Patrick O. Brown - Publications

Affiliations: 
Biochemistry Stanford University, Palo Alto, CA 
Area:
gene expression
Website:
http://brownlab.stanford.edu/Pat_Brown_Lab_Home_Page/Home.html

207 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Hogan GJ, Brown PO, Herschlag D. Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. Plos Biology. 13: e1002307. PMID 26587879 DOI: 10.1371/journal.pbio.1002307  1
2015 Riordan DP, Varma S, West RB, Brown PO. Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling. Plos One. 10: e0128975. PMID 26176839 DOI: 10.1371/journal.pone.0128975  0.44
2014 Isobe T, Hisamori S, Hogan DJ, Zabala M, Hendrickson DG, Dalerba P, Cai S, Scheeren F, Kuo AH, Sikandar SS, Lam JS, Qian D, Dirbas FM, Somlo G, Lao K, ... Brown PO, et al. miR-142 regulates the tumorigenicity of human breast cancer stem cells through the canonical WNT signaling pathway. Elife. 3. PMID 25406066 DOI: 10.7554/eLife.01977  1
2014 Lovejoy AF, Riordan DP, Brown PO. Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. Plos One. 9: e110799. PMID 25353621 DOI: 10.1371/journal.pone.0110799  1
2014 Lareau LF, Hite DH, Hogan GJ, Brown PO. Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments. Elife. 3: e01257. PMID 24842990 DOI: 10.7554/eLife.01257  1
2014 Wang PL, Bao Y, Yee MC, Barrett SP, Hogan GJ, Olsen MN, Dinneny JR, Brown PO, Salzman J. Circular RNA is expressed across the eukaryotic tree of life. Plos One. 9: e90859. PMID 24609083 DOI: 10.1371/journal.pone.0090859  1
2013 Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Cell-type specific features of circular RNA expression. Plos Genetics. 9: e1003777. PMID 24039610 DOI: 10.1371/journal.pgen.1003777  1
2013 Klass DM, Scheibe M, Butter F, Hogan GJ, Mann M, Brown PO. Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae. Genome Research. 23: 1028-38. PMID 23636942 DOI: 10.1101/gr.153031.112  1
2013 Brown PO. An interview with Patrick O Brown on the origins and future of open access. Bmc Biology. 11: 33. PMID 23587113 DOI: 10.1186/1741-7007-11-33  1
2013 Salzman J, Klass DM, Brown PO. Improved discovery of molecular interactions in genome-scale data with adaptive model-based normalization. Plos One. 8: e53930. PMID 23349766 DOI: 10.1371/journal.pone.0053930  1
2012 Tsvetanova NG, Riordan DP, Brown PO. The yeast Rab GTPase Ypt1 modulates unfolded protein response dynamics by regulating the stability of HAC1 RNA. Plos Genetics. 8: e1002862. PMID 22844259 DOI: 10.1371/journal.pgen.1002862  1
2012 Bates JG, Salzman J, May D, Garcia PB, Hogan GJ, McIntosh M, Schlissel MS, Brown PO. Extensive gene-specific translational reprogramming in a model of B cell differentiation and Abl-dependent transformation. Plos One. 7: e37108. PMID 22693568 DOI: 10.1371/journal.pone.0037108  1
2012 Casolari JM, Thompson MA, Salzman J, Champion LM, Moerner WE, Brown PO. Widespread mRNA association with cytoskeletal motor proteins and identification and dynamics of myosin-associated mRNAs in S. cerevisiae. Plos One. 7: e31912. PMID 22359641 DOI: 10.1371/journal.pone.0031912  1
2012 Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. Plos One. 7: e30733. PMID 22319583 DOI: 10.1371/journal.pone.0030733  1
2012 Wong D, Kea B, Pesich R, Higgs BW, Zhu W, Brown P, Yao Y, Fiorentino D. Interferon and biologic signatures in dermatomyositis skin: Specificity and heterogeneity across diseases Plos One. 7. PMID 22235269 DOI: 10.1371/journal.pone.0029161  1
2011 Salzman J, Marinelli RJ, Wang PL, Green AE, Nielsen JS, Nelson BH, Drescher CW, Brown PO. ESRRA-C11orf20 is a recurrent gene fusion in serous ovarian carcinoma. Plos Biology. 9: e1001156. PMID 21949640 DOI: 10.1371/journal.pbio.1001156  1
2011 del Alamo M, Hogan DJ, Pechmann S, Albanese V, Brown PO, Frydman J. Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes. Plos Biology. 9: e1001100. PMID 21765803 DOI: 10.1371/journal.pbio.1001100  1
2011 Weaver A, Brown P, Huey S, Magallon M, Bollman EB, Mares D, Streit TG, Lieberman M. A low-tech analytical method for diethylcarbamazine citrate in medicated salt. Plos Neglected Tropical Diseases. 5: e1005. PMID 21347443 DOI: 10.1371/journal.pntd.0001005  1
2011 Rubins KH, Hensley LE, Relman DA, Brown PO. Stunned silence: gene expression programs in human cells infected with monkeypox or vaccinia virus. Plos One. 6: e15615. PMID 21267444 DOI: 10.1371/journal.pone.0015615  1
2011 Riordan DP, Herschlag D, Brown PO. Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome. Nucleic Acids Research. 39: 1501-9. PMID 20959291 DOI: 10.1093/nar/gkq920  1
2010 Thompson MA, Casolari JM, Badieirostami M, Brown PO, Moerner WE. Three-dimensional tracking of single mRNA particles in Saccharomyces cerevisiae using a double-helix point spread function. Proceedings of the National Academy of Sciences of the United States of America. 107: 17864-71. PMID 20921361 DOI: 10.1073/pnas.1012868107  1
2010 Tsvetanova NG, Klass DM, Salzman J, Brown PO. Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. Plos One. 5. PMID 20844764 DOI: 10.1371/journal.pone.0012671  1
2010 Waddell SJ, Popper SJ, Rubins KH, Griffiths MJ, Brown PO, Levin M, Relman DA. Dissecting interferon-induced transcriptional programs in human peripheral blood cells. Plos One. 5: e9753. PMID 20339534 DOI: 10.1371/journal.pone.0009753  1
2010 Houshdaran S, Hawley S, Palmer C, Campan M, Olsen MN, Ventura AP, Knudsen BS, Drescher CW, Urban ND, Brown PO, Laird PW. DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines. Plos One. 5: e9359. PMID 20179752 DOI: 10.1371/journal.pone.0009359  1
