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Patrick Brown
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62
Botstein, David
24
van de Rijn, Matt
18
Diehn, Maximilian
15
Eisen, Michael
12
Alizadeh, Ash
10
Tibshirani, Robert
10
Montgomery, Kelli
10
Perou, Charles
9
Pollack, Jonathan
9
West, Robert
9
Chi, Jen-Tsan
9
Hernandez-Boussard, Tina
9
DeRisi, Joe
9
Sherlock, Gavin
8
Chang, Howard
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All Publications
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2009: Hendrickson David G; Hogan Daniel J; McCullough Heather L; Myers Jason W; Herschlag Daniel; Ferrell James E; Brown Patrick O
Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA.
PLoS biology 2009;7(11):e1000238.
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2009: Brown Patrick O; Palmer Chana
The preclinical natural history of serous ovarian cancer: defining the target for early detection.
PLoS medicine 2009;6(7):e1000114.
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2008: Marinelli Robert J; Montgomery Kelli; Liu Chih Long; Shah Nigam H; Prapong Wijan; Nitzberg Michael; Zachariah Zachariah K; Sherlock Gavin J; Natkunam Yasodha; West Robert B; van de Rijn Matt; Brown Patrick O; Ball Catherine A
The Stanford Tissue Microarray Database.
Nucleic acids research 2008;36(Database issue):D871-7.
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2008: Rubins Kathleen H; Hensley Lisa E; Bell George W; Wang Chunlin; Lefkowitz Elliot J; Brown Patrick O; Relman David A
Comparative analysis of viral gene expression programs during poxvirus infection: a transcriptional map of the vaccinia and monkeypox genomes.
PloS one 2008;3(7):e2628.
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2008: Hendrickson David G; Hogan Daniel J; Herschlag Daniel; Ferrell James E; Brown Patrick O
Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance.
PloS one 2008;3(5):e2126.
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2007: Halbleib Jennifer M; Sääf Annika M; Brown Patrick O; Nelson W James
Transcriptional modulation of genes encoding structural characteristics of differentiating enterocytes during development of a polarized epithelium in vitro.
Molecular biology of the cell 2007;18(11):4261-78.
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2007: Sääf Annika M; Halbleib Jennifer M; Chen Xin; Yuen Siu Tsan; Leung Suet Yi; Nelson W James; Brown Patrick O
Parallels between global transcriptional programs of polarizing Caco-2 intestinal epithelial cells in vitro and gene expression programs in normal colon and colon cancer.
Molecular biology of the cell 2007;18(11):4245-60.
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2007: Chi Jen-Tsan; Rodriguez Edwin H; Wang Zhen; Nuyten Dimitry S A; Mukherjee Sayan; van de Rijn Matt; van de Vijver Marc J; Hastie Trevor; Brown Patrick O
Gene expression programs of human smooth muscle cells: tissue-specific differentiation and prognostic significance in breast cancers.
PLoS genetics 2007;3(9):1770-84.
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2007: Palmer Chana; Bik Elisabeth M; DiGiulio Daniel B; Relman David A; Brown Patrick O
Development of the human infant intestinal microbiota.
PLoS biology 2007;5(7):e177.
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2007: Demeter Janos; Beauheim Catherine; Gollub Jeremy; Hernandez-Boussard Tina; Jin Heng; Maier Donald; Matese John C; Nitzberg Michael; Wymore Farrell; Zachariah Zachariah K; Brown Patrick O; Sherlock Gavin; Ball Catherine A
The Stanford Microarray Database: implementation of new analysis tools and open source release of software.
Nucleic acids research 2007;35(Database issue):D766-70.
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2007: Popper Stephen J; Shimizu Chisato; Shike Hiroko; Kanegaye John T; Newburger Jane W; Sundel Robert P; Brown Patrick O; Burns Jane C; Relman David A
Gene-expression patterns reveal underlying biological processes in Kawasaki disease.
Genome biology 2007;8(12):R261.
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2007: Klapholz-Brown Zach; Walmsley Graham G; Nusse Ysbrand M; Nusse Roel; Brown Patrick O
Transcriptional program induced by Wnt protein in human fibroblasts suggests mechanisms for cell cooperativity in defining tissue microenvironments.
PloS one 2007;2(9):e945.
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2007: Buess Martin; Nuyten Dimitry S A; Hastie Trevor; Nielsen Torsten; Pesich Robert; Brown Patrick O
Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.
Genome biology 2007;8(9):R191.
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2007: Rubins Kathleen H; Hensley Lisa E; Wahl-Jensen Victoria; Daddario DiCaprio Kathleen M; Young Howard A; Reed Douglas S; Jahrling Peter B; Brown Patrick O; Relman David A; Geisbert Thomas W
The temporal program of peripheral blood gene expression in the response of nonhuman primates to Ebola hemorrhagic fever.
Genome biology 2007;8(8):R174.
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2007: Hurowitz Evan H; Drori Iddo; Stodden Victoria C; Donoho David L; Brown Patrick O
Virtual Northern analysis of the human genome.
PloS one 2007;2(5):e460.
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2006: Sneddon Julie B; Zhen Hanson H; Montgomery Kelli; van de Rijn Matt; Tward Aaron D; West Robert; Gladstone Hayes; Chang Howard Y; Morganroth Greg S; Oro Anthony E; Brown Patrick O
Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(40):14842-7.
