Alejandro-Osorio, Adriana L, Huebert, Dana J, Porcaro, Dominic T, Sonntag, Megan E, Nillasithanukroh, Songdet, Will, Jessica L, ...
Abstract Background Yeast responding to stress activate a large gene expression program called the Environmental Stress Response that consists of approximately 600 repressed genes and approximately...
Audrey P Gasch, Michael B Eisen
the conditional coregulation of yeast gene expression
Flexible promoter architecture requirements for coactivator recruitment (2006)
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
Abstract Background The spatial organization of transcription factor binding sites in regulatory DNA, and the composition of intersite sequences, influences the assembly of the multiprotein complexes...
Derek Y Chiang, David A Nix, Ryan K Shultzaberger, Audrey P Gasch, Michael B Eisen, Derek Y Chiang, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available shortly after the date of publication, from the URL listed below....
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
A systematic examination of the gene regulatory elements in ascomycete fungi reveals striking conservation along with some examples of the ways in which regulatory systems can evolve.
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Conservation and evolution of cis-regulatory systems in ascomycete fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Gasch, Audrey P, Eisen, Michael B
Abstract Background Organisms simplify the orchestration of gene expression by coregulating genes whose products function together in the cell. Many proteins serve different roles depending on the...
Audrey P Gasch, Michael B Eisen
the conditional coregulation of yeast gene expression
Genomic expression programs in the response of yeast cells to environmental changes (2000)
Audrey P. Gasch, Paul T. Spellman, Camilla M. Kao, Orna Carmel-harel, Michael B. Eisen, Gisela Storz, ...
We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over...
Genomic Expression Programs in the Response of Yeast Cells to Environmental ChangesD⃞
Gasch, Audrey P., Spellman, Paul T., Kao, Camilla M., Carmel-Harel, Orna, Eisen, Michael B., Storz, Gisela, ...
We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over...
Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast
Lyons, Thomas J., Gasch, Audrey P., Gaither, L. Alex, Botstein, David, Brown, Patrick O., Eide, David J.
The Zap1p transcription factor senses cellular zinc status and increases expression of its target genes in response to zinc deficiency. Previously known Zap1p-regulated genes encode the Zrt1p, Zrt2p,...
Gasch, Audrey P., Huang, Mingxia, Metzner, Sandra, Botstein, David, Elledge, Stephen J., Brown, Patrick O.
Eukaryotic cells respond to DNA damage by arresting the cell cycle and modulating gene expression to ensure efficient DNA repair. The human ATR kinase and its homolog in yeast, MEC1, play central...
Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
Gasch, Audrey P, Eisen, Michael B
A heuristically modified version of fuzzy k-means clustering has been used to identify overlapping clusters of yeast genes based on published gene-expression data following the response of yeast...
Koc, Ahmet, Gasch, Audrey P., Rutherford, Julian C., Kim, Hwa-Young, Gladyshev, Vadim N.
Aging is thought to be caused by the accumulation of damage, primarily from oxidative modifications of cellular components by reactive oxygen species (ROS). Here we used yeast methionine sulfoxide...
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi
Gasch, Audrey P, Moses, Alan M, Chiang, Derek Y, Fraser, Hunter B, Berardini, Mark, Eisen, Michael B
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Flexible promoter architecture requirements for coactivator recruitment
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
Genomic Expression Programs in the Response of Yeast Cells to Environmental ChangesD⃞
Gasch, Audrey P., Spellman, Paul T., Kao, Camilla M., Carmel-Harel, Orna, Eisen, Michael B., Storz, Gisela, ...
We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over...
Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast
Lyons, Thomas J., Gasch, Audrey P., Gaither, L. Alex, Botstein, David, Brown, Patrick O., Eide, David J.
The Zap1p transcription factor senses cellular zinc status and increases expression of its target genes in response to zinc deficiency. Previously known Zap1p-regulated genes encode the Zrt1p, Zrt2p,...
Gasch, Audrey P., Huang, Mingxia, Metzner, Sandra, Botstein, David, Elledge, Stephen J., Brown, Patrick O.
Eukaryotic cells respond to DNA damage by arresting the cell cycle and modulating gene expression to ensure efficient DNA repair. The human ATR kinase and its homolog in yeast, MEC1, play central...
Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
Gasch, Audrey P, Eisen, Michael B
A heuristically modified version of fuzzy k-means clustering has been used to identify overlapping clusters of yeast genes based on published gene-expression data following the response of yeast...
Koc, Ahmet, Gasch, Audrey P., Rutherford, Julian C., Kim, Hwa-Young, Gladyshev, Vadim N.
Aging is thought to be caused by the accumulation of damage, primarily from oxidative modifications of cellular components by reactive oxygen species (ROS). Here we used yeast methionine sulfoxide...
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi
Gasch, Audrey P, Moses, Alan M, Chiang, Derek Y, Fraser, Hunter B, Berardini, Mark, Eisen, Michael B
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Flexible promoter architecture requirements for coactivator recruitment
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates
Kvitek, Daniel J., Will, Jessica L., Gasch, Audrey P.
Interactions between an organism and its environment can significantly influence phenotypic evolution. A first step toward understanding this process is to characterize phenotypic diversity within...
Stress-activated Genomic Expression Changes Serve a Preparative Role for Impending Stress in Yeast
Berry, David B., Gasch, Audrey P.
Yeast cells respond to stress by mediating condition-specific gene expression changes and by mounting a common response to many stresses, called the environmental stress response (ESR). Giaever et...
Alejandro-Osorio, Adriana L, Huebert, Dana J, Porcaro, Dominic T, Sonntag, Megan E, Nillasithanukroh, Songdet, Will, Jessica L, ...
Chromatin-immunoprecipitation and computational analysis implicate Rpd3p as an important co-factor in the network of genes regulating the yeast environmental stress response.