Patrick O. Brown

Publications

• An interview with Patrick O Brown on the origins and future of open access. Brown PO, BMC Biol. 2013: 11 33
• Improved discovery of molecular interactions in genome-scale data with adaptive model-based normalization. Salzman J, Klass DM, Brown PO. PLoS One. 2013; 8 (1): e53930
• Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae. Klass DM, Scheibe M, Butter F, Hogan GJ, Mann M, Brown PO. Genome Res. 2013
• Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. PLoS One. 2012; 7 (2): e30733
• Extensive gene-specific translational reprogramming in a model of B cell differentiation and Abl-dependent transformation. Bates JG, Salzman J, May D, Garcia PB, Hogan GJ, McIntosh M, Schlissel MS, Brown PO. PLoS One. 2012; 7 (5): e37108
• Interferon and biologic signatures in dermatomyositis skin: specificity and heterogeneity across diseases. Wong D, Kea B, Pesich R, Higgs BW, Zhu W, Brown P, Yao Y, Fiorentino D. PLoS One. 2012; 7 (1): e29161
• The yeast Rab GTPase Ypt1 modulates unfolded protein response dynamics by regulating the stability of HAC1 RNA. Tsvetanova NG, Riordan DP, Brown PO. PLoS Genet. 2012; 8 (7): e1002862
• Widespread mRNA association with cytoskeletal motor proteins and identification and dynamics of myosin-associated mRNAs in S. cerevisiae. Casolari JM, Thompson MA, Salzman J, Champion LM, Moerner WE, Brown PO. PLoS One. 2012; 7 (2): e31912
• Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes. del Alamo M, Hogan DJ, Pechmann S, Albanese V, Brown PO, Frydman J. PLoS Biol. 2011; 9 (7): e1001100
• ESRRA-C11orf20 is a recurrent gene fusion in serous ovarian carcinoma. Salzman J, Marinelli RJ, Wang PL, Green AE, Nielsen JS, Nelson BH, Drescher CW, Brown PO. PLoS Biol. 2011; 9 (9): e1001156
• Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome. Riordan DP, Herschlag D, Brown PO. Nucleic Acids Res. 2011; 39 (4): 1501-9
• Stunned silence: gene expression programs in human cells infected with monkeypox or vaccinia virus. Rubins KH, Hensley LE, Relman DA, Brown PO. PLoS One. 2011; 6 (1): e15615
• Dissecting interferon-induced transcriptional programs in human peripheral blood cells. Waddell SJ, Popper SJ, Rubins KH, Griffiths MJ, Brown PO, Levin M, Relman DA. PLoS One. 2010; 5 (3): e9753
• Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. Tsvetanova NG, Klass DM, Salzman J, Brown PO. PLoS One. 2010; 5 (9)
• Three-dimensional tracking of single mRNA particles in Saccharomyces cerevisiae using a double-helix point spread function. Thompson MA, Casolari JM, Badieirostami M, Brown PO, Moerner WE. Proc Natl Acad Sci U S A. 2010; 107 (42): 17864-71
• Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, Brown PO. PLoS Biol. 2009; 7 (11): e1000238
• The preclinical natural history of serous ovarian cancer: defining the target for early detection. Brown PO, Palmer C. PLoS Med. 2009; 6 (7): e1000114
• Comparative analysis of viral gene expression programs during poxvirus infection: a transcriptional map of the vaccinia and monkeypox genomes. Rubins KH, Hensley LE, Bell GW, Wang C, Lefkowitz EJ, Brown PO, Relman DA. PLoS One. 2008; 3 (7): e2628
• Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO. PLoS Biol. 2008; 6 (10): e255
• Systematic evaluation of candidate blood markers for detecting ovarian cancer. Palmer C, Duan X, Hawley S, Scholler N, Thorpe JD, Sahota RA, Wong MQ, Wray A, Bergan LA, Drescher CW, McIntosh MW, Brown PO, Nelson BH, Urban N. PLoS One. 2008; 3 (7): e2633
• Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE, Brown PO. PLoS One. 2008; 3 (5): e2126
• The Stanford Tissue Microarray Database. Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, van de Rijn M, Brown PO, Ball CA. Nucleic Acids Res. 2008; 36 (Database issue): D871-7
• Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer. Buess M, Nuyten DS, Hastie T, Nielsen T, Pesich R, Brown PO. Genome Biol. 2007; 8 (9): R191
• Development of the human infant intestinal microbiota. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. PLoS Biol. 2007; 5 (7): e177
• Gene expression patterns in pancreatic tumors, cells and tissues. Lowe AW, Olsen M, Hao Y, Lee SP, Taek Lee K, Chen X, van de Rijn M, Brown PO. PLoS One. 2007; 2 (3): e323
• Gene expression programs of human smooth muscle cells: tissue-specific differentiation and prognostic significance in breast cancers. Chi JT, Rodriguez EH, Wang Z, Nuyten DS, Mukherjee S, van de Rijn M, van de Vijver MJ, Hastie T, Brown PO. PLoS Genet. 2007; 3 (9): 1770-84
• Gene-expression patterns reveal underlying biological processes in Kawasaki disease. Popper SJ, Shimizu C, Shike H, Kanegaye JT, Newburger JW, Sundel RP, Brown PO, Burns JC, Relman DA. Genome Biol. 2007; 8 (12): R261
• Parallels between global transcriptional programs of polarizing Caco-2 intestinal epithelial cells in vitro and gene expression programs in normal colon and colon cancer. Sääf AM, Halbleib JM, Chen X, Yuen ST, Leung SY, Nelson WJ, Brown PO. Mol Biol Cell. 2007; 18 (11): 4245-60
• The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G, Ball CA. Nucleic Acids Res. 2007; 35 (Database issue): D766-70
