30 Result(s)

Article

Microarray scanner calibration curves: characteristics and implications

Microarray-based measurement of mRNA abundance assumes a linear relationship between the fluorescence intensity and the dye concentration. In reality, however, the calibration curve can be nonlinear.

Leming Shi, Weida Tong, Zhenqiang Su, Tao Han, **g Han, Raj K Puri… in BMC Bioinformatics (2005)

Article

A microarray study of MPP⁺-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools

This paper describes a microarray study including data quality control, data analysis and the analysis of the mechanism of toxicity (MOT) induced by 1-methyl-4-phenylpyridinium (MPP⁺) in a rat adrenal pheochromoc...

Zengjun Xu, Tucker A Patterson, Jonathan D Wren, Tao Han, Leming Shi… in BMC Bioinformatics (2005)

Article

Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential

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. Marshall, Science, 306, 630–631, 2004...

Leming Shi, Weida Tong, Hong Fang, Uwe Scherf, **g Han, Raj K Puri… in BMC Bioinformatics (2005)

Article

Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions

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 drugs and toxins. This is leading ...

Tao Han, Cathy D Melvin, Leming Shi, William S Branham… in BMC Bioinformatics (2006)

Article

Microarray analysis distinguishes differential gene expression patterns from large and small colony Thymidine kinase mutants of L5178Y mouse lymphoma cells

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 colonies grow at a normal rate while cell...

Tao Han, Jianyong Wang, Weida Tong, Martha M Moore, James C Fuscoe… in BMC Bioinformatics (2006)

Article

Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Map** 500 K array set using 270 HapMap samples

Genome-wide association studies (GWAS) aim to identify genetic variants (usually single nucleotide polymorphisms [SNPs]) across the entire human genome that are associated with phenotypic traits such as diseas...

Huixiao Hong, Zhenqiang Su, Weigong Ge, Leming Shi, Roger Perkins… in BMC Bioinformatics (2008)

Article

Characterization of whole genome amplified (WGA) DNA for use in genoty** assay development

Genoty** assays often require substantial amounts of DNA. To overcome the problem of limiting amounts of available DNA, Whole Genome Amplification (WGA) methods have been developed. The multiple displacement...

Tao Han, Ching-Wei Chang, Joshua C Kwekel, Ying Chen, Yun Ge… in BMC Genomics (2012)

Article

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

Realizing personalized medicine requires integrating diverse data types with bioinformatics. The most vital data are genomic information for individuals that are from advanced next-generation sequencing (NGS) ...

Hui**ao Hong, WenQian Zhang, Jie Shen, ZhenQiang Su… in Science China Life Sciences (2013)

Article

Erratum to: Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

Hui**ao Hong, WenQian Zhang, Jie Shen, ZhenQiang Su… in Science China Life Sciences (2013)

Article

Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice

Nonalcoholic fatty liver disease (NAFLD) is a major health problem and a leading cause of chronic liver disease in the United States and Western countries. In humans, genetic factors greatly influence individu...

Volodymyr P. Tryndyak, Tao Han, James C. Fuscoe, Sharon A. Ross… in BMC Genomics (2016)

Article

Pioglitazone prevents cholesterol gallstone formation through the regulation of cholesterol homeostasis in guinea pigs with a lithogenic diet

The cholesterol gallstones diseases (CGD) is highly correlated with metabolic syndrome and type 2 diabetes. The present study aimed to investigate preventive effects of pioglitazone (PIO), an antidiabetic drug...

Tao Han, Yangge Lv, Shijia Wang, Tao Hu, Hao Hong, Zan Fu in Lipids in Health and Disease (2019)

Article

Silencing lncRNA Lfar1 alleviates the classical activation and pyoptosis of macrophage in hepatic fibrosis

Hepatic fibrosis is a common pathological consequence of a sustained wound healing response to continuous liver injury, characterized by increased production and accumulation of extracellular matrix. If unreso...

Kun Zhang, Zhemin Shi, Mengxia Zhang, Xueyi Dong, Lina Zheng… in Cell Death & Disease (2020)

Article

Transcriptional factor ATF3 promotes liver fibrosis via activating hepatic stellate cells

The excessive accumulation of extracellular matrix (ECM) is a key feature of liver fibrosis and the activated hepatic stellate cells (HSCs) are the major producer of ECM proteins. However, the precise mechanis...

Zhemin Shi, Kun Zhang, Ting Chen, Yu Zhang, **aoxiao Du… in Cell Death & Disease (2020)

Article

XDeathDB: a visualization platform for cell death molecular interactions

Lots of cell death initiator and effector molecules, signalling pathways and subcellular sites have been identified as key mediators in both cell death processes in cancer. The XDeathDB visualization platform ...

Venkat Sundar Gadepalli, Hangil Kim, Yueze Liu, Tao Han… in Cell Death & Disease (2021)