D Botstein

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11
    Koichi Sayama
    Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
    BMC Immunol 3:5. 2002
  2. ncbi request reprint Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease
    David Botstein
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Nat Genet 33:228-37. 2003
  3. ncbi request reprint Lack of evidence for an association between alpha-adducin and blood pressure regulation in Asian populations
    K Ranade
    Department of Genetics, Stanford University School of Medicine, California 94305-5120, USA
    Am J Hypertens 13:704-9. 2000
  4. pmc Structure-function relationships in yeast tubulins
    K L Richards
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 11:1887-903. 2000
  5. pmc 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns
    T Hastie
    Department of Statistics, Sequoia Hall, Stanford University, Stanford, CA 94305, USA
    Genome Biol 1:RESEARCH0003. 2000
  6. pmc High-throughput genotyping with single nucleotide polymorphisms
    K Ranade
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
    Genome Res 11:1262-8. 2001
  7. pmc BIM1 encodes a microtubule-binding protein in yeast
    K Schwartz
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 8:2677-91. 1997
  8. pmc Dominant-lethal alpha-tubulin mutants defective in microtubule depolymerization in yeast
    K R Anders
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Mol Biol Cell 12:3973-86. 2001
  9. 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
  10. pmc Aip3p/Bud6p, a yeast actin-interacting protein that is involved in morphogenesis and the selection of bipolar budding sites
    D C Amberg
    Department of Genetics, Stanford University School of Medicine, California 94305 5120, USA
    Mol Biol Cell 8:729-53. 1997

Detail Information

Publications109 found, 100 shown here

  1. pmc Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11
    Koichi Sayama
    Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
    BMC Immunol 3:5. 2002
    ..To search for new mast cell products, we used complementary DNA microarrays to analyze gene expression in human umbilical cord blood-derived mast cells stimulated via the high-affinity IgE receptor (Fc(epsilon)RI)...
  2. ncbi request reprint Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease
    David Botstein
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Nat Genet 33:228-37. 2003
    ....
  3. ncbi request reprint Lack of evidence for an association between alpha-adducin and blood pressure regulation in Asian populations
    K Ranade
    Department of Genetics, Stanford University School of Medicine, California 94305-5120, USA
    Am J Hypertens 13:704-9. 2000
    ..30). In contrast, in the Japanese population, there was no evidence for a positive association under any model. For the combined Chinese and Japanese samples, the evidence for association with alpha-adducin was not significant...
  4. pmc Structure-function relationships in yeast tubulins
    K L Richards
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 11:1887-903. 2000
    ....
  5. pmc 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns
    T Hastie
    Department of Statistics, Sequoia Hall, Stanford University, Stanford, CA 94305, USA
    Genome Biol 1:RESEARCH0003. 2000
    ..The technique can be 'unsupervised', that is, the genes and samples are treated as unlabeled, or partially or fully supervised by using known properties of the genes or samples to assist in finding meaningful groupings...
  6. pmc High-throughput genotyping with single nucleotide polymorphisms
    K Ranade
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
    Genome Res 11:1262-8. 2001
    ..Indeed, large-scale genotyping has been accomplished for 23 other SNPs in 13 different genes using this method. In addition, we identified three "pseudo-SNPs" (WIAF1161, WIAF2566, and WIAF335) that are probably a result of duplication...
  7. pmc BIM1 encodes a microtubule-binding protein in yeast
    K Schwartz
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 8:2677-91. 1997
    ..One of the human homologues, EB1, has been reported previously as binding APC, itself a microtubule-binding protein and the product of a gene implicated in the etiology of human colon cancer...
  8. pmc Dominant-lethal alpha-tubulin mutants defective in microtubule depolymerization in yeast
    K R Anders
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Mol Biol Cell 12:3973-86. 2001
    ..These data support the view that alpha-tubulin is a GTPase-activating protein that acts, during microtubule polymerization, to stimulate GTP hydrolysis in beta-tubulin and thereby account for the dynamic instability of microtubules...
  9. 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...