2009 Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, Brown PO. Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. Plos Biology. 7: e1000238. PMID 19901979 DOI: 10.1371/journal.pbio.1000238  1
2009 Brown PO, Palmer C. The preclinical natural history of serous ovarian cancer: defining the target for early detection. Plos Medicine. 6: e1000114. PMID 19636370 DOI: 10.1371/journal.pmed.1000114  1
2008 Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. Plos Biology. 6: e255. PMID 18959479 DOI: 10.1371/journal.pbio.0060255  1
2008 McIntosh M, Anderson G, Drescher C, Hanash S, Urban N, Brown P, Gambhir SS, Coukos G, Laird PW, Nelson B, Palmer C. Ovarian cancer early detection claims are biased. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 14: 7574; author reply 7. PMID 18948385 DOI: 10.1158/1078-0432.CCR-08-0623  1
2008 Rubins KH, Hensley LE, Bell GW, Wang C, Lefkowitz EJ, Brown PO, Relman DA. Comparative analysis of viral gene expression programs during poxvirus infection: a transcriptional map of the vaccinia and monkeypox genomes. Plos One. 3: e2628. PMID 18612436 DOI: 10.1371/journal.pone.0002628  1
2008 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. Systematic evaluation of candidate blood markers for detecting ovarian cancer. Plos One. 3: e2633. PMID 18612378 DOI: 10.1371/journal.pone.0002633  1
2008 Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE, Brown PO. Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. Plos One. 3: e2126. PMID 18461144 DOI: 10.1371/journal.pone.0002126  1
2008 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. The Stanford Tissue Microarray Database. Nucleic Acids Research. 36: D871-7. PMID 17989087 DOI: 10.1093/nar/gkm861  1
2007 Popper SJ, Shimizu C, Shike H, Kanegaye JT, Newburger JW, Sundel RP, Brown PO, Burns JC, Relman DA. Gene-expression patterns reveal underlying biological processes in Kawasaki disease. Genome Biology. 8: R261. PMID 18067656 DOI: 10.1186/gb-2007-8-12-r261  1
2007 Chi JT, Rodriguez EH, Wang Z, Nuyten DS, Mukherjee S, van de Rijn M, van de Vijver MJ, Hastie T, Brown PO. Gene expression programs of human smooth muscle cells: tissue-specific differentiation and prognostic significance in breast cancers. Plos Genetics. 3: 1770-84. PMID 17907811 DOI: 10.1371/journal.pgen.0030164  1
2007 Klapholz-Brown Z, Walmsley GG, Nusse YM, Nusse R, Brown PO. Transcriptional program induced by Wnt protein in human fibroblasts suggests mechanisms for cell cooperativity in defining tissue microenvironments. Plos One. 2: e945. PMID 17895986 DOI: 10.1371/journal.pone.0000945  1
2007 Buess M, Nuyten DS, Hastie T, Nielsen T, Pesich R, Brown PO. Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer. Genome Biology. 8: R191. PMID 17868458 DOI: 10.1186/gb-2007-8-9-r191  1
2007 Rubins KH, Hensley LE, Wahl-Jensen V, Daddario DiCaprio KM, Young HA, Reed DS, Jahrling PB, Brown PO, Relman DA, Geisbert TW. The temporal program of peripheral blood gene expression in the response of nonhuman primates to Ebola hemorrhagic fever. Genome Biology. 8: R174. PMID 17725815 DOI: 10.1186/gb-2007-8-8-r174  1
2007 Halbleib JM, Sääf AM, Brown PO, Nelson WJ. Transcriptional modulation of genes encoding structural characteristics of differentiating enterocytes during development of a polarized epithelium in vitro. Molecular Biology of the Cell. 18: 4261-78. PMID 17699590 DOI: 10.1091/mbc.E07-04-0308  1
2007 Sääf AM, Halbleib JM, Chen X, Yuen ST, Leung SY, Nelson WJ, Brown PO. 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. 18: 4245-60. PMID 17699589 DOI: 10.1091/mbc.E07-04-0309  1
2007 Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. Plos Biology. 5: e177. PMID 17594176 DOI: 10.1371/journal.pbio.0050177  1
2007 Hurowitz EH, Drori I, Stodden VC, Donoho DL, Brown PO. Virtual Northern analysis of the human genome. Plos One. 2: e460. PMID 17520019 DOI: 10.1371/journal.pone.0000460  1
2007 Lowe AW, Olsen M, Hao Y, Lee SP, Taek Lee K, Chen X, van de Rijn M, Brown PO. Gene expression patterns in pancreatic tumors, cells and tissues. Plos One. 2: e323. PMID 17389914 DOI: 10.1371/journal.pone.0000323  1
2007 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. The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Research. 35: D766-70. PMID 17182626 DOI: 10.1093/nar/gkl1019  1
2006 Myers JW, Chi JT, Gong D, Schaner ME, Brown PO, Ferrell JE. 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. 2: 181-94. PMID 19771225  0.44
2006 Nuyten DS, Kreike B, Hart AA, Chi JT, Sneddon JB, Wessels LF, Peterse HJ, Bartelink H, Brown PO, Chang HY, van de Vijver MJ. Predicting a local recurrence after breast-conserving therapy by gene expression profiling. Breast Cancer Research : Bcr. 8: R62. PMID 17069664 DOI: 10.1186/bcr1614  1
2006 Sneddon JB, Zhen HH, Montgomery K, van de Rijn M, Tward AD, West R, Gladstone H, Chang HY, Morganroth GS, Oro AE, Brown PO. 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. 103: 14842-7. PMID 17003113 DOI: 10.1073/pnas.0606857103  1
2006 Kapp AV, Jeffrey SS, Langerød A, Børresen-Dale AL, Han W, Noh DY, Bukholm IR, Nicolau M, Brown PO, Tibshirani R. Discovery and validation of breast cancer subtypes. Bmc Genomics. 7: 231. PMID 16965636 DOI: 10.1186/1471-2164-7-231  1
2006 Brown PO. 2005 Curt Stern Award address. Exploring along a crooked path. American Journal of Human Genetics. 79: 429-33. PMID 16909380 DOI: 10.1086/507689  1
2006 Rinn JL, Bondre C, Gladstone HB, Brown PO, Chang HY. Anatomic demarcation by positional variation in fibroblast gene expression programs. Plos Genetics. 2: e119. PMID 16895450 DOI: 10.1371/journal.pgen.0020119  1
