Faculty & Research
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Molecular Biology Faculty

David Botstein

Anthony B. Evnin '62 Professor of Genomics
Professor of molecular biology and the lewis-sigler institute for integrative genomics

director, lewis-sigler institute for integrative genomics
Director, certificate program in quantitative and computational biology

David Botstein

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Phone (609) 258-7005
locationCarl Icahn Lab, 143
Phone Lab (609) 258-8585
Faculty Assistant
Marybeth Fedele
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Phone (609) 258-7058

Research Focus

Molecular Genetics in the Post-Genome-Sequence Era

The genomic sequences of humans, several eukaryotic model organisms, and numerous bacteria have opened up new opportunities and challenges for molecular genetics. Now one can study all the genes of an organism at once, promising a level of biological inference at the "system level", beyond that possible from studying separate, individual genes, gene assemblies or pathways. A major challenge is the analysis and display of huge volumes of information in ways that allow biologists to fully interpret them.

Research areas: (1) genome-wide studies of gene expression through the life cycle and experimental evolution of budding yeast (Saccharomyces cerevisiae), (2) mechanisms by which yeast maintain metabolic homeostasis in the face of environmental and genetic perturbations, and (3) quantitative analysis and intuitive display of genome-scale biological information in the context of genomic databases.

Genome-Scale Studies of Metabolic Homeostasis in Yeast

We are studying the ability of yeast to maintain metabolic homeostasis under a variety of steady-state (chemostat) and changing (perturbation of chemostat cultures or batch cultures) growth environments. We have found that many features of growth regulation are shared among chemostat cultures regardless of the nature of the nutrient limitation, whereas other general features (e.g. cell cycle arrest in starving batch cultures) vary according to the nature of the limitation. We have found a way to avoid a stress response after temperature shifts and are exploiting this to study transcriptional responses in response to limitations imposed by conditional lethal mutations in essential genes (e.g. those encoding actin and the tubulins). We have already found that different actin alleles with different phenotypes show characteristically different patterns of transcriptional response in this system. In this way we are beginning to learn how cells respond to specific defects in essential intracellular functions.

Genome-Wide Gene Expression During Experimental Evolution in Yeast

When cultures of Saccharomyces cerevisiae are exposed to persistent strong selection in a constant environment, such as a limiting nutrient in continuous culture, fitter variant strains arise that "sweep" the culture. Based on the repeated observation of similar changes in patterns of genome-wide gene expression and underlying genomic rearrangements found in strains that have "evolved" independently under these conditions, it appears that yeast can adapt to glucose limitation in chemostats in only a small number of ways, in part by characteristic rearrangements of their genomes. We infer from these results that there must be constraints in the relevant regulatory networks that limit the ways in which gene expression can be altered in a way that improves fitness.

Both the evolution and homeostasis studies aim to define the many interactions of metabolic regulatory networks in yeast. Ultimately we hope to amass a body of data sufficient to support realistic mathematical and computational models of these networks. The methods we are developing should also provide the means for experimental tests of such models.

Analysis and Display of Genome-Scale Biological Data

The full value of highly parallel, genome-scale data acquisition methods such as DNA microarray hybridization can only be realized if there are comparably powerful analytical facilities in place, namely ways of storing, searching, recovering, analyzing and displaying the data. To this end we have established a microarray database at the Lewis-Sigler Institute that integrates these functions, and have moved some of the functionalities of the Saccharomyces Genome Database to Princeton. Essential to any useful display of results from genome-wide studies is an efficient system and intuitively understood linkages of genetic data with biological annotation for the bacterial, yeast, human or mouse genes under study. To this end we plan to establish and develop representation of genome-scale results that can be computationally parsed (using the Gene Ontology) and used in the interpretation and display of new data.


