Very Important Pool (VIP) genes – an application for microarray-based molecular signatures (2008)
Su, Zhenqiang, Hong, Huixiao, Fang, Hong, Shi, Leming, Perkins, Roger, Tong, Weida
Abstract Background Advances in DNA microarray technology portend that molecular signatures from which microarray will eventually be used in clinical environments and personalized medicine....
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...
The First RSBI (ISA-TAB) Workshop: "Can a Simple Format Work for Complex Studies?" (2008)
Sansone, Susanna-Assunta, Rocca-Serra, Philippe, Brandizi, Marco, Brazma, Alvis, Field, Dawn, Fostel, Jennifer, ...
This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6–8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of...
Zhong Wang, Zhan-jun Zhang, Yi Wang, Yiyu Cheng, Weida Tong, Yongyan Wang
A major challenge in post-genomic research is to understand how physiological and pathological phenotypes arise from the networks of expressed genes and to develop powerful tools for translating the...
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...
Guo, Lei, Fang, Hong, Collins, Jim, Fan, Xiao-hui, Dial, Stacey, Wong, Alex, ...
Abstract Background Fibrates are a unique hypolipidemic drugs that lower plasma triglyceride and cholesterol levels through their action as peroxisome proliferator-activated receptor alpha (PPARα)...
Sun, Hongmei, Fang, Hong, Chen, Tao, Perkins, Roger, Tong, Weida
Abstract Background Gene Ontology (GO) characterizes and categorizes the functions of genes and their products according to biological processes, molecular functions and cellular components,...
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....
Xie, Qian, Ratnasinghe, Luke D, Hong, Huixiao, Perkins, Roger, Tang, Ze-Zhong, Hu, Nan, ...
Abstract Background Systematic evaluation and study of single nucleotide polymorphisms (SNPs) made possible by high throughput genotyping technologies and bioinformatics promises to provide...
Hong, Huixiao, Dragan, Yvonne, Epstein, Joshua, Teitel, Candee, Chen, Bangzheng, Xie, Qian, ...
Abstract Background Proteomic profiling of complex biological mixtures by the ProteinChip technology of surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS)...
QSAR Models Using a Large Diverse Set of Estrogens (2001)
Leming M. Shi, Hong Fang, Weida Tong, Jie Wu, Roger Perkins, Robert M. Blair, ...
this paper, these two techniques are further investigated and compared, particularly for their predictivity, by using the NCTR data set.
Tan, Yongxi, Shi, Leming, Tong, Weida, Wang, Charles
DNA microarray technology provides a promising approach to the diagnosis and prognosis of tumors on a genome-wide scale by monitoring the expression levels of thousands of genes simultaneously. One...
Hong, Huixiao, Tong, Weida, Fang, Hong, Shi, Leming, Xie, Qian, Wu, Jie, ...
A number of environmental chemicals, by mimicking natural hormones, can disrupt endocrine function in experimental animals, wildlife, and humans. These chemicals, called "endocrine-disrupting...
Tong, Weida, Cao, Xiaoxi, Harris, Stephen, Sun, Hongmei, Fang, Hong, Fuscoe, James, ...
The mapping of the human genome and the determination of corresponding gene functions, pathways, and biological mechanisms are driving the emergence of the new research fields of toxicogenomics and...
Tong, Weida, Xie, Qian, Hong, Huixiao, Fang, Hong, Shi, Leming, Perkins, Roger, ...
Class prediction using “omics” data is playing an increasing role in toxicogenomics, diagnosis/prognosis, and risk assessment. These data are usually noisy and represented by relatively few...
Tong, Weida, Xie, Qian, Hong, Huixiao, Shi, Leming, Fang, Hong, Perkins, Roger
Quantitative structure–activity relationship (QSAR) methods have been widely applied in drug discovery, lead optimization, toxicity prediction, and regulatory decisions. Despite major advances in...
Corvi, Raffaella, Ahr, Hans-Jürgen, Albertini, Silvio, Blakey, David H., Clerici, Libero, Coecke, Sandra, ...
This is the report of the first workshop “Validation of Toxicogenomics-Based Test Systems” held 11–12 December 2003 in Ispra, Italy. The workshop was hosted by the European Centre for the...
Microarray scanner calibration curves: characteristics and implications
Shi, Leming, Tong, Weida, Su, Zhenqiang, Han, Tao, Han, Jing, Puri, Raj K, ...
Tan, Yongxi, Shi, Leming, Tong, Weida, Wang, Charles
DNA microarray technology provides a promising approach to the diagnosis and prognosis of tumors on a genome-wide scale by monitoring the expression levels of thousands of genes simultaneously. One...
Hong, Huixiao, Tong, Weida, Fang, Hong, Shi, Leming, Xie, Qian, Wu, Jie, ...
A number of environmental chemicals, by mimicking natural hormones, can disrupt endocrine function in experimental animals, wildlife, and humans. These chemicals, called "endocrine-disrupting...
Tong, Weida, Cao, Xiaoxi, Harris, Stephen, Sun, Hongmei, Fang, Hong, Fuscoe, James, ...
The mapping of the human genome and the determination of corresponding gene functions, pathways, and biological mechanisms are driving the emergence of the new research fields of toxicogenomics and...
Tong, Weida, Xie, Qian, Hong, Huixiao, Fang, Hong, Shi, Leming, Perkins, Roger, ...
Class prediction using “omics” data is playing an increasing role in toxicogenomics, diagnosis/prognosis, and risk assessment. These data are usually noisy and represented by relatively few...
Tong, Weida, Xie, Qian, Hong, Huixiao, Shi, Leming, Fang, Hong, Perkins, Roger
Quantitative structure–activity relationship (QSAR) methods have been widely applied in drug discovery, lead optimization, toxicity prediction, and regulatory decisions. Despite major advances in...
Corvi, Raffaella, Ahr, Hans-Jürgen, Albertini, Silvio, Blakey, David H., Clerici, Libero, Coecke, Sandra, ...
This is the report of the first workshop “Validation of Toxicogenomics-Based Test Systems” held 11–12 December 2003 in Ispra, Italy. The workshop was hosted by the European Centre for the...
Microarray scanner calibration curves: characteristics and implications
Shi, Leming, Tong, Weida, Su, Zhenqiang, Han, Tao, Han, Jing, Puri, Raj K, ...
Very Important Pool (VIP) genes – an application for microarray-based molecular signatures
Su, Zhenqiang, Hong, Huixiao, Fang, Hong, Shi, Leming, Perkins, Roger, Tong, Weida