2006 Soen Y, Mori A, Palmer TD, Brown PO. Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments. Molecular Systems Biology. 2: 37. PMID 16820778 DOI: 10.1038/msb4100076  1
2006 Palmer C, Diehn M, Alizadeh AA, Brown PO. Cell-type specific gene expression profiles of leukocytes in human peripheral blood. Bmc Genomics. 7: 115. PMID 16704732 DOI: 10.1186/1471-2164-7-115  1
2006 Sood R, Zehnder JL, Druzin ML, Brown PO. Gene expression patterns in human placenta. Proceedings of the National Academy of Sciences of the United States of America. 103: 5478-83. PMID 16567644 DOI: 10.1073/pnas.0508035103  1
2006 Gerber AP, Luschnig S, Krasnow MA, Brown PO, Herschlag D. 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. 103: 4487-92. PMID 16537387 DOI: 10.1073/pnas.0509260103  1
2006 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, et al. Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. Plos Medicine. 3: e47. PMID 16417408 DOI: 10.1371/journal.pmed.0030047  1
2006 Diehn M, Bhattacharya R, Botstein D, Brown PO. Genome-scale identification of membrane-associated human mRNAs. Plos Genetics. 2: e11. PMID 16415983 DOI: 10.1371/journal.pgen.0020011  1
2006 Palmer C, Bik EM, Eisen MB, Eckburg PB, Sana TR, Wolber PK, Relman DA, Brown PO. Rapid quantitative profiling of complex microbial populations. Nucleic Acids Research. 34: e5. PMID 16407321 DOI: 10.1093/nar/gnj007  1
2006 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, et al. 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. 103: 690-5. PMID 16407111 DOI: 10.1073/pnas.0507321103  1
2005 Diehn JJ, Diehn M, Marmor MF, Brown PO. Differential gene expression in anatomical compartments of the human eye. Genome Biology. 6: R74. PMID 16168081 DOI: 10.1186/gb-2005-6-9-r74  1
2005 Chen DS, Soen Y, Stuge TB, Lee PP, Weber JS, Brown PO, Davis MM. Marked differences in human melanoma antigen-specific T cell responsiveness after vaccination using a functional microarray. Plos Medicine. 2: e265. PMID 16162034 DOI: 10.1371/journal.pmed.0020265  1
2005 West RB, Nuyten DS, Subramanian S, Nielsen TO, Corless CL, Rubin BP, Montgomery K, Zhu S, Patel R, Hernandez-Boussard T, Goldblum JR, Brown PO, van de Vijver M, van de Rijn M. Determination of stromal signatures in breast carcinoma. Plos Biology. 3: e187. PMID 15869330 DOI: 10.1371/journal.pbio.0030187  1
2005 Arava Y, Boas FE, Brown PO, Herschlag D. Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Research. 33: 2421-32. PMID 15860778 DOI: 10.1093/nar/gki331  1
2005 Liang Y, Diehn M, Watson N, Bollen AW, Aldape KD, Nicholas MK, Lamborn KR, Berger MS, Botstein D, Brown PO, Israel MA. Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proceedings of the National Academy of Sciences of the United States of America. 102: 5814-9. PMID 15827123 DOI: 10.1073/pnas.0402870102  1
2005 Shyamsundar R, Kim YH, Higgins JP, Montgomery K, Jorden M, Sethuraman A, van de Rijn M, Botstein D, Brown PO, Pollack JR. A DNA microarray survey of gene expression in normal human tissues. Genome Biology. 6: R22. PMID 15774023 DOI: 10.1186/gb-2005-6-3-r22  1
2005 Ellsworth RE, Ellsworth DL, Neatrour DM, Deyarmin B, Lubert SM, Sarachine MJ, Brown P, Hooke JA, Shriver CD. Allelic imbalance in primary breast carcinomas and metastatic tumors of the axillary lymph nodes. Molecular Cancer Research : McR. 3: 71-7. PMID 15755873 DOI: 10.1158/1541-7786.MCR-04-0180  1
2005 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. 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. 102: 3738-43. PMID 15701700 DOI: 10.1073/pnas.0409462102  1
2005 Ball CA, Awad IA, Demeter J, Gollub J, Hebert JM, Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G. The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Research. 33: D580-2. PMID 15608265 DOI: 10.1093/nar/gki006  1
2004 Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, Cozzarelli NR. Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biology. 5: R87. PMID 15535863 DOI: 10.1186/gb-2004-5-11-r87  1
2004 Rubins KH, Hensley LE, Jahrling PB, Whitney AR, Geisbert TW, Huggins JW, Owen A, Leduc JW, Brown PO, Relman DA. The host response to smallpox: analysis of the gene expression program in peripheral blood cells in a nonhuman primate model. Proceedings of the National Academy of Sciences of the United States of America. 101: 15190-5. PMID 15477590 DOI: 10.1073/pnas.0405759101  1
2004 Tu IP, Schaner M, Diehn M, Sikic BI, Brown PO, Botstein D, Fero MJ. A method for detecting and correcting feature misidentification on expression microarrays. Bmc Genomics. 5: 64. PMID 15357875 DOI: 10.1186/1471-2164-5-64  1
2004 McCaffrey RL, Fawcett P, O'Riordan M, Lee KD, Havell EA, Brown PO, Portnoy DA. A specific gene expression program triggered by Gram-positive bacteria in the cytosol. Proceedings of the National Academy of Sciences of the United States of America. 101: 11386-91. PMID 15269347 DOI: 10.1073/pnas.0403215101  1
2004 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. Apo D in soft tissue tumors: a novel marker for dermatofibrosarcoma protuberans. The American Journal of Surgical Pathology. 28: 1063-9. PMID 15252314 DOI: 10.1097/01.pas.0000126857.86186.4c  1
2004 West RB, Corless CL, Chen X, Rubin BP, Subramanian S, Montgomery K, Zhu S, Ball CA, Nielsen TO, Patel R, Goldblum JR, Brown PO, Heinrich MC, van de Rijn M. The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status. The American Journal of Pathology. 165: 107-13. PMID 15215166 DOI: 10.1016/S0002-9440(10)63279-8  1
2004 Munagala K, Tibshirani R, Brown PO. Cancer characterization and feature set extraction by discriminative margin clustering. Bmc Bioinformatics. 5: 21. PMID 15070405 DOI: 10.1186/1471-2105-5-21  1