• The temporal program of peripheral blood gene expression in the response of nonhuman primates to Ebola hemorrhagic fever. Rubins KH, Hensley LE, Wahl-Jensen V, Daddario DiCaprio KM, Young HA, Reed DS, Jahrling PB, Brown PO, Relman DA, Geisbert TW. Genome Biol. 2007; 8 (8): R174
• Transcriptional modulation of genes encoding structural characteristics of differentiating enterocytes during development of a polarized epithelium in vitro. Halbleib JM, Sääf AM, Brown PO, Nelson WJ. Mol Biol Cell. 2007; 18 (11): 4261-78
• Transcriptional program induced by Wnt protein in human fibroblasts suggests mechanisms for cell cooperativity in defining tissue microenvironments. Klapholz-Brown Z, Walmsley GG, Nusse YM, Nusse R, Brown PO. PLoS One. 2007; 2 (9): e945
• Virtual Northern analysis of the human genome. Hurowitz EH, Drori I, Stodden VC, Donoho DL, Brown PO. PLoS One. 2007; 2 (5): e460
• 2005 Curt Stern Award address. Exploring along a crooked path. Brown PO, Am J Hum Genet. 2006; 79 (3): 429-33
• A landscape effect in tenosynovial giant-cell tumor from activation of CSF1 expression by a translocation in a minority of tumor cells. West RB, Rubin BP, Miller MA, Subramanian S, Kaygusuz G, Montgomery K, Zhu S, Marinelli RJ, De Luca A, Downs-Kelly E, Goldblum JR, Corless CL, Brown PO, Gilks CB, Nielsen TO, Huntsman D, van de Rijn M. Proc Natl Acad Sci U S A. 2006; 103 (3): 690-5
• Anatomic demarcation by positional variation in fibroblast gene expression programs. Rinn JL, Bondre C, Gladstone HB, Brown PO, Chang HY. PLoS Genet. 2006; 2 (7): e119
• Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation. Sneddon JB, Zhen HH, Montgomery K, van de Rijn M, Tward AD, West R, Gladstone H, Chang HY, Morganroth GS, Oro AE, Brown PO. Proc Natl Acad Sci U S A. 2006; 103 (40): 14842-7
• Cell-type specific gene expression profiles of leukocytes in human peripheral blood. Palmer C, Diehn M, Alizadeh AA, Brown PO. BMC Genomics. 2006: 7 115
• Discovery and validation of breast cancer subtypes. Kapp AV, Jeffrey SS, Langerød A, Børresen-Dale AL, Han W, Noh DY, Bukholm IR, Nicolau M, Brown PO, Tibshirani R. BMC Genomics. 2006: 7 231
• Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments. Soen Y, Mori A, Palmer TD, Brown PO. Mol Syst Biol. 2006: 2 37
• Gene expression patterns in human placenta. Sood R, Zehnder JL, Druzin ML, Brown PO. Proc Natl Acad Sci U S A. 2006; 103 (14): 5478-83
• Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. Chi JT, Wang Z, Nuyten DS, Rodriguez EH, Schaner ME, Salim A, Wang Y, Kristensen GB, Helland A, Børresen-Dale AL, Giaccia A, Longaker MT, Hastie T, Yang GP, van de Vijver MJ, Brown PO. PLoS Med. 2006; 3 (3): e47
• Genome-scale identification of membrane-associated human mRNAs. Diehn M, Bhattacharya R, Botstein D, Brown PO. PLoS Genet. 2006; 2 (1): e11
• Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Gerber AP, Luschnig S, Krasnow MA, Brown PO, Herschlag D. Proc Natl Acad Sci U S A. 2006; 103 (12): 4487-92
• Minimizing off-target effects by using diced siRNAs for RNA interference. Myers JW, Chi JT, Gong D, Schaner ME, Brown PO, Ferrell JE. J RNAi Gene Silencing. 2006; 2 (2): 181-94
• Predicting a local recurrence after breast-conserving therapy by gene expression profiling. Nuyten DS, Kreike B, Hart AA, Chi JT, Sneddon JB, Wessels LF, Peterse HJ, Bartelink H, Brown PO, Chang HY, van de Vijver MJ. Breast Cancer Res. 2006; 8 (5): R62
• Rapid quantitative profiling of complex microbial populations. Palmer C, Bik EM, Eisen MB, Eckburg PB, Sana TR, Wolber PK, Relman DA, Brown PO. Nucleic Acids Res. 2006; 34 (1): e5
• A DNA microarray survey of gene expression in normal human tissues. Shyamsundar R, Kim YH, Higgins JP, Montgomery K, Jorden M, Sethuraman A, van de Rijn M, Botstein D, Brown PO, Pollack JR. Genome Biol. 2005; 6 (3): R22
• Determination of stromal signatures in breast carcinoma. 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. PLoS Biol. 2005; 3 (6): e187
• Differential gene expression in anatomical compartments of the human eye. Diehn JJ, Diehn M, Marmor MF, Brown PO. Genome Biol. 2005; 6 (9): R74
• Dissecting eukaryotic translation and its control by ribosome density mapping. Arava Y, Boas FE, Brown PO, Herschlag D. Nucleic Acids Res. 2005; 33 (8): 2421-32
• Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Liang Y, Diehn M, Watson N, Bollen AW, Aldape KD, Nicholas MK, Lamborn KR, Berger MS, Botstein D, Brown PO, Israel MA. Proc Natl Acad Sci U S A. 2005; 102 (16): 5814-9
• Marked differences in human melanoma antigen-specific T cell responsiveness after vaccination using a functional microarray. Chen DS, Soen Y, Stuge TB, Lee PP, Weber JS, Brown PO, Davis MM. PLoS Med. 2005; 2 (10): e265
• Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Chang HY, Nuyten DS, Sneddon JB, Hastie T, Tibshirani R, Sørlie T, Dai H, He YD, van't Veer LJ, Bartelink H, van de Rijn M, Brown PO, van de Vijver MJ. Proc Natl Acad Sci U S A. 2005; 102 (10): 3738-43
• The Stanford Microarray Database accommodates additional microarray platforms and data formats. 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. Nucleic Acids Res. 2005; 33 (Database issue): D580-2