Selected Publications

McIsaac RS, Silverman SJ, Parsons L,...Botstein D. (2013) Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae. J Vis Exp. e50382. Pubmed

McIsaac RS, Gibney PA, Chandran SS, Benjamin KR, Botstein D. (2014) Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae. Nucleic Acids Res. 42: e48. Pubmed

McIsaac RS, Oakes BL, Botstein D, Noyes MB. (2013) Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters. J Vis Exp. e51153. Pubmed

Gibney PA, Lu C, Caudy AA, Hess DC, Botstein D. (2013) Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes. Proc Natl Acad Sci. 110: E4393-402. Pubmed

Caudy AA, Guan Y, Jia Y,...Botstein D,...Dunham MJ. (2013) A new system for comparative functional genomics of Saccharomyces yeasts. Genetics. 195: 275-87. Pubmed

Lang GI, Rice DP, Hickman MJ,...Botstein D, Desai MM. (2013) Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature. 500: 571-74. Pubmed

McIsaac RS, Silverman SJ, Parsons L,...Botstein D. (2013) Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae. J Vis Exp. e50382. Pubmed

Gibney PA, Hickman MJ, Bradley PH, Matese JC, Botstein D. (2013) Phylogenetic portrait of the Saccharomyces cerevisiae functional genome. G3 (Bethesda). 3: 1335-40. Pubmed

McIsaac RS, Oakes BL, Wang X, Dummit KA, Botstein D, Noyes MB. (2013) Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast. Nucleic Acids Res. 41: e57. PubMed

Dolinski K, Botstein D. (2013) Automating the construction of gene ontologies. Nat Biotechnol. 31: 34-35. Pubmed

Welch AZ, Gibney PA, Botstein D, Koshland DE. (2012) TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae. Mol Biol Cell. 24: 115-28. Pubmed

Slavov N, Botstein D. (2012) Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression. Mol Biol Cell. 24: 157-68. Pubmed

Botstein D. (2012) Why we need more basic biology research, not less. Mol Biol Cell. 23: 4160-61. Pubmed

Doherty KM, Pride LD, Lukose J,...Botstein D, Moore CW. (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 diverse mechanisms of action. G3 (Bethesda). 2: 943-59. Pubmed

Petti AA, McIsaac RS, Ho-Shing O, Bussemaker HJ, Botstein D. (2012) Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway. Mol Biol Cell. 23: 3008-24. Pubmed

McIsaac RS, Petti AA, Bussemaker HJ, Botstein D. (2012) Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol Biol Cell. 23: 2993-3007. Pubmed

McIsaac RS, Silverman SJ, McClean MN,...Botstein D. (2011) Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae. Mol Biol Cell. 22: 4447-59. PubMed

Botstein D, Fink GR. (2011) Yeast: an experimental organism for 21st Century biology. Genetics.  189: 695-704. PubMed

Lang GI, Botstein D. (2011) A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast. PLoS One. 6: e25290. PubMed

Lang GI, Botstein D, Desai MM. (2011) Genetic variation and the fate of beneficial mutations in asexual populations. Genetics. 188: 647-61. PubMed

Slavov N, Botstein D. (2011) Coupling among growth rate response, metabolic cycle and cell division cycle in yeast. Mol Biol Cell. 22: 1997-2009. PubMed

Gresham D, Boer VM, Caudy A,...Botstein D. (2011) System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae. Genetics. 187: 299-317. PubMed

Botstein D. (2011) Genome-sequencing anniversary. Fruits of genome sequences for biology. Science. 331: 1025. PubMed

Wyart M, Botstein D, Wingreen NS. (2010) Evaluating gene expression dynamics using pairwise RNA FISH data. PLoS Comput Biol. 6: e1000979. PubMed

Botstein D. (2010) Technological innovation leads to fundamental understanding in cell biology. Mol Biol Cell. 21: 3791-92. PubMed

Silverman SJ, Petti AA, Slavov N,...Botstein D. (2010) Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate. Proc Natl Acad Sci. 107: 6946-51. PubMed

Gresham D, Curry B, Ward A,...Botstein D. (2010) Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes. Proc Natl Acad Sci. 107: 1482-87. PubMed