2004 Gerber AP, Herschlag D, Brown PO. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. Plos Biology. 2: E79. PMID 15024427 DOI: 10.1371/journal.pbio.0020079  1
2004 Murray JI, Whitfield ML, Trinklein ND, Myers RM, Brown PO, Botstein D. Diverse and specific gene expression responses to stresses in cultured human cells. Molecular Biology of the Cell. 15: 2361-74. PMID 15004229 DOI: 10.1091/mbc.E03-11-0799  1
2004 Piedras-Rentería ES, Pyle JL, Diehn M, Glickfeld LL, Harata NC, Cao Y, Kavalali ET, Brown PO, Tsien RW. 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. 101: 3609-14. PMID 14990796 DOI: 10.1073/pnas.0308188100  1
2004 Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, van de Rijn M, Botstein D, Brown PO. Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. Plos Biology. 2: E7. PMID 14737219 DOI: 10.1371/journal.pbio.0020007  1
2004 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, et al. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proceedings of the National Academy of Sciences of the United States of America. 101: 811-6. PMID 14711987 DOI: 10.1073/pnas.0304146101  1
2004 Shakoury-Elizeh M, Tiedeman J, Rashford J, Ferea T, Demeter J, Garcia E, Rolfes R, Brown PO, Botstein D, Philpott CC. Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae. Molecular Biology of the Cell. 15: 1233-43. PMID 14668481 DOI: 10.1091/mbc.E03-09-0642  1
2004 Higgins JP, Wang L, Kambham N, Montgomery K, Mason V, Vogelmann SU, Lemley KV, Brown PO, Brooks JD, van de Rijn M. Gene expression in the normal adult human kidney assessed by complementary DNA microarray. Molecular Biology of the Cell. 15: 649-56. PMID 14657249 DOI: 10.1091/mbc.E03-06-0432  1
2004 Eisen MB, Brown PO, Varmus HE. PLoS Medicine - A medical journal for the internet age Plos Medicine. 1: 002-003. DOI: 10.1371/journal.pmed.0010031  1
2004 Alter O, Golub GH, Brown PO, Botstein D. Integrative data-driven mathematical models predict novel genome-scale correlation between DNA replication initiation and RNA transcription during the cell cycle in yeast Aiche Annual Meeting, Conference Proceedings. 1007-1008.  0.56
2004 Alter O, Golub GH, Brown PO, Botstein D. Integrative data-driven mathematical models predict novel genome-scale correlation between DNA replication initiation and RNA transcription during the cell cycle in yeast Aiche Annual Meeting, Conference Proceedings. 1007-1008.  1
2004 Alter O, Golub GH, Brown PO, Botstein D. Integrative data-driven mathematical models predict novel genomescale correlation between DNA replication initiation and RNA transcription during the cell cycle in yeast Aiche Annual Meeting, Conference Proceedings. 8303-8304.  1
2003 Hurowitz EH, Brown PO. Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biology. 5: R2. PMID 14709174 DOI: 10.1186/gb-2003-5-1-r2  1
2003 Soen Y, Chen DS, Kraft DL, Davis MM, Brown PO. Detection and characterization of cellular immune responses using peptide-MHC microarrays. Plos Biology. 1: E65. PMID 14691537 DOI: 10.1371/journal.pbio.0000065  1
2003 Linn SC, West RB, Pollack JR, Zhu S, Hernandez-Boussard T, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Siegmund D, Botstein D, Brown PO, Gilks CB, van de Rijn M. Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. The American Journal of Pathology. 163: 2383-95. PMID 14633610 DOI: 10.1016/S0002-9440(10)63593-6  1
2003 Roose JP, Diehn M, Tomlinson MG, Lin J, Alizadeh AA, Botstein D, Brown PO, Weiss A. T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression. Plos Biology. 1: E53. PMID 14624253 DOI: 10.1371/journal.pbio.0000053  1
2003 Sperger JM, Chen X, Draper JS, Antosiewicz JE, Chon CH, Jones SB, Brooks JD, Andrews PW, Brown PO, Thomson JA. Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proceedings of the National Academy of Sciences of the United States of America. 100: 13350-5. PMID 14595015 DOI: 10.1073/pnas.2235735100  1
2003 Brown PO, Eisen MB, Varmus HE. Why PLoS became a publisher. Plos Biology. 1: E36. PMID 14551926 DOI: 10.1371/journal.pbio.0000036  1
2003 Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, McCalmont TH, Brown PO, Botstein D, Connolly MK. Systemic and cell type-specific gene expression patterns in scleroderma skin. Proceedings of the National Academy of Sciences of the United States of America. 100: 12319-24. PMID 14530402 DOI: 10.1073/pnas.1635114100  1
2003 Nielsen TO, Hsu FD, O'Connell JX, Gilks CB, Sorensen PH, Linn S, West RB, Liu CL, Botstein D, Brown PO, van de Rijn M. Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology. The American Journal of Pathology. 163: 1449-56. PMID 14507652 DOI: 10.1016/S0002-9440(10)63502-X  1
2003 Shepard KA, Gerber AP, Jambhekar A, Takizawa PA, Brown PO, Herschlag D, DeRisi JL, Vale RD. Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis. Proceedings of the National Academy of Sciences of the United States of America. 100: 11429-34. PMID 13679573 DOI: 10.1073/pnas.2033246100  1
2003 Chi JT, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, van de Rijn M, Botstein D, Brown PO. Endothelial cell diversity revealed by global expression profiling. Proceedings of the National Academy of Sciences of the United States of America. 100: 10623-8. PMID 12963823 DOI: 10.1073/pnas.1434429100  1
2003 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, ... ... Brown PO, et al. Gene expression patterns in ovarian carcinomas. Molecular Biology of the Cell. 14: 4376-86. PMID 12960427 DOI: 10.1091/mbc.E03-05-0279  1
2003 Chen X, Leung SY, Yuen ST, Chu KM, Ji J, Li R, Chan AS, Law S, Troyanskaya OG, Wong J, So S, Botstein D, Brown PO. Variation in gene expression patterns in human gastric cancers. Molecular Biology of the Cell. 14: 3208-15. PMID 12925757 DOI: 10.1091/mbc.E02-12-0833  1