• A method for detecting and correcting feature misidentification on expression microarrays. Tu IP, Schaner M, Diehn M, Sikic BI, Brown PO, Botstein D, Fero MJ. BMC Genomics. 2004: 5 64
• A specific gene expression program triggered by Gram-positive bacteria in the cytosol. McCaffrey RL, Fawcett P, O'Riordan M, Lee KD, Havell EA, Brown PO, Portnoy DA. Proc Natl Acad Sci U S A. 2004; 101 (31): 11386-91
• Apo D in soft tissue tumors: a novel marker for dermatofibrosarcoma protuberans. West RB, Harvell J, Linn SC, Liu CL, Prapong W, Hernandez-Boussard T, Montgomery K, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Brown PO, van de Rijn M, Lui CL. Am J Surg Pathol. 2004; 28 (8): 1063-9
• Cancer characterization and feature set extraction by discriminative margin clustering. Munagala K, Tibshirani R, Brown PO. BMC Bioinformatics. 2004: 5 21
• Diverse and specific gene expression responses to stresses in cultured human cells. Murray JI, Whitfield ML, Trinklein ND, Myers RM, Brown PO, Botstein D. Mol Biol Cell. 2004; 15 (5): 2361-74
• Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. Gerber AP, Herschlag D, Brown PO. PLoS Biol. 2004; 2 (3): E79
• Gene expression in the normal adult human kidney assessed by complementary DNA microarray. Higgins JP, Wang L, Kambham N, Montgomery K, Mason V, Vogelmann SU, Lemley KV, Brown PO, Brooks JD, van de Rijn M. Mol Biol Cell. 2004; 15 (2): 649-56
• Gene expression profiling identifies clinically relevant subtypes of prostate cancer. 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. Proc Natl Acad Sci U S A. 2004; 101 (3): 811-6
• Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, van de Rijn M, Botstein D, Brown PO. PLoS Biol. 2004; 2 (2): E7
• Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, Cozzarelli NR. Genome Biol. 2004; 5 (11): R87
• PLoS Medicine - a medical journal for the internet age Eisen MB, Brown PO, Varmus HE. PLoS Medicine. 2004; 1 (1): e31
• Presynaptic homeostasis at CNS nerve terminals compensates for lack of a key Ca2+ entry pathway. Piedras-Rentería ES, Pyle JL, Diehn M, Glickfeld LL, Harata NC, Cao Y, Kavalali ET, Brown PO, Tsien RW. Proc Natl Acad Sci U S A. 2004; 101 (10): 3609-14
• The host response to smallpox: analysis of the gene expression program in peripheral blood cells in a nonhuman primate model. Rubins KH, Hensley LE, Jahrling PB, Whitney AR, Geisbert TW, Huggins JW, Owen A, Leduc JW, Brown PO, Relman DA. Proc Natl Acad Sci U S A. 2004; 101 (42): 15190-5
• The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status. 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. Am J Pathol. 2004; 165 (1): 107-13
• Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae. Shakoury-Elizeh M, Tiedeman J, Rashford J, Ferea T, Demeter J, Garcia E, Rolfes R, Brown PO, Botstein D, Philpott CC. Mol Biol Cell. 2004; 15 (3): 1233-43
• A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes. Baldwin DN, Vanchinathan V, Brown PO, Theriot JA. Genome Biol. 2003; 4 (1): R2
• Detection and characterization of cellular immune responses using peptide-MHC microarrays. Soen Y, Chen DS, Kraft DL, Davis MM, Brown PO. PLoS Biol. 2003; 1 (3): E65
• 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. Holterhus PM, Hiort O, Demeter J, Brown PO, Brooks JD. Genome Biol. 2003; 4 (6): R37
• Endothelial cell diversity revealed by global expression profiling. Chi JT, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, van de Rijn M, Botstein D, Brown PO. Proc Natl Acad Sci U S A. 2003; 100 (19): 10623-8
• Exploration of global gene expression patterns in pancreatic adenocarcinoma using cDNA microarrays. 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. Am J Pathol. 2003; 162 (4): 1151-62
• Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. 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. Am J Pathol. 2003; 163 (6): 2383-95
• Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Sperger JM, Chen X, Draper JS, Antosiewicz JE, Chon CH, Jones SB, Brooks JD, Andrews PW, Brown PO, Thomson JA. Proc Natl Acad Sci U S A. 2003; 100 (23): 13350-5
• Gene expression patterns in ovarian carcinomas. 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. Mol Biol Cell. 2003; 14 (11): 4376-86
• Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Alter O, Brown PO, Botstein D. Proc Natl Acad Sci U S A. 2003; 100 (6): 3351-6
• Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Hurowitz EH, Brown PO. Genome Biol. 2003; 5 (1): R2
• Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D. Proc Natl Acad Sci U S A. 2003; 100 (7): 3889-94
• Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. Nagy PL, Cleary ML, Brown PO, Lieb JD. Proc Natl Acad Sci U S A. 2003; 100 (11): 6364-9
• Genomewide view of gene silencing by small interfering RNAs. Chi JT, Chang HY, Wang NN, Chang DS, Dunphy N, Brown PO. Proc Natl Acad Sci U S A. 2003; 100 (11): 6343-6
• Individuality and variation in gene expression patterns in human blood. Whitney AR, Diehn M, Popper SJ, Alizadeh AA, Boldrick JC, Relman DA, Brown PO. Proc Natl Acad Sci U S A. 2003; 100 (4): 1896-901