  10. pmc Aip3p/Bud6p, a yeast actin-interacting protein that is involved in morphogenesis and the selection of bipolar budding sites
    D C Amberg
    Department of Genetics, Stanford University School of Medicine, California 94305 5120, USA
    Mol Biol Cell 8:729-53. 1997
    ..Surprisingly, the localization of Aip3p does not appear to require either polarized actin or the septin proteins of the neck filaments...
  11. ncbi request reprint The glycine allele of a glycine/arginine polymorphism in the beta2-adrenergic receptor gene is associated with essential hypertension in a population of Chinese origin
    K Ranade
    Department of Genetics, Stanford University School of Medicine, California, USA
    Am J Hypertens 14:1196-200. 2001
    ..We sought to replicate these results in a population of Chinese origin primarily from Taiwan and the San Francisco Bay area...
  12. pmc Genetic and physical maps of Saccharomyces cerevisiae
    J M Cherry
    Department of Genetics, Stanford University School of Medicine, California 94305 5120, USA
    Nature 387:67-73. 1997
    ..The data for the maps are accessible electronically from the Saccharomyces Genome Database (SGD: http://genome-www.stanford. edu/Saccharomyces/)...
  13. 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...
  14. ncbi request reprint Subcellular localization of yeast CDC46 varies with the cell cycle
    K M Hennessy
    Department of Genetics, Stanford University, California 94305
    Genes Dev 4:2252-63. 1990
    ..This partitioning of proteins in a cell cycle-dependent manner illustrates a general means of regulating events that must occur only once in each cycle, such as DNA initiation...
  15. 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...
  16. pmc Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation
    Wei Wang
    Department of Genetics, Stanford University, Stanford, CA 94305 5120, USA
    Proc Natl Acad Sci U S A 102:1998-2003. 2005
    ..We show that this model accounts for the temporal control of the "middle" sporulation genes and suggest a similar regulatory arrangement can be found in developmental programs in higher organisms...
  17. pmc Ultrastructure of the yeast actin cytoskeleton and its association with the plasma membrane
    J Mulholland
    Department of Genetics, Beckman Center, Stanford University Medical Center, California 94305
    J Cell Biol 125:381-91. 1994
    ..We propose a possible role for this unique cortical structure in wall growth and osmotic regulation...
  18. ncbi request reprint Diverse essential functions revealed by complementing yeast calmodulin mutants
    Y Ohya
    Department of Genetics, Stanford University School of Medicine, CA 94305
    Science 263:963-6. 1994
    ....
  19. 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...
  20. 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
    ....
  21. pmc Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
    Selina S Dwight
    Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5120, USA
    Nucleic Acids Res 30:69-72. 2002
    ..geneontology.org. SGD gene associations to GO can be found by visiting our site at http://genome-www.stanford.edu/Saccharomyces/...
  22. pmc Yeast actin cytoskeleton mutants accumulate a new class of Golgi-derived secretary vesicle
    J Mulholland
    Department of Genetics, Stanford University Medical School, California 94305, USA
    Mol Biol Cell 8:1481-99. 1997
    ....
  23. 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...
  24. pmc Nutritional homeostasis in batch and steady-state culture of yeast
    Alok J Saldanha
    Department of Genetics, Stanford University Medical School, Stanford, CA 94305, USA
    Mol Biol Cell 15:4089-104. 2004
    ....
  25. pmc A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
    Olga G Troyanskaya
    Department of Genetics, Stanford University School of Medicine, CA 94305, USA
    Proc Natl Acad Sci U S A 100:8348-53. 2003
    ..We found that by creating functional groupings based on heterogeneous data types, MAGIC improved accuracy of the groupings compared with microarray analysis alone. We describe several of the biological gene groupings identified...
  26. pmc Saccharomyces Genome Database provides mutant phenotype data
    Stacia R Engel
    Department of Genetics, Stanford University, Stanford, CA, USA
    Nucleic Acids Res 38:D433-6. 2010
    ..Here we describe how published phenotypes and genetic interaction data are annotated and displayed in SGD...
