Bmc Bioinformatics, Tao Han, Jianyong Wang, Weida Tong, Martha M Moore, James C Fuscoe, ...
Proceedings Microarray analysis distinguishes differential gene expression patterns from large and small colony Thymidine kinase mutants of L5178Y mouse lymphoma cells
Hong, Huixiao, Su, Zhenqiang, Ge, Weigong, Shi, Leming, Perkins, Roger, Fang, Hong, ...
Abstract Background Genome-wide association studies (GWAS) aim to identify genetic variants (usually single nucleotide polymorphisms [SNPs]) across the entire human genome that are associated with...
Shi, Leming, Jones, Wendell D, Jensen, Roderick V, Harris, Stephen C, Perkins, Roger G, Goodsaid, Federico M, ...
Abstract Background Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially...
Wren, Jonathan D, Wilkins, Dawn, Fuscoe, James C, Bridges, Susan, Winters-Hilt, Stephen, Gusev, Yuriy
Bmc Bioinformatics, Tao Han, Cathy D Melvin, Leming Shi, William S Branham, Carrie L Mol, ...
© 2006 Han et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License
Designing Toxicogenomics Studies that use DNA Array Technology (2008)
Robert R. Delongchamp, Cruz Velasco, Varsha G. Desai, Taewon Lee, James C. Fuscoe
Background: Bioassays are routinely used to evaluate the toxicity of test agents. Experimental designs for bioassays are largely encompassed by fixed effects linear models. In toxicogenomics studies...
Mei, Nan, Guo, Lei, Liu, Ruqing, Fuscoe, James C, Chen, Tao
Abstract Background Pyrrolizidine alkaloids (PAs) are probably the most common plant constituents that poison livestock, wildlife, and humans worldwide. Riddelliine is isolated from plants grown in...
The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies (2007)
Leming D. Shi, Wendell D. Jones, Roderick V. Jensen, Stephen C. Harris, Roger G. Perkins, Federico M. Goodsaid, ...
Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent...
The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies (2007)
Leming Shi, Wendell D. Jones, Roderick V. Jensen, Stephen C. Harris, Roger G. Perkins, Federico M. Goodsaid, ...
Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent...
Branham, William S, Melvin, Cathy D, Han, Tao, Desai, Varsha G, Moland, Carrie L, Scully, Adam T, ...
Abstract Background Environmental ozone can rapidly degrade cyanine 5 (Cy5), a fluorescent dye commonly used in microarray gene expression studies. Cyanine 3 (Cy3) is much less affected by...
BMC Biotechnology BioMed Central Methodology article (2007)
William S Branham, Cathy D Melvin, Tao Han, Varsha G Desai, Carrie L Mol, ...
Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements
Mei, Nan, Guo, Lei, Zhang, Lu, Shi, Leming, Sun, Yongming, Fung, Chris, ...
Abstract Background Comfrey is consumed by humans as a vegetable and a tea, and has been used as an herbal medicine for more than 2000 years. Comfrey, however, is hepatotoxic in livestock and humans...
Han, Tao, Melvin, Cathy D, Shi, Leming, Branham, William S, Moland, Carrie L, Pine, P Scott, ...
Abstract Background DNA microarrays, which have been increasingly used to monitor mRNA transcripts at a global level, can provide detailed insight into cellular processes involved in response to...
Chen, Tao, Guo, Lei, Zhang, Lu, Shi, Leming, Fang, Hong, Sun, Yongming, ...
Abstract Background Aristolochic acid (AA) is the active component of herbal drugs derived from Aristolochia species that have been used for medicinal purposes since antiquity. AA, however, induced...
Han, Tao, Wang, Jianyong, Tong, Weida, Moore, Martha M, Fuscoe, James C, Chen, Tao
Abstract Background The Thymidine kinase ( Tk ) mutants generated from the widely used L5178Y mouse lymphoma assay fall into two categories, small colony and large colony. Cells from the large...
Microarray scanner calibration curves: characteristics and implications (2005)
Shi, Leming, Tong, Weida, Su, Zhenqiang, Han, Tao, Han, Jing, Puri, Raj K, ...
Abstract Background Microarray-based measurement of mRNA abundance assumes a linear relationship between the fluorescence intensity and the dye concentration. In reality, however, the calibration...
Shi, Leming, Tong, Weida, Fang, Hong, Scherf, Uwe, Han, Jing, Puri, Raj K, ...
Abstract Background The acceptance of microarray technology in regulatory decision-making is being challenged by the existence of various platforms and data analysis methods. A recent report (E....
