List of Faculty Publications
Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua
Filters: Keyword is Saccharomyces cerevisiae [Clear All Filters]
“Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes.”, Proc Natl Acad Sci U S A, vol. 110, no. 46, pp. E4393-402, 2013.
, “Yeast cells can access distinct quiescent states.”, Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
, “Yeast: an experimental organism for 21st Century biology.”, Genetics, vol. 189, no. 3, pp. 695-704, 2011.
, “Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae.”, J Vis Exp, no. 76, p. e50382, 2013.
, “Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source.”, Proc Natl Acad Sci U S A, vol. 103, no. 2, pp. 389-94, 2006.
, “Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 15, no. 3, pp. 1233-43, 2004.
, “TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 24, no. 2, pp. 115-28, 2013.
, “A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast.”, PLoS One, vol. 6, no. 9, p. e25290, 2011.
, “System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.”, Genetics, vol. 187, no. 1, pp. 299-317, 2011.
, “Systematic planning of genome-scale experiments in poorly studied species.”, PLoS Comput Biol, vol. 6, no. 3, p. e1000698, 2010.
, “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
, “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.”, Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
, “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
, “Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function.”, Proc Natl Acad Sci U S A, vol. 108, no. 45, pp. E1089-98, 2011.
, “Slow growth induces heat-shock resistance in normal and respiratory-deficient yeast.”, Mol Biol Cell, vol. 20, no. 3, pp. 891-903, 2009.
, “Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.”, PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
, “Simple topological features reflect dynamics and modularity in protein interaction networks.”, PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
, “A scalable method for integration and functional analysis of multiple microarray datasets.”, Bioinformatics, vol. 22, no. 23, pp. 2890-7, 2006.
, “Saccharomyces genome database: underlying principles and organisation.”, Brief Bioinform, vol. 5, no. 1, pp. 9-22, 2004.
, “Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.”, Nucleic Acids Res, vol. 32, no. Database issue, pp. D311-4, 2004.
, “Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).”, Nucleic Acids Res, vol. 30, no. 1, pp. 69-72, 2002.
, “Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.”, Nucleic Acids Res, vol. 31, no. 1, pp. 216-8, 2003.
, “Saccharomyces Genome Database provides mutant phenotype data.”, Nucleic Acids Res, vol. 38, no. Database issue, pp. D433-6, 2010.
, “Saccharomyces Genome Database.”, Methods Enzymol, vol. 350, pp. 329-46, 2002.
, “Saccharomyces cerevisiae S288C genome annotation: a working hypothesis.”, Yeast, vol. 23, no. 12, pp. 857-65, 2006.
, “Riboneogenesis in yeast.”, Cell, vol. 145, no. 6, pp. 969-80, 2011.
, “The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.”, PLoS Genet, vol. 4, no. 12, p. e1000303, 2008.
, “Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation.”, Mol Cell, vol. 48, no. 1, pp. 52-62, 2012.
, “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
, “Predicting gene function in a hierarchical context with an ensemble of classifiers.”, Genome Biol, vol. 9 Suppl 1, p. S3, 2008.
, “Predicting cellular growth from gene expression signatures.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
, “Phylogenetic portrait of the Saccharomyces cerevisiae functional genome.”, G3 (Bethesda), vol. 3, no. 8, pp. 1335-40, 2013.
, “Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations.”, Nature, vol. 500, no. 7464, pp. 571-4, 2013.
, “Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 2993-3007, 2012.
, “Orthology and functional conservation in eukaryotes.”, Annu Rev Genet, vol. 41, pp. 465-507, 2007.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes.”, Proc Natl Acad Sci U S A, vol. 107, no. 4, pp. 1482-7, 2010.
, “Nutritional homeostasis in batch and steady-state culture of yeast.”, Mol Biol Cell, vol. 15, no. 9, pp. 4089-104, 2004.
, “Nucleotide degradation and ribose salvage in yeast.”, Mol Syst Biol, vol. 9, p. 665, 2013.
, “Nucleosome-coupled expression differences in closely-related species.”, BMC Genomics, vol. 12, p. 466, 2011.
, “Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.”, BMC Bioinformatics, vol. 8, p. 250, 2007.
, “Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.”, Nat Genet, vol. 34, no. 2, pp. 166-76, 2003.
, “Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.”, Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.
, “Missing value estimation methods for DNA microarrays.”, Bioinformatics, vol. 17, no. 6, pp. 520-5, 2001.
, “Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 47, pp. 44817-25, 2002.
, “Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer.”, Anal Chem, vol. 82, no. 8, pp. 3212-21, 2010.
, “Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.”, Proc Natl Acad Sci U S A, vol. 107, no. 15, pp. 6946-51, 2010.
, “Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.”, BMC Genomics, vol. 10, p. 221, 2009.
, “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), vol. 2, no. 8, pp. 943-59, 2012.
, “It's the data!”, Mol Biol Cell, vol. 21, no. 1, pp. 4-6, 2010.
, “Isotope ratio-based profiling of microbial folates.”, J Am Soc Mass Spectrom, vol. 18, no. 5, pp. 898-909, 2007.
, “Information-based clustering.”, Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18297-302, 2005.
, “Influence of genotype and nutrition on survival and metabolism of starving yeast.”, Proc Natl Acad Sci U S A, vol. 105, no. 19, pp. 6930-5, 2008.
, “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
, “The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.”, Bioinformatics, vol. 25, no. 18, pp. 2404-10, 2009.
