Integrated analysis of breast cancer cell lines reveals unique signaling pathways (2009)
Heiser, Laura M, Wang, Nicholas J, Talcott, Carolyn L, Laderoute, Keith R, Knapp, Merrill, Guan, Yinghui, ...
Abstract Background Cancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis....
Wang, Yuker, Carlton, Victoria EH, Karlin-Neumann, George, Sapolsky, Ronald, Zhang, Li, Moorhead, Martin, ...
Abstract Background A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded...
GenomeGraphs: integrated genomic data visualization with R (2009)
Durinck, Steffen, Bullard, James, Spellman, Paul T, Dudoit, Sandrine
Abstract Background Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different...
Sparse combinatorial inference with an application in cancer biology (2009)
Mukherjee, Sach, Pelech, Steven, Neve, Richard M., Kuo, Wen-Lin, Ziyad, Safiyyah, Spellman, Paul T., ...
Motivation: Combinatorial effects, in which several variables jointly influence an output or response, play an important role in biological systems. In many settings, Boolean functions provide a...
Bmc Bioinformatics, Steffen Durinck, James Bullard, Paul T Spellman
Software GenomeGraphs: integrated genomic data visualization with R
Press, Joshua Z., De Luca, Alessandro, Boyd, Niki, Young, Sean, Troussard, Armelle, Ridge, Yolanda, ...
Performance of Molecular Inversion Probes (MIP) in Allele Copy Number Determination (2008)
Wang, Yuker, Moorhead, Martin, Karlin-Neumann, George, Wang, Nicolas J., Ireland, James, Lin, Steven, ...
We have developed a new protocol for using Molecular Inversion Probes (MIP) to accurately and specifically measure allele copy number (ACN). The new protocol provides for significant improvements...
Kenny, Paraic A., Lee, Genee Y., Myers, Connie A., Neve, Richard M., Semeiks, Jeremy R., Spellman, Paul T., ...
Richard M. Neve, Koei Chin, Jane Fridly, Jennifer Yeh, Frederick L. Baehner, Tea Fevr, ...
collection of breast cancer cell lines for the study of functionally
Press, Joshua Z, De Luca, Alessandro, Boyd, Niki, Young, Sean, Troussard, Armelle, Ridge, Yolanda, ...
Background Subclassification of ovarian carcinomas can be used to guide treatment and determine prognosis. Germline and somatic mutations, loss of heterozygosity (LOH), and epigenetic events such as...
Analysis of molecular inversion probe performance for allele copy number determination (2007)
Wang, Yuker, Moorhead, Martin, Karlin-Neumann, George, Wang, Nicholas J, Ireland, James, Lin, Steven, ...
Abstract We have developed a new protocol for using molecular inversion probes to accurately and specifically measure allele copy number. The new protocol provides for significant improvements,...
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...
* Corresponding authors (2006)
Tim F Rayner, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, ...
A simple spreadsheet-based, MIAME-supportive format for
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...
Evidence for large domains of similarly expressed genes in the Drosophila genome (2002)
Spellman, Paul T, Rubin, Gerald M
Abstract Background Transcriptional regulation in eukaryotes generally operates at the level of individual genes. Regulation of sets of adjacent genes by mechanisms operating at the level of...
© 2002 Spellman et al., licensee BioMed Central Ltd (2002)
Paul T Spellman, Michael Miller, Jason Stewart, Charles Troup, Steve Chervitz, Derek Bernhart, ...
The electronic version of this article is the complete one and can be found online at
The Stanford Microarray Database (2001)
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...
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...
Microarray Hybridization □d, Paul T. Spellman, Gavin Sherlock, Michael Q. Zhang, Vishwanath R, Kirk Anders, ...
this article is available at www.molbiolcell.org.
Koei Chin, Y Devries, Jane Fridly, Paul T. Spellman, Ritu Roydasgupta, Wen-lin Kuo, ...
and transcriptional aberrations linked to breast cancer pathophysiologies
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...
Cluster analysis and display of genome-wide expression patterns
Eisen, Michael B., Spellman, Paul T., Brown, Patrick O., Botstein, David
A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in...
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...
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...
Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays
De Gregorio, Ennio, Spellman, Paul T., Rubin, Gerald M., Lemaitre, Bruno
To identify new Drosophila genes involved in the immune response, we monitored the gene expression profile of adult flies in response to microbial infection by using high-density oligonucleotide...
The Toll and Imd pathways are the major regulators of the immune response in Drosophila
De Gregorio, Ennio, Spellman, Paul T., Tzou, Phoebe, Rubin, Gerald M., Lemaitre, Bruno
Microarray studies have shown recently that microbial infection leads to extensive changes in the Drosophila gene expression programme. However, little is known about the control of most of the fly...
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...
Ceramic Capillaries for Use in Microarray Fabrication
George, Reed A., Woolley, John Patrick, Spellman, Paul T.
We have used ceramic capillary tips generally used in the microelectronics industry for the production of DNA microarrays. The ceramic tips improve the morphology of microarray elements, allow higher...
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, ...
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...
Cluster analysis and display of genome-wide expression patterns
Eisen, Michael B., Spellman, Paul T., Brown, Patrick O., Botstein, David
A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in...
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...
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...
Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays
De Gregorio, Ennio, Spellman, Paul T., Rubin, Gerald M., Lemaitre, Bruno
To identify new Drosophila genes involved in the immune response, we monitored the gene expression profile of adult flies in response to microbial infection by using high-density oligonucleotide...
The Toll and Imd pathways are the major regulators of the immune response in Drosophila
De Gregorio, Ennio, Spellman, Paul T., Tzou, Phoebe, Rubin, Gerald M., Lemaitre, Bruno
Microarray studies have shown recently that microbial infection leads to extensive changes in the Drosophila gene expression programme. However, little is known about the control of most of the fly...
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...
Ceramic Capillaries for Use in Microarray Fabrication
George, Reed A., Woolley, John Patrick, Spellman, Paul T.
We have used ceramic capillary tips generally used in the microelectronics industry for the production of DNA microarrays. The ceramic tips improve the morphology of microarray elements, allow higher...
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, ...
Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities
Press, Joshua Z, De Luca, Alessandro, Boyd, Niki, Young, Sean, Troussard, Armelle, Ridge, Yolanda, ...
Analysis of molecular inversion probe performance for allele copy number determination
Wang, Yuker, Moorhead, Martin, Karlin-Neumann, George, Wang, Nicholas J, Ireland, James, Lin, Steven, ...
A new protocol for using molecular inversion probes to specifically and accurately measure allele copy numbers.
GenomeGraphs: integrated genomic data visualization with R
Durinck, Steffen, Bullard, James, Spellman, Paul T, Dudoit, Sandrine
Wang, Yuker, Carlton, Victoria EH, Karlin-Neumann, George, Sapolsky, Ronald, Zhang, Li, Moorhead, Martin, ...
Integrated analysis of breast cancer cell lines reveals unique signaling pathways
Heiser, Laura M, Wang, Nicholas J, Talcott, Carolyn L, Laderoute, Keith R, Knapp, Merrill, Guan, Yinghui, ...
Mapping of sub-networks in the EGFR-MAPK pathway in different breast cancer cell lines reveals that PAK1 may be a marker for sensitivity to MEK inhibitors.