The XBabelPhish MAGE-ML and XML Translator (2008)
Maier, Don, Wymore, Farrell, Sherlock, Gavin, Ball, Catherine A
Abstract Background MAGE-ML has been promoted as a standard format for describing microarray experiments and the data they produce. Two characteristics of the MAGE-ML format compromise its use as a...
OntologyWidget – a reusable, embeddable widget for easily locating ontology terms (2007)
Beauheim, Catherine C, Wymore, Farrell, Nitzberg, Michael, Zachariah, Zachariah K, Jin, Heng, Skene, JH Pate, ...
Abstract Background Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity,...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB (2006)
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
Abstract Background Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the...
A Human-Curated Annotation of the Candida albicans Genome (2005)
Burkhard R. Braun, Christophe D'Enfert, Mikhail Martchenko, Jan Dungan, Alan Kuo, ...
Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly,...
Dunn, Barbara, Levine, R Paul, Sherlock, Gavin
Abstract Background Genetic differences between yeast strains used in wine-making may account for some of the variation seen in their fermentation properties and may also produce differing sensory...
Caryoscope: An Open Source Java application for viewing microarray data in a genomic context (2004)
Awad, Ihab AB, Rees, Christian A, Hernandez-Boussard, Tina, Ball, Catherine A, Sherlock, Gavin
Abstract Background Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically...
GeneXplorer: an interactive web application for microarray data visualization and analysis (2004)
Rees, Christian A, Demeter, Janos, Matese, John C, Botstein, David, Sherlock, Gavin
Abstract Background When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures...
Submission of Microarray Data to Public Repositories (2004)
Catherine A. Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication.
Submission of Microarray Data to Public Repositories (2004)
Catherine A. Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, ...
Killion, Patrick J, Sherlock, Gavin, Iyer, Vishwanath R
Abstract Background The power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms. Description The...
Design and implementation of microarray gene expression markup language (MAGE-ML) (2002)
Spellman, Paul T, Miller, Michael, Stewart, Jason, Troup, Charles, Sarkans, Ugis, Chervitz, Steve, ...
Abstract Background Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one...
Olga Troyanskaya, Gavin Sherlock, Trevor Hastie, Robert Tibshirani, David Botstein, Russ B. Altman
Motivation: Gene expression microarray experiments can generate data sets with multiple missing expression values. Unfortunately, many algorithms for gene expression analysis require a complete...
Imputing Missing Data for Gene Expression Arrays (2001)
Trevor Hastie, Robert Tibshirani, Gavin Sherlock, Michael Eisen, Patrick Brown, David Botstein
this report. 1.2 SVD imputation using all the data
Exploratory Screening of Genes and Clusters (2001)
Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, Michael Eisen, Gavin Sherlock, Pat Brownil
We discuss a method called "cluster scoring" for supervised learning from a set of gene expression experiments. Cluster scoring generalizes methods that rank individual genes based on their...
Missing value estimation methods for DNA microarrays (2001)
Olga Troyanskaya, Gavin Sherlock, Pat Brown, Trevor Hastie, Robert Tibshirani, David Botstein, ...
Motivation: Gene expression microarray experiments can generate data sets with multiple missing expression values. Unfortunately, many algorithms for gene expression analysis require a complete...
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...
Microarray Hybridization, Paul T. Spellman, Gavin Sherlock, Michael Q. Zhang, Vishwanath R, Kirk Anders, ...
this article is available at www.molbiolcell.org.
A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains
Salama, Nina, Guillemin, Karen, McDaniel, Timothy K., Sherlock, Gavin, Tompkins, Lucy, Falkow, Stanley
Helicobacter pylori colonizes the stomach of half of the world's population, causing a wide spectrum of disease ranging from asymptomatic gastritis to ulcers to gastric cancer. Although the basis for...
Spellman, Paul T., Sherlock, Gavin, Zhang, Michael Q., Iyer, Vishwanath R., Anders, Kirk, Eisen, Michael B., ...
We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures...
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...
Whitfield, Michael L., Sherlock, Gavin, Saldanha, Alok J., Murray, John I., Ball, Catherine A., Alexander, Karen E., ...
The genome-wide program of gene expression during the cell division cycle in a human cancer cell line (HeLa) was characterized using cDNA microarrays. Transcripts of >850 genes showed periodic...
Design and implementation of microarray gene expression markup language (MAGE-ML)
Spellman, Paul T, Miller, Michael, Stewart, Jason, Troup, Charles, Sarkans, Ugis, Chervitz, Steve, ...
Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to...
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...
The Stanford Microarray Database: data access and quality assessment tools
Gollub, Jeremy, Ball, Catherine A., Binkley, Gail, Demeter, Janos, Finkelstein, David B., Hebert, Joan M., ...
The Stanford Microarray Database (SMD; http://genome-www.stanford.edu/microarray/) serves as a microarray research database for Stanford investigators and their collaborators. In addition, SMD...