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2006: Brown Patrick O
2005 Curt Stern Award address. Exploring along a crooked path.
American journal of human genetics 2006;79(3):429-33.
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2006: Rinn John L; Bondre Chanda; Gladstone Hayes B; Brown Patrick O; Chang Howard Y
Anatomic demarcation by positional variation in fibroblast gene expression programs.
PLoS genetics 2006;2(7):e119.
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2006: Sood Ruchira; Zehnder James L; Druzin Maurice L; Brown Patrick O
Gene expression patterns in human placenta.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(14):5478-83.
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2006: Gerber André P; Luschnig Stefan; Krasnow Mark A; Brown Patrick O; Herschlag Daniel
Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(12):4487-92.
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2006: Chi Jen-Tsan; Wang Zhen; Nuyten Dimitry S A; Rodriguez Edwin H; Schaner Marci E; Salim Ali; Wang Yun; Kristensen Gunnar B; Helland Aslaug; Børresen-Dale Anne-Lise; Giaccia Amato; Longaker Michael T; Hastie Trevor; Yang George P; van de Vijver Marc J; Brown Patrick O
Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers.
PLoS medicine 2006;3(3):e47.
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2006: Diehn Maximilian; Bhattacharya Ramona; Botstein David; Brown Patrick O
Genome-scale identification of membrane-associated human mRNAs.
PLoS genetics 2006;2(1):e11.
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2006: West Robert B; Rubin Brian P; Miller Melinda A; Subramanian Subbaya; Kaygusuz Gulsah; Montgomery Kelli; Zhu Shirley; Marinelli Robert J; De Luca Alessandro; Downs-Kelly Erinn; Goldblum John R; Corless Christopher L; Brown Patrick O; Gilks C Blake; Nielsen Torsten O; Huntsman David; van de Rijn Matt
A landscape effect in tenosynovial giant-cell tumor from activation of CSF1 expression by a translocation in a minority of tumor cells.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(3):690-5.
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2006: Myers Jason W; Chi Jen-Tsan; Gong Delquin; Schaner Marci E; Brown Patrick O; Ferrell James E
Minimizing off-target effects by using diced siRNAs for RNA interference.
Journal of RNAi and gene silencing : an international journal of RNA and gene targeting research 2006;2(2):181-94.
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2006: Nuyten Dimitry S A; Kreike Bas; Hart Augustinus A M; Chi Jen-Tsan Ashley; Sneddon Julie B; Wessels Lodewyk F A; Peterse Hans J; Bartelink Harry; Brown Patrick O; Chang Howard Y; van de Vijver Marc J
Predicting a local recurrence after breast-conserving therapy by gene expression profiling.
Breast cancer research : BCR 2006;8(5):R62.
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2006: Kapp Amy V; Jeffrey Stefanie S; Langerød Anita; Børresen-Dale Anne-Lise; Han Wonshik; Noh Dong-Young; Bukholm Ida R K; Nicolau Monica; Brown Patrick O; Tibshirani Robert
Discovery and validation of breast cancer subtypes.
BMC genomics 2006;7():231.
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2006: Soen Yoav; Mori Akiko; Palmer Theo D; Brown Patrick O
Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments.
Molecular systems biology 2006;2():37.
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2006: Palmer Chana; Diehn Maximilian; Alizadeh Ash A; Brown Patrick O
Cell-type specific gene expression profiles of leukocytes in human peripheral blood.
BMC genomics 2006;7():115.
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2006: Palmer Chana; Bik Elisabeth M; Eisen Michael B; Eckburg Paul B; Sana Theodore R; Wolber Paul K; Relman David A; Brown Patrick O
Rapid quantitative profiling of complex microbial populations.
Nucleic acids research 2006;34(1):e5.
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2005: Chen Daniel S; Soen Yoav; Stuge Tor B; Lee Peter P; Weber Jeffrey S; Brown Patrick O; Davis Mark M
Marked differences in human melanoma antigen-specific T cell responsiveness after vaccination using a functional microarray.
PLoS medicine 2005;2(10):e265.
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2005: West Robert B; Nuyten Dimitry S A; Subramanian Subbaya; Nielsen Torsten O; Corless Christopher L; Rubin Brian P; Montgomery Kelli; Zhu Shirley; Patel Rajiv; Hernandez-Boussard Tina; Goldblum John R; Brown Patrick O; van de Vijver Marc; van de Rijn Matt
Determination of stromal signatures in breast carcinoma.
PLoS biology 2005;3(6):e187.
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2005: Liang Yu; Diehn Maximilian; Watson Nathan; Bollen Andrew W; Aldape Ken D; Nicholas M Kelly; Lamborn Kathleen R; Berger Mitchel S; Botstein David; Brown Patrick O; Israel Mark A
Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(16):5814-9.
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2005: Chang Howard Y; Nuyten Dimitry S A; Sneddon Julie B; Hastie Trevor; Tibshirani Robert; Sørlie Therese; Dai Hongyue; He Yudong D; van't Veer Laura J; Bartelink Harry; van de Rijn Matt; Brown Patrick O; van de Vijver Marc J
Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(10):3738-43.
