Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
Abstract Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions....
Discovery of biological networks from diverse functional genomic data (2005)
Myers, Chad L, Robson, Drew, Wible, Adam, Hibbs, Matthew A, Chiriac, Camelia, Theesfeld, Chandra L, ...
Abstract We have developed a general probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data. This framework was validated by...
Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures (2005)
Brauer, Matthew J., Saldanha, Alok J., Dolinski, Kara, Botstein, David
We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited...
Dolinski, Kara, Muir, Scott, Cardenas, Maria, Heitman, Joseph
The cyclophilins and FK506 binding proteins (FKBPs) bind to cyclosporin A, FK506, and rapamycin and mediate their immunosuppressive and toxic effects, but the physiological functions of these...
Dolinski, Kara, Scholz, Christian, Muir, R. Scott, Rospert, Sabine, Schmid, Franz X., Cardenas, Maria E., ...
Cyclophilin and FK506 binding protein (FKBP) accelerate cis–trans peptidyl-prolyl isomerization and bind to and mediate the effects of the immunosuppressants cyclosporin A and FK506. The normal...
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data
Ball, Catherine A., Jin, Heng, Sherlock, Gavin, Weng, Shuai, Matese, John C., Andrada, Rey, ...
Upon the completion of the Saccharomyces cerevisiae genomic sequence in 1996 [Goffeau,A. et al. (1997) Nature, 387, 5], several creative and ambitious projects have been initiated to explore the...
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
Dwight, Selina S., Harris, Midori A., Dolinski, Kara, Ball, Catherine A., Binkley, Gail, Christie, Karen R., ...
The Saccharomyces Genome Database (SGD) resources, ranging from genetic and physical maps to genome-wide analysis tools, reflect the scientific progress in identifying genes and their functions over...
Integrating functional genomic information into the Saccharomyces Genome Database
Ball, Catherine A., Dolinski, Kara, Dwight, Selina S., Harris, Midori A., Issel-Tarver, Laurie, Kasarskis, Andrew, ...
The Saccharomyces Genome Database (SGD) stores and organizes information about the nearly 6200 genes in the yeast genome. The information is organized around the ‘locus page’ and directs users to...
Weng, Shuai, Dong, Qing, Balakrishnan, Rama, Christie, Karen, Costanzo, Maria, Dolinski, Kara, ...
The Saccharomyces Genome Database (SGD: http://genome-www.stanford.edu/Saccharomyces/) has recently developed new resources to provide more complete information about proteins from the budding yeast...
Troyanskaya, Olga G., Dolinski , Kara, Owen, Art B., Altman, Russ B., Botstein , David
Genomic sequencing is no longer a novelty, but gene function annotation remains a key challenge in modern biology. A variety of functional genomics experimental techniques are available, from classic...
Christie, Karen R., Weng, Shuai, Balakrishnan, Rama, Costanzo, Maria C., Dolinski, Kara, Dwight, Selina S., ...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/), a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, has recently developed several...
Balakrishnan, Rama, Christie, Karen R., Costanzo, Maria C., Dolinski, Kara, Dwight, Selina S., Engel, Stacia R., ...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is a scientific database of gene, protein and genomic information for the yeast Saccharomyces cerevisiae. SGD has recently...
Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast CulturesD⃞
Brauer, Matthew J., Saldanha, Alok J., Dolinski, Kara, Botstein, David
We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited...
Hirschman, Jodi E., Balakrishnan, Rama, Christie, Karen R., Costanzo, Maria C., Dwight, Selina S., Engel, Stacia R., ...
Sequencing and annotation of the entire Saccharomyces cerevisiae genome has made it possible to gain a genome-wide perspective on yeast genes and gene products. To make this information available on...
Discovery of biological networks from diverse functional genomic data
Myers, Chad L, Robson, Drew, Wible, Adam, Hibbs, Matthew A, Chiriac, Camelia, Theesfeld, Chandra L, ...
BioPIXIE is a probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data.
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
Dolinski, Kara, Muir, Scott, Cardenas, Maria, Heitman, Joseph
The cyclophilins and FK506 binding proteins (FKBPs) bind to cyclosporin A, FK506, and rapamycin and mediate their immunosuppressive and toxic effects, but the physiological functions of these...
Dolinski, Kara, Scholz, Christian, Muir, R. Scott, Rospert, Sabine, Schmid, Franz X., Cardenas, Maria E., ...