• Repeated observation of breast tumor subtypes in independent gene expression data sets. Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, Lønning PE, Brown PO, Børresen-Dale AL, Botstein D. Proc Natl Acad Sci U S A. 2003; 100 (14): 8418-23
• SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA. Nucleic Acids Res. 2003; 31 (1): 219-23
• Systemic and cell type-specific gene expression patterns in scleroderma skin. Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, McCalmont TH, Brown PO, Botstein D, Connolly MK. Proc Natl Acad Sci U S A. 2003; 100 (21): 12319-24
• T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression. Roose JP, Diehn M, Tomlinson MG, Lin J, Alizadeh AA, Botstein D, Brown PO, Weiss A. PLoS Biol. 2003; 1 (2): E53
• The Stanford Microarray Database: data access and quality assessment tools. 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. Nucleic Acids Res. 2003; 31 (1): 94-6
• Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology. 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. Am J Pathol. 2003; 163 (4): 1449-56
• Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R. Proc Natl Acad Sci U S A. 2003; 100 (4): 1926-30
• Variation in gene expression patterns in human gastric cancers. 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. Mol Biol Cell. 2003; 14 (8): 3208-15
• Why PLoS became a publisher. Brown PO, Eisen MB, Varmus HE. PLoS Biol. 2003; 1 (1): E36
• Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis. Shepard KA, Gerber AP, Jambhekar A, Takizawa PA, Brown PO, Herschlag D, DeRisi JL, Vale RD. Proc Natl Acad Sci U S A. 2003; 100 (20): 11429-34
• A transcriptional response to Wnt protein in human embryonic carcinoma cells. Willert J, Epping M, Pollack JR, Brown PO, Nusse R. BMC Dev Biol. 2002: 2 8
• Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Tani TH, Khodursky A, Blumenthal RM, Brown PO, Matthews RG. Proc Natl Acad Sci U S A. 2002; 99 (21): 13471-6
• Autoantigen microarrays for multiplex characterization of autoantibody responses. 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. Nat Med. 2002; 8 (3): 295-301
• Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D. Proc Natl Acad Sci U S A. 2002; 99 (25): 16144-9
• Diversity, topographic differentiation, and positional memory in human fibroblasts. Chang HY, Chi JT, Dudoit S, Bondre C, van de Rijn M, Botstein D, Brown PO. Proc Natl Acad Sci U S A. 2002; 99 (20): 12877-82
• Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. van de Rijn M, Perou CM, Tibshirani R, Haas P, Kallioniemi O, Kononen J, Torhorst J, Sauter G, Zuber M, Köchli OR, Mross F, Dieterich H, Seitz R, Ross D, Botstein D, Brown P. Am J Pathol. 2002; 161 (6): 1991-6
• Gene expression patterns in human liver cancers. 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. Mol Biol Cell. 2002; 13 (6): 1929-39
• Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS. J Biol Chem. 2002; 277 (34): 31079-88
• Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Diehn M, Alizadeh AA, Rando OJ, Liu CL, Stankunas K, Botstein D, Crabtree GR, Brown PO. Proc Natl Acad Sci U S A. 2002; 99 (18): 11796-801
• Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D. Mol Biol Cell. 2002; 13 (6): 1977-2000
• In vivo regulation of human skeletal muscle gene expression by thyroid hormone. Clément K, Viguerie N, Diehn M, Alizadeh A, Barbe P, Thalamas C, Storey JD, Brown PO, Barsh GS, Langin D. Genome Res. 2002; 12 (2): 281-91
• Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Pollack JR, Sørlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Børresen-Dale AL, Brown PO. Proc Natl Acad Sci U S A. 2002; 99 (20): 12963-8
• Molecular characterisation of soft tissue tumours: a gene expression study. 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. Lancet. 2002; 359 (9314): 1301-7
• Nonparametric methods for identifying differentially expressed genes in microarray data. Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. Bioinformatics. 2002; 18 (11): 1454-61
• Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis. 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. Proc Natl Acad Sci U S A. 2002; 99 (25): 16203-8
• Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays. Lin JY, Pollack JR, Chou FL, Rees CA, Christian AT, Bedford JS, Brown PO, Ginsberg MH. Genome Biol. 2002; 3 (6): RESEARCH0026
• Precision and functional specificity in mRNA decay. Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Proc Natl Acad Sci U S A. 2002; 99 (9): 5860-5
• Public-access group supports PubMed Central. Eisen MB, Brown PO, Varmus HE. Nature. 2002; 419 (6903): 111
• Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, Belcher CE, Botstein D, Staudt LM, Brown PO, Relman DA. Proc Natl Acad Sci U S A. 2002; 99 (2): 972-7
• Transcriptional programs activated by exposure of human prostate cancer cells to androgen. DePrimo SE, Diehn M, Nelson JB, Reiter RE, Matese J, Fero M, Tibshirani R, Brown PO, Brooks JD. Genome Biol. 2002; 3 (7): RESEARCH0032
• Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11. Sayama K, Diehn M, Matsuda K, Lunderius C, Tsai M, Tam SY, Botstein D, Brown PO, Galli SJ. BMC Immunol. 2002: 3 5
• Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes. Lossos IS, Alizadeh AA, Diehn M, Warnke R, Thorstenson Y, Oefner PJ, Brown PO, Botstein D, Levy R. Proc Natl Acad Sci U S A. 2002; 99 (13): 8886-91
• Genomic analysis of renal allograft dysfunction using cDNA microarrays. Sarwal M, Chang S, Barry C, Chen X, Alizadeh A, Salvatierra O, Brown P. Transplant Proc. 2001 Feb-Mar; 33 (1-2): 297-8
• A second iron-regulatory system in yeast independent of Aft1p. Rutherford JC, Jaron S, Ray E, Brown PO, Winge DR. Proc Natl Acad Sci U S A. 2001; 98 (25): 14322-7
• Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC. Genetics. 2001; 158 (1): 41-64
• Comparative genome-scale analysis of gene expression profiles in T cell lymphoma cells during malignant progression using a complementary DNA microarray. Li S, Ross DT, Kadin ME, Brown PO, Wasik MA. Am J Pathol. 2001; 158 (4): 1231-7
• Comprehensive mutational analysis of the Moloney murine leukemia virus envelope protein. Rothenberg SM, Olsen MN, Laurent LC, Crowley RA, Brown PO. J Virol. 2001; 75 (23): 11851-62
• Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Sato K, Tokusumi Y, Kikuchi N, Ishii Y, Hamaguchi Y, Nishizuka I, Goto H, Nitanda H, Satomi S, Yoshiki A, Kusakabe M, DeRisi JL, Eisen MB, Iyer VR, Brown PO, Muramatsu M, Shimada H, Okazaki Y, Hayashizaki Y. Proc Natl Acad Sci U S A. 2001; 98 (5): 2199-204
• Diversity of gene expression in adenocarcinoma of the lung. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I. Proc Natl Acad Sci U S A. 2001; 98 (24): 13784-9
• Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Sørlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Lønning PE, Børresen-Dale AL. Proc Natl Acad Sci U S A. 2001; 98 (19): 10869-74
• Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO. Nature. 2001; 409 (6819): 533-8
• Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO. Mol Biol Cell. 2001; 12 (10): 2987-3003
• Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Kuhn KM, DeRisi JL, Brown PO, Sarnow P. Mol Cell Biol. 2001; 21 (3): 916-27
• Haa1, a protein homologous to the copper-regulated transcription factor Ace1, is a novel transcriptional activator. Keller G, Ray E, Brown PO, Winge DR. J Biol Chem. 2001; 276 (42): 38697-702
• Information access. Building a "GenBank" of the published literature. Roberts RJ, Varmus HE, Ashburner M, Brown PO, Eisen MB, Khosla C, Kirschner M, Nusse R, Scott M, Wold B. Science. 2001; 291 (5512): 2318-9
• Microarrays in primary breast cancer--lessons from chemotherapy studies. Lønning PE, Sørlie T, Perou CM, Brown PO, Botstein D, Børresen-Dale AL. Endocr Relat Cancer. 2001; 8 (3): 259-63
• Missing value estimation methods for DNA microarrays. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Bioinformatics. 2001; 17 (6): 520-5
• Modulation of cellular and viral gene expression by the latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus. Renne R, Barry C, Dittmer D, Compitello N, Brown PO, Ganem D. J Virol. 2001; 75 (1): 458-68
• Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Lieb JD, Liu X, Botstein D, Brown PO. Nat Genet. 2001; 28 (4): 327-34
• Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Haab BB, Dunham MJ, Brown PO. Genome Biol. 2001; 2 (2): RESEARCH0004
• RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer. Finlin BS, Gau CL, Murphy GA, Shao H, Kimel T, Seitz RS, Chiu YF, Botstein D, Brown PO, Der CJ, Tamanoi F, Andres DA, Perou CM. J Biol Chem. 2001; 276 (45): 42259-67
• Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Liu R, Liu H, Chen X, Kirby M, Brown PO, Zhao K. Cell. 2001; 106 (3): 309-18
• Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia. Rosenwald A, Alizadeh AA, Widhopf G, Simon R, Davis RE, Yu X, Yang L, Pickeral OK, Rassenti LZ, Powell J, Botstein D, Byrd JC, Grever MR, Cheson BD, Chiorazzi N, Wilson WH, Kipps TJ, Brown PO, Staudt LM. J Exp Med. 2001; 194 (11): 1639-47
• Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae. Carmel-Harel O, Stearman R, Gasch AP, Botstein D, Brown PO, Storz G. Mol Microbiol. 2001; 39 (3): 595-605
• Supervised harvesting of expression trees. Hastie T, Tibshirani R, Botstein D, Brown P. Genome Biol. 2001; 2 (1): RESEARCH0003
• The Stanford Microarray Database. Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM. Nucleic Acids Res. 2001; 29 (1): 152-5
• Three cell wall mannoproteins facilitate the uptake of iron in Saccharomyces cerevisiae. Protchenko O, Ferea T, Rashford J, Tiedeman J, Brown PO, Botstein D, Philpott CC. J Biol Chem. 2001; 276 (52): 49244-50
• Use of cDNA microarrays to analyze dioxin-induced changes in human liver gene expression. Frueh FW, Hayashibara KC, Brown PO, Whitlock JP. Toxicol Lett. 2001; 122 (3): 189-203
• Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Chiang DY, Brown PO, Eisen MB. Bioinformatics. 2001: 17 Suppl 1 S49-55
• 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, Chan WC, Botstein D, Brown P. Genome Biol. 2000; 1 (2): RESEARCH0003
