David Botstein

Changing perspectives in yeast research nearly a decade after the genome sequence.

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).

Stereotyped and specific gene expression programs in human innate immune responses to bacteria.

A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.

Molecular characterisation of soft tissue tumours: a gene expression study.

Systematic structure-function analysis of the small GTPase Arf1 in yeast.

Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.

Gene expression patterns in human liver cancers.

Identification of genes periodically expressed in the human cell cycle and their expression in tumors.

Challenges in developing a molecular characterization of cancer.

Saccharomyces Genome Database.

Immunoelectron microscopy of aldehyde-fixed yeast cells.

Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.

Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.

Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.

Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae.

Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.

Diversity, topographic differentiation, and positional memory in human fibroblasts.

Nonparametric methods for identifying differentially expressed genes in microarray data.

Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae.

Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis.

Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome.

Overview of the Alliance for Cellular Signaling.

A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.

The Stanford Microarray Database: data access and quality assessment tools.

Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.

SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.

A genome scan for hypertension susceptibility loci in populations of Chinese and Japanese origins.

Variation in gene expression patterns in follicular lymphoma and the response to rituximab.

Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease.

Planning the genome institute's future.

Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).

Repeated observation of breast tumor subtypes in independent gene expression data sets.

Variation in gene expression patterns in human gastric cancers.

Gene expression patterns in ovarian carcinomas.

Endothelial cell diversity revealed by global expression profiling.

Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology.

Systemic and cell type-specific gene expression patterns in scleroderma skin.

Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1.

Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells.

T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.

Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.

The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response.

Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae.

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.

Gene expression profiling identifies clinically relevant subtypes of prostate cancer.

Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds.

Introductory science and mathematics education for 21st-Century biologists.

Expression array technology in the diagnosis and treatment of breast cancer.

Diverse and specific gene expression responses to stresses in cultured human cells.

Ira Herskowitz: 1946-2003.

Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.

Universal Reference RNA as a standard for microarray experiments.

Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes.

Saccharomyces genome database: underlying principles and organisation.

Nutritional homeostasis in batch and steady-state culture of yeast.

GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.

A method for detecting and correcting feature misidentification on expression microarrays.

Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress.

GeneXplorer: an interactive web application for microarray data visualization and analysis.

Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD).

Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.

Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.

A DNA microarray survey of gene expression in normal human tissues.

Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.

Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source.

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.

Genome-scale identification of membrane-associated human mRNAs.

Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray.

Willing to do the math: an interview with David Botstein. Interview by Jane Gitschier.

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.

Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements.

Back to the future: education for systems-level biologists.

Saccharomyces cerevisiae S288C genome annotation: a working hypothesis.

Ammonium toxicity and potassium limitation in yeast.

Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer.

Expanded protein information at SGD: new pages and proteome browser.

Conservation of the metabolomic response to starvation across two divergent microbes.

Identification of alterations in DNA copy number in host stromal cells during tumor progression.

Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains.

Orthology and functional conservation in eukaryotes.

The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.

Gene Ontology annotations at SGD: new data sources and annotation methods.

Comparing whole genomes using DNA microarrays.

Influence of genotype and nutrition on survival and metabolism of starving yeast.

Slow growth induces heat-shock resistance in normal and respiratory-deficient yeast.

The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.

Predicting cellular growth from gene expression signatures.

The cost of gene expression underlies a fitness trade-off in yeast.

A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.

Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.

Saccharomyces Genome Database provides mutant phenotype data.

Recurated protein interaction datasets.

It's the data!

Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes.

Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.

Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus.

System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.

Technological innovation leads to fundamental understanding in cell biology.

Evaluating gene expression dynamics using pairwise RNA FISH data.

Genome-sequencing anniversary. Fruits of genome sequences for biology.

Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast.

Genetic variation and the fate of beneficial mutations in asexual populations.

Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function.

Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.

Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae.

A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast.

Metabolic cycling without cell division cycling in respiring yeast.

Yeast: an experimental organism for 21st Century biology.

A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.

Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.

Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.

Loss of a 20S proteasome activator in Saccharomyces cerevisiae downregulates genes important for genomic integrity, increases DNA damage, and selectively sensitizes cells to agents with diverse mechanisms of action.

Why we need more basic biology research, not less.

Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression.

TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae.

Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.

Automating the construction of gene ontologies.

Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case.

Phylogenetic portrait of the Saccharomyces cerevisiae functional genome.

A new system for comparative functional genomics of Saccharomyces yeasts.

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations.

Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes.

Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.

Lasker∼Koshland to genetics pioneer.

Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter.

Extrachromosomal circular DNA is common in yeast.

Analysis of Polygenic Mutants Suggests a Role for Mediator in Regulating Transcriptional Activation Distance in Saccharomyces cerevisiae.