Search Results - "STOUGHTON, Roland"

Applications of DNA microarrays in biology by Stoughton, Roland B

“…DNA microarrays have enabled biology researchers to conduct large-scale quantitative experiments. This capacity has produced qualitative changes in the breadth…”
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How molecular profiling could revolutionize drug discovery by Stoughton, Roland B, Friend, Stephen H

“…Information from genomic, proteomic and metabolomic measurements has already benefited target discovery and validation, assessment of efficacy and toxicity of…”
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Integrated Genomic and Proteomic Analyses of Gene Expression in Mammalian Cells by Tian, Qiang, Stepaniants, Serguei B, Mao, Mao, Weng, Lee, Feetham, Megan C, Doyle, Michelle J, Yi, Eugene C, Dai, Hongyue, Thorsson, Vesteinn, Eng, Jimmy, Goodlett, David, Berger, Joel P, Gunter, Bert, Linseley, Peter S, Stoughton, Roland B, Aebersold, Ruedi, Collins, Steven J, Hanlon, William A, Hood, Leroy E

“…Using DNA microarrays together with quantitative proteomic techniques (ICAT reagents, two-dimensional DIGE, and MS), we evaluated the correlation of mRNA and…”
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Genetics of gene expression surveyed in maize, mouse and man by Schadt, Eric E, Friend, Stephen H, Monks, Stephanie A, Drake, Thomas A, Lusis, Aldons J, Che, Nam, Colinayo, Veronica, Ruff, Thomas G, Milligan, Stephen B, Lamb, John R, Cavet, Guy, Linsley, Peter S, Mao, Mao, Stoughton, Roland B

“…Treating messenger RNA transcript abundances as quantitative traits and mapping gene expression quantitative trait loci for these traits has been pursued in…”
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A cell proliferation signature is a marker of extremely poor outcome in a subpopulation of breast cancer patients by HONGYUE DAI, VAN'T VEER, Laura, STOUGHTON, Roland, FRIEND, Stephen, LAMB, John, HE, Yudong D, MAO MAO, FINE, Bernard M, BERNARDS, Rene, VAN DE VIJVER, Marc, DEUTSCH, Paul, SACHS, Alan

“…Breast cancer comprises a group of distinct subtypes that despite having similar histologic appearances, have very different metastatic potentials. Being able…”
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Functional Discovery via a Compendium of Expression Profiles by Hughes, Timothy R, Marton, Matthew J, Jones, Allan R, Roberts, Christopher J, Stoughton, Roland, Armour, Christopher D, Bennett, Holly A, Coffey, Ernest, Dai, Hongyue, He, Yudong D, Kidd, Matthew J, King, Amy M, Meyer, Michael R, Slade, David, Lum, Pek Y, Stepaniants, Sergey B, Shoemaker, Daniel D, Gachotte, Daniel, Chakraburtty, Kalpana, Simon, Julian, Bard, Martin, Friend, Stephen H

“…Ascertaining the impact of uncharacterized perturbations on the cell is a fundamental problem in biology. Here, we describe how a single assay can be used to…”
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Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters by Altschuler, Steven J, Wu, Lani F, Hughes, Timothy R, Davierwala, Armaity P, Robinson, Mark D, Stoughton, Roland

“…Genome sequencing has led to the discovery of tens of thousands of potential new genes. Six years after the sequencing of the well-studied yeast Saccharomyces…”
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Effects of Atmospheric Ozone on Microarray Data Quality by Fare, Thomas L, Coffey, Ernest M, Dai, Hongyue, He, Yudong D, Kessler, Deborah A, Kilian, Kristopher A, Koch, John E, LeProust, Eric, Marton, Matthew J, Meyer, Michael R, Stoughton, Roland B, Tokiwa, George Y, Wang, Yanqun

“…A data anomaly was observed that affected the uniformity and reproducibility of fluorescent signal across DNA microarrays. Results from experimental sets…”
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Signaling and Circuitry of Multiple MAPK Pathways Revealed by a Matrix of Global Gene Expression Profiles by Roberts, Christopher J., Nelson, Bryce, Marton, Matthew J., Stoughton, Roland, Meyer, Michael R., Bennett, Holly A., He, Yudong D., Dai, Hongyue, Walker, Wynn L., Hughes, Timothy R., Tyers, Mike, Boone, Charles, Friend, Stephen H.

“…Genome-wide transcript profiling was used to monitor signal transduction during yeast pheromone response. Genetic manipulations allowed analysis of changes in…”
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Microarray standard data set and figures of merit for comparing data processing methods and experiment designs by HE, Yudong D, DAI, Hongyue, STOUGHTON, Roland B, SCHADT, Eric E, CAVET, Guy, EDWARDS, Stephen W, STEPANIANTS, Sergey B, DUENWALD, Sven, KLEINHANZ, Robert, JONES, Allan R, SHOEMAKER, Daniel D

“…There is a very large and growing level of effort toward improving the platforms, experiment designs, and data analysis methods for microarray expression…”
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Drug target validation and identification of secondary drug target effects using DNA microarrays by Marton, Matthew J., DeRisi, Joseph L., Bennett, Holly A., Iyer, Vishwanath R., Meyer, Michael R., Roberts, Christopher J., Stoughton, Roland, Burchard, Julja, Slade, David, Dai, Hongyue, Bassett, Douglas E., Hartwell, Leland H., Brown, Patrick O., Friend, Stephen H.

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Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing by Castle, John, Garrett-Engele, Phil, Armour, Christopher D, Duenwald, Sven J, Loerch, Patrick M, Meyer, Michael R, Schadt, Eric E, Stoughton, Roland, Parrish, Mark L, Shoemaker, Daniel D, Johnson, Jason M

“…Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that…”
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Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays by Johnson, Jason M., Castle, John, Garrett-Engele, Philip, Kan, Zhengyan, Loerch, Patrick M., Armour, Christopher D., Santos, Ralph, Schadt, Eric E., Stoughton, Roland, Shoemaker, Daniel D.

“…Alternative pre-messenger RNA (pre-mRNA) splicing plays important roles in development, physiology, and disease, and more than half of human genes are…”
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Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer by Linsley, Peter S, Hughes, Timothy R, Mao, Mao, Jones, Allan R, Burchard, Julja, Marton, Matthew J, Shannon, Karen W, Lefkowitz, Steven M, Ziman, Michael, Schelter, Janell M, Meyer, Michael R, Kobayashi, Sumire, Davis, Colleen, Dai, Hongyue, He, Yudong D, Stephaniants, Sergey B, Cavet, Guy, Walker, Wynn L, West, Anne, Coffey, Ernest, Shoemaker, Daniel D, Stoughton, Roland, Blanchard, Alan P, Friend, Stephen H

“…We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing…”
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Use of hybridization kinetics for differentiating specific from non‐specific binding to oligonucleotide microarrays by Dai, Hongyue, Meyer, Michael, Stepaniants, Sergey, Ziman, Michael, Stoughton, Roland

“…Hybridization kinetics were found to be significantly different for specific and non‐specific binding of labeled cRNA to surface‐bound oligonucleotides on…”
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Measurements of small-caliber ballistic shock waves in air by Stoughton, Roland

“…Megahertz bandwidth pressure measurements of airborne ballistic shock waves from bullets are presented which confirm weak-shock theoretical predictions of…”
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Drug target validation and identification of secondary drug target effects using DNA microarrays by Friend, Stephen H, Marton, Matthew J, DeRisi, Joseph L, Bennett, Holly A, Iyer, Vishwanath R, Meyer, Michael R, Roberts, Christopher J, Stoughton, Roland, Burchard, Julja, Slade, David, Dai, Hongyue, Bassett, Douglas E, Hartwell, Leland H, Brown, Patrick O

“…We describe here a method for drug target validation and identification of secondary drug target effects based on genome-wide gene expression patterns. The…”
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Development of a DNA Microarray for Toxicology Based on Hepatotoxin- regulated Sequences by Waring, Jeffrey F., Cavet, Guy, Jolly, Robert A., McDowell, Jeff, Dai, Hongye, Ciurlionis, Rita, Zhang, Chunsheng, Stoughton, Roland, Lum, Pek, Ferguson, Allan, Roberts, Christopher J., Ulrich, Roger G.

“…Toxicogenomics is an emerging field combining genomics and bioinformatics to identify and characterize mechanisms of toxicity of compounds. One of the main…”
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Development of a DNA Microarray for Toxicology Based on Hepatotoxin-Regulated Sequences by Waring, Jeffrey F., Cavet, Guy, Jolly, Robert A., McDowell, Jeff, Dai, Hongye, Ciurlionis, Rita, Zhang, Chunsheng, Stoughton, Roland, Lum, Pek, Ferguson, Allan, Roberts, Christopher J., Ulrich, Roger G.

“…Toxicogenomics is an emerging field combining genomics and bioinformatics to identify and characterize mechanisms of toxicity of compounds. One of the main…”
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Optimal estimation of acoustic intensity from pressure in the presence of mean flow by Strait, Stewart, Stoughton, Roland

“…Bayesian minimum mean-squared error (MMSE) estimators are constructed for obtaining pressure, velocity, and intensity in the near- or far-field of an extended…”
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