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2005: Ball Catherine A; Awad Ihab A B; Demeter Janos; Gollub Jeremy; Hebert Joan M; Hernandez-Boussard Tina; Jin Heng; Matese John C; Nitzberg Michael; Wymore Farrell; Zachariah Zachariah K; Brown Patrick O; Sherlock Gavin
The Stanford Microarray Database accommodates additional microarray platforms and data formats.
Nucleic acids research 2005;33(Database issue):D580-2.
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2005: Diehn Jennifer J; Diehn Maximilian; Marmor Michael F; Brown Patrick O
Differential gene expression in anatomical compartments of the human eye.
Genome biology 2005;6(9):R74.
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2005: Arava Yoav; Boas F Edward; Brown Patrick O; Herschlag Daniel
Dissecting eukaryotic translation and its control by ribosome density mapping.
Nucleic acids research 2005;33(8):2421-32.
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2005: Shyamsundar Radha; Kim Young H; Higgins John P; Montgomery Kelli; Jorden Michelle; Sethuraman Anand; van de Rijn Matt; Botstein David; Brown Patrick O; Pollack Jonathan R
A DNA microarray survey of gene expression in normal human tissues.
Genome biology 2005;6(3):R22.
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2004: Rubins Kathleen H; Hensley Lisa E; Jahrling Peter B; Whitney Adeline R; Geisbert Thomas W; Huggins John W; Owen Art; Leduc James W; Brown Patrick O; Relman David A
The host response to smallpox: analysis of the gene expression program in peripheral blood cells in a nonhuman primate model.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(42):15190-5.
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2004: Tu I-Ping; Schaner Marci; Diehn Maximilian; Sikic Branimir I; Brown Patrick O; Botstein David; Fero Michael J
A method for detecting and correcting feature misidentification on expression microarrays.
BMC genomics 2004;5(1):64.
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2004: McCaffrey Ramona L; Fawcett Paul; O'Riordan Mary; Lee Kyung-Dall; Havell Edward A; Brown Patrick O; Portnoy Daniel A
A specific gene expression program triggered by Gram-positive bacteria in the cytosol.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(31):11386-91.
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2004: West Robert B; Harvell Jeff; Linn Sabine C; Liu Chih Long; Prapong Wijan; Hernandez-Boussard Tina; Montgomery Kelli; Nielsen Torsten O; Rubin Brian P; Patel Rajiv; Goldblum John R; Brown Patrick O; van de Rijn Matt;
Apo D in soft tissue tumors: a novel marker for dermatofibrosarcoma protuberans.
The American journal of surgical pathology 2004;28(8):1063-9.
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2004: West Robert B; Corless Christopher L; Chen Xin; Rubin Brian P; Subramanian Subbaya; Montgomery Kelli; Zhu Shirley; Ball Catherine A; Nielsen Torsten O; Patel Rajiv; Goldblum John R; Brown Patrick O; Heinrich Michael C; van de Rijn Matt
The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status.
The American journal of pathology 2004;165(1):107-13.
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2004: Murray John Isaac; Whitfield Michael L; Trinklein Nathan D; Myers Richard M; Brown Patrick O; Botstein David
Diverse and specific gene expression responses to stresses in cultured human cells.
Molecular biology of the cell 2004;15(5):2361-74.
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2004: Munagala Kamesh; Tibshirani Robert; Brown Patrick O
Cancer characterization and feature set extraction by discriminative margin clustering.
BMC bioinformatics 2004;5():21.
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2004: Gerber André P; Herschlag Daniel; Brown Patrick O
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast.
PLoS biology 2004;2(3):E79.
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2004: Piedras-Rentería Erika S; Pyle Jason L; Diehn Max; Glickfeld Lindsey L; Harata Nobutoshi C; Cao Yuqing; Kavalali Ege T; Brown Patrick O; Tsien Richard W
Presynaptic homeostasis at CNS nerve terminals compensates for lack of a key Ca2+ entry pathway.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(10):3609-14.
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2004: Chang Howard Y; Sneddon Julie B; Alizadeh Ash A; Sood Ruchira; West Rob B; Montgomery Kelli; Chi Jen-Tsan; van de Rijn Matt; Botstein David; Brown Patrick O
Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds.
PLoS biology 2004;2(2):E7.
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2004: Higgins John P T; Wang Lingli; Kambham Neeraja; Montgomery Kelli; Mason Veronica; Vogelmann Stefanie U; Lemley Kevin V; Brown Patrick O; Brooks James D; van de Rijn Matt
Gene expression in the normal adult human kidney assessed by complementary DNA microarray.
Molecular biology of the cell 2004;15(2):649-56.
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2004: Lapointe Jacques; Li Chunde; Higgins John P; van de Rijn Matt; Bair Eric; Montgomery Kelli; Ferrari Michelle; Egevad Lars; Rayford Walter; Bergerheim Ulf; Ekman Peter; DeMarzo Angelo M; Tibshirani Robert; Botstein David; Brown Patrick O; Brooks James D; Pollack Jonathan R
Gene expression profiling identifies clinically relevant subtypes of prostate cancer.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(3):811-6.
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2004: Peter Brian J; Arsuaga Javier; Breier Adam M; Khodursky Arkady B; Brown Patrick O; Cozzarelli Nicholas R
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli.
Genome biology 2004;5(11):R87.
