P O Brown

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Virtual Northern analysis of the human genome
    Evan H Hurowitz
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 2:e460. 2007
  2. pmc Detection and characterization of cellular immune responses using peptide-MHC microarrays
    Yoav Soen
    Department of Biochemistry, Stanford University, Stanford, California, USA
    PLoS Biol 1:E65. 2003
  3. pmc Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    Andre P Gerber
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E79. 2004
  4. pmc Differential gene expression in anatomical compartments of the human eye
    Jennifer J Diehn
    Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Genome Biol 6:R74. 2005
  5. pmc Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae
    Evan H Hurowitz
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5307, USA
    Genome Biol 5:R2. 2003
  6. pmc 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
    Paul Martin Holterhus
    Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Genome Biol 4:R37. 2003
  7. pmc A DNA microarray survey of gene expression in normal human tissues
    Radha Shyamsundar
    Department of Pathology, Stanford University School of Medicine, 269 Campus Drive, CCSR 3245A, Stanford, CA 94305 5176, USA
    Genome Biol 6:R22. 2005
  8. pmc A method for detecting and correcting feature misidentification on expression microarrays
    I Ping Tu
    Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
    BMC Genomics 5:64. 2004
  9. pmc A transcriptional response to Wnt protein in human embryonic carcinoma cells
    Jennifer Willert
    Department of Developmental Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305 USA
    BMC Dev Biol 2:8. 2002
  10. pmc Cancer characterization and feature set extraction by discriminative margin clustering
    Kamesh Munagala
    Department of Biochemistry, Stanford University School of Medicine, 466 Gates Computer Science, Stanford, CA 94305, USA
    BMC Bioinformatics 5:21. 2004

Collaborators

Detail Information

Publications55

  1. pmc Virtual Northern analysis of the human genome
    Evan H Hurowitz
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 2:e460. 2007
    ..We applied the Virtual Northern technique to human brain mRNA to systematically measure human mRNA transcript lengths on a genome-wide scale...
  2. pmc Detection and characterization of cellular immune responses using peptide-MHC microarrays
    Yoav Soen
    Department of Biochemistry, Stanford University, Stanford, California, USA
    PLoS Biol 1:E65. 2003
    ....
  3. pmc Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    Andre P Gerber
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E79. 2004
    ....
  4. pmc Differential gene expression in anatomical compartments of the human eye
    Jennifer J Diehn
    Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Genome Biol 6:R74. 2005
    ..We set out to systematically characterize the global gene expression patterns that specify the distinctive characteristics of the various eye compartments...
  5. pmc Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae
    Evan H Hurowitz
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5307, USA
    Genome Biol 5:R2. 2003
    ..Although the protein-coding sequences in the Saccharomyces cerevisiae genome have been studied and annotated extensively, much less is known about the extent and characteristics of the untranslated regions of yeast mRNAs...
  6. pmc 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
    Paul Martin Holterhus
    Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Genome Biol 4:R37. 2003
    ....
  7. pmc A DNA microarray survey of gene expression in normal human tissues
    Radha Shyamsundar
    Department of Pathology, Stanford University School of Medicine, 269 Campus Drive, CCSR 3245A, Stanford, CA 94305 5176, USA
    Genome Biol 6:R22. 2005
    ....
  8. pmc A method for detecting and correcting feature misidentification on expression microarrays
    I Ping Tu
    Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
    BMC Genomics 5:64. 2004
    ..In this paper, we describe our statistical methods to detect the inconsistencies in microarray data that arise from process errors, and discuss our technique to locate and fix these errors...
  9. pmc A transcriptional response to Wnt protein in human embryonic carcinoma cells
    Jennifer Willert
    Department of Developmental Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305 USA
    BMC Dev Biol 2:8. 2002
    ..Wnt signaling is implicated in many developmental decisions, including stem cell control, as well as in cancer. There are relatively few target genes known of the Wnt pathway...
  10. pmc Cancer characterization and feature set extraction by discriminative margin clustering
    Kamesh Munagala
    Department of Biochemistry, Stanford University School of Medicine, 466 Gates Computer Science, Stanford, CA 94305, USA
    BMC Bioinformatics 5:21. 2004
    ..A central challenge in the molecular diagnosis and treatment of cancer is to define a set of molecular features that, taken together, distinguish a given cancer, or type of cancer, from all normal cells and tissues...
  11. pmc Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions
    B B Haab
    Department of Biochemistry and Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Genome Biol 2:RESEARCH0004. 2001
    ....
