David Botstein

Summary

Affiliation: Princeton University
Country: USA

Publications

  1. pmc Why we need more basic biology research, not less
    David Botstein
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 23:4160-1. 2012
  2. 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
  3. 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
  4. pmc Universal Reference RNA as a standard for microarray experiments
    Natalia Novoradovskaya
    Stratagene, 11011 N, Torrey Pines Road, La Jolla, CA 92037, USA
    BMC Genomics 5:20. 2004
  5. 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
  6. pmc Ira Herskowitz: 1946-2003
    David Botstein
    Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA
    Genetics 166:653-60. 2004
  7. pmc It's the data!
    David Botstein
    Lewis Sigler Institute for Integrative Genomics, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 21:4-6. 2010
  8. pmc Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains
    Joseph Schacherer
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
    PLoS ONE 2:e322. 2007
  9. pmc The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast
    David Gresham
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
    PLoS Genet 4:e1000303. 2008
  10. pmc Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway
    Allegra A Petti
    The Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 23:3008-24. 2012

Detail Information

Publications91

  1. pmc Why we need more basic biology research, not less
    David Botstein
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 23:4160-1. 2012
    ..I believe this idea to be deeply mistaken. Recent history suggests instead that what we have learned in the last 50 years is only the beginning. The way forward is to invest more in basic science, not less...
  2. 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
    ....
  3. 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...
  4. pmc Universal Reference RNA as a standard for microarray experiments
    Natalia Novoradovskaya
    Stratagene, 11011 N, Torrey Pines Road, La Jolla, CA 92037, USA
    BMC Genomics 5:20. 2004
    ..Measuring signal at each spot as the ratio of experimental RNA to reference RNA targets, rather than relying on absolute signal intensity, decreases variability by normalizing signal output in any two-color hybridization experiment...
  5. 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...
  6. pmc Ira Herskowitz: 1946-2003
    David Botstein
    Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA
    Genetics 166:653-60. 2004
  7. pmc It's the data!
    David Botstein
    Lewis Sigler Institute for Integrative Genomics, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 21:4-6. 2010
    ....
  8. pmc Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains
    Joseph Schacherer
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
    PLoS ONE 2:e322. 2007
    ..These data and new visualization tools are accessible online in a new resource: the Yeast SNPs Browser (YSB; http://gbrowse.princeton.edu/cgi-bin/gbrowse/yeast_strains_snps) that is available to all researchers...
  9. pmc The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast
    David Gresham
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
    PLoS Genet 4:e1000303. 2008
    ..Thus, in addition to answering basic mechanistic questions about evolutionary mechanisms, our work suggests that experimental evolution can also shed light on the function and regulation of individual metabolic pathways...
  10. pmc Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway
    Allegra A Petti
    The Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 23:3008-24. 2012
    ..Finally, CBF1 deletion sometimes has the opposite effect on gene expression from MET31 and MET32 deletion...
  11. pmc Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations
    Viktor M Boer
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 21:198-211. 2010
    ..The complete data can be accessed at the interactive website http://growthrate.princeton.edu/metabolome...
  12. pmc Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae
    R Scott McIsaac
    The Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Amyris, Inc, Emeryville, CA 94608, USA, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Nucleic Acids Res 42:e48. 2014
    ....
  13. pmc Predicting cellular growth from gene expression signatures
    Edoardo M Airoldi
    Lewis Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Princeton, New Jersey, United States of America
    PLoS Comput Biol 5:e1000257. 2009
    ..Data and tools enabling others to apply our methods are available at http://function.princeton.edu/growthrate...
  14. pmc Phylogenetic portrait of the Saccharomyces cerevisiae functional genome
    Patrick A Gibney
    The Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    G3 (Bethesda) 3:1335-40. 2013
    ..Gene ontology analysis of the phylogroups revealed that they were associated with specific, distinct trends in gene function, generalizations likely to be of interest to a wide range of biologists. ..
  15. pmc Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes
    David Gresham
    Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 107:1482-7. 2010
    ..Moreover, designing microarray probes with optimized sensitivity to mismatches should increase the accuracy of standard microarray applications such as copy-number variation detection and gene expression analysis...
  16. pmc Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway
    R Scott McIsaac
    The Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 23:2993-3007. 2012
    ....
  17. pmc Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae
    R Scott McIsaac
    The Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 22:4447-59. 2011