• A gene expression database for the molecular pharmacology of cancer. Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO, Weinstein JN. Nat Genet. 2000; 24 (3): 236-44
• Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Khodursky AB, Peter BJ, Schmid MB, DeRisi J, Botstein D, Brown PO, Cozzarelli NR. Proc Natl Acad Sci U S A. 2000; 97 (17): 9419-24
• Arrest, adaptation, and recovery following a chromosome double-strand break in Saccharomyces cerevisiae. Lee SE, Pellicioli A, Demeter J, Vaze MP, Gasch AP, Malkova A, Brown PO, Botstein D, Stearns T, Foiani M, Haber JE. Cold Spring Harb Symp Quant Biol. 2000: 65 303-14
• Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Reid JL, Iyer VR, Brown PO, Struhl K. Mol Cell. 2000; 6 (6): 1297-307
• DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Khodursky AB, Peter BJ, Cozzarelli NR, Botstein D, Brown PO, Yanofsky C. Proc Natl Acad Sci U S A. 2000; 97 (22): 12170-5
• Degradation of proteins from the ER of S. cerevisiae requires an intact unfolded protein response pathway. Casagrande R, Stern P, Diehn M, Shamu C, Osario M, Zúñiga M, Brown PO, Ploegh H. Mol Cell. 2000; 5 (4): 729-35
• Desferrioxamine-mediated iron uptake in Saccharomyces cerevisiae. Evidence for two pathways of iron uptake. Yun CW, Ferea T, Rashford J, Ardon O, Brown PO, Botstein D, Kaplan J, Philpott CC. J Biol Chem. 2000; 275 (14): 10709-15
• Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM. Nature. 2000; 403 (6769): 503-11
• Examining the living genome in health and disease with DNA microarrays. Diehn M, Alizadeh AA, Brown PO. JAMA. 2000; 283 (17): 2298-9
• Functional characterization of the human immunodeficiency virus type 1 genome by genetic footprinting. Laurent LC, Olsen MN, Crowley RA, Savilahti H, Brown PO. J Virol. 2000; 74 (6): 2760-9
• Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants. DeRisi J, van den Hazel B, Marc P, Balzi E, Brown P, Jacq C, Goffeau A. FEBS Lett. 2000; 470 (2): 156-60
• Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Lyons TJ, Gasch AP, Gaither LA, Botstein D, Brown PO, Eide DJ. Proc Natl Acad Sci U S A. 2000; 97 (14): 7957-62
• Genomic expression programs in the response of yeast cells to environmental changes. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Mol Biol Cell. 2000; 11 (12): 4241-57
• Genomic views of the immune system*. Staudt LM, Brown PO. Annu Rev Immunol. 2000: 18 829-59
• Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, Petes TD. Proc Natl Acad Sci U S A. 2000; 97 (21): 11383-90
• Identification of clinically distinct types of diffuse large B-cell lymphoma based on gene expression patterns. Brown, P.O., Alizadeh, A., Eisen, M.B., Davis, R.E., Ma, C., Rosenwald, A., Sherlock, G., Boldrick, J.C., Sabet, H., Tran, T., Yu, X., Powell, J.I., Yang, L., Marti, G.E., Moore, T., Hudson, J., Chan, W.C., Greiner, T., Weisenberger, D., Tibshirani, R., Armitage, J.O., Lossos, I., Levy, R., Wilson, W., Grever, M., Byrd, J., Botstein, D., Staudt, L.. Nature. 2000; (403): 503-511
• Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays. Gross C, Kelleher M, Iyer VR, Brown PO, Winge DR. J Biol Chem. 2000; 275 (41): 32310-6
• Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Diehn M, Eisen MB, Botstein D, Brown PO. Nat Genet. 2000; 25 (1): 58-62
• Molecular portraits of human breast tumours. Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lønning PE, Børresen-Dale AL, Brown PO, Botstein D. Nature. 2000; 406 (6797): 747-52
• New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Ogawa N, DeRisi J, Brown PO. Mol Biol Cell. 2000; 11 (12): 4309-21
• Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas. Lossos IS, Alizadeh AA, Eisen MB, Chan WC, Brown PO, Botstein D, Staudt LM, Levy R. Proc Natl Acad Sci U S A. 2000; 97 (18): 10209-13
• Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK. Mol Microbiol. 2000; 35 (1): 6-14
• Singular value decomposition for genome-wide expression data processing and modeling. Alter O, Brown PO, Botstein D. Proc Natl Acad Sci U S A. 2000; 97 (18): 10101-6
• Systematic variation in gene expression patterns in human cancer cell lines. Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO. Nat Genet. 2000; 24 (3): 227-35
• Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B. Nature. 2000; 406 (6791): 90-4
• Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Sudarsanam P, Iyer VR, Brown PO, Winston F. Proc Natl Acad Sci U S A. 2000; 97 (7): 3364-9
• Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes. Yang GP, Ross DT, Kuang WW, Brown PO, Weigel RJ. Nucleic Acids Res. 1999; 27 (6): 1517-23
• DNA arrays for analysis of gene expression. Eisen MB, Brown PO. Methods Enzymol. 1999: 303 179-205
• Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Perou CM, Jeffrey SS, van de Rijn M, Rees CA, Eisen MB, Ross DT, Pergamenschikov A, Williams CF, Zhu SX, Lee JC, Lashkari D, Shalon D, Brown PO, Botstein D. Proc Natl Acad Sci U S A. 1999; 96 (16): 9212-7
• Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Wilson M, DeRisi J, Kristensen HH, Imboden P, Rane S, Brown PO, Schoolnik GK. Proc Natl Acad Sci U S A. 1999; 96 (22): 12833-8