  12. pmc 2005 Curt Stern Award address. Exploring along a crooked path
    Patrick O Brown
    Department of Biochemistry, Stanford University School of Medicine and Howard Hughes Medical Institute, Stanford, CA 94350, USA
    Am J Hum Genet 79:429-33. 2006
  13. ncbi request reprint Exploring the new world of the genome with DNA microarrays
    P O Brown
    Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, California 94305, USA
    Nat Genet 21:33-7. 1999
    ..Exploration of the genome using DNA microarrays and other genome-scale technologies should narrow the gap in our knowledge of gene function and molecular biology between the currently-favoured model organisms and other species...
  14. ncbi request reprint Functional analysis of the genes of yeast chromosome V by genetic footprinting
    V Smith
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA Medicine, Stanford, CA 94305, USA
    Science 274:2069-74. 1996
    ..Results could not be obtained for fewer than 3 percent of the genes tested (7 of 268). Previously known mutant phenotypes were confirmed, and, for about 30 percent of the genes, new mutant phenotypes were identified...
  15. ncbi request reprint Exploring the metabolic and genetic control of gene expression on a genomic scale
    J L DeRisi
    Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA 94305 5428, USA
    Science 278:680-6. 1997
    ..These results demonstrate the feasibility and utility of this approach to genomewide exploration of gene expression patterns...
  16. pmc Genomic expression programs in the response of yeast cells to environmental changes
    A P Gasch
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5428, USA
    Mol Biol Cell 11:4241-57. 2000
    ..Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell...
  17. ncbi request reprint Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    J D Lieb
    Department of Biochemistry, Stanford University, Stanford, California 94305 5428, USA
    Nat Genet 28:327-34. 2001
    ..This global phenomenon, which may be a general characteristic of sequence-specific transcriptional factors, indicates the existence of a genome-wide molecular mechanism for marking promoter regions...
  18. pmc Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p
    A P Gasch
    Departments of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Mol Biol Cell 12:2987-3003. 2001
    ..The complete data set as well as supplemental materials is available at http://www-genome.stanford.edu/mec1...
  19. pmc Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source
    K M Kuhn
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Cell Biol 21:916-27. 2001
    ..cerevisiae reacts to the carbon source shift with a remarkable variety of responses, including translational regulation of specific mRNAs and activation of specific enzymes involved in a nonconventional splicing mechanism...
  20. ncbi request reprint Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    V R Iyer
    Department of Biochemistry, Stanford University Medical Center, California 94305, USA
    Nature 409:533-8. 2001
    ..The functional specialization of these factors may provide a mechanism for independent regulation of distinct molecular processes that normally occur in synchrony during the mitotic cell cycle...
  21. pmc Singular value decomposition for genome-wide expression data processing and modeling
    O Alter
    Departments of Genetics and Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 97:10101-6. 2000
    ....
  22. ncbi request reprint Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth
    G Zhu
    Department of Biochemistry, University of Washington, Seattle 98195 7350, USA
    Nature 406:90-4. 2000
    ..Thus, a cascade of transcription factors operates late in the cell cycle. Finally, the fkh1 fkh2 mutant displays a constitutive pseudohyphal morphology, indicating that Fkh1 and Fkh2 may help control the switch to this mode of growth...
  23. ncbi request reprint Molecular portraits of human breast tumours
    C M Perou
    Department of Genetics, Stanford University School of Medicine, California 94305, USA
    Nature 406:747-52. 2000
    ..The tumours could be classified into subtypes distinguished by pervasive differences in their gene expression patterns...
  24. pmc Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes
    G P Yang
    Department of Surgery and Department of Biochemistry, Stanford University, Stanford, CA 94305 5414, USA
    Nucleic Acids Res 27:1517-23. 1999
    ..This approach allowed the identification of differentially expressed genes without the need to obtain previously cloned cDNAs...
  25. pmc New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis
    N Ogawa
    Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305 5307, USA
    Mol Biol Cell 11:4309-21. 2000
    ..Taken together, the results reveal important new features of a genetic system that plays a critical role in P(i) acquisition and polyP metabolism in yeast...
  26. pmc DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli
    A B Khodursky
    Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, CA 94305, USA
    Proc Natl Acad Sci U S A 97:12170-5. 2000
    ..We uncovered a plethora of likely indirect effects of changes in tryptophan metabolism on intracellular mRNA pools, most prominent of which was the sensitivity of arginine biosynthetic operons to tryptophan starvation...
  27. ncbi request reprint Observing the living genome
    T L Ferea
    Department of Genetics, L311, Stanford University School of Medicine, Stanford 94305 5120, USA
    Curr Opin Genet Dev 9:715-22. 1999
    ..The rich information represented in the variation in each gene's expression provides the basis for a new kind of genomic map...
  28. ncbi request reprint Use of cDNA microarrays to analyze dioxin-induced changes in human liver gene expression
    F W Frueh
    Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, CA 95305 5332, USA
    Toxicol Lett 122:189-203. 2001
    ..We observed direct and indirect responses to TCDD implying that adaptation to TCDD (and other related environmental stimuli) is substantially more complex than we previously realized...
