PubMed

Expression profiling of a hemopoietic cell survival transcriptome implicates osteopontin as a functional prognostic factor in AML.

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, Haylock DN, Nilsson SK, D'Andrea RJ, Lopez AF, Guthridge MA.

Blood. 2009 Oct 5. [Epub ahead of print]PMID: 19805619 [PubMed - as supplied by publisher]Related articles

Unliganded estrogen receptor-beta regulation of genes is inhibited by tamoxifen.

Levy N, Paruthiyil S, Zhao X, Vivar OI, Saunier EF, Griffin C, Tagliaferri M, Cohen I, Speed TP, Leitman DC.

Mol Cell Endocrinol. 2009 Sep 8. [Epub ahead of print]PMID: 19744542 [PubMed - as supplied by publisher]Related articles

Drug and cell type-specific regulation of genes with different classes of estrogen receptor beta-selective agonists.

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, Leitman DC.

PLoS One. 2009 Jul 17;4(7):e6271.PMID: 19609440 [PubMed - indexed for MEDLINE]Related articlesFree article

Gene expression profiling identifies activated growth factor signaling in poor prognosis (Luminal-B) estrogen receptor positive breast cancer.

Loi S, Sotiriou C, Haibe-Kains B, Lallemand F, Conus NM, Piccart MJ, Speed TP, McArthur GA.

BMC Med Genomics. 2009 Jun 24;2:37.PMID: 19552798 [PubMed - in process]Related articlesFree article

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6.

Bengtsson H, Wirapati P, Speed TP.

Bioinformatics. 2009 Sep 1;25(17):2149-56. Epub 2009 Jun 17.PMID: 19535535 [PubMed - indexed for MEDLINE]Related articlesFree article

Differential splicing using whole-transcript microarrays.

Robinson MD, Speed TP.

BMC Bioinformatics. 2009 May 22;10:156.PMID: 19463149 [PubMed - indexed for MEDLINE]Related articlesFree article

Sir2 paralogues cooperate to regulate virulence genes and antigenic variation in Plasmodium falciparum.

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.

PLoS Biol. 2009 Apr 14;7(4):e84.PMID: 19402747 [PubMed - indexed for MEDLINE]Related articlesFree article

A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods.

Bengtsson H, Ray A, Spellman P, Speed TP.

Bioinformatics. 2009 Apr 1;25(7):861-7. Epub 2009 Feb 4.PMID: 19193730 [PubMed - indexed for MEDLINE]Related articlesFree article

Temporal global expression data reveal known and novel salicylate-impacted processes and regulators mediating powdery mildew growth and reproduction on Arabidopsis.

Chandran D, Tai YC, Hather G, Dewdney J, Denoux C, Burgess DG, Ausubel FM, Speed TP, Wildermuth MC.

Plant Physiol. 2009 Mar;149(3):1435-51. Epub 2009 Jan 28.PMID: 19176722 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of the platypus genome suggests a transposon origin for mammalian imprinting.

Pask AJ, Papenfuss AT, Ager EI, McColl KA, Speed TP, Renfree MB.

Genome Biol. 2009;10(1):R1. Epub 2009 Jan 2.PMID: 19121219 [PubMed - indexed for MEDLINE]Related articlesFree article

Cell type- and estrogen receptor-subtype specific regulation of selective estrogen receptor modulator regulatory elements.

Ball LJ, Levy N, Zhao X, Griffin C, Tagliaferri M, Cohen I, Ricke WA, Speed TP, Firestone GL, Leitman DC.

Mol Cell Endocrinol. 2009 Feb 27;299(2):204-11. Epub 2008 Nov 18.PMID: 19059307 [PubMed - indexed for MEDLINE]Related articles

Sparse combinatorial inference with an application in cancer biology.

Mukherjee S, Pelech S, Neve RM, Kuo WL, Ziyad S, Spellman PT, Gray JW, Speed TP.

Bioinformatics. 2009 Jan 15;25(2):265-71. Epub 2008 Nov 27.PMID: 19038985 [PubMed - indexed for MEDLINE]Related articles

SOME STEP-DOWN PROCEDURES CONTROLLING THE FALSE DISCOVERY RATE UNDER DEPENDENCE.

Ge Y, Sealfon SC, Speed TP.

Stat Sin. 2008;18(3):881-904.PMID: 19018297 [PubMed]Related articlesFree article

Network inference using informative priors.

Mukherjee S, Speed TP.

Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14313-8. Epub 2008 Sep 17.PMID: 18799736 [PubMed - indexed for MEDLINE]Related articlesFree article

Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

Cancer Genome Atlas Research Network.

Nature. 2008 Oct 23;455(7216):1061-8. Epub 2008 Sep 4.PMID: 18772890 [PubMed - indexed for MEDLINE]Related articlesFree article

Integrative analysis of RUNX1 downstream pathways and target genes.

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, Kavallaris M, Smyth GK, Scott HS.

BMC Genomics. 2008 Jul 31;9:363.PMID: 18671852 [PubMed - indexed for MEDLINE]Related articlesFree article

On gene ranking using replicated microarray time course data.

Tai YC, Speed TP.

Biometrics. 2009 Mar;65(1):40-51. Epub 2008 Jun 5.PMID: 18537947 [PubMed - indexed for MEDLINE]Related articles

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.

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, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD.

PLoS Biol. 2008 Feb;6(2):e27.PMID: 18271625 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of gene expression during neurite outgrowth and regeneration.

Szpara ML, Vranizan K, Tai YC, Goodman CS, Speed TP, Ngai J.

BMC Neurosci. 2007 Nov 23;8:100.PMID: 18036227 [PubMed - indexed for MEDLINE]Related articlesFree article

A comparison of Affymetrix gene expression arrays.

Robinson MD, Speed TP.

BMC Bioinformatics. 2007 Nov 15;8:449.PMID: 18005448 [PubMed - indexed for MEDLINE]Related articlesFree article