MacAlpine DM, Cheung E. Lewis PW, Beal EL, Speed TP, Manak JR and MR Botchan. (2007) Genomic
profiling and expression studies reveal both positive and negative activities for the Drosophila Myb-MuvB/dREAM complex in
proliferating cel s. Genes and Development. Nov 15;21(22):2880-96.
Zhang NR, Wildermuth, M, Speed TP. (2007) Transcription Factor Binding Site Prediction with Multivariate Gene Expression Data.
Annals of Applied Statistics, 2(1):332-365.
Szpara ML, Vranizan K, Tai YC, Goodman CS, Speed TP and Ngai J (2007) Analysis of Gene Expression during Neurite
Outgrowth and Regeneration. BMC Neuroscience. Nov 23;8(1):100
Ge Y, Sealfon SC and Speed TP (2008) Some Step-down Procedures Control ing the False Discovery Rate under Dependence
Statistica Sinica, (18):881-904.
Guipponi M, Toh MY, Tan J, Park D, Hanson K, Bal ana E, Kwong D, Cannon PZ, Wu Q, Gout A, Delorenzi M, Speed TP, Smith
RJ, Dahl HH, Petersen M, Teasdale RD, Estivil X, Park WJ, Scott HS. (2008) An integrated genetic and functional analysis of the
role of type I transmembrane serine proteases (TMPRSSs) in hearing loss. Hum Mutat. Jan;29(1):130-41.
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, Kilpatrick TJ and Rubio JP. (2008) 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.
Jan;71(1):42-50.
Levy N, Tatomer D, Herber CB, Zhao X, Tang H, Sargeant T, Bal LJ, Summers J, Speed TP, Leitman DC. (2008) Differential
regulation of Native Estrogen Receptor Regulatory Elements by Estradiol, Tamoxifen, and Raloxifene. Mol Endocrinol. 22(2):287-
303.
Li XY, Macarthur S, Bourgon R, Nix D, Pol ard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Hendriks CL, Chu HC, Ogawa
N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin
MD. (2008) Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm. PLoS Biol. Feb
12;6(2):e27
Bengtsson H, Irizarry R, Carvalho B and TP Speed (2008) Estimation and assessment of raw copy numbers at the single locus
level. Bioinformatics, 24 (6): 759-767.
Chuan Tai Y, Speed TP. (2008) On Gene Ranking Using Replicated Microarray Time Course Data Biometrics. 2008 Jun 5. [Epub
ahead of print]
Purdom E, Simpson KM, Robinson MD, Conboy JG, Lapuk AV, Speed TP. (2008) FIRMA: a method for detection of alternative
splicing from exon array data. Bioinformatics. 24(15):1707-14.
Rubio JP, Stankovich J, Field J, Tubridy N, Marriot M, Chapman C, Bahlo M, Perera D, Johnson LJ, Tait BD, Varney MD, Speed
TP, Taylor BV, Foote SJ, Butzkueven H, Kilpatrick TJ. (2008) Replication of KIAA0350, IL2RA, RPL5 and CD58 as multiple
sclerosis susceptibility genes in Australians. Genes Immun. 624–630; doi:10.1038/gene.2008.59.
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, Turner DR, Speed TP, Kaval aris M, Smyth GK, Scott HS. (2008) Integrative analysis
of RUNX1 downstream pathways and target genes. BMC Genomics. Jul 31;9:363.
The Cancer Genome Research Atlas Network (2008) Comprehensive genomic characterization defines human glioblastoma
genes and core pathways. Nature. 2008 Oct 23;455(7216):1061-8.
Mukherjee S, Speed TP. (2008) Network inference using informative priors. Proc Natl Acad Sci U S A. 2008 Sep
23;105(38):14313-8
Ge Y, Sealfon SC, Speed TP. Some step-down procedures control ing the false discovery rate under dependence. Stat Sin.
2008;18(3):881-904.
Pask AJ, Papenfuss AT, Ager EI, McCol KA, Speed TP, Renfree MB. Analysis of the platypus genome suggests a transposon
origin for mammalian imprinting. Genome Biol. 10(1):R1, 2009 Chandran D, Tai YC, Hather G, Dewdney J, Denoux C, Burgess DG, Ausubel FM, Speed TP, Wildermuth MC. Temporal Global
Expression Data Reveals Known and Novel Salicylate-Impacted Processes and Regulators Mediating Powdery Mildew Growth
and Reproduction on Arabidopsis. Plant Physiol. 2009 Jan.
Bengtsson H, Ray A, Spel man P, Speed TP. A single-sample method for normalizing and combining ful -resolution copy numbers
from multiple platforms, labs and analysis methods. Bioinformatics. 2009, Feb.
Mukherjee S, Pelech S, Neve RM, Kuo WL, Ziyad S, Spel man PT, Gray JW, Speed TP. Sparse combinatorial inference with an
application in cancer biology. Bioinformatics. 25(2):265-71, 2009.