Use of a mixed tissue RNA design for performance assessments on multiple microarray formats (2005)
Karol L. Thompson, Barry A. Rosenzweig, P. Scott Pine, Jacques Retief, Yaron Turpaz, Cynthia A. Afshari, ...
The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range...
Use of a mixed tissue RNA design for performance assessments on multiple microarray formats (2005)
Thompson, Karol L., Rosenzweig, Barry A., Pine, P. Scott, Retief, Jacques, Turpaz, Yaron, Afshari, Cynthia A., ...
The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range...
Analysis of variance components in gene expression data (2004)
Chen, James J., Delongchamp, Robert R., Tsai, Chen-An, Hsueh, Huey-miin, Sistare, Frank, Thompson, Karol L., ...
Motivation: A microarray experiment is a multi-step process and each step is a potential source of variation. There are two major sources of variation: biological variation and technical variation....
Analysis of variance components in gene expression data (2004)
Chen, James J., Delongchamp, Robert R., Tsai, Chen-An, Hsueh, Huey-miin, Sistare, Frank, Thompson, Karol L., ...
Motivation: A microarray experiment is a multi-step process, and each step is a potential source of variation. There are two major sources of variation: biological variation and technical variation....
Analysis of variance components in gene expression data (2004)
Chen, James J., Delongchamp, Robert R., Tsai, Chen-An, Hsueh, Huey-miin, Sistare, Frank, Thompson, Karol L., ...
Motivation: A microarray experiment is a multi-step process and each step is a potential source of variation. There are two major sources of variation: biological variation and technical variation....
Thai, Sheau-Fung, Allen, James W., DeAngelo, Anthony B., George, Michael H., Fuscoe, James C.
Dichloroacetic acid (DCA) is a major by-product of water disinfection by chlorination. Several studies have demonstrated the hepatocarcinogenicity of DCA in mice when administered in drinking water....
Chen, Chun-Lin, Fuscoe, James C., Liu, Qing, Pui, Ching-Hon, Mahmoud, Hazem H., Relling, Mary V.
Background Etoposide, an inhibitor of the normal religation activity of the nuclear enzyme topoisomerase II, can induce a secondary acute myeloid leukemia characterized by site-specific DNA...
Fuscoe, James C., Setzer, R.Woodrow, Collard, Deborah D., Moore, Martha M.
A t(14; 18) chromosomal translocation is found in ∼85% of follicular lymphomas by both cytogenetic and molecular analyses. This rearrangement deregulates expression of the bcl-2 proto-oncogene by...
Fuscoe, James C., Zimmerman, Lisa J., Harrington-Brock, Karen, Moore, Martha M.
The DNA sequence of 11 in vivo-arising intragenic deletion junctions occurring in the hypoxanthine-guanine phospho-ribosyltransferase (hprt) gene of human T-lymphocytes was determined. These...
Konecki, David S., Brennand, John, Fuscoe, James C., Caskey, C.Thomas, Chinault, A.Craig
Recombinant plasmids containing DNA inserts complementary to mRNA coding for hypoxanthine–guanine phosphoribosyltransferase (HPRT) from mouse and Chinese hamster cell lines have been isolated from...
Use of a mixed tissue RNA design for performance assessments on multiple microarray formats
Thompson, Karol L., Rosenzweig, Barry A., Pine, P. Scott, Retief, Jacques, Turpaz, Yaron, Afshari, Cynthia A., ...
The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range...
Microarray scanner calibration curves: characteristics and implications
Shi, Leming, Tong, Weida, Su, Zhenqiang, Han, Tao, Han, Jing, Puri, Raj K, ...
Chen, Tao, Guo, Lei, Zhang, Lu, Shi, Leming, Fang, Hong, Sun, Yongming, ...
Use of a mixed tissue RNA design for performance assessments on multiple microarray formats
Thompson, Karol L., Rosenzweig, Barry A., Pine, P. Scott, Retief, Jacques, Turpaz, Yaron, Afshari, Cynthia A., ...
The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range...
Microarray scanner calibration curves: characteristics and implications
Shi, Leming, Tong, Weida, Su, Zhenqiang, Han, Tao, Han, Jing, Puri, Raj K, ...
Chen, Tao, Guo, Lei, Zhang, Lu, Shi, Leming, Fang, Hong, Sun, Yongming, ...
Branham, William S, Melvin, Cathy D, Han, Tao, Desai, Varsha G, Moland, Carrie L, Scully, Adam T, ...
Wren, Jonathan D, Wilkins, Dawn, Fuscoe, James C, Bridges, Susan, Winters-Hilt, Stephen, Gusev, Yuriy
Shi, Leming, Jones, Wendell D, Jensen, Roderick V, Harris, Stephen C, Perkins, Roger G, Goodsaid, Federico M, ...