    ..These gene induction and protein degradation systems provide important tools for studying the dynamics and functional relationships of genes and their respective regulatory networks...
  18. pmc Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes
    Patrick A Gibney
    Lewis Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544
    Proc Natl Acad Sci U S A 110:E4393-402. 2013
    ..We suggest that survival after heat shock depends on a small number of genes that function in assessing the metabolic health of the cell and/or regulate its growth in a changing environment...
  19. pmc Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function
    Allegra A Petti
    Lewis Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 108:E1089-98. 2011
    ....
  20. pmc Evaluating gene expression dynamics using pairwise RNA FISH data
    Matthieu Wyart
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
    PLoS Comput Biol 6:e1000979. 2010
    ..The approach to FISH data presented here can be applied in general to reconstruct dynamics from snapshots of pairs of correlated quantities including, for example, protein concentrations obtained from immunofluorescence assays...
  21. pmc Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast
    R Scott McIsaac
    The Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Nucleic Acids Res 41:e57. 2013
    ..These new tools allow for the elucidation of regulatory network elements dynamically, which we demonstrate with a major metabolic regulator, Gcn4p...
  22. 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...
  23. pmc Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate
    Sanford J Silverman
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 107:6946-51. 2010
    ..We conclude that the yeast metabolic cycle is an intrinsic property of yeast metabolism and does not depend on either synchronization or external limitation of growth by the carbon source...
  24. 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
    ....
  25. pmc Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast
    Mark J Hickman
    Lewis Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 22:4192-204. 2011
    ..Our results show that rapidly growing cells require significant methylation, likely for the biosynthesis of phospholipids...
  26. pmc Slow growth induces heat-shock resistance in normal and respiratory-deficient yeast
    Charles Lu
    Carl Icahn Laboratory, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 20:891-903. 2009
    ....
  27. pmc Influence of genotype and nutrition on survival and metabolism of starving yeast
    Viktor M Boer
    Lewis Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 105:6930-5. 2008
    ..Furthermore, we suggest that our results on condition-dependent chronological lifespan have important implications for the interpretation and design of studies on chronological aging...
  28. pmc The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists
    Sven Heinicke
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
    PLoS ONE 2:e766. 2007
    ..Thus, bioinformaticians and software developers may also find P-POD useful because they can use the P-POD database infrastructure when developing their own comparative genomics resources and database tools...
  29. pmc Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations
    Gregory I Lang
    Lewis Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    Nature 500:571-4. 2013
    ....
  30. 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...
  31. pmc Conservation of the metabolomic response to starvation across two divergent microbes
    Matthew J Brauer
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 103:19302-7. 2006
    ..Metabolic similarity across organisms extends from the covalent reaction network of metabolism to include many elements of metabolome response to nutrient deprivation as well...
  32. pmc A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast
    Gregory I Lang
    Department of Molecular and Cellular Biology and The Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
    PLoS ONE 6:e25290. 2011
    ....
  33. 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...
  34. 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...
  35. ncbi request reprint Orthology and functional conservation in eukaryotes
    Kara Dolinski
    Department of Molecular Biology, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Annu Rev Genet 41:465-507. 2007
    ..Data and illustrations are derived from specific comparison of eight species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Saccharomyces cerevisiae, and Plasmodium falciparum...
  36. pmc Genetic variation and the fate of beneficial mutations in asexual populations
    Gregory I Lang
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Genetics 188:647-61. 2011
    ..Rather, underlying "background" genetic variation is quickly generated in our initially clonal populations and plays a crucial role in determining the fate of each individual beneficial mutation in the evolving population...
  37. ncbi request reprint Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray
    David Gresham
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Science 311:1932-6. 2006
    ..We applied this approach to elucidate the genetic basis of phenotypic variants and to identify the small number of single-base pair changes accumulated during experimental evolution of yeast...
  38. pmc The cost of gene expression underlies a fitness trade-off in yeast
    Gregory I Lang
    Lewis Sigler Institute for Integrative Genomics and the Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 106:5755-60. 2009
    ....
  39. ncbi request reprint Changing perspectives in yeast research nearly a decade after the genome sequence
    Kara Dolinski
    Lewis Sigler Institute for Integrative Genomics, Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544 USA