2003 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, et al. 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. 100: 8418-23. PMID 12829800 DOI: 10.1073/pnas.0932692100  1
2003 Holterhus PM, Hiort O, Demeter J, Brown PO, Brooks JD. Differential gene-expression patterns in genital fibroblasts of normal males and 46,XY females with androgen insensitivity syndrome: evidence for early programming involving the androgen receptor. Genome Biology. 4: R37. PMID 12801411 DOI: 10.1186/gb-2003-4-6-r37  1
2003 Nagy PL, Cleary ML, Brown PO, Lieb JD. 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. 100: 6364-9. PMID 12750471 DOI: 10.1073/pnas.1131966100  1
2003 Chi JT, Chang HY, Wang NN, Chang DS, Dunphy N, Brown PO. Genomewide view of gene silencing by small interfering RNAs. Proceedings of the National Academy of Sciences of the United States of America. 100: 6343-6. PMID 12730368 DOI: 10.1073/pnas.1037853100  1
2003 Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America. 100: 3889-94. PMID 12660367 DOI: 10.1073/pnas.0635171100  1
2003 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, ... ... Brown PO, et al. Exploration of global gene expression patterns in pancreatic adenocarcinoma using cDNA microarrays. The American Journal of Pathology. 162: 1151-62. PMID 12651607 DOI: 10.1016/S0002-9440(10)63911-9  1
2003 Alter O, Brown PO, Botstein D. 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. 100: 3351-6. PMID 12631705 DOI: 10.1073/pnas.0530258100  1
2003 Whitney AR, Diehn M, Popper SJ, Alizadeh AA, Boldrick JC, Relman DA, Brown PO. Individuality and variation in gene expression patterns in human blood. Proceedings of the National Academy of Sciences of the United States of America. 100: 1896-901. PMID 12578971 DOI: 10.1073/pnas.252784499  1
2003 Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R. Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proceedings of the National Academy of Sciences of the United States of America. 100: 1926-30. PMID 12571354 DOI: 10.1073/pnas.0437875100  1
2003 Baldwin DN, Vanchinathan V, Brown PO, Theriot JA. A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes. Genome Biology. 4: R2. PMID 12537547  1
2003 Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA. SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Research. 31: 219-23. PMID 12519986 DOI: 10.1093/nar/gkg014  1
2003 Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown PO, Botstein D, Sherlock G. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Research. 31: 94-6. PMID 12519956 DOI: 10.1093/nar/gkg078  1
2002 Leung SY, Chen X, Chu KM, Yuen ST, Mathy J, Ji J, Chan AS, Li R, Law S, Troyanskaya OG, Tu IP, Wong J, So S, Botstein D, Brown PO. Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis. Proceedings of the National Academy of Sciences of the United States of America. 99: 16203-8. PMID 12456890 DOI: 10.1073/pnas.212646299  1
2002 Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America. 99: 16144-9. PMID 12446845 DOI: 10.1073/pnas.242624799  1
2002 Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics (Oxford, England). 18: 1454-61. PMID 12424116  1
2002 Tani TH, Khodursky A, Blumenthal RM, Brown PO, Matthews RG. Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proceedings of the National Academy of Sciences of the United States of America. 99: 13471-6. PMID 12374860 DOI: 10.1073/pnas.212510999  1
2002 Chang HY, Chi JT, Dudoit S, Bondre C, van de Rijn M, Botstein D, Brown PO. Diversity, topographic differentiation, and positional memory in human fibroblasts. Proceedings of the National Academy of Sciences of the United States of America. 99: 12877-82. PMID 12297622 DOI: 10.1073/pnas.162488599  1
2002 Pollack JR, Sørlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Børresen-Dale AL, Brown PO. 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. 99: 12963-8. PMID 12297621 DOI: 10.1073/pnas.162471999  1
2002 Eisen MB, Brown PO, Varmus HE. Public-access group supports PubMed Central. Nature. 419: 111. PMID 12226637 DOI: 10.1038/419111c  1
2002 Diehn M, Alizadeh AA, Rando OJ, Liu CL, Stankunas K, Botstein D, Crabtree GR, Brown PO. Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Proceedings of the National Academy of Sciences of the United States of America. 99: 11796-801. PMID 12195013 DOI: 10.1073/pnas.092284399  1
2002 DePrimo SE, Diehn M, Nelson JB, Reiter RE, Matese J, Fero M, Tibshirani R, Brown PO, Brooks JD. Transcriptional programs activated by exposure of human prostate cancer cells to androgen. Genome Biology. 3: RESEARCH0032. PMID 12184806  1
2002 Willert J, Epping M, Pollack JR, Brown PO, Nusse R. A transcriptional response to Wnt protein in human embryonic carcinoma cells. Bmc Developmental Biology. 2: 8. PMID 12095419  1
2002 Lin JY, Pollack JR, Chou FL, Rees CA, Christian AT, Bedford JS, Brown PO, Ginsberg MH. Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays. Genome Biology. 3: RESEARCH0026. PMID 12093373  1
2002 Sayama K, Diehn M, Matsuda K, Lunderius C, Tsai M, Tam SY, Botstein D, Brown PO, Galli SJ. Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11. Bmc Immunology. 3: 5. PMID 12079505  1
2002 Lossos IS, Alizadeh AA, Diehn M, Warnke R, Thorstenson Y, Oefner PJ, Brown PO, Botstein D, Levy R. Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes. Proceedings of the National Academy of Sciences of the United States of America. 99: 8886-91. PMID 12077300 DOI: 10.1073/pnas.132253599  1
