Publications (2002-Recent):
(updated 06/21/05)

Publications (1995-2001)

West RB, Nuyten DS, Subramanian S, Nielsen TO, Corless CL, Rubin BP, Montgomery K, Zhu S, Patel R, Hernandez-Boussard T, Goldblum JR, Brown PO, van de Vijver M, van de Rijn M.
Determination of stromal signatures in breast carcinoma.
PLOS Biology. 2005 Jun 3; 6(187): e187.
Pubmed PLOS Biology
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Arava Y, Boas FE, Brown PO, Herschlag D.
Dissecting eukaryotic translation and its control by ribosome density mapping.
Nucleic Acids Res. 2005 Apr 28; 33(8): 2421-32.
Pubmed Nucleic Acids Res
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Liang Y, Diehn M, Watson N, Bollen AW, Aldape KD, Nicholas MK, Lamborn KR, Berger MS, Botstein D, Brown PO, Israel MA.
Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.
Proc Natl Acad Sci U S A. 2005 Apr 19; 102(16): 5814-9.
Pubmed PNAS PDF

Shyamsundar R, Kim YH, Higgins JP, Montgomery K, Jorden M, Sethuraman A, van de Rijn M, Botstein D, Brown PO, Pollack JR.
A DNA microarray survey of gene expression in normal human tissues.
Genome Biology. Feb 14 2005; 6(3): R22.
Pubmed Genome Biology
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Chang HY, Nuyten DS, Sneddon JB, Hastie T, Tibshirani R, Sorlie T, Dai H, He YD, Van't Veer LJ, Bartelink H, van de Rijn M, Brown PO, van de Vijver MJ.
Robustness, scalability and integration of a wound-response gene expression signature in predicting breast cancer survival.
Proc Natl Acad Sci U S A. 2005 Feb 8; (): .
Pubmed PNAS
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Ball CA, Awad IA, Demeter J, Gollub J, Hebert JM, Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G.
The Stanford Microarray Database accommodates additional microarray platforms and data formats.
Nucleic Acids Res. 2005 Jan; 1(33): D580-2.
Pubmed Nucleic Acids Res
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Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, Cozzarelli NR.
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli.
Genome Biol. 2004; 5(11): R87.
Pubmed Genome Biology
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Eisen MB, Brown PO, Varmus HE.
PLoS Medicine-A Medical Journal for the Internet Age.
PLoS Medicine. 2004 Oct; 1(1): E31.
Pubmed PLoS Medicine
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Rubins KH, Hensley LE, Jahrling PB, Whitney AR, Geisbert TW, Huggins JW, Owen A, Leduc JW, Brown PO, Relman DA.
The host response to smallpox:analysis of the gene expression program in peripheral blood cells in a nonhuman primate model.
Pro Natl Acad Sci U S A. 2004 Oct 19; 101(42): 15190-5.
Pubmed PNAS
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Tu IP, Schaner M, Diehn M, Sikic BI, Brown PO, Botstein D, Fero MJ.
A method for detecting and correcting feature misidentification on expression microarrays.
BMC Genomics. 2004 Sept 09; 5(1): 64.
Pubmed BMC Genomics
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McCaffrey RL, Fawcett P, O'Riordan M, Lee KD, Havell EA, Brown PO, Portnoy DA.
A specific gene expression program triggered by Gram-positive bacteria in the cytosol.
Proc Natl Acad Sci U S A. 2004 Aug 3; 101(31): 11386-91.
Pubmed PNAS
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West RB, Harvell J, Linn SC, Liu CL, Prapong W, Hernandez-Bousard T, Montgomery K, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Brown PO, van de Rijn M.
Apo D in soft tissue tumors: a novel marker for dermatofibrosarcoma protuberans.
Am J Surg Pathol. 2004 Aug; 28(8): 1063-9.
Pubmed Am J Surg Pathol
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West RB, Corless CL, Chen X, Rubin BP, Subramanian S, Montgomery K, Zhu S, Ball CA, Nielsen TO, Patel R, Goldblum JR, Brown PO, Heinrich MC, van de Rijn M.
The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status.
Am J Pathol.. 2004 Jul; 165(1): 107-13.
Pubmed Am J. Pathol
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Munagala K, Tibshirani R, Brown PO.
Cancer characterization and feature set extraction by discriminative margin clustering.
BMC Bioinformatics. 2004 Mar 03; 5(1): 21.
Pubmed BMC Bioinformatics
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Gerber AP, Herschlag D, Brown PO.
Extensive association of funtionally and cytopically related mRNAs with Puf family RNA-binding proteins in yeast.
PLoS Biology. 2004 Mar; 2(3): E79.
Pubmed PLoS Biology PDF

Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, van de Rijn M, Botstein D, Brown PO.
Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds.
PLoS Biol. 2004 Feb; 2(2): 1.
Pubmed PLoS Biology Web Supplement PDF

Lapointe J, Li C, Higgins JP, Van De Rijn M, Bair E, Montgomery K, Ferrari M, Egevad L, Rayford W, Bergerheim U, Ekman P, DeMarzo AM, Tibshirani R, Botstein D, Brown PO, Brooks JD, Pollack JR.
Gene expression profiling identifies clinically relevant subtypes of prostate cancer.
Proc Natl Acad Sci U S A. 2004 Jan 20; 101(3): 811.
Pubmed PNAS Web Supplement PDF

Hurowitz EH, Brown PO.
Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae.
Genome Biol. 2003 Dec 22; 5(1): R2.
Pubmed Genome Biol Web Supplement PDF

Soen Y, Chen DS, Kraft DL, Davis MM, Brown PO.
Detection and characterization of cellular immune responses using peptide-MHC microarrays.
PLoS Biol. 2003 Dec; 1(3): E65.
Pubmed PLoS Biology Web Supplement PDF

Shakoury-Elizeh M, Tiedeman J, Rashford J, Ferea T, Demeter J, Garcia E, Rolfes R, Brown PO, Botstein D, Philpott CC.
Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae.
Mol Biol Cell. 2003 Dec 10; (): .
Pubmed Mol Biol Cell Web Supplement PDF

Higgins JP, Wang L, Kambham N, Montgomery K, Mason V, Vogelmann SU, Lemley KV, Brown PO, Brooks JD, Van De Rijn M.
Gene expression in the normal adult human kidney assessed by complementary DNA microarray.
Mol Biol Cell. 2003 Dec 2; (): .
Pubmed Mol Biol Cell Web Supplement PDF

Linn SC, West RB, Pollack JR, Zhu S, Hernandez-Boussard T, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Siegmund D, Botstein D, Brown PO, Gilks CB, van de Rijn M.
Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.
Am J Pathol. 2003 Dec; 163(6): 2383-95.
Pubmed Am J Pathol Web Supplement PDF

Roose JP, Diehn M, Tomlinson MG, Lin J, Alizadeh AA, Botstein D, Brown PO, Weiss A.
T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.
PLoS Biol. 2003 Nov; 1(2): E53.
Pubmed PLoS Biology Web Supplement PDF

Sperger JM, Chen X, Draper JS, Antosiewicz JE, Chon CH, Jones SB, Brooks JD, Andrews PW, Brown PO, Thomson JA.
Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors.
Proc Natl Acad Sci U S A. 2003 Nov 11; 100(23): 13350-5.
Pubmed PNAS Web Supplement PDF

Schaner ME, Ross DT, Ciaravino G, Sorlie T, Troyanskaya O, Diehn M, Wang YC, Duran GE, Sikic TL, Caldeira S, Skomedal H, Tu IP, Hernandez-Boussard T, Johnson SW, O'Dwyer PJ, Fero MJ, Kristensen GB, Borresen-Dale AL, Hastie T, Tibshirani R, van de Rijn M, Teng NN, Longacre TA, Botstein D, Brown PO, Sikic BI.
Gene expression patterns in ovarian carcinomas.
Mol Biol Cell. 2003 Nov; 14(11): 4376-86.
Pubmed Mol Biol Cell Web Supplement PDF

Brown PO, Eisen MB, Varmus HE.
Why PLoS became a publisher.
PLoS Biol. 2003 Oct; 1(1): E36.
Pubmed PLoS Biology
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Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, McCalmont TH, Brown PO, Botstein D, Connolly MK.
Systemic and cell type-specific gene expression patterns in scleroderma skin.
Proc Natl Acad Sci U S A. 2003 Oct 14; 100(21): 12319-24.
Pubmed PNAS Web Supplement PDF

Nielsen TO, Hsu FD, O'Connell JX, Gilks CB, Sorensen PH, Linn S, West RB, Liu CL, Botstein D, Brown PO, van de Rijn M.
Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology.
Am J Pathol. 2003 Oct; 163(4): 1449-56.
Pubmed Am J Pathol Web Supplement PDF

Shepard KA, Gerber AP, Jambhekar A, Takizawa PA, Brown PO, Herschlag D, DeRisi JL, Vale RD.
Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis.
Proc Natl Acad Sci U S A. 2003 Sep 30; 100(20): 11429-34.
Pubmed PNAS Web Supplement PDF

Chi JT, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, van de Rijn M, Botstein D, Brown PO.
Endothelial cell diversity revealed by global expression profiling.
Proc Natl Acad Sci U S A. 2003 Sep 16; 100(19): 10623-8.
Pubmed PNAS Web Supplement PDF

