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
Bmc Bioinformatics, Zhenqiang Su, Huixiao Hong, Hong Fang, Leming Shi, Roger Perkins, ...
Proceedings Very Important Pool (VIP) genes – an application for microarray-based molecular signatures
ebTrack: an environmental bioinformatics system built upon ArrayTrack™ (2009)
Chen, Minjun, Martin, Jackson, Fang, Hong, Isukapalli, Sastry, Georgopoulos, Panos G, Welsh, William J, ...
Abstract ebTrack is being developed as an integrated bioinformatics system for environmental research and analysis by addressing the issues of integration, curation, management, first level analysis...
Fan, Xiaohui, Shi, Leming, Fang, Hong, Harris, Stephen, Perkins, Roger, Tong, Weida
Abstract Recent publications have raised concerns about the reliability of microarray technology because of the lack of reproducibility of differentially expressed genes (DEGs) from highly similar...
Bushel, Pierre R, Nielsen, Dahlia, Tong, Weida
Abstract The First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007) was held at the North Carolina State University McKimmon Center in Raleigh, North...
Joseph R. Votano, Marc Parham, Lowell H. Hall, Lemont B. Kier, Scott Oloff, Er Tropsha, ...
Three new consensus QSAR models for the prediction of Ames
Toxicogenomics and Cell-based Assays for Toxicology (2009)
Weida Tong, Hong Fang, Donna Mendrick
Toxicity is usually investigated using a set of standardized animal-based studies which, unfortunately, fail to detect all compounds that induce human adverse events and do not provide detailed...
Weida Tong, Qian Xie, Huixiao Hong, Hong Fang, Leming Shi, Roger Perkins, ...
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...
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...
cytotoxicity for identification of biomarkers (2008)
Yongxi Tan, Leming Shi, Saber M. Hussain, Jun Xu, Weida Tong, John M, ...
Integrating time-course microarray gene expression profiles with
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...
Huixiao Hong, Candee Teitel, Laura P. James, Weida Tong, Jack A. Hinson, Et Al.
Drug induced toxicities account for nearly half of the cases of acute liver failure in adults over age 50 in the US. Acetaminophen (APAP) is a commonly used non-prescription drug that can be...
Toward a Checklist for Exchange and Interpretation of Data from a Toxicology Study (2007)
Fostel, Jennifer M., Burgoon, Lyle, Zwickl, Craig, Lord, Peter, Corton, J. Christopher, Bushel, Pierre R., ...
Data from toxicology and toxicogenomics studies are valuable, and can be combined for meta-analysis using public data repositories such as Chemical Effects in Biological Systems Knowledgebase,...
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...
Tan, Yongxi, Shi, Leming, Hussain, Saber M., Xu, Jun, Tong, Weida, Frazier, John M., ...
Motivation: DNA microarrays can provide information about the expression levels of thousands of genes simultaneously at the transcriptomic level, while conventional cell viability and cytotoxicity...
Bmc Bioinformatics, Hongmei Sun, Hong Fang, Tao Chen, Roger Perkins, Weida Tong, ...
© 2006 Sun et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Lei Guo, Hong Fang, Jim Collins, Xiao-hui Fan, Stacey Dial, ...
Proceedings Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor α agonists
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)...
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...
Fostel, Jennifer, Choi, Danielle, Zwickl, Craig, Morrison, Norman, Rashid, Asif, Hasan, Atif, ...
A critical component in the design of the Chemical Effects in Biological Systems (CEBS) Knowledgebase is a strategy to capture toxicogenomics study protocols and the toxicity endpoint data (clinical...
Fostel, Jennifer, Choi, Danielle, Zwickl, Craig, Morrison, Norman, Rashid, Asif, Hasan, Atif, ...
A critical component in the design of the Chemical Effects in Biological Systems (CEBS) Knowledgebase is a strategy to capture toxicogenomics study protocols and the toxicity endpoint data (clinical...
Tan, Yongxi, Shi, Leming, Hussain, Saber M., Xu, Jun, Tong, Weida, Frazier, John M., ...
Motivation: DNA microarrays can provide information about the expression levels of thousands of genes simultaneously at the transcriptomic level, while conventional cell viability and cytotoxicity...
Bmc Bioinformatics, Qian Xie, Luke D Ratnasinghe, Huixiao Hong, Roger Perkins, Zhong Tang, ...
<supplement> <title> <p>Second Annual MidSouth Computational Biology and Bioinformatics Society Conference. Bioinformatics: a systems approach</p> </title>...
Three new consensus QSAR models for the prediction of Ames genotoxicity (2004)
Votano, Joseph R., Parham, Marc, Hall, Lowell H., Kier, Lemont B., Oloff, Scott, Tropsha, Alexander, ...
Three QSAR methods, artificial neural net (ANN), k-nearest neighbors (kNN), and Decision Forest (DF), were applied to 3363 diverse compounds tested for their Ames genotoxicity. The ratio of mutagens...
Weida Tong, Xiaoxi Cao, Stephen Harris, Hongmei Sun, Hong Fang, James Fuscoe, ...
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...
Blair, Robert M., Fang, Hong, Branham, William S., Hass, Bruce S., Dial, Stacey L., Moland, Carrie L., ...
We have utilized a validated (standardized) estrogen receptor (ER) competitive-binding assay to determine the ER affinity for a large, structurally diverse group of chemicals. Uteri from...
Government of the United States; the Large Scale Networking Working (1998)
Leming M. Shi, Hong Fang, Weida Tong, Jie Wu, Roger Perkins, Robert M. Blair, ...
Endocrine disruptors (EDs) have a variety of adverse effects in humans and animals. About 58 000 chemicals, most having little safety data, must be tested in a group of tiered assays. As assays will...
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
Shi, Leming, Jones, Wendell D, Jensen, Roderick V, Harris, Stephen C, Perkins, Roger G, Goodsaid, Federico M, ...
Bushel, Pierre R, Nielsen, Dahlia, Tong, Weida
The First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007) was held at the North Carolina State University McKimmon Center in Raleigh, North Carolina on...
Fan, Xiaohui, Shi, Leming, Fang, Hong, Harris, Stephen, Perkins, Roger, Tong, Weida
Recent publications have raised concerns about the reliability of microarray technology because of the lack of reproducibility of differentially expressed genes (DEGs) from highly similar studies...
ebTrack: an environmental bioinformatics system built upon ArrayTrack™
Chen, Minjun, Martin, Jackson, Fang, Hong, Isukapalli, Sastry, Georgopoulos, Panos G, Welsh, William J, ...
ebTrack is being developed as an integrated bioinformatics system for environmental research and analysis by addressing the issues of integration, curation, management, first level analysis and...