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2003: Soen Yoav; Chen Daniel S; Kraft Daniel L; Davis Mark M; Brown Patrick O
Detection and characterization of cellular immune responses using peptide-MHC microarrays.
PLoS biology 2003;1(3):E65.
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2003: Linn Sabine C; West Rob B; Pollack Jonathan R; Zhu Shirley; Hernandez-Boussard Tina; Nielsen Torsten O; Rubin Brian P; Patel Rajiv; Goldblum John R; Siegmund David; Botstein David; Brown Patrick O; Gilks C Blake; van de Rijn Matt
Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.
The American journal of pathology 2003;163(6):2383-95.
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2003: Roose Jeroen P; Diehn Maximilian; Tomlinson Michael G; Lin Joseph; Alizadeh Ash A; Botstein David; Brown Patrick O; Weiss Arthur
T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.
PLoS biology 2003;1(2):E53.
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2003: Schaner Marci E; Ross Douglas T; Ciaravino Giuseppe; Sorlie Therese; Troyanskaya Olga; Diehn Maximilian; Wang Yan C; Duran George E; Sikic Thomas L; Caldeira Sandra; Skomedal Hanne; Tu I-Ping; Hernandez-Boussard Tina; Johnson Steven W; O'Dwyer Peter J; Fero Michael J; Kristensen Gunnar B; Borresen-Dale Anne-Lise; Hastie Trevor; Tibshirani Robert; van de Rijn Matt; Teng Nelson N; Longacre Teri A; Botstein David; Brown Patrick O; Sikic Branimir I
Gene expression patterns in ovarian carcinomas.
Molecular biology of the cell 2003;14(11):4376-86.
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2003: Whitfield Michael L; Finlay Deborah R; Murray John Isaac; Troyanskaya Olga G; Chi Jen-Tsan; Pergamenschikov Alexander; McCalmont Timothy H; Brown Patrick O; Botstein David; Connolly M Kari
Systemic and cell type-specific gene expression patterns in scleroderma skin.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(21):12319-24.
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2003: Nielsen Torsten O; Hsu Forrest D; O'Connell John X; Gilks C Blake; Sorensen Poul H B; Linn Sabine; West Robert B; Liu Chih Long; Botstein David; Brown Patrick O; van de Rijn Matt
Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology.
The American journal of pathology 2003;163(4):1449-56.
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2003: Shepard K A; Gerber A P; Jambhekar A; Takizawa P A; Brown P O; Herschlag D; DeRisi J L; Vale R D
Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(20):11429-34.
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2003: Chi Jen-Tsan; Chang Howard Y; Haraldsen Guttorm; Jahnsen Frode L; Troyanskaya Olga G; Chang Dustin S; Wang Zhen; Rockson Stanley G; van de Rijn Matt; Botstein David; Brown Patrick O
Endothelial cell diversity revealed by global expression profiling.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(19):10623-8.
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2003: Chen Xin; Leung Suet Y; Yuen Siu T; Chu Kent-Man; Ji Jiafu; Li Rui; Chan Annie S Y; Law Simon; Troyanskaya Olga G; Wong John; So Samuel; Botstein David; Brown Patrick O
Variation in gene expression patterns in human gastric cancers.
Molecular biology of the cell 2003;14(8):3208-15.
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2003: Sorlie Therese; Tibshirani Robert; Parker Joel; Hastie Trevor; Marron J S; Nobel Andrew; Deng Shibing; Johnsen Hilde; Pesich Robert; Geisler Stephanie; Demeter Janos; Perou Charles M; Lønning Per E; Brown Patrick O; Børresen-Dale Anne-Lise; Botstein David
Repeated observation of breast tumor subtypes in independent gene expression data sets.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(14):8418-23.
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2003: Nagy Peter L; Cleary Michael L; Brown Patrick O; Lieb Jason D
Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(11):6364-9.
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2003: Chi Jen-Tsan; Chang Howard Y; Wang Nancy N; Chang Dustin S; Dunphy Nina; Brown Patrick O
Genomewide view of gene silencing by small interfering RNAs.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(11):6343-6.
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2003: Arava Yoav; Wang Yulei; Storey John D; Liu Chih Long; Brown Patrick O; Herschlag Daniel
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(7):3889-94.
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2003: Alter Orly; Brown Patrick O; Botstein David
Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(6):3351-6.
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2003: Whitney Adeline R; Diehn Maximilian; Popper Stephen J; Alizadeh Ash A; Boldrick Jennifer C; Relman David A; Brown Patrick O
Individuality and variation in gene expression patterns in human blood.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(4):1896-901.
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2003: Bohen Sean P; Troyanskaya Olga G; Alter Orly; Warnke Roger; Botstein David; Brown Patrick O; Levy Ronald
Variation in gene expression patterns in follicular lymphoma and the response to rituximab.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(4):1926-30.
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2003: Diehn Maximilian; Sherlock Gavin; Binkley Gail; Jin Heng; Matese John C; Hernandez-Boussard Tina; Rees Christian A; Cherry J Michael; Botstein David; Brown Patrick O; Alizadeh Ash A
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.
Nucleic acids research 2003;31(1):219-23.
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2003: Gollub Jeremy; Ball Catherine A; Binkley Gail; Demeter Janos; Finkelstein David B; Hebert Joan M; Hernandez-Boussard Tina; Jin Heng; Kaloper Miroslava; Matese John C; Schroeder Mark; Brown Patrick O; Botstein David; Sherlock Gavin
The Stanford Microarray Database: data access and quality assessment tools.
