Research Topics
Genomes and Genes | P O BrownSummaryAffiliation: Stanford University Country: USA Publications
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Publications
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeastAndre P Gerber
Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
PLoS Biol 2:E79. 2004....- Detection and characterization of cellular immune responses using peptide-MHC microarraysYoav Soen
Department of Biochemistry, Stanford University, Stanford, California, USA
PLoS Biol 1:E65. 2003.... - Differential gene expression in anatomical compartments of the human eyeJennifer 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... - Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiaeEvan H Hurowitz
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
Genome Biol 5:R2. 2003..A systematic relationship between the lengths of the untranslated regions in yeast mRNAs and the functions of the proteins they encode may point to an important regulatory role for these sequences... - 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 receptorPaul Martin Holterhus
Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
Genome Biol 4:R37. 2003.... - A DNA microarray survey of gene expression in normal human tissuesRadha Shyamsundar
Department of Pathology, Stanford University School of Medicine, 269 Campus Drive, CCSR 3245A, Stanford, CA 94305 5176, USA
Genome Biol 6:R22. 2005.... - A method for detecting and correcting feature misidentification on expression microarraysI 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... - A transcriptional response to Wnt protein in human embryonic carcinoma cellsJennifer 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... - Cancer characterization and feature set extraction by discriminative margin clusteringKamesh 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... - 2005 Curt Stern Award address. Exploring along a crooked pathPatrick 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 - Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutionsB B Haab
Department of Biochemistry and Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Genome Biol 2:RESEARCH0004. 2001.... - Functional analysis of the genes of yeast chromosome V by genetic footprintingV 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... - Exploring the new world of the genome with DNA microarraysP 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... - Exploring the metabolic and genetic control of gene expression on a genomic scaleJ 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... - Genomic expression programs in the response of yeast cells to environmental changesA 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... - Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA associationJ 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... - Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1pA 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... - Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon sourceK 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... - Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBFV 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... - Singular value decomposition for genome-wide expression data processing and modelingO Alter
Departments of Genetics and Biochemistry, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 97:10101-6. 2000.... - Two yeast forkhead genes regulate the cell cycle and pseudohyphal growthG 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... - Combining SSH and cDNA microarrays for rapid identification of differentially expressed genesG 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... - New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysisN 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... - DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coliA 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... - Observing the living genomeT 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... - Use of cDNA microarrays to analyze dioxin-induced changes in human liver gene expressionF 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... - Parallel human genome analysis: microarray-based expression monitoring of 1000 genesM 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... - Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridizationM 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... - Human immunodeficiency virus type 1 vectors efficiently transduce human hematopoietic stem cellsR 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... - Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coliJ 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... - Mediator protein mutations that selectively abolish activated transcriptionL 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... - Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomasI 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... - The Stanford Microarray DatabaseG 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... - Comprehensive mutational analysis of the Moloney murine leukemia virus envelope proteinS 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... - Diversity of gene expression in adenocarcinoma of the lungM 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... - 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 codonZ 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... - A second iron-regulatory system in yeast independent of Aft1pJ 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... - Three cell wall mannoproteins facilitate the uptake of iron in Saccharomyces cerevisiaeO 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... - The transcriptional program of sporulation in budding yeastS 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... - Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarraysC 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... - Visualizing associations between genome sequences and gene expression data using genome-mean expression profilesD 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/... - Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiaeO 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.... - Haa1, a protein homologous to the copper-regulated transcription factor Ace1, is a novel transcriptional activatorG 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... - Desferrioxamine-mediated iron uptake in Saccharomyces cerevisiae. Evidence for two pathways of iron uptakeC 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... - Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarraysA 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... - Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiaeL 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... - Comparative genome-scale analysis of gene expression profiles in T cell lymphoma cells during malignant progression using a complementary DNA microarrayS 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.... - Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysisK 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... - Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arraysR 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.... - Regulation of CSF1 promoter by the SWI/SNF-like BAF complexR 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... - RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancerB 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...