  27. pmc Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source
    Michal Ronen
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:389-94. 2006
    ..With these estimates, for two regulatory circuits involving interaction among multiple regulators we could generate dynamical models that quantitatively account for the observed transcriptional responses to the transient perturbations...
  28. pmc Genetic variation in aldosterone synthase predicts plasma glucose levels
    K Ranade
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
    Proc Natl Acad Sci U S A 98:13219-24. 2001
    ..51; 95% confidence interval (C.I.) 1.39-3.92; P = 0.0015] and have impaired fasting glucose levels (odds ratio 3.53; 95% C.I. 2.02-5.5; P = 0.0000036). These results suggest a new role for aldosterone in glucose homeostasis...
  29. 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...
  30. pmc Gene Ontology annotations at SGD: new data sources and annotation methods
    Eurie L Hong
    Department of Genetics, Stanford University, Stanford, CA, USA
    Nucleic Acids Res 36:D577-81. 2008
    ..In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current...
  31. pmc Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome
    Jodi E Hirschman
    Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5120, USA
    Nucleic Acids Res 34:D442-5. 2006
    ..Detailed lists are accessible through SGD's Advanced Search tool (http://db.yeastgenome.org/cgi-bin/search/featureSearch), and all the data presented on this page are available from the SGD ftp site (ftp://ftp.yeastgenome.org/yeast/)...
  32. pmc The Stanford Microarray Database: data access and quality assessment tools
    Jeremy Gollub
    Department of Genetics, Center for Clinical Sciences Research, 269 Campus Drive, Room 2255b, Stanford University, Stanford, CA 94305 5163, USA
    Nucleic Acids Res 31:94-6. 2003
    ..In this article, we describe some of SMD's newer tools for accessing public data, assessing data quality and for data analysis...
  33. pmc Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms
    Karen R Christie
    Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5120, USA
    Nucleic Acids Res 32:D311-4. 2004
    ..Finally, the Find Chromosomal Features search interface provides a versatile tool for querying multiple types of information in SGD...
  34. 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...
  35. 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...
  36. ncbi request reprint Genetic variation in the human urea transporter-2 is associated with variation in blood pressure
    K Ranade
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
    Hum Mol Genet 10:2157-64. 2001
    ..5 (95% CI 1.2-1.8, P < 0.001), respectively. There was a similar trend for systolic BP, and odds ratios for the Ile227 and Ala357 alleles were 1.7 (95% CI 1.2-2.3, P = 0.002) and 1.3 (95% CI 1.1-1.6, P = 0.007), respectively, in men...
  37. pmc SGD: Saccharomyces Genome Database
    J M Cherry
    Department of Genetics, Stanford University, Stanford, CA 94305 5120, USA
    Nucleic Acids Res 26:73-9. 1998
    ..SGD can be accessed via the World Wide Web at http://genome-www.stanford.edu/Saccharomyces/..
  38. ncbi request reprint Missing value estimation methods for DNA microarrays
    O Troyanskaya
    Stanford Medical Informatics Stanford University School of Medicine, Stanford, CA, USA
    Bioinformatics 17:520-5. 2001
    ..We report results of the comparative experiments and provide recommendations and tools for accurate estimation of missing microarray data under a variety of conditions...
  39. pmc Supervised harvesting of expression trees
    T Hastie
    Department of Health, Research and Policy, Stanford University, Stanford, CA 94305, USA
    Genome Biol 2:RESEARCH0003. 2001
    ..CONCLUSIONS: Tree harvesting is a potentially useful tool for exploration of gene expression data and identification of interesting clusters of genes worthy of further investigation...
  40. ncbi request reprint Specificity domains distinguish the Ras-related GTPases Ypt1 and Sec4
    B Dunn
    Department of Genetics, Stanford University School of Medicine, California 94305
    Nature 362:563-5. 1993
    ....