Chen X, Leung SY, Yuen ST, Chu KM, Ji J, Li R, Chan AS, Law S, Troyanskaya OG, Wong J, So S, Botstein D, Brown PO.
Variation in gene expression patterns in human gastric cancers.
Mol Biol Cell. 2003 Aug; 14(8): 3208-15.
Pubmed Mol Biol Cell Web Supplement PDF

Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, Lonning PE, Brown PO, Borresen-Dale AL, Botstein D.
Repeated observation of breast tumor subtypes in independent gene expression data sets.
Proc Natl Acad Sci U S A. 2003 Jul 8; 100(14): 8418-23.
Pubmed PNAS Web Supplement PDF

Holterhus PM, Hiort O, Demeter J, Brown PO, Brooks JD.
Differential gene-expression patterns in genital fibroblasts of normal males and 46,XY females with androgen insensitivity syndrome: evidence for early programming involving the androgen receptor.
Genome Biol. 2003 May 15; 4(6): R37.
Pubmed Genome Biol Web Supplement PDF

Nagy PL, Cleary ML, Brown PO, Lieb JD.
Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin.
Proc Natl Acad Sci U S A. 2003 May 27; 100(11): 6364-9.
Pubmed PNAS Web Supplement PDF

Chi JT, Chang HY, Wang NN, Chang DS, Dunphy N, Brown PO.
Genomewide view of gene silencing by small interfering RNAs.
Proc Natl Acad Sci U S A. 2003 May 27; 100(11): 6343-6.
Pubmed PNAS Web Supplement PDF

Iacobuzio-Donahue CA, Maitra A, Olsen M, Lowe AW, van Heek NT, Rosty C, Walter K, Sato N, Parker A, Ashfaq R, Jaffee E, Ryu B, Jones J, Eshleman JR, Yeo CJ, Cameron JL, Kern SE, Hruban RH, Brown PO, Goggins M.
Exploration of global gene expression patterns in pancreatic adenocarcinoma using cDNA microarrays.
Am J Pathol.. 2003 Apr; 162(4): 1151-62.
Pubmed Am J Pathol Web Supplement PDF

Arava Y,Wang Y, Storey JD, Liu C-L,Brown PO, Herschlag D.
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae.
Proc Natl Acad Sci U S A. 2003 Apr 1; 100(7): 3889-3894.
Pubmed PNAS PDF

Alter O, Brown PO, Botstein D.
Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.
Proc Natl Acad Sci U S A. 2003 Mar 18; 100(6): 3351-6.
Pubmed PNAS Web Supplement PDF

Whitney AR, Diehn M, Popper SJ, Alizadeh AA, Boldrick JC, Relman DA, Brown PO.
Individuality and variation in gene expression patterns in human blood.
Proc Natl Acad Sci U S A. 2003 Feb 18; 100(4): 1896-901.
Pubmed PNAS Web Supplement PDF

Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO Levy R.
Variation in gene expression patterns in follicular lymphoma and the response to rituximab.
Proc Natl Acad Sci U S A. 2003 Feb 18; 100(4): 1926-30.
Pubmed PNAS Web Supplement PDF

Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA.
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.
Nucleic Acids Res.. 2003 Jan 1; 31(1): 219-23.
Pubmed Nucleic Acids Res. Web Supplement PDF

Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown PO, Botstein D, Sherlock G.
The Stanford Microarray Database: data access and quality assessment tools.
Nucleic Acids Res.. 2003 Jan 1; 31(1): 94-6.
Pubmed Nucleic Acids Res. Web Supplement PDF

Baldwin DN, Vanchinathan V, Brown PO, Theriot JA.
A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes.
Genome Biol.. 2002 December 23; 4(1): R2.
Pubmed Genome Biol. Web Supplement PDF

Leung SY, Chen X, Chu KM, Yuen ST, Mathy J, Ji J, Chan AS, Li R, Law S, Troyanskaya OG, Tu IP, Wong J, So S, Botstein D, Brown PO.
Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis.
Proc Natl Acad Sci U S A. 2002 Dec 10; 99(25): 16203-8.
Pubmed PNAS Web Supplement PDF

Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D.
Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae.
Proc Natl Acad Sci U S A. 2002 Dec 10; 99(25): 16144-9.
Pubmed PNAS Web Supplement PDF

Troyanskaya OG, Garber ME, Brown PO, Botstein D.
Nonparametric methods for identifying differentially expressed genes in microarray data.
Bioinformatics. 2002 Nov; 18(11): 1454-61.
Pubmed Bioinformatics
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Tani TH, Khodursky A, Blumenthal RM, Brown PO, Matthews RG.
Adaptation to famine: A family of stationary-phase genes revealed by microarray analysis.
Proc Natl Acad Sci U S A. 2002 Oct 15; 99(21): 13471-13476.
Pubmed PNAS
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Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO.
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.
Proc Natl Acad Sci U S A. 2002 Oct 1; 99(20): 12963-8.
Pubmed PNAS Web Supplement PDF