• Exploring the new world of the genome with DNA microarrays. Brown PO, Botstein D. Nat Genet. 1999; 21 (1 Suppl): 33-7
• Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO. Nat Genet. 1999; 23 (1): 41-6
• Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Johannes G, Carter MS, Eisen MB, Brown PO, Sarnow P. Proc Natl Acad Sci U S A. 1999; 96 (23): 13118-23
• Mediator protein mutations that selectively abolish activated transcription. Myers LC, Gustafsson CM, Hayashibara KC, Brown PO, Kornberg RD. Proc Natl Acad Sci U S A. 1999; 96 (1): 67-72
• Observing the living genome. Ferea TL, Brown PO. Curr Opin Genet Dev. 1999; 9 (6): 715-22
• Stereospecificity of reactions catalyzed by HIV-1 integrase. Gerton JL, Herschlag D, Brown PO. J Biol Chem. 1999; 274 (47): 33480-7
• Systematic changes in gene expression patterns following adaptive evolution in yeast. Ferea TL, Botstein D, Brown PO, Rosenzweig RF. Proc Natl Acad Sci U S A. 1999; 96 (17): 9721-6
• The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes. Alizadeh A, Eisen M, Davis RE, Ma C, Sabet H, Tran T, Powell JI, Yang L, Marti GE, Moore DT, Hudson JR, Chan WC, Greiner T, Weisenburger D, Armitage JO, Lossos I, Levy R, Botstein D, Brown PO, Staudt LM. Cold Spring Harb Symp Quant Biol. 1999: 64 71-8
• The transcriptional program in the response of human fibroblasts to serum. Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JC, Trent JM, Staudt LM, Hudson J, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO. Science. 1999; 283 (5398): 83-7
• Transduction of human progenitor hematopoietic stem cells by human immunodeficiency virus type 1-based vectors is cell cycle dependent. Sutton RE, Reitsma MJ, Uchida N, Brown PO. J Virol. 1999; 73 (5): 3649-60
• Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae. Lutfiyya LL, Iyer VR, DeRisi J, DeVit MJ, Brown PO, Johnston M. Genetics. 1998; 150 (4): 1377-91
• Cluster analysis and display of genome-wide expression patterns. Eisen MB, Spellman PT, Brown PO, Botstein D. Proc Natl Acad Sci U S A. 1998; 95 (25): 14863-8
• Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Mol Biol Cell. 1998; 9 (12): 3273-97
• Drug target validation and identification of secondary drug target effects using DNA microarrays. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE, Hartwell LH, Brown PO, Friend SH. Nat Med. 1998; 4 (11): 1293-301
• Effects of mutations in residues near the active site of human immunodeficiency virus type 1 integrase on specific enzyme-substrate interactions. Gerton JL, Ohgi S, Olsen M, DeRisi J, Brown PO. J Virol. 1998; 72 (6): 5046-55
• Enrichment for loci identical-by-descent between pairs of mouse or human genomes by genomic mismatch scanning. McAllister L, Penland L, Brown PO. Genomics. 1998; 47 (1): 7-11
• Genomics and human disease--variations on variation. Brown PO, Hartwell L. Nat Genet. 1998; 18 (2): 91-3
• Human immunodeficiency virus type 1 vectors efficiently transduce human hematopoietic stem cells. Sutton RE, Wu HT, Rigg R, Böhnlein E, Brown PO. J Virol. 1998; 72 (7): 5781-8
• Photo-cross-linking studies suggest a model for the architecture of an active human immunodeficiency virus type 1 integrase-DNA complex. Heuer TS, Brown PO. Biochemistry. 1998; 37 (19): 6667-78
• Probing lymphocyte biology by genomic-scale gene expression analysis. Alizadeh A, Eisen M, Botstein D, Brown PO, Staudt LM. J Clin Immunol. 1998; 18 (6): 373-9
• Supramolecular organization of immature and mature murine leukemia virus revealed by electron cryo-microscopy: implications for retroviral assembly mechanisms. Yeager M, Wilson-Kubalek EM, Weiner SG, Brown PO, Rein A. Proc Natl Acad Sci U S A. 1998; 95 (13): 7299-304
• The transcriptional program of sporulation in budding yeast. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. Science. 1998; 282 (5389): 699-705
• 3'-end processing and kinetics of 5'-end joining during retroviral integration in vivo. Roe T, Chow SA, Brown PO. J Virol. 1997; 71 (2): 1334-40
• Disruption of the terminal base pairs of retroviral DNA during integration. Scottoline BP, Chow S, Ellison V, Brown PO. Genes Dev. 1997; 11 (3): 371-82
• Exploring the metabolic and genetic control of gene expression on a genomic scale. DeRisi JL, Iyer VR, Brown PO. Science. 1997; 278 (5338): 680-6
• High-resolution functional mapping of a cloned gene by genetic footprinting. Singh IR, Crowley RA, Brown PO. Proc Natl Acad Sci U S A. 1997; 94 (4): 1304-9
• Mapping features of HIV-1 integrase near selected sites on viral and target DNA molecules in an active enzyme-DNA complex by photo-cross-linking. Heuer TS, Brown PO. Biochemistry. 1997; 36 (35): 10655-65
• The core domain of HIV-1 integrase recognizes key features of its DNA substrates. Gerton JL, Brown PO. J Biol Chem. 1997; 272 (41): 25809-15
• Yeast microarrays for genome wide parallel genetic and gene expression analysis. Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW. Proc Natl Acad Sci U S A. 1997; 94 (24): 13057-62
• A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Shalon D, Smith SJ, Brown PO. Genome Res. 1996; 6 (7): 639-45