  41. pmc Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome
    Matt van de Rijn
    L235 Department of Pathology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, CA 94305, USA
    Am J Pathol 161:1991-6. 2002
    ..Moreover, multivariate analysis showed that in node-negative breast carcinoma, expression of these cytokeratins was a prognostic factor independent of tumor size and tumor grade...
  42. pmc Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae
    Maitreya J Dunham
    Department of Genetics, and Howard Hughes Medical Institute and Department of Biochemistry, Stanford University Medical School, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:16144-9. 2002
    ....
  43. ncbi request reprint Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
    Eran Segal
    Computer Science Department, Stanford University, Stanford, California, 94305, USA
    Nat Genet 34:166-76. 2003
    ..We present microarray experiments supporting three novel predictions, suggesting regulatory roles for previously uncharacterized proteins...
  44. pmc Repeated observation of breast tumor subtypes in independent gene expression data sets
    Therese Sorlie
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:8418-23. 2003
    ..Our results strongly support the idea that many of these breast tumor subtypes represent biologically distinct disease entities...
  45. pmc SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
    Maximilian Diehn
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Nucleic Acids Res 31:219-23. 2003
    ..SOURCE is available at http://source.stanford.edu...
  46. pmc Gene expression patterns in ovarian carcinomas
    Marci E Schaner
    Stanford University School of Medicine, Stanford, California 94305 5151, USA
    Mol Biol Cell 14:4376-86. 2003
    ....
  47. pmc GeneXplorer: an interactive web application for microarray data visualization and analysis
    Christian A Rees
    Dept of Genetics, 300 Pasteur Drive, Stanford University Medical School, Stanford, CA 94305 5120, USA
    BMC Bioinformatics 5:141. 2004
    ..We set out to create a CGI application containing many of the features of some of the existing standalone software for the visualization of clustered microarray data...
  48. pmc Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress
    Michael Shapira
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Mol Biol Cell 15:5659-69. 2004
    ..The apparent involvement of a forkhead protein in HP-induced cell cycle arrest, similar to that reported for Caenorhabditis elegans and human, describes a potentially novel stress response pathway in yeast...
  49. pmc GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    Elizabeth I Boyle
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3710-5. 2004
    ..GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script...
  50. pmc Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures
    Matthew J Brauer
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94122, USA
    Mol Biol Cell 16:2503-17. 2005
    ..These results suggest that some aspect of actual starvation, possibly a component of the stress response, may be required for triggering the metabolic remodeling associated with the diauxic shift...
  51. pmc Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors
    Jonathan R Pollack
    Departments of Pathology, Genetics, Surgery, Health Research and Policy, and Biochemistry, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:12963-8. 2002
    ..These findings provide evidence that widespread DNA copy number alteration can lead directly to global deregulation of gene expression, which may contribute to the development or progression of cancer...
  52. ncbi request reprint Expression array technology in the diagnosis and treatment of breast cancer
    Stefanie S Jeffrey
    Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
    Mol Interv 2:101-9. 2002
    ..Thus, microarray analysis may translate basic research data into more confident diagnoses, specifically designed treatment regimens geared to each patient's needs, and better clinical prognoses...
  53. pmc Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms
    Orly Alter
    Department of Genetics, Stanford University, Stanford, CA 94305
    Proc Natl Acad Sci U S A 100:3351-6. 2003
    ..This framework enables comparative reconstruction and classification of the genes and arrays of both data sets. We illustrate this framework with a comparison of yeast and human cell-cycle expression data sets...
  54. ncbi request reprint Defining protein interactions with yeast actin in vivo
    D C Amberg
    Department of Genetics, Stanford University School of Medicine, California 94305 5120
    Nat Struct Biol 2:28-35. 1995
    ..In contrast, the patterns for profilin and the SH3 domain proteins suggest a shared binding site and commonality in mechanism...
  55. 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...
  56. pmc A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae
    Wei Wang
    Department of Genetics, Stanford University, Stanford, CA 94305 5120, USA
    Proc Natl Acad Sci U S A 99:16893-8. 2002
    ..Correlating the activation of a module to a specific perturbation predicts links in the cell's regulatory networks, and examining coactivated modules suggests specific instances of crosstalk between regulatory pathways...
