David Botstein

The Lewis-Sigler Institute for Integrative Genomics, Princeton University

Affiliated withPrinceton University Calico Life Sciences LLC

Research Area

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JoVE Journal Publications

ArticleTotal : 3	Year
Publication title Cited by 25	2013
Publication title Cited by 11	2013
Publication title Cited by 59	2016

Other Publications

Article	Year
Changing perspectives in yeast research nearly a decade after the genome sequence. Genome research\| PubMed ID: 16339358	2005
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic acids research\| PubMed ID: 11752257	2002
Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 11805339	2002
A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate. American journal of human genetics\| PubMed ID: 11854867	2002
Molecular characterisation of soft tissue tumours: a gene expression study. Lancet\| PubMed ID: 11965276	2002
Systematic structure-function analysis of the small GTPase Arf1 in yeast. Molecular biology of the cell\| PubMed ID: 12006660	2002
Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. The Journal of biological chemistry\| PubMed ID: 12058033	2002
Gene expression patterns in human liver cancers. Molecular biology of the cell\| PubMed ID: 12058060	2002
Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Molecular biology of the cell\| PubMed ID: 12058064	2002
Challenges in developing a molecular characterization of cancer. Seminars in oncology\| PubMed ID: 12063681	2002
Saccharomyces Genome Database. Methods in enzymology\| PubMed ID: 12073322	2002
Immunoelectron microscopy of aldehyde-fixed yeast cells. Methods in enzymology\| PubMed ID: 12073367	2002
Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12077300	2002
Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11. BMC immunology\| PubMed ID: 12079505	2002
Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12195013	2002
Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae. The Journal of biological chemistry\| PubMed ID: 12239211	2002
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12297621	2002
Diversity, topographic differentiation, and positional memory in human fibroblasts. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12297622	2002
Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics (Oxford, England)\| PubMed ID: 12424116	2002
Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12446845	2002
Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12456890	2002
Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. The American journal of pathology\| PubMed ID: 12466114	2002
Overview of the Alliance for Cellular Signaling. Nature\| PubMed ID: 12478301	2002
A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12482955	2002
The Stanford Microarray Database: data access and quality assessment tools. Nucleic acids research\| PubMed ID: 12519956	2003
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic acids research\| PubMed ID: 12519985	2003
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic acids research\| PubMed ID: 12519986	2003
A genome scan for hypertension susceptibility loci in populations of Chinese and Japanese origins. American journal of hypertension\| PubMed ID: 12559686	2003
Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12571354	2003
Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nature genetics\| PubMed ID: 12610532	2003
Planning the genome institute's future. Science (New York, N.Y.)\| PubMed ID: 12624247	2003
Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12631705	2003
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature genetics\| PubMed ID: 12740579	2003
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12826619	2003
Repeated observation of breast tumor subtypes in independent gene expression data sets. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12829800	2003
Variation in gene expression patterns in human gastric cancers. Molecular biology of the cell\| PubMed ID: 12925757	2003
Gene expression patterns in ovarian carcinomas. Molecular biology of the cell\| PubMed ID: 12960427	2003
Endothelial cell diversity revealed by global expression profiling. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12963823	2003
Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology. The American journal of pathology\| PubMed ID: 14507652	2003
Systemic and cell type-specific gene expression patterns in scleroderma skin. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 14530402	2003
Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1. Molecular cell\| PubMed ID: 14536079	2003
Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells. Molecular biology of the cell\| PubMed ID: 14617803	2004
T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression. PLoS biology\| PubMed ID: 14624253	2003
Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. The American journal of pathology\| PubMed ID: 14633610	2003
The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response. Molecular biology of the cell\| PubMed ID: 14668476	2004
Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae. Molecular biology of the cell\| PubMed ID: 14668481	2004
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic acids research\| PubMed ID: 14681421	2004
Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 14711987	2004
Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS biology\| PubMed ID: 14737219	2004
Introductory science and mathematics education for 21st-Century biologists. Science (New York, N.Y.)\| PubMed ID: 14764865	2004
Expression array technology in the diagnosis and treatment of breast cancer. Molecular interventions\| PubMed ID: 14993355	2002
Diverse and specific gene expression responses to stresses in cultured human cells. Molecular biology of the cell\| PubMed ID: 15004229	2004
Ira Herskowitz: 1946-2003. Genetics\| PubMed ID: 15020456	2004
Different gene expression patterns in invasive lobular and ductal carcinomas of the breast. Molecular biology of the cell\| PubMed ID: 15034139	2004
Universal Reference RNA as a standard for microarray experiments. BMC genomics\| PubMed ID: 15113400	2004
Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. The New England journal of medicine\| PubMed ID: 15115829	2004
Saccharomyces genome database: underlying principles and organisation. Briefings in bioinformatics\| PubMed ID: 15153302	2004
Nutritional homeostasis in batch and steady-state culture of yeast. Molecular biology of the cell\| PubMed ID: 15240820	2004
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics (Oxford, England)\| PubMed ID: 15297299	2004
A method for detecting and correcting feature misidentification on expression microarrays. BMC genomics\| PubMed ID: 15357875	2004
Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. Molecular biology of the cell\| PubMed ID: 15371544	2004
GeneXplorer: an interactive web application for microarray data visualization and analysis. BMC bioinformatics\| PubMed ID: 15458579	2004
Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic acids research\| PubMed ID: 15608219	2005
Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15684073	2005
Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Molecular biology of the cell\| PubMed ID: 15758028	2005
A DNA microarray survey of gene expression in normal human tissues. Genome biology\| PubMed ID: 15774023	2005
Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15827123	2005
Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 16381818	2006
Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic acids research\| PubMed ID: 16381907	2006
Genome-scale identification of membrane-associated human mRNAs. PLoS genetics\| PubMed ID: 16415983	2006
Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science (New York, N.Y.)\| PubMed ID: 16527929	2006
Willing to do the math: an interview with David Botstein. Interview by Jane Gitschier. PLoS genetics\| PubMed ID: 16733551	2006
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. Journal of biology\| PubMed ID: 16762047	2006
Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements. Genetics\| PubMed ID: 16816424	2006
Back to the future: education for systems-level biologists. Nature reviews. Molecular cell biology\| PubMed ID: 16990789	2006
Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast (Chichester, England)\| PubMed ID: 17001629	2006
Ammonium toxicity and potassium limitation in yeast. PLoS biology\| PubMed ID: 17048990	2006
Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer. Molecular cancer therapeutics\| PubMed ID: 17121939	2006
Expanded protein information at SGD: new pages and proteome browser. Nucleic acids research\| PubMed ID: 17142221	2007
Conservation of the metabolomic response to starvation across two divergent microbes. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17159141	2006
Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17167050	2006
Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PloS one\| PubMed ID: 17389913	2007
Orthology and functional conservation in eukaryotes. Annual review of genetics\| PubMed ID: 17678444	2007
The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PloS one\| PubMed ID: 17712414	2007
Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Molecular biology of the cell\| PubMed ID: 17959824	2008
Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic acids research\| PubMed ID: 17982175	2008
Comparing whole genomes using DNA microarrays. Nature reviews. Genetics\| PubMed ID: 18347592	2008
Influence of genotype and nutrition on survival and metabolism of starving yeast. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18456835	2008
Slow growth induces heat-shock resistance in normal and respiratory-deficient yeast. Molecular biology of the cell\| PubMed ID: 19056679	2009
The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS genetics\| PubMed ID: 19079573	2008
Predicting cellular growth from gene expression signatures. PLoS computational biology\| PubMed ID: 19119411	2009
The cost of gene expression underlies a fitness trade-off in yeast. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 19299502	2009
A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nature biotechnology\| PubMed ID: 19349972	2009
Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Molecular biology of the cell\| PubMed ID: 19889834	2010
Saccharomyces Genome Database provides mutant phenotype data. Nucleic acids research\| PubMed ID: 19906697	2010
Recurated protein interaction datasets. Nature methods\| PubMed ID: 19935838	2009
It's the data! Molecular biology of the cell\| PubMed ID: 20048255	2010
Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20080586	2010
Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20335538	2010
Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20937885	2010
System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae. Genetics\| PubMed ID: 20944018	2011
Technological innovation leads to fundamental understanding in cell biology. Molecular biology of the cell\| PubMed ID: 21079013	2010
Evaluating gene expression dynamics using pairwise RNA FISH data. PLoS computational biology\| PubMed ID: 21079668	2010
Genome-sequencing anniversary. Fruits of genome sequences for biology. Science (New York, N.Y.)\| PubMed ID: 21350164	2011
Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast. Molecular biology of the cell\| PubMed ID: 21525243	2011
Genetic variation and the fate of beneficial mutations in asexual populations. Genetics\| PubMed ID: 21546542	2011
Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 21734149	2011
Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast. Molecular biology of the cell\| PubMed ID: 21900497	2011
Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae. Molecular biology of the cell\| PubMed ID: 21965290	2011
A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast. PloS one\| PubMed ID: 21966486	2011
Metabolic cycling without cell division cycling in respiring yeast. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 22065748	2011
Yeast: an experimental organism for 21st Century biology. Genetics\| PubMed ID: 22084421	2011
A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes. Molecular biology of the cell\| PubMed ID: 22456505	2012
Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway. Molecular biology of the cell\| PubMed ID: 22696679	2012
Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Molecular biology of the cell\| PubMed ID: 22696683	2012
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 dive... G3 (Bethesda, Md.)\| PubMed ID: 22908043	2012
Why we need more basic biology research, not less. Molecular biology of the cell\| PubMed ID: 23112227	2012
Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression. Molecular biology of the cell\| PubMed ID: 23135997	2013
TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae. Molecular biology of the cell\| PubMed ID: 23171550	2013
Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast. Nucleic acids research\| PubMed ID: 23275543	2013
Automating the construction of gene ontologies. Nature biotechnology\| PubMed ID: 23302932	2013
Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case. G3 (Bethesda, Md.)\| PubMed ID: 23550140	2013
Phylogenetic portrait of the Saccharomyces cerevisiae functional genome. G3 (Bethesda, Md.)\| PubMed ID: 23749449	2013
A new system for comparative functional genomics of Saccharomyces yeasts. Genetics\| PubMed ID: 23852385	2013
Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature\| PubMed ID: 23873039	2013
Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 24167267	2013
Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae. Nucleic acids research\| PubMed ID: 24445804	2014
Lasker∼Koshland to genetics pioneer. Cell\| PubMed ID: 25215481	2014
Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 25918382	2015
Extrachromosomal circular DNA is common in yeast. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 26038577	2015
Analysis of Polygenic Mutants Suggests a Role for Mediator in Regulating Transcriptional Activation Distance in Saccharomyces cerevisiae. Genetics\| PubMed ID: 26281848	2015