Botstein D. (2010) It's the Data! Mol Biol Cell. 21: 4-6. PubMed

Engel SR, Balakrishnan R, Binkley G,...Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 38: D433-36. PubMed

Boer VM, Crutchfield CA, Bradley PH, Botstein D, Rabinowitz JD. (2009) Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Mol Biol Cell. 21: 198-211. PubMed

Lang GI, Murray AW, Botstein D. (2009) The cost of gene expression underlies a fitness trade-off in yeast. Proc Natl Acad Sci. 106: 5755-60. PubMed

Airoldi EM, Huttenhower C, Gresham D,...Botstein D, Troyanskaya OG. (2009) Predicting cellular growth from gene expression signatures. PLoS Comput Biol. 5: e1000257. PubMed

Gresham D, Desai MM, Tucker CM,...Botstein D, Dunham MJ. (2008) The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet. 4: e1000303. PubMed

Lu C, Brauer MJ, Botstein D. (2008) Slow growth induces heat shock resistance in normal and respiratory-deficient yeast. Mol Biol Cell. 20: 891-903. PubMed

Boer VM, Amini S, Botstein D. (2008) Influence of genotype and nutrition on survival and metabolism of starving yeast. Proc Natl Acad Sci. 105: 6930-35. PubMed

Gresham D, Dunham MJ, Botstein D. (2008) Comparing whole genomes using DNA microarrays. Nat Rev Genet. 9: 291-302. PubMed

Hong EL, Balakrishnan R, Dong Q,...Botstein D, Cherry JM. (2007) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 36: D577-81. PubMed

Brauer MJ, Huttenhower C, Airoldi EM,...Botstein D. (2007) Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell. 19: 352-67. PubMed

Dolinski K, Botstein D. (2007) Orthology and functional conservation in eukaryotes. Annu Rev Genet. 41: 465-507. PubMed

Heinicke S, Livstone MS, Lu C,...Botstein D, Dolinski K. (2007) The Princeton Protein Orthology Database (P-POD): A comparative genomics analysis tool for biologists. PLoS ONE. 2: e766. PubMed

Pelham RJ, Rodgers L, Hall I,...Botstein D. (2006) Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proc Natl Acad Sci. 103: 19848-53. PubMed

Hess DC, Lu W, Rabinowitz JD, Botstein D. (2006) Ammonium toxicity and potassium limitation in yeast. Ammonium toxicity and potassium limitation in yeast. PLoS Biol. 4: e351. PubMed

Brauer MJ, Yuan J, Bennett BD,...Botstein D, Rabinowitz JD. (2006) Conservation of the metabolomic response to starvation across two divergent microbes. Proc Natl Acad Sci. 103: 19302-07. PubMed

Wingreen N, Botstein D. (2006) Back to the future: education for systems-level biologists. Nat Rev Mol Cell Biol. 7: 829-32. PubMed

Dolinski K, Botstein D. (2006) Changing perspectives in yeast research nearly a decade after the genome sequence. Genome Res. 15: 1611-19. PubMed

Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, Li H. (2005) Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc Natl Acad Sci. 102: 1998-2003. PubMed

Brauer MJ, Saldanha AJ, Dolinski K, Botstein D. (2005) Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Mol Biol Cell. 16: 2503-17. PubMed

Saldanha AJ, Brauer MJ, Botstein D. (2004) Nutritional homeostasis in batch and steady-state culture of yeast. Mol Biol Cell. 15: 4089-104. PubMed

Bialek W, Botstein D. (2004) Introductory science and mathematics education for 21st-Century biologists. Science. 303: 788-90. PubMed

Botstein D, Risch N. (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet. 33 Suppl: 228-37. PubMed

Alter O, Brown PO, Botstein D. (2003) Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc Natl Acad Sci. 100: 3351-56. PubMed

Whitfield ML, Sherlock G, Saldanha AJ,...Botstein D. (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell. 13: 1977-2000. PubMed

Dunham MJ, Badrane H, Ferea T,...Botstein D. (2002) Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci. 99: 16144-49. PubMed


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