  57. pmc Saccharomyces genome database: underlying principles and organisation
    Selina S Dwight
    Department of Genetics, School of Medicine, Standford University, Standford, CA 94305 5120, USA
    Brief Bioinform 5:9-22. 2004
    ..This paper aims to detail these philosophies and how they shape the organisation and presentation of the database...
  58. pmc Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)
    Rama Balakrishnan
    Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5120, USA
    Nucleic Acids Res 33:D374-7. 2005
    ..cerevisiae protein, the single most similar protein from several model organisms and presents links to the database pages of those proteins, facilitating access to curated information about potential orthologs of yeast proteins...
  59. ncbi request reprint Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes
    Izidore S Lossos
    Division of Oncology, Department of Medicine, Stanford University Medical Center, Stanford, Calif, USA
    N Engl J Med 350:1828-37. 2004
    ..Several gene-expression signatures can be used to predict the prognosis in diffuse large-B-cell lymphoma, but the lack of practical tests for a genome-scale analysis has restricted the use of this method...
  60. ncbi request reprint Nonparametric methods for identifying differentially expressed genes in microarray data
    Olga G Troyanskaya
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
    Bioinformatics 18:1454-61. 2002
    ..We systematically assess the performance of each method based on simulated and biological data under varying noise levels and p-value cutoffs...
  61. ncbi request reprint Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae
    Hiroyuki Yoshimoto
    Department of Biological Sciences, Stanford University, 371 Serra Mall, Stanford, CA 94305 5020, USA
    J Biol Chem 277:31079-88. 2002
    ..A similar sequence, 5'-GAGGCTG-3', was identified as a common sequence motif in the upstream regions of calcineurin/ Crz1p-dependent genes. This finding is consistent with direct regulation of these genes by Crz1p...
  62. pmc Expanded protein information at SGD: new pages and proteome browser
    Robert Nash
    Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5120, USA
    Nucleic Acids Res 35:D468-71. 2007
    ..Finally, SGD continues to improve upon the availability of genetic and physical interaction data in an ongoing collaboration with BioGRID by providing direct access to more than 82,000 manually-curated interactions...
  63. pmc Identification of genes periodically expressed in the human cell cycle and their expression in tumors
    Michael L Whitfield
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 13:1977-2000. 2002
    ..The data in this report provide a comprehensive catalog of cell cycle regulated genes that can serve as a starting point for functional discovery. The full dataset is available at http://genome-www.stanford.edu/Human-CellCycle/HeLa/...
  64. ncbi request reprint A group of interacting yeast DNA replication genes
    K M Hennessy
    Department of Genetics, Stanford University, California 94305
    Genes Dev 5:958-69. 1991
    ....
  65. pmc Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans
    Sabine C Linn
    Departments of Pathology, Genetics, and Biochemistry, and Howard Hughes Medical Institute, Stanford University Medical Center, Stanford, California 94305, USA
    Am J Pathol 163:2383-95. 2003
    ....
  66. pmc Different gene expression patterns in invasive lobular and ductal carcinomas of the breast
    Hongjuan Zhao
    Department of Surgery, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 15:2523-36. 2004
    ..The remaining ILCs closely resemble IDCs in their transcription patterns. Further studies are needed to explore the differences between ILC molecular subtypes and to determine whether they require different therapeutic strategies...
  67. pmc Gene expression profiling identifies clinically relevant subtypes of prostate cancer
    Jacques Lapointe
    Department of Pathology, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 101:811-6. 2004
    ..Our results suggest that prostate tumors can be usefully classified according to their gene expression patterns, and these tumor subtypes may provide a basis for improved prognostication and treatment stratification...
  68. pmc Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells
    Hongjuan Zhao
    Department of Urology, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 15:506-19. 2004
    ..Our results suggest that MSA may protect against prostate cancer by inhibiting cell proliferation, by modulating the expression of AR and AR-regulated genes and by inducing carcinogen defenses...