Nucleic acids research 2003;31(1):94-6.
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2003: Hurowitz Evan H; Brown Patrick O
Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae.
Genome biology 2003;5(1):R2.
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2003: Holterhus Paul-Martin; Hiort Olaf; Demeter Janos; Brown Patrick O; Brooks James D
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 biology 2003;4(6):R37.
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2003: Baldwin David N; Vanchinathan Veena; Brown Patrick O; Theriot Julie A
A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes.
Genome biology 2003;4(1):R2.
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2002: Leung Suet Y; Chen Xin; Chu Kent M; Yuen Siu T; Mathy Jonathan; Ji Jiafu; Chan Annie S Y; Li Rui; Law Simon; Troyanskaya Olga G; Tu I-Ping; Wong John; So Samuel; Botstein David; Brown Patrick O
Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(25):16203-8.
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2002: Dunham Maitreya J; Badrane Hassan; Ferea Tracy; Adams Julian; Brown Patrick O; Rosenzweig Frank; Botstein David
Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(25):16144-9.
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2002: Troyanskaya Olga G; Garber Mitchell E; Brown Patrick O; Botstein David; Altman Russ B
Nonparametric methods for identifying differentially expressed genes in microarray data.
Bioinformatics (Oxford, England) 2002;18(11):1454-61.
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2002: Chang Howard Y; Chi Jen-Tsan; Dudoit Sandrine; Bondre Chanda; van de Rijn Matt; Botstein David; Brown Patrick O
Diversity, topographic differentiation, and positional memory in human fibroblasts.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(20):12877-82.
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2002: Pollack Jonathan R; Sørlie Therese; Perou Charles M; Rees Christian A; Jeffrey Stefanie S; Lonning Per E; Tibshirani Robert; Botstein David; Børresen-Dale Anne-Lise; Brown Patrick O
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(20):12963-8.
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2002: Diehn Maximilian; Alizadeh Ash A; Rando Oliver J; Liu Chih Long; Stankunas Kryn; Botstein David; Crabtree Gerald R; Brown Patrick O
Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(18):11796-801.
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2002: Yoshimoto Hiroyuki; Saltsman Kirstie; Gasch Audrey P; Li Hong Xia; Ogawa Nobuo; Botstein David; Brown Patrick O; Cyert Martha S
Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.
The Journal of biological chemistry 2002;277(34):31079-88.
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2002: Willert Jennifer; Epping Mirjam; Pollack Jonathan R; Brown Patrick O; Nusse Roel
A transcriptional response to Wnt protein in human embryonic carcinoma cells.
BMC developmental biology 2002;2():8.
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2002: DePrimo Samuel E; Diehn Maximilian; Nelson Joel B; Reiter Robert E; Matese John; Fero Mike; Tibshirani Robert; Brown Patrick O; Brooks James D
Transcriptional programs activated by exposure of human prostate cancer cells to androgen.
Genome biology 2002;3(7):RESEARCH0032.
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2002: Sayama Koichi; Diehn Maximilian; Matsuda Kentaro; Lunderius Carolina; Tsai Mindy; Tam See-Ying; Botstein David; Brown Patrick O; Galli Stephen J
Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.
BMC immunology 2002;3():5.
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2002: Lossos Izidore S; Alizadeh Ash A; Diehn Maximilian; Warnke Roger; Thorstenson Yvonne; Oefner Peter J; Brown Patrick O; Botstein David; Levy Ronald
Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(13):8886-91.
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2002: Whitfield Michael L; Sherlock Gavin; Saldanha Alok J; Murray John I; Ball Catherine A; Alexander Karen E; Matese John C; Perou Charles M; Hurt Myra M; Brown Patrick O; Botstein David
Identification of genes periodically expressed in the human cell cycle and their expression in tumors.
Molecular biology of the cell 2002;13(6):1977-2000.
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2002: Chen Xin; Cheung Siu Tim; So Samuel; Fan Sheung Tat; Barry Christopher; Higgins John; Lai Kin-Man; Ji Jiafu; Dudoit Sandrine; Ng Irene O L; Van De Rijn Matt; Botstein David; Brown Patrick O
Gene expression patterns in human liver cancers.
Molecular biology of the cell 2002;13(6):1929-39.
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2002: Wang Yulei; Liu Chih Long; Storey John D; Tibshirani Robert J; Herschlag Daniel; Brown Patrick O
Precision and functional specificity in mRNA decay.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(9):5860-5.
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2002: Nielsen Torsten O; West Rob B; Linn Sabine C; Alter Orly; Knowling Margaret A; O'Connell John X; Zhu Shirley; Fero Mike; Sherlock Gavin; Pollack Jonathan R; Brown Patrick O; Botstein David; van de Rijn Matt
Molecular characterisation of soft tissue tumours: a gene expression study.
Lancet 2002;359(9314):1301-7.
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2002: Clément Karine; Viguerie Nathalie; Diehn Maximilian; Alizadeh Ash; Barbe Pierre; Thalamas Claire; Storey John D; Brown Patrick O; Barsh Greg S; Langin Dominique
In vivo regulation of human skeletal muscle gene expression by thyroid hormone.
Genome research 2002;12(2):281-91.
