Analysis of variance components in gene expression data. - James J. Chen; Robert R. Delongchamp; Chen-An Tsai; Huey-miin Hsueh; Frank Sistare; Karol L. Thompson; Varsha G. Desai; James C. Fuscoe (Bioinform., 2004)

Sample Size for Identifying Differentially Expressed Genes in Microarray Experiments. - Sue-Jane Wang; James J. Chen (J. Comput. Biol., 2004)

Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates. - Dung-Tsa Chen; James J. Chen; Seng-jaw Soong (Bioinform., 2005)

Sample size for gene expression microarray experiments. - Chen-An Tsai; Sue-Jane Wang; Dung-Tsa Chen; James J. Chen (Bioinform., 2005)

Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential. - Leming M. Shi; Weida Tong; Hong Fang; Uwe Scherf; Jing Han 003; Raj K. Puri; Felix W. Frueh; Federico M. Goodsaid; Lei Guo 006; Zhenqiang Su; Tao Han 007; James C. Fuscoe; et al. (BMC Bioinform., 2005)

Microarray scanner calibration curves: characteristics and implications. - Leming M. Shi; Weida Tong; Zhenqiang Su; Tao Han 007; Jing Han 003; Raj K. Puri; Hong Fang; Felix W. Frueh; Federico M. Goodsaid; Lei Guo 006; William S. Branham; James J. Chen; et al. (BMC Bioinform., 2005)

Regression trees for analysis of count data with extra Poisson variation. - Yunhee Choi; Hongshik Ahn; James J. Chen (Comput. Stat. Data Anal., 2005)

Ensemble methods for classification of patients for personalized medicine with high-dimensional data. - Hojin Moon; Hongshik Ahn; Ralph L. Kodell; Songjoon Baek; Chien-Ju Lin; James J. Chen (Artif. Intell. Medicine, 2007)

Significance analysis of groups of genes in expression profiling studies. - James J. Chen; Taewon Lee; Robert R. Delongchamp; Tao Chen; Chen-An Tsai (Bioinform., 2007)

Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data. - James J. Chen; Huey-miin Hsueh; Robert R. Delongchamp; Chien-Ju Lin; Chen-An Tsai (BMC Bioinform., 2007)

Gene selection with multiple ordering criteria. - James J. Chen; Chen-An Tsai; ShengLi Tzeng; Chun-Houh Chen (BMC Bioinform., 2007)

Classification by ensembles from random partitions of high-dimensional data. - Hongshik Ahn; Hojin Moon; Melissa J. Fazzari; Noha Lim; James J. Chen; Ralph L. Kodell (Comput. Stat. Data Anal., 2007)

Kernel estimation for adjusted p. - Chen-An Tsai; James J. Chen (Comput. Stat. Data Anal., 2007)

Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples. - Huixiao Hong; Zhenqiang Su; Weigong Ge; Leming M. Shi; Roger Perkins; Hong Fang; Joshua Xu; James J. Chen; Tao Han 007; Jim Kaput; James C. Fuscoe; Weida Tong (BMC Bioinform., 2008)

A model-free ensemble method for class prediction with application to biomedical decision making. - Ralph L. Kodell; Bruce A. Pearce; Songjoon Baek; Hojin Moon; Hongshik Ahn; John F. Young; James J. Chen (Artif. Intell. Medicine, 2009)

Development of biomarker classifiers from high-dimensional data. - Songjoon Baek; Chen-An Tsai; James J. Chen (Briefings Bioinform., 2009)

Multivariate analysis of variance test for gene set analysis. - Chen-An Tsai; James J. Chen (Bioinform., 2009)

An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays. - Hong Fang; Joshua Xu; Don Ding; Scott A. Jackson; Isha R. Patel; Jonathan G. Frye; Wen Zou; Rajesh Nayak; Steven L. Foley; James J. Chen; Zhenqiang Su; Yanbin Ye; et al. (BMC Bioinform., 2010)

Power and sample size estimation in microarray studies. - Wei-Jiun Lin; Huey-miin Hsueh; James J. Chen (BMC Bioinform., 2010)

Class-imbalanced classifiers for high-dimensional data. - Wei-Jiun Lin; James J. Chen (Briefings Bioinform., 2013)

Identification of reproducible gene expression signatures in lung adenocarcinoma. - Tzu-Pin Lu; Eric Y. Chuang; James J. Chen (BMC Bioinform., 2013)

Data mining tools for Salmonella characterization: application to gel-based fingerprinting analysis. - Wen Zou; Hailin Tang; Weizhong Zhao; Joe Meehan; Steven L. Foley; Wei-Jiun Lin; Hung-Chia Chen; Hong Fang; Rajesh Nayak; James J. Chen (BMC Bioinform., 2013)

Topic modeling for cluster analysis of large biological and medical datasets. - Weizhong Zhao; Wen Zou; James J. Chen (BMC Bioinform., 2014)

A heuristic approach to determine an appropriate number of topics in topic modeling. - Weizhong Zhao; James J. Chen; Roger Perkins; Zhichao Liu; Weigong Ge; Yijun Ding; Wen Zou (BMC Bioinform., 2015)

A novel procedure on next generation sequencing data analysis using text mining algorithm. - Weizhong Zhao; James J. Chen; Roger Perkins; Yuping Wang; Zhichao Liu; Huixiao Hong; Weida Tong; Wen Zou (BMC Bioinform., 2016)

Erratum to: A novel procedure on next generation sequencing data analysis using text mining algorithm. - Weizhong Zhao; James J. Chen; Roger Perkins; Yuping Wang; Zhichao Liu; Huixiao Hong; Weida Tong; Wen Zou (BMC Bioinform., 2016)

Use of data mining at the Food and Drug Administration. - Hesha J. Duggirala; Joseph M. Tonning; Ella Smith; Roselie A. Bright; John D. Baker; Robert Ball; Carlos Bell; Susan J. Bright-Ponte; Taxiarchis Botsis; Khaled Bouri; Marc Boyer; Keith Burkhart; et al. (J. Am. Medical Informatics Assoc., 2016)

Best Setting of Model Parameters in Applying Topic Modeling on Textual Documents. - Wen Zou; Weizhong Zhao; James J. Chen; Roger Perkins (BCB, 2017)

Discovering Drug-Drug Associations in the FDA Adverse Event Reporting System Database with Data Mining Approaches. - Weizhong Zhao; Huyen Le; James J. Chen; Hesha J. Duggirala; Richard Forshee; Taxiarchis Botsis; Henry Francis; Huixiao Hong; Weida Tong; Yi-Ting Hwang; Wen Zou (BIBM, 2021)