  69. pmc Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation
    Maximilian Diehn
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:11796-801. 2002
    ....
  70. 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
    ....
  71. pmc The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response
    Nathan D Trinklein
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
    Mol Biol Cell 15:1254-61. 2004
    ....
  72. pmc A locus for Fanconi anemia on 16q determined by homozygosity mapping
    M Gschwend
    Department of Genetics, Stanford University School of Medicine, CA 94305 5120, USA
    Am J Hum Genet 59:377-84. 1996
    ..We also demonstrate the strong effect of marker allele frequencies on LOD scores obtained in homozygosity mapping and discuss ways to avoid false positives arising from this effect...
  73. 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...
  74. 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...
  75. pmc Genome-scale identification of membrane-associated human mRNAs
    Maximilian Diehn
    Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
    PLoS Genet 2:e11. 2006
    ..The large-scale annotation of subcellular localization reported here will serve as a reference database and will aid in the rational design of diagnostic tests and molecular therapies for diverse diseases...
  76. pmc Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins
    Shuai Weng
    Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5120, USA
    Nucleic Acids Res 31:216-8. 2003
    ..A third new resource is the Protein Information page, which contains protein physical and chemical properties, such as molecular weight and hydropathicity scores, predicted from the translated ORF sequence...
  77. 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...
  78. pmc Diversity, topographic differentiation, and positional memory in human fibroblasts
    Howard Y Chang
    Departments of Dermatology, Biochemistry, Pathology, and Genetics, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:12877-82. 2002
    ....
  79. pmc Stereotyped and specific gene expression programs in human innate immune responses to bacteria
    Jennifer C Boldrick
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:972-7. 2002
    ..Modulation of this host-response program by bacterial virulence mechanisms was an important source of variation in the response to different bacteria...
  80. pmc Variation in gene expression patterns in human gastric cancers
    Xin Chen
    Department of Surgery, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 14:3208-15. 2003
    ..The variations in gene expression patterns among cancers in different patients suggest differences in pathogenetic pathways and potential therapeutic strategies...
  81. pmc Diverse and specific gene expression responses to stresses in cultured human cells
    John Isaac Murray
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 15:2361-74. 2004
    ..The dataset is freely available for search and download at http://microarray-pubs.stanford.edu/human_stress/Home.shtml...
  82. pmc Gene expression patterns in human liver cancers
    Xin Chen
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 13:1929-39. 2002
    ..Some features of the gene expression patterns were associated with specific phenotypic and genotypic characteristics of the tumors, including growth rate, vascular invasion, and p53 overexpression...
  83. pmc Endothelial cell diversity revealed by global expression profiling
    Jen Tsan Chi
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:10623-8. 2003
    ..Tissue-specific expression patterns in different tissue microvascular ECs suggest they are distinct differentiated cell types that play roles in the local physiology of their respective organs and tissues...
  84. ncbi request reprint Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1
    Kevin S Smith
    Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Mol Cell 12:393-400. 2003
    ..These results link E2a-Pbx1 with Bmi-1 on an oncogenic pathway that is likely to play a role in the pathogenesis of human lymphoid leukemias through downregulation of the INK4A-ARF gene...
  85. ncbi request reprint Challenges in developing a molecular characterization of cancer
    Jonathan R Pollack
    Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Semin Oncol 29:280-5. 2002
    ..Here, we detail some of the challenges in developing a molecular characterization of cancer and in translating these new discoveries towards clinical utility...
  86. pmc Saccharomyces cerevisiae S288C genome annotation: a working hypothesis
    Dianna G Fisk
    Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5120, USA
    Yeast 23:857-65. 2006
    ..cerevisiae sequence and annotation have changed, consider the multiple sources of experimental and comparative data on which these changes are based, and describe our methods for evaluating, incorporating and documenting these new data...
  87. ncbi request reprint Saccharomyces Genome Database
    Laurie Issel-Tarver
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Methods Enzymol 350:329-46. 2002
  88. pmc A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate
    Koustubh Ranade
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Am J Hum Genet 70:935-42. 2002
    ..Neither the Arg389Gly polymorphism in the beta1 adrenergic receptor nor polymorphisms in the beta2 and beta3 adrenergic receptors were associated with resting heart rate. The heritability of heart rate was 39.7% +/- 7.1% (P<10-7)...