  29. pmc Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization
    M Wilson
    Department of Microbiology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 96:12833-8. 1999
    ..Insights gained from this approach may define new drug targets and suggest new methods for identifying compounds that inhibit those targets...
  30. pmc Parallel human genome analysis: microarray-based expression monitoring of 1000 genes
    M Schena
    Department of Biochemistry, Beckman Center, Stanford University Medical Center, CA 94305, USA
    Proc Natl Acad Sci U S A 93:10614-9. 1996
    ..Parallel gene analysis with microarrays provides a rapid and efficient method for large-scale human gene discovery...
  31. pmc Human immunodeficiency virus type 1 vectors efficiently transduce human hematopoietic stem cells
    R E Sutton
    Department of Biochemistry and Howard Hughes Medical Institute, Stanford University Medical Center, Stanford, California 94305, USA
    J Virol 72:5781-8. 1998
    ..These results extend the utility of this lentivirus vector system...
  32. pmc Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli
    J Courcelle
    Department of Biochemistry, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
    Genetics 158:41-64. 2001
    ..These newly identified UV-responsive genes are discussed with respect to their possible roles in cellular recovery following exposure to UV irradiation...
  33. pmc DNA strand exchange and selective DNA annealing promoted by the human immunodeficiency virus type 1 nucleocapsid protein
    Z Tsuchihashi
    Howard Hughes Medical Institute, Standford, California
    J Virol 68:5863-70. 1994
    ..This activity of NC may be important for correct folding of viral genomic RNA and may have practical applications...
  34. pmc Mediator protein mutations that selectively abolish activated transcription
    L C Myers
    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 96:67-72. 1999
    ..These findings make an important connection between transcriptional activation in vitro and in vivo, and identify Mediator as a "global" transcriptional coactivator...
  35. pmc Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas
    I S Lossos
    Departments of Medicine, Biochemistry, and Genetics, Division of Oncology and Howard Hughes Medical Institute, Stanford University Medical Center, Stanford, CA 94305 5306, USA
    Proc Natl Acad Sci U S A 97:10209-13. 2000
    ..Our findings validate the concept that lymphoid malignancies are derived from cells at discrete stages of normal lymphocyte maturation and that the malignant cells retain the genetic program of those normal cells...
  36. pmc The Stanford Microarray Database
    G Sherlock
    Department of Genetics, Center for Clinical Sciences Research, 269 Campus Drive, Room 2255b, Stanford University, Stanford, CA 94305 5163, USA
    Nucleic Acids Res 29:152-5. 2001
    ..S., Lowe,T.M. and Tolstoshev,C.M. (1993) Nature Genet., 4, 332-333] and SWISS-PROT [Bairoch,A. and Apweiler,R. (2000) Nucleic Acids Res., 28, 45-48] and can be accessed at http://genome-www.stanford.edu/microarray...
  37. pmc Diversity of gene expression in adenocarcinoma of the lung
    M E Garber
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 98:13784-9. 2001
    ..Gene expression analysis thus promises to extend and refine standard pathologic analysis...
  38. pmc Comprehensive mutational analysis of the Moloney murine leukemia virus envelope protein
    S M Rothenberg
    Program in Cancer Biology, Stanford University Medical Center, Palo Alto, California 94305, USA
    J Virol 75:11851-62. 2001
    ..The high-resolution functional map reported here will be valuable for the engineering of the Env protein for a variety of uses, including gene therapy...
  39. ncbi request reprint 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
    Z Tsuchihashi
    Howard Hughes Medical Institute, Stanford University Medical Center, California 94305
    Genes Dev 6:511-9. 1992
    ..coli. Expression in E. coli of a mutant tRNA(Lys) with a CUU anticodon specifically inhibited the frameshifting at the AAG codon, suggesting that the absence of this tRNA in E. coli contributes to the efficiency of the dnaX frameshift...
  40. ncbi request reprint The transcriptional program of sporulation in budding yeast
    S Chu
    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143 0448, USA
    Science 282:699-705. 1998
    ..The temporal expression pattern provided clues to potential functions of hundreds of previously uncharacterized genes, some of which have vertebrate homologs that may function during gametogenesis...
  41. ncbi request reprint Three cell wall mannoproteins facilitate the uptake of iron in Saccharomyces cerevisiae
    O Protchenko
    Liver Diseases Section, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-1800, USA
    J Biol Chem 276:49244-50. 2001
    ..Fit1p, Fit2p, and Fit3p may function by increasing the amount of iron associated with the cell wall and periplasmic space...