Cyclophilin and FK506 binding protein (FKBP) accelerate cis–trans peptidyl-prolyl isomerization and bind to and mediate the effects of the immunosuppressants cyclosporin A and FK506. The normal...
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data
Ball, Catherine A., Jin, Heng, Sherlock, Gavin, Weng, Shuai, Matese, John C., Andrada, Rey, ...
Upon the completion of the Saccharomyces cerevisiae genomic sequence in 1996 [Goffeau,A. et al. (1997) Nature, 387, 5], several creative and ambitious projects have been initiated to explore the...
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
Dwight, Selina S., Harris, Midori A., Dolinski, Kara, Ball, Catherine A., Binkley, Gail, Christie, Karen R., ...
The Saccharomyces Genome Database (SGD) resources, ranging from genetic and physical maps to genome-wide analysis tools, reflect the scientific progress in identifying genes and their functions over...
Integrating functional genomic information into the Saccharomyces Genome Database
Ball, Catherine A., Dolinski, Kara, Dwight, Selina S., Harris, Midori A., Issel-Tarver, Laurie, Kasarskis, Andrew, ...
The Saccharomyces Genome Database (SGD) stores and organizes information about the nearly 6200 genes in the yeast genome. The information is organized around the ‘locus page’ and directs users to...
Weng, Shuai, Dong, Qing, Balakrishnan, Rama, Christie, Karen, Costanzo, Maria, Dolinski, Kara, ...
The Saccharomyces Genome Database (SGD: http://genome-www.stanford.edu/Saccharomyces/) has recently developed new resources to provide more complete information about proteins from the budding yeast...
Troyanskaya, Olga G., Dolinski , Kara, Owen, Art B., Altman, Russ B., Botstein , David
Genomic sequencing is no longer a novelty, but gene function annotation remains a key challenge in modern biology. A variety of functional genomics experimental techniques are available, from classic...
Christie, Karen R., Weng, Shuai, Balakrishnan, Rama, Costanzo, Maria C., Dolinski, Kara, Dwight, Selina S., ...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/), a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, has recently developed several...
Balakrishnan, Rama, Christie, Karen R., Costanzo, Maria C., Dolinski, Kara, Dwight, Selina S., Engel, Stacia R., ...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is a scientific database of gene, protein and genomic information for the yeast Saccharomyces cerevisiae. SGD has recently...
Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast CulturesD⃞
Brauer, Matthew J., Saldanha, Alok J., Dolinski, Kara, Botstein, David
We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited...
Hirschman, Jodi E., Balakrishnan, Rama, Christie, Karen R., Costanzo, Maria C., Dwight, Selina S., Engel, Stacia R., ...
Sequencing and annotation of the entire Saccharomyces cerevisiae genome has made it possible to gain a genome-wide perspective on yeast genes and gene products. To make this information available on...
Discovery of biological networks from diverse functional genomic data
Myers, Chad L, Robson, Drew, Wible, Adam, Hibbs, Matthew A, Chiriac, Camelia, Theesfeld, Chandra L, ...
BioPIXIE is a probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data.
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
Expanded protein information at SGD: new pages and proteome browser
Nash, Robert, Weng, Shuai, Hitz, Ben, Balakrishnan, Rama, Christie, Karen R., Costanzo, Maria C., ...
The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available protein information and has...
Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains
Schacherer, Joseph, Ruderfer, Douglas M., Gresham, David, Dolinski, Kara, Botstein, David, Kruglyak, Leonid
Ten years have passed since the genome of Saccharomyces cerevisiae–more precisely, the S288c strain–was completely sequenced. However, experimental work in yeast is commonly performed using...
Heinicke, Sven, Livstone, Michael S., Lu, Charles, Oughtred, Rose, Kang, Fan, Angiuoli, Samuel V., ...
Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases...
The BioGRID Interaction Database: 2008 update
Breitkreutz, Bobby-Joe, Stark, Chris, Reguly, Teresa, Boucher, Lorrie, Breitkreutz, Ashton, Livstone, Michael, ...
The Biological General Repository for Interaction Datasets (BioGRID) database (http://www.thebiogrid.org) was developed to house and distribute collections of protein and genetic interactions from...
Gene Ontology annotations at SGD: new data sources and annotation methods
Hong, Eurie L., Balakrishnan, Rama, Dong, Qing, Christie, Karen R., Park, Julie, Binkley, Gail, ...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces...