Tian, Weidong, Zhang, Lan V, Taşan, Murat, Gibbons, Francis D, King, Oliver D, Park, Julie, ...
Abstract Background: Learning the function of genes is a major goal of computational genomics. Methods for inferring gene function have typically fallen into two categories: 'guilt-by-profiling',...
Lockshon, Daniel, Kerr, Emily O., Learmonth, Robert P., Kennedy, Brian K., Cherry, J. Michael, Macreadie, Ian G.
[Abstract] The mechanisms which control the fluidity of eukaryotic membranes are unknown. We have identified S.cerevisiae deletion strains whose growth is impaired by palmitoleic (PO; C16:1) but not...
Learmonth, Robert P., Butcher, Brett, Cherry, J. Michael, Macreadie, Ian G.
Adaptation of yeasts to changing environments during growth, fermentation and bioprocessing requires rapid modulation of membrane fluidity. We studied fluidity modulation in S. cerevisiae FY1679-28c...
Lockshon, Daniel, Kerr, Emily O., Learmonth, Robert P., Kennedy, Brian K., Cherry, J. Michael, Macreadie, Ian G.
[Abstract] The mechanisms which control the fluidity of eukaryotic membranes are unknown. We have identified S.cerevisiae deletion strains whose growth is impaired by palmitoleic (PO; C16:1) but not...
Learmonth, Robert P., Butcher, Brett, Cherry, J. Michael, Macreadie, Ian G.
Adaptation of yeasts to changing environments during growth, fermentation and bioprocessing requires rapid modulation of membrane fluidity. We studied fluidity modulation in S. cerevisiae FY1679-28c...
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. (2006)
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Jonathan A. Eisen, Robert S. Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R. Wortman, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
David B. Finkelstein, Jeremy Gollub, Rob Ewing, Fredrik Sterky, Shauna Somerville, J. Michael Cherry
Two-color DNA microarray data has proven valuable in high-throughput expression profiling. However microarray expression ratios (log 2 ratios) are subject to measurement error from multiple causes....
The Stanford Microarray Database (2001)
Gavin Sherlock, Tina Hern, Andrew Kasarskis, Gail Binkley, John C. Matese, Selina S. Dwight, ...
The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two...
J. Michael Cherry, Caroline Adler, Catherine Ball, Stephen A. Chervitz, Selina S. Dwight, Erich T. Hester, ...
The Saccharomyces GenomeDatabase (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic sequence, its genes and their products, the phenotypes of its mutants, and the...
David J. Fl, Shuai Weng, Fabien X. Petel, J. Michael Cherry
AtDB, the Arabidopsis thaliana Database, has a primary role to provide public access to the collected genomic information for A.thaliana via the WorldWideWeb (URL: http://genome-www.stanford.edu/ )....
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...
The Stanford Microarray Database
Sherlock, Gavin, Hernandez-Boussard, Tina, Kasarskis, Andrew, Binkley, Gail, Matese, John C., Dwight, Selina S., ...
The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two...
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...
Gutiérrez, Rodrigo A., Ewing, Rob M., Cherry, J. Michael, Green, Pamela J.
mRNA degradation provides a powerful means for controlling gene expression during growth, development, and many physiological transitions in plants and other systems. Rates of decay help define the...
A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae
Wang, Wei, Cherry, J. Michael, Botstein, David, Li, Hao
Decomposing regulatory networks into functional modules is a first step toward deciphering the logical structure of complex networks. We propose a systematic approach to reconstructing transcription...
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
Diehn, Maximilian, Sherlock, Gavin, Binkley, Gail, Jin, Heng, Matese, John C., Hernandez-Boussard, Tina, ...
The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale...
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...
Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation
Wang, Wei, Cherry, J. Michael, Nochomovitz, Yigal, Jolly, Emmitt, Botstein, David, Li, Hao
Decomposing transcriptional regulatory networks into functional modules and determining logical relations between them is the first step toward understanding transcriptional regulation at the system...
PatMatch: a program for finding patterns in peptide and nucleotide sequences
Yan, Thomas, Yoo, Danny, Berardini, Tanya Z., Mueller, Lukas A., Weems, Dan C., Weng, Shuai, ...
Here, we present PatMatch, an efficient, web-based pattern-matching program that enables searches for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small...
Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research
Stover, Nicholas A., Krieger, Cynthia J., Binkley, Gail, Dong, Qing, Fisk, Dianna G., Nash, Robert, ...
We have developed a web-based resource (available at ) for researchers studying the model ciliate organism Tetrahymena thermophila. Employing the underlying database structure and programming of the...
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...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
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...
The Stanford Microarray Database
Sherlock, Gavin, Hernandez-Boussard, Tina, Kasarskis, Andrew, Binkley, Gail, Matese, John C., Dwight, Selina S., ...
The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two...
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...
Gutiérrez, Rodrigo A., Ewing, Rob M., Cherry, J. Michael, Green, Pamela J.
mRNA degradation provides a powerful means for controlling gene expression during growth, development, and many physiological transitions in plants and other systems. Rates of decay help define the...
A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae
Wang, Wei, Cherry, J. Michael, Botstein, David, Li, Hao
Decomposing regulatory networks into functional modules is a first step toward deciphering the logical structure of complex networks. We propose a systematic approach to reconstructing transcription...
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
Diehn, Maximilian, Sherlock, Gavin, Binkley, Gail, Jin, Heng, Matese, John C., Hernandez-Boussard, Tina, ...
The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale...
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...
Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation
Wang, Wei, Cherry, J. Michael, Nochomovitz, Yigal, Jolly, Emmitt, Botstein, David, Li, Hao
Decomposing transcriptional regulatory networks into functional modules and determining logical relations between them is the first step toward understanding transcriptional regulation at the system...
PatMatch: a program for finding patterns in peptide and nucleotide sequences
Yan, Thomas, Yoo, Danny, Berardini, Tanya Z., Mueller, Lukas A., Weems, Dan C., Weng, Shuai, ...
Here, we present PatMatch, an efficient, web-based pattern-matching program that enables searches for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small...
Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research
Stover, Nicholas A., Krieger, Cynthia J., Binkley, Gail, Dong, Qing, Fisk, Dianna G., Nash, Robert, ...
We have developed a web-based resource (available at ) for researchers studying the model ciliate organism Tetrahymena thermophila. Employing the underlying database structure and programming of the...
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...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
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...
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...