Research Topics
| David BotsteinSummaryAffiliation: Princeton University Country: USA Publications
| Collaborators
|
Detail Information
Publications
Why we need more basic biology research, not lessDavid 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...- 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... - Universal Reference RNA as a standard for microarray experimentsNatalia 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... - GeneXplorer: an interactive web application for microarray data visualization and analysisChristian 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... - Ira Herskowitz: 1946-2003David Botstein
Lewis-Sigler Institute, Princeton University, Princeton, NJ 08544, USA
Genetics 166:653-60. 2004 - 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.... - Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strainsJoseph 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... - The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeastDavid 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... - Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathwayAllegra 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... - Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitationsViktor 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... - Predicting cellular growth from gene expression signaturesEdoardo 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... - Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probesDavid 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... - Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathwayR Scott McIsaac
The Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
Mol Biol Cell 23:2993-3007. 2012.... - Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiaeR 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... - Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial functionAllegra 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.... - Evaluating gene expression dynamics using pairwise RNA FISH dataMatthieu 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... - Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeastR 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... - Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeastMatthew 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..quot; This concept is useful in interpreting the system-level connections among growth rate, metabolism, stress, and the cell cycle... - Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphateSanford 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... 
Comparing whole genomes using DNA microarraysDavid 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....- Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeastMark 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... - The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologistsSven 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... - Influence of genotype and nutrition on survival and metabolism of starving yeastViktor 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... - Slow growth induces heat-shock resistance in normal and respiratory-deficient yeastCharles Lu
Carl Icahn Laboratory, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
Mol Biol Cell 20:891-903. 2009.... - Ammonium toxicity and potassium limitation in yeastDavid 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... - Conservation of the metabolomic response to starvation across two divergent microbesMatthew 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... - A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeastGregory 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.... - Identification of alterations in DNA copy number in host stromal cells during tumor progressionRobert 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... - Homeostatic adjustment and metabolic remodeling in glucose-limited yeast culturesMatthew 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... 
Orthology and functional conservation in eukaryotesKara 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...- Genetic variation and the fate of beneficial mutations in asexual populationsGregory 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... - Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarrayDavid 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... - The cost of gene expression underlies a fitness trade-off in yeastGregory 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.... - Changing perspectives in yeast research nearly a decade after the genome sequenceKara Dolinski
Lewis-Sigler Institute for Integrative Genomics, Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544 USA
Genome Res 15:1611-9. 2005.... - Back to the future: education for systems-level biologistsNed 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... - Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expressionNikolai 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... - TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiaeAaron 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... - Yeast: an experimental organism for 21st Century biologyDavid 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... - Gene Ontology annotations at SGD: new data sources and annotation methodsEurie 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... - SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression dataMaximilian 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... - Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex diseaseDavid Botstein
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
Nat Genet 33:228-37. 2003.... - Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organismsOrly 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... - Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasisSuet 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... - Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiaeMaitreya 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.... - Stereotyped and specific gene expression programs in human innate immune responses to bacteriaJennifer 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... - Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiaeEleanor 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... - Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiaeHiroyuki 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... - Identification of genes periodically expressed in the human cell cycle and their expression in tumorsMichael 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/... - Module networks: identifying regulatory modules and their condition-specific regulators from gene expression dataEran 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... - Challenges in developing a molecular characterization of cancerJonathan 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... - Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumorsJonathan 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... - Nonparametric methods for identifying differentially expressed genes in microarray dataOlga G Troyanskaya
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Bioinformatics 18:1454-61. 2002..Thus the methods described and evaluated here provide a convenient and robust way to identify differentially expressed genes for further biological and clinical analysis... - 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/... - Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteinsShuai 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... - Expanded protein information at SGD: new pages and proteome browserRobert 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... - Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulationWei 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... - 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... - Disruption of yeast forkhead-associated cell cycle transcription by oxidative stressMichael 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... - Nutritional homeostasis in batch and steady-state culture of yeastAlok J Saldanha
Department of Genetics, Stanford University Medical School, Stanford, CA 94305, USA
Mol Biol Cell 15:4089-104. 2004.... - Saccharomyces genome database: underlying principles and organisationSelina 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... - Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberansSabine 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.... - Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiaeMinoo 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... - Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organismsKaren 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... - Diverse and specific gene expression responses to stresses in cultured human cellsJohn 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... - 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... - Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genomeJodi 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/)... - Willing to do the math: an interview with David Botstein. Interview by Jane GitschierDavid Botstein
PLoS Genet 2:e79. 2006 - Transcriptional response of steady-state yeast cultures to transient perturbations in carbon sourceMichal 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... - Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genesIzidore S Lossos
Division of Oncology, Department of Medicine, Stanford University Medical Center, Stanford, Calif, USA
N Engl J Med 350:1828-37. 2004..The model was independent of the International Prognostic Index and added to its predictive power. CONCLUSIONS: Measurement of the expression of six genes is sufficient to predict overall survival in diffuse large-B-cell lymphoma... - Molecular characterisation of soft tissue tumours: a gene expression studyTorsten O Nielsen
Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
Lancet 359:1301-7. 2002..Large numbers of uncharacterised genes contributed to distinctions between the tumours, and some of these could be useful markers for diagnosis, have prognostic significance, or prove possible targets for treatment... - Expression array technology in the diagnosis and treatment of breast cancerStefanie 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... - Saccharomyces cerevisiae S288C genome annotation: a working hypothesisDianna 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... - Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiaeTeresa 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... - Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and woundsHoward 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... - Systematic structure-function analysis of the small GTPase Arf1 in yeastEleanor 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... - Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiformeYu 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... - GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genesElizabeth I Boyle
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Bioinformatics 20:3710-5. 2004..AVAILABILITY: The full source code and documentation for GO::TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/... - Variation in gene expression patterns in human gastric cancersXin 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... - Saccharomyces Genome DatabaseLaurie Issel-Tarver
Department of Genetics, Stanford University, Stanford, California 94305, USA
Methods Enzymol 350:329-46. 2002 - Diversity, topographic differentiation, and positional memory in human fibroblastsHoward 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.... - Repeated observation of breast tumor subtypes in independent gene expression data setsTherese 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... - The Stanford Microarray Database: data access and quality assessment toolsJeremy 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... - Gene expression profiling identifies clinically relevant subtypes of prostate cancerJacques 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... - A systematic approach to reconstructing transcription networks in SaccharomycescerevisiaeWei 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... - Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancerTherese 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...