• Functional analysis of the genes of yeast chromosome V by genetic footprinting. Smith V, Chou KN, Lashkari D, Botstein D, Brown PO. Science. 1996; 274 (5295): 2069-74
• Monoclonal antibodies against human immunodeficiency virus type 1 integrase: epitope mapping and differential effects on integrase activities in vitro. Nilsen BM, Haugan IR, Berg K, Olsen L, Brown PO, Helland DE. J Virol. 1996; 70 (3): 1580-7
• Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. Proc Natl Acad Sci U S A. 1996; 93 (20): 10614-9
• Use of a cDNA microarray to analyse gene expression patterns in human cancer. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. Nat Genet. 1996; 14 (4): 457-60
• An essential interaction between distinct domains of HIV-1 integrase mediates assembly of the active multimer. Ellison V, Gerton J, Vincent KA, Brown PO. J Biol Chem. 1995; 270 (7): 3320-6
• Characterization of recombinant murine leukemia virus integrase. Dotan I, Scottoline BP, Heuer TS, Brown PO. J Virol. 1995; 69 (1): 456-68
• Genetic footprinting: a genomic strategy for determining a gene's function given its sequence. Smith V, Botstein D, Brown PO. Proc Natl Acad Sci U S A. 1995; 92 (14): 6479-83
• Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Schena M, Shalon D, Davis RW, Brown PO. Science. 1995; 270 (5235): 467-70
• Statistical methods for linkage analysis of complex traits from high-resolution maps of identity by descent. Dupuis J, Brown PO, Siegmund D. Genetics. 1995; 140 (2): 843-56
• Two-dimensional crystallization of histidine-tagged, HIV-1 reverse transcriptase promoted by a novel nickel-chelating lipid. Kubalek EW, Le Grice SF, Brown PO. J Struct Biol. 1994 Sep-Oct; 113 (2): 117-23
• A stable complex between integrase and viral DNA ends mediates human immunodeficiency virus integration in vitro. Ellison V, Brown PO. Proc Natl Acad Sci U S A. 1994; 91 (15): 7316-20
• DNA strand exchange and selective DNA annealing promoted by the human immunodeficiency virus type 1 nucleocapsid protein. Tsuchihashi Z, Brown PO. J Virol. 1994; 68 (9): 5863-70
• Genome scanning methods. Brown PO, Curr Opin Genet Dev. 1994; 4 (3): 366-73
• Juxtaposition of two viral DNA ends in a bimolecular disintegration reaction mediated by multimers of human immunodeficiency virus type 1 or murine leukemia virus integrase. Chow SA, Brown PO. J Virol. 1994; 68 (12): 7869-78
• Substrate features important for recognition and catalysis by human immunodeficiency virus type 1 integrase identified by using novel DNA substrates. Chow SA, Brown PO. J Virol. 1994; 68 (6): 3896-907
• Characterization of human immunodeficiency virus type 1 integrase expressed in Escherichia coli and analysis of variants with amino-terminal mutations. Vincent KA, Ellison V, Chow SA, Brown PO. J Virol. 1993; 67 (1): 425-37
• Gaussian models for genetic linkage analysis using complete high-resolution maps of identity by descent. Feingold E, Brown PO, Siegmund D. Am J Hum Genet. 1993; 53 (1): 234-51
• Genomic mismatch scanning: a new approach to genetic linkage mapping. Nelson SF, McCusker JH, Sander MA, Kee Y, Modrich P, Brown PO. Nat Genet. 1993; 4 (1): 11-8
• Integration of murine leukemia virus DNA depends on mitosis. Roe T, Reynolds TC, Yu G, Brown PO. EMBO J. 1993; 12 (5): 2099-108
• Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. Chow SA, Vincent KA, Ellison V, Brown PO. Science. 1992; 255 (5045): 723-6
• Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon. Tsuchihashi Z, Brown PO. Genes Dev. 1992; 6 (3): 511-9
• Host sequences flanking the HIV provirus. Vincent KA, York-Higgins D, Quiroga M, Brown PO. Nucleic Acids Res. 1990; 18 (20): 6045-7
• Human immunodeficiency virus integration in a cell-free system. Ellison V, Abrams H, Roe T, Lifson J, Brown P. J Virol. 1990; 64 (6): 2711-5
• Integration of retroviral DNA. Brown PO, Curr Top Microbiol Immunol. 1990: 157 19-48
• A nucleoprotein complex mediates the integration of retroviral DNA. Bowerman B, Brown PO, Bishop JM, Varmus HE. Genes Dev. 1989; 3 (4): 469-78
• Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein. Brown PO, Bowerman B, Varmus HE, Bishop JM. Proc Natl Acad Sci U S A. 1989; 86 (8): 2525-9
• Correct integration of retroviral DNA in vitro. Brown PO, Bowerman B, Varmus HE, Bishop JM. Cell. 1987; 49 (3): 347-56
• Catenation and knotting of duplex DNA by type 1 topoisomerases: a mechanistic parallel with type 2 topoisomerases. Brown PO, Cozzarelli NR. Proc Natl Acad Sci U S A. 1981; 78 (2): 843-7
• A sign inversion mechanism for enzymatic supercoiling of DNA. Brown PO, Cozzarelli NR. Science. 1979; 206 (4422): 1081-3
• A topoisomerase from Escherichia coli related to DNA gyrase. Brown PO, Peebles CL, Cozzarelli NR. Proc Natl Acad Sci U S A. 1979; 76 (12): 6110-4
• Structure and activities of Escherichia coli DNA gyrase. Peebles CL, Higgins NP, Kreuzer KN, Morrison A, Brown PO, Sugino A, Cozzarelli NR. Cold Spring Harb Symp Quant Biol. 1979: 43 Pt 1 41-52
• Energy coupling in DNA gyrase and the mechanism of action of novobiocin. Sugino A, Higgins NP, Brown PO, Peebles CL, Cozzarelli NR. Proc Natl Acad Sci U S A. 1978; 75 (10): 4838-42