, “How and when should interactome-derived clusters be used to predict functional modules and protein function?”, Bioinformatics, vol. 25, no. 23, pp. 3143-50, 2009.
, “Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.”, Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
, “Hierarchical multi-label prediction of gene function.”, Bioinformatics, vol. 22, no. 7, pp. 830-6, 2006.
, “Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.”, Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
, “G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
, “Global analysis of gene function in yeast by quantitative phenotypic profiling.”, Mol Syst Biol, vol. 2, p. 2006.0001, 2006.
, “Genomic analysis using a yeast artificial chromosome library with mouse DNA inserts.”, Proc Natl Acad Sci U S A, vol. 89, no. 6, pp. 2456-60, 1992.
, “A genomewide functional network for the laboratory mouse.”, PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
, “Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray.”, Science, vol. 311, no. 5769, pp. 1932-6, 2006.
, “Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains.”, PLoS One, vol. 2, no. 3, p. e322, 2007.
, “Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.”, J Biol Chem, vol. 277, no. 34, pp. 31079-88, 2002.
, “Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.”, Nucleic Acids Res, vol. 34, no. Database issue, pp. D442-5, 2006.
, “Genetic variation and the fate of beneficial mutations in asexual populations.”, Genetics, vol. 188, no. 3, pp. 647-61, 2011.
, “The genetic landscape of a cell.”, Science, vol. 327, no. 5964, pp. 425-31, 2010.
, “Genetic basis of metabolome variation in yeast.”, PLoS Genet, vol. 10, no. 3, p. e1004142, 2014.
, “Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.”, Proc Natl Acad Sci U S A, vol. 100, no. 6, pp. 3351-6, 2003.
, “Gene Ontology annotations at SGD: new data sources and annotation methods.”, Nucleic Acids Res, vol. 36, no. Database issue, pp. D577-81, 2008.
, “Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD).”, Nucleic Acids Res, vol. 33, no. Database issue, pp. D374-7, 2005.
, “Functional analysis of gene duplications in Saccharomyces cerevisiae.”, Genetics, vol. 175, no. 2, pp. 933-43, 2007.
, “Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 22, no. 22, pp. 4447-59, 2011.
, “Exploring the functional landscape of gene expression: directed search of large microarray compendia.”, Bioinformatics, vol. 23, no. 20, pp. 2692-9, 2007.
, “Expanded protein information at SGD: new pages and proteome browser.”, Nucleic Acids Res, vol. 35, no. Database issue, pp. D468-71, 2007.
, “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
, “Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress.”, Mol Biol Cell, vol. 15, no. 12, pp. 5659-69, 2004.
, “Discovery of biological networks from diverse functional genomic data.”, Genome Biol, vol. 6, no. 13, p. R114, 2005.
, “Directing experimental biology: a case study in mitochondrial biogenesis.”, PLoS Comput Biol, vol. 5, no. 3, p. e1000322, 2009.
, “Design and analysis of Bar-seq experiments.”, G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
, “Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast.”, Mol Biol Cell, vol. 22, no. 12, pp. 1997-2009, 2011.
, “The cost of gene expression underlies a fitness trade-off in yeast.”, Proc Natl Acad Sci U S A, vol. 106, no. 14, pp. 5755-60, 2009.
, “Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.”, Mol Biol Cell, vol. 19, no. 1, pp. 352-67, 2008.
, “Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.”, Mol Biol Cell, vol. 22, no. 21, pp. 4192-204, 2011.
, “Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
, “Cooperation among microorganisms.”, PLoS Biol, vol. 4, no. 9, p. e299, 2006.
, “A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.”, Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
, “Conservation of the metabolomic response to starvation across two divergent microbes.”, Proc Natl Acad Sci U S A, vol. 103, no. 51, pp. 19302-7, 2006.
, “Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.”, PLoS Genet, vol. 5, no. 3, p. e1000407, 2009.
, “Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.”, Methods Mol Biol, vol. 548, pp. 273-93, 2009.
, “Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.”, J Biol, vol. 5, no. 4, p. 11, 2006.
, “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
, “Comparative gene expression between two yeast species.”, BMC Genomics, vol. 14, p. 33, 2013.
, “Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 3008-24, 2012.
, “Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae.”, Cell Rep, vol. 5, no. 6, pp. 1725-36, 2013.
, “Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 25, pp. 16144-9, 2002.
, “Changing perspectives in yeast research nearly a decade after the genome sequence.”, Genome Res, vol. 15, no. 12, pp. 1611-9, 2005.
, “Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies.”, BMC Bioinformatics, vol. 9, p. 458, 2008.
, “A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).”, Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8348-53, 2003.
, “Bayesian data integration: a functional perspective.”, Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
, “Assessing the functional structure of genomic data.”, Bioinformatics, vol. 24, no. 13, pp. i330-8, 2008.
, “Ammonium toxicity and potassium limitation in yeast.”, PLoS Biol, vol. 4, no. 11, p. e351, 2006.
, “Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus.”, Proc Natl Acad Sci U S A, vol. 107, no. 43, pp. 18551-6, 2010.
, “Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements.”, Genetics, vol. 174, no. 1, pp. 519-23, 2006.
, “A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae.”, PLoS One, vol. 12, no. 5, p. e0176085, 2017.
, “A global genetic interaction network maps a wiring diagram of cellular function.”, Science, vol. 353, no. 6306, 2016.
, “Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast.”, Mol Biol Cell, vol. 29, no. 8, pp. 897-910, 2018.
, “Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase.”, ACS Chem Biol, vol. 13, no. 10, pp. 3011-3020, 2018.
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