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2002: Boldrick Jennifer C; Alizadeh Ash A; Diehn Maximilian; Dudoit Sandrine; Liu Chih Long; Belcher Christopher E; Botstein David; Staudt Louis M; Brown Patrick O; Relman David A
Stereotyped and specific gene expression programs in human innate immune responses to bacteria.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(2):972-7.
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2002: Lin Johann Y; Pollack Jonathan R; Chou Fan-Li; Rees Christian A; Christian Allen T; Bedford Joel S; Brown Patrick O; Ginsberg Mark H
Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays.
Genome biology 2002;3(6):RESEARCH0026.
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2001: Garber M E; Troyanskaya O G; Schluens K; Petersen S; Thaesler Z; Pacyna-Gengelbach M; van de Rijn M; Rosen G D; Perou C M; Whyte R I; Altman R B; Brown P O; Botstein D; Petersen I
Diversity of gene expression in adenocarcinoma of the lung.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(24):13784-9.
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2001: Gasch A P; Huang M; Metzner S; Botstein D; Elledge S J; Brown P O
Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p.
Molecular biology of the cell 2001;12(10):2987-3003.
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2001: Lønning P E; Sørlie T; Perou C M; Brown P O; Botstein D; Børresen-Dale A L
Microarrays in primary breast cancer--lessons from chemotherapy studies.
Endocrine-related cancer 2001;8(3):259-63.
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2001: Sørlie T; Perou C M; Tibshirani R; Aas T; Geisler S; Johnsen H; Hastie T; Eisen M B; van de Rijn M; Jeffrey S S; Thorsen T; Quist H; Matese J C; Brown P O; Botstein D; Eystein Lønning P; Børresen-Dale A L
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(19):10869-74.
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2001: Lieb J D; Liu X; Botstein D; Brown P O
Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association.
Nature genetics 2001;28(4):327-34.
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2001: Courcelle J; Khodursky A; Peter B; Brown P O; Hanawalt P C
Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli.
Genetics 2001;158(1):41-64.
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2001: Li S; Ross D T; Kadin M E; Brown P O; Wasik M A
Comparative genome-scale analysis of gene expression profiles in T cell lymphoma cells during malignant progression using a complementary DNA microarray.
The American journal of pathology 2001;158(4):1231-7.
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2001: Carmel-Harel O; Stearman R; Gasch A P; Botstein D; Brown P O; Storz G
Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae.
Molecular microbiology 2001;39(3):595-605.
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2001: Kuhn K M; DeRisi J L; Brown P O; Sarnow P
Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source.
Molecular and cellular biology 2001;21(3):916-27.
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2001: Iyer V R; Horak C E; Scafe C S; Botstein D; Snyder M; Brown P O
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.
Nature 2001;409(6819):533-8.
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2001: Sherlock G; Hernandez-Boussard T; Kasarskis A; Binkley G; Matese J C; Dwight S S; Kaloper M; Weng S; Jin H; Ball C A; Eisen M B; Spellman P T; Brown P O; Botstein D; Cherry J M
The Stanford Microarray Database.
Nucleic acids research 2001;29(1):152-5.
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2001: Haab B B; Dunham M J; Brown P O
Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions.
Genome biology 2001;2(2):RESEARCH0004.
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2000: Ogawa N; DeRisi J; Brown P O
New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis.
Molecular biology of the cell 2000;11(12):4309-21.
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2000: Gasch A P; Spellman P T; Kao C M; Carmel-Harel O; Eisen M B; Storz G; Botstein D; Brown P O
Genomic expression programs in the response of yeast cells to environmental changes.
Molecular biology of the cell 2000;11(12):4241-57.
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2000: Gerton J L; DeRisi J; Shroff R; Lichten M; Brown P O; Petes T D
Inaugural article: global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(21):11383-90.
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2000: Khodursky A B; Peter B J; Cozzarelli N R; Botstein D; Brown P O; Yanofsky C
DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(22):12170-5.
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2000: Alter O; Brown P O; Botstein D
Singular value decomposition for genome-wide expression data processing and modeling.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(18):10101-6.
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2000: Perou C M; Sørlie T; Eisen M B; van de Rijn M; Jeffrey S S; Rees C A; Pollack J R; Ross D T; Johnsen H; Akslen L A; Fluge O; Pergamenschikov A; Williams C; Zhu S X; Lønning P E; Børresen-Dale A L; Brown P O; Botstein D
Molecular portraits of human breast tumours.
Nature 2000;406(6797):747-52.
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2000: Khodursky A B; Peter B J; Schmid M B; DeRisi J; Botstein D; Brown P O; Cozzarelli N R
Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(17):9419-24.
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2000: Zhu G; Spellman P T; Volpe T; Brown P O; Botstein D; Davis T N; Futcher B
Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth.
Nature 2000;406(6791):90-4.
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2000: Diehn M; Alizadeh A A; Brown P O
Examining the living genome in health and disease with DNA microarrays.
JAMA : the journal of the American Medical Association 2000;283(17):2298-9.
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2000: Diehn M; Eisen M B; Botstein D; Brown P O
Large-scale identification of secreted and membrane-associated gene products using DNA microarrays.
Nature genetics 2000;25(1):58-62.
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2000: Scherf U; Ross D T; Waltham M; Smith L H; Lee J K; Tanabe L; Kohn K W; Reinhold W C; Myers T G; Andrews D T; Scudiero D A; Eisen M B; Sausville E A; Pommier Y; Botstein D; Brown P O; Weinstein J N
A gene expression database for the molecular pharmacology of cancer.
Nature genetics 2000;24(3):236-44.
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2000: Ross D T; Scherf U; Eisen M B; Perou C M; Rees C; Spellman P; Iyer V; Jeffrey S S; Van de Rijn M; Waltham M; Pergamenschikov A; Lee J C; Lashkari D; Shalon D; Myers T G; Weinstein J N; Botstein D; Brown P O
Systematic variation in gene expression patterns in human cancer cell lines.
Nature genetics 2000;24(3):227-35.
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2000: Lee S E; Pellicioli A; Demeter J; Vaze M P; Gasch A P; Malkova A; Brown P O; Botstein D; Stearns T; Foiani M; Haber J E
Arrest, adaptation, and recovery following a chromosome double-strand break in Saccharomyces cerevisiae.
Cold Spring Harbor symposia on quantitative biology 2000;65():303-14.
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1999: Ferea T L; Brown P O
Observing the living genome.
Current opinion in genetics & development 1999;9(6):715-22.
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1999: Gerton J L; Herschlag D; Brown P O
Stereospecificity of reactions catalyzed by HIV-1 integrase.
The Journal of biological chemistry 1999;274(47):33480-7.
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1999: Johannes G; Carter M S; Eisen M B; Brown P O; Sarnow P
Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(23):13118-23.
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1999: Wilson M; DeRisi J; Kristensen H H; Imboden P; Rane S; Brown P O; Schoolnik G K
Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(22):12833-8.
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1999: Pollack J R; Perou C M; Alizadeh A A; Eisen M B; Pergamenschikov A; Williams C F; Jeffrey S S; Botstein D; Brown P O
Genome-wide analysis of DNA copy-number changes using cDNA microarrays.
Nature genetics 1999;23(1):41-6.
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1999: Ferea T L; Botstein D; Brown P O; Rosenzweig R F
Systematic changes in gene expression patterns following adaptive evolution in yeast.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(17):9721-6.
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1999: Perou C M; Jeffrey S S; van de Rijn M; Rees C A; Eisen M B; Ross D T; Pergamenschikov A; Williams C F; Zhu S X; Lee J C; Lashkari D; Shalon D; Brown P O; Botstein D
Distinctive gene expression patterns in human mammary epithelial cells and breast cancers.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(16):9212-7.
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1999: Yang G P; Ross D T; Kuang W W; Brown P O; Weigel R J
Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes.
Nucleic acids research 1999;27(6):1517-23.
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1999: Brown P O; Botstein D
Exploring the new world of the genome with DNA microarrays.
Nature genetics 1999;21(1 Suppl):33-7.
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1999: Myers L C; Gustafsson C M; Hayashibara K C; Brown P O; Kornberg R D
Mediator protein mutations that selectively abolish activated transcription.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(1):67-72.
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1999: Iyer V R; Eisen M B; Ross D T; Schuler G; Moore T; Lee J C; Trent J M; Staudt L M; Hudson J; Boguski M S; Lashkari D; Shalon D; Botstein D; Brown P O
The transcriptional program in the response of human fibroblasts to serum.
Science (New York, N.Y.) 1999;283(5398):83-7.
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1999: Alizadeh A; Eisen M; Davis R E; Ma C; Sabet H; Tran T; Powell J I; Yang L; Marti G E; Moore D T; Hudson J R; Chan W C; Greiner T; Weisenburger D; Armitage J O; Lossos I; Levy R; Botstein D; Brown P O; Staudt L M
The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes.
Cold Spring Harbor symposia on quantitative biology 1999;64():71-8.
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1999: Eisen M B; Brown P O
DNA arrays for analysis of gene expression.
Methods in enzymology 1999;303():179-205.
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1998: Eisen M B; Spellman P T; Brown P O; Botstein D
Cluster analysis and display of genome-wide expression patterns.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(25):14863-8.
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1998: Spellman P T; Sherlock G; Zhang M Q; Iyer V R; Anders K; Eisen M B; Brown P O; Botstein D; Futcher B
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
Molecular biology of the cell 1998;9(12):3273-97.
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1998: Alizadeh A; Eisen M; Botstein D; Brown P O; Staudt L M
Probing lymphocyte biology by genomic-scale gene expression analysis.
Journal of clinical immunology 1998;18(6):373-9.
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1998: Chu S; DeRisi J; Eisen M; Mulholland J; Botstein D; Brown P O; Herskowitz I
The transcriptional program of sporulation in budding yeast.
Science (New York, N.Y.) 1998;282(5389):699-705.
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1998: Yeager M; Wilson-Kubalek E M; Weiner S G; Brown P O; Rein A
Supramolecular organization of immature and mature murine leukemia virus revealed by electron cryo-microscopy: implications for retroviral assembly mechanisms.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(13):7299-304.
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1998: Gerton J L; Ohgi S; Olsen M; DeRisi J; Brown P O
Effects of mutations in residues near the active site of human immunodeficiency virus type 1 integrase on specific enzyme-substrate interactions.
Journal of virology 1998;72(6):5046-55.
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1998: Heuer T S; Brown P O
Photo-cross-linking studies suggest a model for the architecture of an active human immunodeficiency virus type 1 integrase-DNA complex.
Biochemistry 1998;37(19):6667-78.
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1997: Lashkari D A; DeRisi J L; McCusker J H; Namath A F; Gentile C; Hwang S Y; Brown P O; Davis R W
Yeast microarrays for genome wide parallel genetic and gene expression analysis.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(24):13057-62.
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1997: DeRisi J L; Iyer V R; Brown P O
Exploring the metabolic and genetic control of gene expression on a genomic scale.
Science (New York, N.Y.) 1997;278(5338):680-6.
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1997: Gerton J L; Brown P O
The core domain of HIV-1 integrase recognizes key features of its DNA substrates.
The Journal of biological chemistry 1997;272(41):25809-15.
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1997: Heuer T S; Brown P O
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.
Biochemistry 1997;36(35):10655-65.
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1997: Singh I R; Crowley R A; Brown P O
High-resolution functional mapping of a cloned gene by genetic footprinting.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(4):1304-9.
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1997: Scottoline B P; Chow S; Ellison V; Brown P O
Disruption of the terminal base pairs of retroviral DNA during integration.
Genes & development 1997;11(3):371-82.
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1997: Roe T; Chow S A; Brown P O
3'-end processing and kinetics of 5'-end joining during retroviral integration in vivo.
Journal of virology 1997;71(2):1334-40.
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1996: Smith V; Chou K N; Lashkari D; Botstein D; Brown P O
Functional analysis of the genes of yeast chromosome V by genetic footprinting.
Science (New York, N.Y.) 1996;274(5295):2069-74.
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1996: DeRisi J; Penland L; Brown P O; Bittner M L; Meltzer P S; Ray M; Chen Y; Su Y A; Trent J M
Use of a cDNA microarray to analyse gene expression patterns in human cancer.
Nature genetics 1996;14(4):457-60.
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1996: Schena M; Shalon D; Heller R; Chai A; Brown P O; Davis R W
Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(20):10614-9.
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1996: Shalon D; Smith S J; Brown P O
A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization.
Genome research 1996;6(7):639-45.
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1995: Schena M; Shalon D; Davis R W; Brown P O
Quantitative monitoring of gene expression patterns with a complementary DNA microarray.
Science (New York, N.Y.) 1995;270(5235):467-70.
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1995: Smith V; Botstein D; Brown P O
Genetic footprinting: a genomic strategy for determining a gene's function given its sequence.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(14):6479-83.
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1995: Ellison V; Gerton J; Vincent K A; Brown P O
An essential interaction between distinct domains of HIV-1 integrase mediates assembly of the active multimer.
The Journal of biological chemistry 1995;270(7):3320-6.
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1995: Dotan I; Scottoline B P; Heuer T S; Brown P O
Characterization of recombinant murine leukemia virus integrase.
Journal of virology 1995;69(1):456-68.
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1994: Chow S A; Brown P O
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.
Journal of virology 1994;68(12):7869-78.
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1994: Tsuchihashi Z; Brown P O
DNA strand exchange and selective DNA annealing promoted by the human immunodeficiency virus type 1 nucleocapsid protein.
Journal of virology 1994;68(9):5863-70.
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1994: Ellison V; Brown P O
A stable complex between integrase and viral DNA ends mediates human immunodeficiency virus integration in vitro.
Proceedings of the National Academy of Sciences of the United States of America 1994;91(15):7316-20.
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1994: Chow S A; Brown P O
Substrate features important for recognition and catalysis by human immunodeficiency virus type 1 integrase identified by using novel DNA substrates.
Journal of virology 1994;68(6):3896-907.
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1993: Nelson S F; McCusker J H; Sander M A; Kee Y; Modrich P; Brown P O
Genomic mismatch scanning: a new approach to genetic linkage mapping.
Nature genetics 1993;4(1):11-8.
-
1993: Roe T; Reynolds T C; Yu G; Brown P O
Integration of murine leukemia virus DNA depends on mitosis.
The EMBO journal 1993;12(5):2099-108.
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1993: Vincent K A; Ellison V; Chow S A; Brown P O
Characterization of human immunodeficiency virus type 1 integrase expressed in Escherichia coli and analysis of variants with amino-terminal mutations.
Journal of virology 1993;67(1):425-37.
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1992: Tsuchihashi Z; Brown P O
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.
Genes & development 1992;6(3):511-9.
-
1992: Chow S A; Vincent K A; Ellison V; Brown P O
Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus.
Science (New York, N.Y.) 1992;255(5045):723-6.
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1990: Vincent K A; York-Higgins D; Quiroga M; Brown P O
Host sequences flanking the HIV provirus.
Nucleic acids research 1990;18(20):6045-7.
-
1989: Bowerman B; Brown P O; Bishop J M; Varmus H E
A nucleoprotein complex mediates the integration of retroviral DNA.
Genes & development 1989;3(4):469-78.
-
1989: Brown P O; Bowerman B; Varmus H E; Bishop J M
Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein.
Proceedings of the National Academy of Sciences of the United States of America 1989;86(8):2525-9.
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1987: Brown P O; Bowerman B; Varmus H E; Bishop J M
Correct integration of retroviral DNA in vitro.
Cell 1987;49(3):347-56.
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