Bal LJ, Levy N, Zhao X, Griffin C, Tagliaferri M, Cohen I, Ricke WA, Speed TP, Firestone GL, Leitman DC. Cel type- and estrogen
receptor-subtype specific regulation of selective estrogen receptor modulator regulatory elements. Mol Cel Endocrinol. 299(2):204-
11, 2009 Feb.
Tonkin CJ, Carret CK, Duraisingh MT, Voss TS, Ralph SA, Hommel M, Duf y 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
Biol. 14;7(4):e84, 2009 April.
Robinson MD, Speed TP. Differential splicing using whole-transcript microarrays. BMC Bioinformatics. 22;10(1):156, 2009 May.
Bengtsson H, Wirapati P, Speed TP. A single-array preprocessing method for estimating ful -resolution raw copy numbers from al
Af ymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics. 2009 Jun 17. [Epub ahead of print] Loi S, Sotiriou C, Haibe-Kains B, Lal emand 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 Med
Genomics. 2009 Jun 24;2:37.
Paruthiyil S, Cvoro A, Zhao X, Wu Z, Sui Y, Staub RE, Bagget S, Herber CB, Griffin C, Tagliaferri M, Harris HA, Cohen I,
Bjeldanes LF, Speed TP, Schaufele F, Leitman DC. Drug and cel type-specific regulation of genes with dif erent classes of
estrogen receptor beta-selective agonists. PLoS One. 2009 Jul 17;4(7):e6271.
Powel JA, Thomas D, Barry EF, Kok CH, McClure BJ, Tsykin A, To LB, Brown A, Lewis ID, Herbert K, Goodal GJ, Speed TP,
Asou N, Jacob B, Osato M, Haylock DN, Nilsson SK, D'Andrea RJ, Lopez AF, Guthridge MA. Expression profiling of a
hemopoietic cel survival transcriptome implicates osteopontin as a functional prognostic factor in AML. Blood. 2009 Oct 5. [Epub
ahead of print]
Levy N, Paruthiyil S, Zhao X, Vivar OI, Saunier EF, Grif in C, Tagliaferri M, Cohen I, Speed TP, Leitman DC. Unliganded estrogen
receptor-beta regulation of genes is inhibited by tamoxifen. Mol Cel Endocrinol. 2009 Sep 8. [Epub ahead of print]
C. Research support.
5R01DC007235-04 (Ngai) 12/15/2004-11/30/2010 0.3 summer, 0.9 academic
Programs of Gene Expression in Olfactory Neurogenesis The major goals of this project are the elucidation of the mechanisms of olfactory discrimination and the developmental mechanisms responsible for specifying odorant receptor expression in olfactory neurons and the path-finding of these cel s’ axons to their appropriate targets. Role: Co-Investigator 5U24CA126551-02 (Gray) 02/01/2007-08/31/2010 0.6 calendar Lawrence Berkeley National Lab, NIH Prime Elizabeth Purdom for the Berkeley Cancer Genome Center The major goals of this project are the gene expression profiling at the exon level of large numbers of mRNA samples from tumors, with a view to characterizing the splice variation exhibited therein, and relating this variation to other phenotypic and genotypic data on the same tumors. Role: Subcontract PI 20000275794 (Irizarry) 09/24/2007-08/31/2010 0.6 calendar Preprocessing and Analysis Tools for Contemporary Microarray Applications
The major goals of this project are to develop statistical y rigorous procedures for five microarray applications with a rapidly growing
user base: high-throughput genotyping, whole-genome chromosomal abnormality detection, discovering promoter binding sites with
ChIPchip technology, high-throughput detection of methylated sites, and alternative splicing detection.
Role: Subcontract PI
6901205 (Speed-Spel man) 01/10/2009-31/07/2014 2.4 academic
LBNL Lawrence Berkeley National Laboratory, NIH/NCI $499,992
TCGA Gene Data Analysis Center at Berkeley
The task of this consultancy is to carry out statistical research concerning the routine analysis of data on mRNA and miRNA
abundance, DNA copy number and methylation data on tissue from many hundreds of fresh frozen tumors.
Pending
20093662 (Gray ) 1/09/2009-31/08/2010 0.6 calendar
LBNL Lawrence Berkeley National Laboratory , NIH/NCI $161,000
The Berkeley Cancer Genome Center
The major goals of this project are the gene expression profiling at the exon level of large numbers of mRNA samples from tumors, with
a view to characterizing the splice variation exhibited therein, and relating this variation to other phenotypic and genotypic data on the
same tumors
20091770 01/08/2009-31/07/2012 2.4 calendar
LBNL Lawrence Berkeley National Laboratory , Stand Up to Cancer $472,974
Personalizing Treatment of Triple Negative, Metastatic Breast Cancer
The main goal of this project is to contribute to the methods development aimed at using preclinical and clinical data to identify drug(s)
that are highly ef ective in the molecularly defined ER-positive, HER2-positive and Triple Negative breast cancer subtypes

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