2002 Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Molecular Biology of the Cell. 13: 1977-2000. PMID 12058064 DOI: 10.1091/mbc.02-02-0030.  1
2002 Chen X, Cheung ST, So S, Fan ST, Barry C, Higgins J, Lai KM, Ji J, Dudoit S, Ng IO, Van De Rijn M, Botstein D, Brown PO. Gene expression patterns in human liver cancers. Molecular Biology of the Cell. 13: 1929-39. PMID 12058060 DOI: 10.1091/mbc.02-02-0023.  1
2002 Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS. Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. The Journal of Biological Chemistry. 277: 31079-88. PMID 12058033 DOI: 10.1074/jbc.M202718200  1
2002 Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proceedings of the National Academy of Sciences of the United States of America. 99: 5860-5. PMID 11972065 DOI: 10.1073/pnas.092538799  1
2002 Nielsen TO, West RB, Linn SC, Alter O, Knowling MA, O'Connell JX, Zhu S, Fero M, Sherlock G, Pollack JR, Brown PO, Botstein D, van de Rijn M. Molecular characterisation of soft tissue tumours: a gene expression study. Lancet (London, England). 359: 1301-7. PMID 11965276 DOI: 10.1016/S0140-6736(02)08270-3  1
2002 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, ... ... Brown PO, et al. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nature Medicine. 8: 295-301. PMID 11875502 DOI: 10.1038/nm0302-295  1
2002 Clément K, Viguerie N, Diehn M, Alizadeh A, Barbe P, Thalamas C, Storey JD, Brown PO, Barsh GS, Langin D. In vivo regulation of human skeletal muscle gene expression by thyroid hormone. Genome Research. 12: 281-91. PMID 11827947 DOI: 10.1101/gr.207702  1
2002 Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, Belcher CE, Botstein D, Staudt LM, Brown PO, Relman DA. Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proceedings of the National Academy of Sciences of the United States of America. 99: 972-7. PMID 11805339 DOI: 10.1073/pnas.231625398  1
2002 Sayama K, Diehn M, Matsuda K, Lunderius C, Tsai M, Tam SY, Botstein D, Brown PO, Galli SJ. Transcriptional response of human mast cells stimulated via the Fcε RI and identification of mast cells as a source of IL-11 Bmc Immunology. 3. DOI: 10.1186/1471-2172-3-5  1
2001 Backhus LE, DeRisi J, Bisson LF. Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions. Fems Yeast Research. 1: 111-25. PMID 12702356 DOI: 10.1016/S1567-1356(01)00019-8  1
2001 Rutherford JC, Jaron S, Ray E, Brown PO, Winge DR. A second iron-regulatory system in yeast independent of Aft1p. Proceedings of the National Academy of Sciences of the United States of America. 98: 14322-7. PMID 11734641 DOI: 10.1073/pnas.261381198  1
2001 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, ... ... Brown PO, et al. Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia. The Journal of Experimental Medicine. 194: 1639-47. PMID 11733578 DOI: 10.1084/jem.194.11.1639  1
2001 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. Diversity of gene expression in adenocarcinoma of the lung. Proceedings of the National Academy of Sciences of the United States of America. 98: 13784-9. PMID 11707590 DOI: 10.1073/pnas.241500798  1
2001 Rothenberg SM, Olsen MN, Laurent LC, Crowley RA, Brown PO. Comprehensive mutational analysis of the Moloney murine leukemia virus envelope protein. Journal of Virology. 75: 11851-62. PMID 11689666 DOI: 10.1128/JVI.75.23.11851-11862.2001  1
2001 Protchenko O, Ferea T, Rashford J, Tiedeman J, Brown PO, Botstein D, Philpott CC. Three cell wall mannoproteins facilitate the uptake of iron in Saccharomyces cerevisiae. The Journal of Biological Chemistry. 276: 49244-50. PMID 11673473 DOI: 10.1074/jbc.M109220200  1
2001 Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Molecular Biology of the Cell. 12: 2987-3003. PMID 11598186  1
2001 Lønning PE, Sørlie T, Perou CM, Brown PO, Botstein D, Børresen-Dale AL. Microarrays in primary breast cancer--lessons from chemotherapy studies. Endocrine-Related Cancer. 8: 259-63. PMID 11566617 DOI: 10.1677/erc.0.0080259  1
2001 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, et al. 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. 98: 10869-74. PMID 11553815 DOI: 10.1073/pnas.191367098  1
2001 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. RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer. The Journal of Biological Chemistry. 276: 42259-67. PMID 11533059 DOI: 10.1074/jbc.M105888200  1
2001 Liu R, Liu H, Chen X, Kirby M, Brown PO, Zhao K. Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Cell. 106: 309-18. PMID 11509180 DOI: 10.1016/S0092-8674(01)00446-9  1
2001 Keller G, Ray E, Brown PO, Winge DR. Haa1, a protein homologous to the copper-regulated transcription factor Ace1, is a novel transcriptional activator. The Journal of Biological Chemistry. 276: 38697-702. PMID 11504737 DOI: 10.1074/jbc.M107131200  1
2001 Frueh FW, Hayashibara KC, Brown PO, Whitlock JP. Use of cDNA microarrays to analyze dioxin-induced changes in human liver gene expression. Toxicology Letters. 122: 189-203. PMID 11489354 DOI: 10.1016/S0378-4274(01)00364-2  1
2001 Chiang DY, Brown PO, Eisen MB. Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics (Oxford, England). 17: S49-55. PMID 11472992  1
2001 Lieb JD, Liu X, Botstein D, Brown PO. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nature Genetics. 28: 327-34. PMID 11455386 DOI: 10.1038/ng569  1
2001 Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC. Role of DNA ligase in the illegitimate recombination that generates λbio-transducing phages in Escherichia coli Genetics. 158: 29-39. PMID 11333216  1
2001 Li S, Ross DT, Kadin ME, Brown PO, Wasik MA. 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. 158: 1231-7. PMID 11290540 DOI: 10.1016/S0002-9440(10)64073-4  1