  42. ncbi request reprint Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae
    O Carmel Harel
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892 5430, USA
    Mol Microbiol 39:595-605. 2001
    ....
  43. ncbi request reprint Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays
    C Gross
    University of Utah Health Sciences Center, Departments of Medicine and Biochemistry, Salt Lake City, Utah 84132, USA
    J Biol Chem 275:32310-6. 2000
    ..Copper-induced FET3 and FTR1 expression arises from an indirect copper effect on cellular iron pools...
  44. ncbi request reprint Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles
    D Y Chiang
    Dept. of Molecular and Cell Biology, U. of California, Berkeley, CA 94720, USA
    Bioinformatics 17:S49-55. 2001
    ..Software that computed GMEP's from sequence and gene expression data is available under the terms of the Gnu Public License from http://rana.lbl.gov/...
  45. ncbi request reprint Haa1, a protein homologous to the copper-regulated transcription factor Ace1, is a novel transcriptional activator
    G Keller
    University of Utah Health Sciences Center, Departments of Medicine and Biochemistry, Salt Lake City, Utah 84132, USA
    J Biol Chem 276:38697-702. 2001
    ..Overexpression of Haa1 does not compensate for cells lacking a functional Ace1. The lack of metalloregulation of Haa1 despite the strong sequence similarity to the copper regulatory domain of Ace1 is discussed...
  46. pmc A second iron-regulatory system in yeast independent of Aft1p
    J C Rutherford
    University of Utah Health Sciences Center, Department of Medicine, Salt Lake City, Utah 84132, USA
    Proc Natl Acad Sci U S A 98:14322-7. 2001
    ..Together, these data suggest that yeast has a second regulatory pathway for the iron regulon, with AFT1 and AFT2 playing partially redundant roles...
  47. pmc Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis
    K A Shepard
    Department of Cellular and Molecular Pharmacology and Biochemistry and Biophysics and Howard Hughes Medical Institute, University of California, San Francisco, CA 94107, USA
    Proc Natl Acad Sci U S A 100:11429-34. 2003
    ..In contrast to findings in metazoans, the untranslated regions are dispensable for mRNA localization in yeast. This study reveals an unanticipated widespread use of RNA transport in budding yeast...
  48. pmc Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays
    A B Khodursky
    Department of Molecular and Cell Biology, University of California, Berkeley 94720, USA
    Proc Natl Acad Sci U S A 97:9419-24. 2000
    ..Topo IV activity was sufficient to prevent accumulation of (+) supercoils in plasmid DNA in vivo, suggesting that topo IV can promote replication by removing (+) supercoils in front of the chromosomal fork...
  49. pmc Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays
    R Miki
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC, Yokohama 230-0045, Japan
    Proc Natl Acad Sci U S A 98:2199-204. 2001
    ....
  50. pmc Comparative genome-scale analysis of gene expression profiles in T cell lymphoma cells during malignant progression using a complementary DNA microarray
    S Li
    Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Founders 7.06, 3400 Spruce Street, Philadelphia, PA 19104, USA
    Am J Pathol 158:1231-7. 2001
    ....
  51. pmc Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae
    L L Lutfiyya
    Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Genetics 150:1377-91. 1998
    ..We found no genes repressed by Yer028. Also, we identified no genes repressed by only Mig1 or Mig2. Thus, Mig1 and Mig2 are redundant glucose repressors of many genes...
  52. ncbi request reprint Desferrioxamine-mediated iron uptake in Saccharomyces cerevisiae. Evidence for two pathways of iron uptake
    C W Yun
    Liver Diseases Section, NIDDK, National Institutes of Health, Bethesda, Maryland 20892 1800, USA
    J Biol Chem 275:10709-15. 2000
    ..These data indicate that S. cerevisiae has two pathways for ferrrioxamine-mediated iron uptake, one occurring at the plasma membrane and the other occurring in an intracellular compartment...
  53. ncbi request reprint RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer
    B S Finlin
    Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40536, USA
    J Biol Chem 276:42259-67. 2001
    ..These features of RERG are strikingly different from most Ras superfamily GTP-binding pro-teins and suggest that the loss of RERG expression may contribute to breast tumorigenesis...
  54. ncbi request reprint Regulation of CSF1 promoter by the SWI/SNF-like BAF complex
    R Liu
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Cell 106:309-18. 2001
    ..The BAF complex facilitates Z-DNA formation in a nucleosomal template in vitro. We propose a model in which the BAF complex promotes Z-DNA formation which, in turn, stabilizes the open chromatin structure at the CSF1 promoter...
  55. pmc Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
    T Sørlie
    Department of Genetics, The Norwegian Radium Hospital, Montebello, N 0310 Oslo, Norway
    Proc Natl Acad Sci U S A 98:10869-74. 2001
    ....