Chang HY, Chi JT, Dudoit S, Bondre C, van de Rijn M, Botstein D, Brown PO.
Diversity, topographic differentiation, and positional memory in human fibroblasts.
Proc Natl Acad Sci U S A. 2002 Oct 1; 99(20): 12877-82.
Pubmed PNAS Web Supplement PDF

Diehn M, Alizadeh AA, Rando OJ, Liu CL, Stankunas K, Botstein D, Crabtree GR, Brown PO.
Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.
Proc Natl Acad Sci U S A. 2002 Sep 3; 99(18): 11796-11801.
Pubmed PNAS Web Supplement PDF

Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS.
Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.
J Biol Chem. 2002 Aug 23; 277(34): 31079-88.
Pubmed JBC Web Supplement PDF

Willert J, Epping M, Pollack JR, Brown PO, Nusse R.
A transcriptional response to Wnt protein in human embryonic carcinoma cells.
BMC Dev Biol. 2002 Jul 2; 2(1): 8.
Pubmed BMC Dev Biol
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DePrimo SE, Diehn M, Nelson JB, Reiter RE, Matese J, Fero M, Tibshirani R, Brown PO, Brooks JD.
Transcriptional programs activated by exposure of human prostate cancer cells to androgen.
Genome Biol. 2002 Jun 14; 3(7): RESEARCH0032.
Pubmed Genome Biol
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Lossos IS, Alizadeh AA, Diehn M, Warnke R, Thorstenson Y, Oefner PJ, Brown PO, Botstein D, Levy R.
Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.
Proc Natl Acad Sci U S A. 2002 Jun 25; 99(13): 8886-91.
Pubmed PNAS
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Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D.
Identification of genes periodically expressed in the human cell cycle and their expression in tumors.
Mol Biol Cell. 2002 Jun; 13(6): 1977-2000.
Pubmed Mol Biol Cell Web Supplement PDF

Sayama K, Diehn M, Matsuda K, Lunderius C, Tsai M, Tam SY, Botstein D, Brown PO, Galli SJ.
Transcriptional response of human mast cells stimulated via the FceRI and identification of mast cells as a source of IL-11.
BMC Immunol. 2002 Jun 12; 3(1): 5.
Pubmed BMC Immunol Web Supplement PDF

Chen X, Cheung ST, So S, Fan ST, Barry C, Higgins J, Lai KM, Ji J, Dudoit S, Ng IO, Van De Rijn M, Botstein D, Brown PO.
Gene expression patterns in human liver cancers.
Mol Biol Cell. 2002 Jun; 13(6): 1929-39.
Pubmed Mol Biol Cell
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Lin JY, Pollack JR, Chou FL, Rees CA, Christian AT, Bedford JS, Brown PO, Ginsberg MH.
Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays.
Genome Biol. 2002 May 14; 3(6): RESEARCH0026.1-7.
Pubmed Genome Biol
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Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO.
Precision and functional specificity in mRNA decay.
Proc Natl Acad Sci U S A. 2002 Apr 30; 99(9): 5860-5865.
Pubmed PNAS Web Supplement PDF

Nielsen TO, West RB, Linn SC, Alter O, Knowling MA, O'Connell JX, Zhu S, Fero M, Sherlock G, Pollack JR, Brown PO, Botstein D, van de Rijn M.
Molecular characterisation of soft tissue tumours: a gene expression study.
Lancet. 2002 Apr 13; 359(9314): 1301-7.
Pubmed Elsevier
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Robinson WH, DiGennaro C, Hueber W, Haab BB, Kamachi M, Dean EJ, Fournel S, Fong D, Genovese MC, de Vegvar HE, Skriner K, Hirschberg DL, Morris RI, Muller S, Pruijn GJ, van Venrooij WJ, Smolen JS, Brown PO, Steinman L, Utz PJ.
Autoantigen microarrays for multiplex characterization of autoantibody responses.
Nat Med. 2002 Mar; 8(3): 295-301.
Pubmed Nat Med
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Clement K, Viguerie N, Diehn M, Alizadeh A, Barbe P, Thalamas C, Storey JD, Brown PO, Barsh GS, Langin D.
In vivo regulation of human skeletal muscle gene expression by thyroid hormone.
Genome Res. 2002 Feb; 12(2): 281-291.
Pubmed Genome Res
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Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, Belcher CE, Botstein D, Staudt LM, Brown PO, Relman DA.
Stereotyped and specific gene expression programs in human innate immune responses to bacteria.
Proc Natl Acad Sci U S A. 2002 Jan 22; 99(2): 972-977.
Pubmed PNAS Web Supplement PDF