2001 Roberts RJ, Varmus HE, Ashburner M, Brown PO, Eisen MB, Khosla C, Kirschner M, Nusse R, Scott M, Wold B. Information access. Building a "GenBank" of the published literature. Science (New York, N.Y.). 291: 2318-9. PMID 11269300  1
2001 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, ... ... Brown PO, et al. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proceedings of the National Academy of Sciences of the United States of America. 98: 2199-204. PMID 11226216 DOI: 10.1073/pnas.041605498  1
2001 Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 409: 533-8. PMID 11206552 DOI: 10.1038/35054095  1
2001 Haab BB, Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biology. 2: RESEARCH0004. PMID 11182887  1
2001 Carmel-Harel O, Stearman R, Gasch AP, Botstein D, Brown PO, Storz G. Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae. Molecular Microbiology. 39: 595-605. PMID 11169101 DOI: 10.1046/j.1365-2958.2001.02255.x  1
2001 Kuhn KM, DeRisi JL, Brown PO, 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. 21: 916-27. PMID 11154278 DOI: 10.1128/MCB.21.3.916-927.2001  1
2001 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. The Stanford Microarray Database. Nucleic Acids Research. 29: 152-5. PMID 11125075  1
2001 Renne R, Barry C, Dittmer D, Compitello N, Brown PO, Ganem D. Modulation of cellular and viral gene expression by the latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus. Journal of Virology. 75: 458-68. PMID 11119614 DOI: 10.1128/JVI.75.1.458-468.2001  1
2001 Alter O, Brown PO, Botstein D. Processing and modeling genome-wide expression data using singular value decomposition Proceedings of Spie - the International Society For Optical Engineering. 4266: 171-186. DOI: 10.1117/12.427986  1
2000 Lee SE, Pellicioli A, Demeter J, Vaze MP, Gasch AP, Malkova A, Brown PO, Botstein D, Stearns T, Foiani M, Haber JE. Arrest, adaptation, and recovery following a chromosome double-strand break in Saccharomyces cerevisiae. Cold Spring Harbor Symposia On Quantitative Biology. 65: 303-14. PMID 12760044  1
2000 Reid JL, Iyer VR, Brown PO, Struhl K. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Molecular Cell. 6: 1297-307. PMID 11163204 DOI: 10.1016/S1097-2765(00)00128-3  1
2000 Ogawa N, DeRisi J, Brown PO. New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Molecular Biology of the Cell. 11: 4309-21. PMID 11102525  1
2000 Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell. 11: 4241-57. PMID 11102521  1
2000 Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, Petes TD. 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. 97: 11383-90. PMID 11027339 DOI: 10.1073/pnas.97.21.11383  1
2000 Khodursky AB, Peter BJ, Cozzarelli NR, Botstein D, Brown PO, 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. 97: 12170-5. PMID 11027315 DOI: 10.1073/pnas.220414297  1
2000 Alter O, Brown PO, 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. 97: 10101-10106. PMID 10963673  1
2000 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, ... ... Brown PO, et al. Molecular portraits of human breast tumours. Nature. 406: 747-52. PMID 10963602 DOI: 10.1038/35021093  1
2000 Lossos IS, Alizadeh AA, Eisen MB, Chan WC, Brown PO, Botstein D, Staudt LM, Levy R. Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas. Proceedings of the National Academy of Sciences of the United States of America. 97: 10209-13. PMID 10954754 DOI: 10.1073/pnas.180316097  1
2000 Khodursky AB, Peter BJ, Schmid MB, DeRisi J, Botstein D, Brown PO, Cozzarelli NR. 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. 97: 9419-24. PMID 10944214  1
2000 Gross C, Kelleher M, Iyer VR, Brown PO, Winge DR. Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays Journal of Biological Chemistry. 275: 32310-32316. PMID 10922376  1
2000 Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature. 406: 90-4. PMID 10894548 DOI: 10.1038/35017581  1
2000 Lyons TJ, Gasch AP, Gaither LA, Botstein D, Brown PO, Eide DJ. Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Proceedings of the National Academy of Sciences of the United States of America. 97: 7957-62. PMID 10884426 DOI: 10.1073/pnas.97.14.7957  1
2000 Casagrande R, Stern P, Diehn M, Shamu C, Osario M, Zúñiga M, Brown PO, Ploegh H. Degradation of proteins from the ER of S. cerevisiae requires an intact unfolded protein response pathway. Molecular Cell. 5: 729-35. PMID 10882108  1
2000 Staudt LM, Brown PO. Genomic views of the immune system Annual Review of Immunology. 18: 829-859. PMID 10837077 DOI: 10.1146/annurev.immunol.18.1.829  1
2000 Diehn M, Alizadeh AA, Brown PO. Examining the living genome in health and disease with DNA microarrays. Jama. 283: 2298-9. PMID 10807394  1
2000 Diehn M, Eisen MB, Botstein D, Brown PO. Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nature Genetics. 25: 58-62. PMID 10802657 DOI: 10.1038/75603  1
2000 Yun CW, Ferea T, Rashford J, Ardon O, Brown PO, Botstein D, Kaplan J, Philpott CC. Desferrioxamine-mediated iron uptake in Saccharomyces cerevisiae. Evidence for two pathways of iron uptake Journal of Biological Chemistry. 275: 10709-10715. PMID 10744769 DOI: 10.1074/jbc.275.14.10709  1
2000 Sudarsanam P, Iyer VR, Brown PO, Winston F. Whole-genome expression analysis of Snf/Swi mutants of Saccharomyces cerevisiae Proceedings of the National Academy of Sciences of the United States of America. 97: 3364-3369. PMID 10725359 DOI: 10.1073/pnas.050407197  1
2000 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, et al. A gene expression database for the molecular pharmacology of cancer. Nature Genetics. 24: 236-44. PMID 10700175 DOI: 10.1038/73439  1