  89. pmc Systematic structure-function analysis of the small GTPase Arf1 in yeast
    Eleanor S Click
    Department of Genetics, Stanford University, California 94305, USA
    Mol Biol Cell 13:1652-64. 2002
    ..In addition, we describe the isolation of a spatially distant intragenic suppressor of a dominant lethal mutation in the guanine nucleotide-binding region of Arf1p...
  90. ncbi request reprint A genome scan for hypertension susceptibility loci in populations of Chinese and Japanese origins
    Koustubh Ranade
    Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
    Am J Hypertens 16:158-62. 2003
    ..Our understanding of genes that predispose to essential hypertension is poor...
  91. pmc Variation in gene expression patterns in follicular lymphoma and the response to rituximab
    Sean P Bohen
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:1926-30. 2003
    ..These findings suggest the possibility that the response of follicular lymphoma to rituximab treatment may be predicted from the gene expression pattern of tumors...
  92. pmc Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds
    Howard Y Chang
    Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E7. 2004
    ..Thus, the transcriptional signature of the response of fibroblasts to serum provides a possible link between cancer progression and wound healing, as well as a powerful predictor of the clinical course in several common carcinomas...
  93. pmc Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis
    Suet Y Leung
    Departments of Pathology and Surgery, University of Hong Kong, Hong Kong, China
    Proc Natl Acad Sci U S A 99:16203-8. 2002
    ..Beyond its potential diagnostic and prognostic significance, this result suggests the intriguing possibility that the activity of PLA2G2A may suppress progression or metastasis of human gastric cancer...
  94. doi request reprint Comparing whole genomes using DNA microarrays
    David Gresham
    Lewis Sigler Institute for Integrative Genomics, Department of Molecular Biology, Carl Icahn Laboratory, Princeton University, Princeton, New Jersey 08544, USA
    Nat Rev Genet 9:291-302. 2008
    ....
  95. pmc T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression
    Jeroen P Roose
    Department of Medicine, University of California, San Francisco, USA
    PLoS Biol 1:E53. 2003
    ..Our data suggest that physiologic gene expression programs depend upon tonic activity of signaling pathways independent of receptor ligation...
  96. pmc Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast
    Matthew J Brauer
    Lewis Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 19:352-67. 2008
    ..This concept is useful in interpreting the system-level connections among growth rate, metabolism, stress, and the cell cycle...
  97. pmc Identification of alterations in DNA copy number in host stromal cells during tumor progression
    Robert J Pelham
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 103:19848-53. 2006
    ..We show that numerous amplifications and deletions are found within the host stromal microenvironment, suggesting that alterations in host DNA copy number can occur and may play a significant role in modifying tumor-stromal interactions...
  98. ncbi request reprint Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer
    Therese Sørlie
    Department of Medicine, Section of Oncology, Haukeland University Hospital, N 5021 Bergen, Norway
    Mol Cancer Ther 5:2914-8. 2006
    ..Using supervised analysis, we could not uncover a gene profile that could reliably (>70% accuracy and specificity) predict response to either treatment regimen...
  99. pmc Ammonium toxicity and potassium limitation in yeast
    David C Hess
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    PLoS Biol 4:e351. 2006
    ..The amounts of amino acids excreted increased in relation to the severity of growth impairment by ammonium, suggesting that amino acid excretion is used by yeast for ammonium detoxification...
  100. pmc Willing to do the math: an interview with David Botstein. Interview by Jane Gitschier
    David Botstein
    PLoS Genet 2:e79. 2006
  101. pmc Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme
    Yu Liang
    Preuss Laboratory for Molecular Neuro oncology and Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 102:5814-9. 2005
    ..Our analyses thus identify and validate a prognostic marker of both biologic and clinical significance and provide a series of putative markers for additional evaluation...