    Genome Res 15:1611-9. 2005
    ....
  40. pmc Back to the future: education for systems-level biologists
    Ned Wingreen
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    Nat Rev Mol Cell Biol 7:829-32. 2006
    ..Close reading and discussion of these papers allows students with backgrounds in physics, computational sciences or biology to learn essential ideas and to communicate in the languages of disciplines other than their own...
  41. pmc Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression
    Nikolai Slavov
    Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Biol Cell 24:157-68. 2013
    ..Our observations suggest that a GR signal, which is a function of the abundance of essential natural nutrients, regulates fermentation/respiration, the GRR, and the CDC...
  42. pmc TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae
    Aaron Z Welch
    Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
    Mol Biol Cell 24:115-28. 2013
    ..We suggest that reduction of a specific intermediate in 60S biogenesis, resulting from conditions such as heat shock and nutrient deprivation, increases desiccation tolerance...
  43. pmc Yeast: an experimental organism for 21st Century biology
    David Botstein
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Genetics 189:695-704. 2011
    ..These new fields look beyond the functions of individual genes and proteins, focusing on how these interact and work together to determine the properties of living cells and organisms...
  44. 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/...
  45. 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...
  46. 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...
  47. 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
    ....
  48. 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...
  49. 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...
  50. 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...
  51. 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
    ....
  52. 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...
  53. 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
    ....
  54. 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...
  55. 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...
  56. 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...
  57. 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/...
  58. ncbi request reprint Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae
    Eleanor W Trotter
    Division of Molecular Genetics, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G11 6NU, United Kingdom
    J Biol Chem 277:44817-25. 2002
    ..However, misfolded proteins did not strongly induce the stress response element regulon. We conclude that misfolded proteins are competent to specifically trigger activation of heat shock factor in response to heat shock...
  59. 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...
  60. 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...
  61. 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...
  62. pmc Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae
    Minoo Shakoury-Elizeh
    Liver Diseases Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Mol Biol Cell 15:1233-43. 2004
    ..We provide evidence that yeast subjected to iron deprivation undergo a transcriptional remodeling, resulting in a shift from iron-dependent to parallel, but iron-independent, metabolic pathways...
  63. 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...
  64. 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...
  65. pmc Willing to do the math: an interview with David Botstein. Interview by Jane Gitschier
    David Botstein
    PLoS Genet 2:e79. 2006
  66. 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
    ....
  67. 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/)...
  68. 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...
  69. 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...
  70. 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...
  71. 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...
  72. 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...
  73. 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...
  74. 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...
  75. 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...
  76. 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...
  77. 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...
  78. 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...
  79. 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...
  80. ncbi request reprint Molecular characterisation of soft tissue tumours: a gene expression study
    Torsten O Nielsen
    Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
    Lancet 359:1301-7. 2002
    ..We aimed to start molecular characterisation of these rare neoplasms and to do a genome-wide search for new diagnostic markers...
  81. 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...
  82. 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...
  83. ncbi request reprint Saccharomyces Genome Database
    Laurie Issel-Tarver
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Methods Enzymol 350:329-46. 2002
  84. 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...
  85. 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...
  86. pmc Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
    Teresa Reguly
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
    J Biol 5:11. 2006
    ..Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference...
  87. 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...
  88. 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...
  89. 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...
  90. 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
    ....