2000 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, ... ... Brown PO, et al. Systematic variation in gene expression patterns in human cancer cell lines. Nature Genetics. 24: 227-35. PMID 10700174 DOI: 10.1038/73432  1
2000 Laurent LC, Olsen MN, Crowley RA, Savilahti H, Brown PO. Functional characterization of the human immunodeficiency virus type 1 genome by genetic footprinting Journal of Virology. 74: 2760-2769. PMID 10684292 DOI: 10.1128/JVI.74.6.2760-2769.2000  1
2000 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, ... ... Brown PO, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 403: 503-11. PMID 10676951 DOI: 10.1038/35000501  1
2000 Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Molecular Microbiology. 35: 6-14. PMID 10632873 DOI: 10.1046/j.1365-2958.2000.01730.x  1
2000 Perou CM, Brown PO, Botstein D. Tumor classification using gene expression patterns from DNA microarrays Trends in Ecology and Evolution. 67-76.  1
1999 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, ... ... Brown PO, et al. 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. 64: 71-8. PMID 11232339  1
1999 Johannes G, Carter MS, Eisen MB, Brown PO, 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. 96: 13118-23. PMID 10557283 DOI: 10.1073/pnas.96.23.13118  1
1999 Wilson M, DeRisi J, Kristensen HH, Imboden P, Rane S, Brown PO, Schoolnik GK. 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. 96: 12833-8. PMID 10536008 DOI: 10.1073/pnas.96.22.12833  1
1999 Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nature Genetics. 23: 41-6. PMID 10471496 DOI: 10.1038/12640  1
1999 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. 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. 96: 9212-7. PMID 10430922 DOI: 10.1073/pnas.96.16.9212  1
1999 Eisen MB, Brown PO. DNA arrays for analysis of gene expression. Methods in Enzymology. 303: 179-205. PMID 10349646 DOI: 10.1016/S0076-6879(99)03014-1  1
1999 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. The transcriptional program in the response of human fibroblasts to serum. Science (New York, N.Y.). 283: 83-7. PMID 9872747 DOI: 10.1126/science.283.5398.83  1
1998 Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America. 95: 14863-8. PMID 9843981 DOI: 10.1073/pnas.95.25.14863  1
1998 Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell. 9: 3273-97. PMID 9843569  1
1998 Lutfiyya LL, Iyer VR, DeRisi J, DeVit MJ, Brown PO, Johnston M. Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae. Genetics. 150: 1377-91. PMID 9832517  1
1998 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. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nature Medicine. 4: 1293-301. PMID 9809554 DOI: 10.1038/3282  1
1998 Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. The transcriptional program of sporulation in budding yeast. Science (New York, N.Y.). 282: 699-705. PMID 9784122 DOI: 10.1126/science.282.5389.699  1
1998 Gerton JL, Ohgi S, Olsen M, DeRisi J, Brown PO. Effects of mutations in residues near the active site of human immunodeficiency virus type 1 integrase on specific enzyme-substrate interactions. Journal of Virology. 72: 5046-55. PMID 9573274  1
1997 DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science (New York, N.Y.). 278: 680-6. PMID 9381177 DOI: 10.1126/science.278.5338.680  1
1997 Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proceedings of the National Academy of Sciences of the United States of America. 94: 13057-62. PMID 9371799 DOI: 10.1073/pnas.94.24.13057  1
1997 Scottoline BP, Chow S, Ellison V, Brown PO. Disruption of the terminal base pairs of retroviral DNA during integration. Genes & Development. 11: 371-82. PMID 9030689  1
1996 DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nature Genetics. 14: 457-60. PMID 8944026 DOI: 10.1038/ng1296-457  1
1995 Dotan I, Scottoline BP, Heuer TS, Brown PO. Characterization of recombinant murine leukemia virus integrase. Journal of Virology. 69: 456-68. PMID 7983742  1
1989 Bowerman B, Brown PO, Bishop JM, Varmus HE. A nucleoprotein complex mediates the integration of retroviral DNA. Genes & Development. 3: 469-78. PMID 2721960  1
1989 Brown PO, Bowerman B, Varmus HE, Bishop JM. 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. 86: 2525-9. PMID 2539592  1
1987 Brown PO, Bowerman B, Varmus HE, Bishop JM. Correct integration of retroviral DNA in vitro. Cell. 49: 347-56. PMID 3032450 DOI: 10.1016/0092-8674(87)90287-X  1
1981 Brown PO, Cozzarelli NR. Catenation and knotting of duplex DNA by type 1 topoisomerases: a mechanistic parallel with type 2 topoisomerases. Proceedings of the National Academy of Sciences of the United States of America. 78: 843-7. PMID 6262776  1
1979 Brown PO, Peebles CL, Cozzarelli NR. A topoisomerase from Escherichia coli related to DNA gyrase. Proceedings of the National Academy of Sciences of the United States of America. 76: 6110-4. PMID 230498  1
1979 Brown PO, Cozzarelli NR. A sign inversion mechanism for enzymatic supercoiling of DNA. Science (New York, N.Y.). 206: 1081-3. PMID 227059  1
1979 Peebles CL, Higgins NP, Kreuzer KN, Morrison A, Brown PO, Sugino A, Cozzarelli NR. Structure and activities of Escherichia coli DNA gyrase. Cold Spring Harbor Symposia On Quantitative Biology. 43: 41-52. PMID 225110  1
1978 Sugino A, Higgins NP, Brown PO, Peebles CL, Cozzarelli NR. Energy coupling in DNA gyrase and the mechanism of action of novobiocin. Proceedings of the National Academy of Sciences of the United States of America. 75: 4838-42. PMID 368801  1
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