Submission of Microarray Data to Public Repositories
Ball, Catherine A, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication
GeneXplorer: an interactive web application for microarray data visualization and analysis
Rees, Christian A, Demeter, Janos, Matese, John C, Botstein, David, Sherlock, Gavin
Caryoscope: An Open Source Java application for viewing microarray data in a genomic context
Awad, Ihab AB, Rees, Christian A, Hernandez-Boussard, Tina, Ball, Catherine A, Sherlock, Gavin
Arnaud, Martha B., Costanzo, Maria C., Skrzypek, Marek S., Binkley, Gail, Lane, Christopher, Miyasato, Stuart R., ...
The Candida Genome Database (CGD) is a new database that contains genomic information about the opportunistic fungal pathogen Candida albicans. CGD is a public resource for the research community...
The Stanford Microarray Database accommodates additional microarray platforms and data formats
Ball, Catherine A., Awad, Ihab A. B., Demeter, Janos, Gollub, Jeremy, Hebert, Joan M., Hernandez-Boussard, Tina, ...
The Stanford Microarray Database (SMD) (http://smd.stanford.edu) is a research tool for hundreds of Stanford researchers and their collaborators. In addition, SMD functions as a resource for the...
A Human-Curated Annotation of the Candida albicans Genome
Braun, Burkhard R, Van Het Hoog, Marco, D'Enfert, Christophe, Martchenko, Mikhail, Dungan, Jan, Kuo, Alan, ...
Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly,...
Microarray Data Standards: An Open Letter
Ball, Catherine, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains
Salama, Nina, Guillemin, Karen, McDaniel, Timothy K., Sherlock, Gavin, Tompkins, Lucy, Falkow, Stanley
Helicobacter pylori colonizes the stomach of half of the world's population, causing a wide spectrum of disease ranging from asymptomatic gastritis to ulcers to gastric cancer. Although the basis for...
Spellman, Paul T., Sherlock, Gavin, Zhang, Michael Q., Iyer, Vishwanath R., Anders, Kirk, Eisen, Michael B., ...
We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures...
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...
Whitfield, Michael L., Sherlock, Gavin, Saldanha, Alok J., Murray, John I., Ball, Catherine A., Alexander, Karen E., ...
The genome-wide program of gene expression during the cell division cycle in a human cancer cell line (HeLa) was characterized using cDNA microarrays. Transcripts of >850 genes showed periodic...
Design and implementation of microarray gene expression markup language (MAGE-ML)
Spellman, Paul T, Miller, Michael, Stewart, Jason, Troup, Charles, Sarkans, Ugis, Chervitz, Steve, ...
Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to...
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...
The Stanford Microarray Database: data access and quality assessment tools
Gollub, Jeremy, Ball, Catherine A., Binkley, Gail, Demeter, Janos, Finkelstein, David B., Hebert, Joan M., ...
The Stanford Microarray Database (SMD; http://genome-www.stanford.edu/microarray/) serves as a microarray research database for Stanford investigators and their collaborators. In addition, SMD...
Submission of Microarray Data to Public Repositories
Ball, Catherine A, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication
GeneXplorer: an interactive web application for microarray data visualization and analysis
Rees, Christian A, Demeter, Janos, Matese, John C, Botstein, David, Sherlock, Gavin
Caryoscope: An Open Source Java application for viewing microarray data in a genomic context
Awad, Ihab AB, Rees, Christian A, Hernandez-Boussard, Tina, Ball, Catherine A, Sherlock, Gavin
Arnaud, Martha B., Costanzo, Maria C., Skrzypek, Marek S., Binkley, Gail, Lane, Christopher, Miyasato, Stuart R., ...
The Candida Genome Database (CGD) is a new database that contains genomic information about the opportunistic fungal pathogen Candida albicans. CGD is a public resource for the research community...
The Stanford Microarray Database accommodates additional microarray platforms and data formats
Ball, Catherine A., Awad, Ihab A. B., Demeter, Janos, Gollub, Jeremy, Hebert, Joan M., Hernandez-Boussard, Tina, ...
The Stanford Microarray Database (SMD) (http://smd.stanford.edu) is a research tool for hundreds of Stanford researchers and their collaborators. In addition, SMD functions as a resource for the...
A Human-Curated Annotation of the Candida albicans Genome
Braun, Burkhard R, Van Het Hoog, Marco, D'Enfert, Christophe, Martchenko, Mikhail, Dungan, Jan, Kuo, Alan, ...
Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly,...
Microarray Data Standards: An Open Letter
Ball, Catherine, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
Global analysis of gene function in yeast by quantitative phenotypic profiling
Brown, James A, Sherlock, Gavin, Myers, Chad L, Burrows, Nicola M, Deng, Changchun, Wu, H Irene, ...
We present a method for the global analysis of the function of genes in budding yeast based on hierarchical clustering of the quantitative sensitivity profiles of the 4756 strains with individual...
Sequence resources at the Candida Genome Database
Arnaud, Martha B., Costanzo, Maria C., Skrzypek, Marek S., Shah, Prachi, Binkley, Gail, Lane, Christopher, ...
The Candida Genome Database (CGD, ) contains a curated collection of genomic information and community resources for researchers who are interested in the molecular biology of the opportunistic...
Demeter, Janos, Beauheim, Catherine, Gollub, Jeremy, Hernandez-Boussard, Tina, Jin, Heng, Maier, Donald, ...
The Stanford Microarray Database (SMD; ) is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology....