MAPS: a microarray project system for gene expression experiment information and data validation. - Pierre R. Bushel; Hisham Hamadeh; Lee Bennett; Stella Sieber; Karla Martin; Emile F. Nuwaysir; Kate Johnson; Kelli Reynolds; Richard S. Paules; Cynthia A. Afshari (Bioinform., 2001)

Assessing Gene Significance from cDNA Microarray Expression Data via Mixed Models. - Russell D. Wolfinger; Greg Gibson; Elizabeth D. Wolfinger; Lee Bennett; Hisham Hamadeh; Pierre R. Bushel; Cynthia A. Afshari; Richard S. Paules (J. Comput. Biol., 2001)

Computational selection of distinct class- and subclass-specific gene expression signatures. - Pierre R. Bushel; Hisham Hamadeh; Lee Bennett; James Green; Alan Ableson; Stephen Misener; Cynthia A. Afshari; Richard S. Paules (J. Biomed. Informatics, 2002)

Systematic Variation Normalization in Microarray Data to Get Gene Expression Comparison Unbiased. - Jeff W. Chou; Richard S. Paules; Pierre R. Bushel (J. Bioinform. Comput. Biol., 2005)

PAGE: phase-shifted analysis of gene expression. - Elo Leung; Pierre R. Bushel (Bioinform., 2006)

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application. - Sandhya Xirasagar; Scott F. Gustafson; Cheng-Cheng Huang; Qinyan Pan; Jennifer Fostel; Paul Boyer; B. Alex Merrick; Kenneth B. Tomer; Denny D. Chan; Kenneth J. Yost III; Danielle Choi; Nianqing Xiao; et al. (Bioinform., 2006)

Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes. - Jeff W. Chou; Tong Zhou; William K. Kaufmann; Richard S. Paules; Pierre R. Bushel (BMC Bioinform., 2007)

Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes. - Pierre R. Bushel; Russell D. Wolfinger; Greg Gibson (BMC Syst. Biol., 2007)

CEBS - Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. - Michael D. Waters; Stanley Stasiewicz; B. Alex Merrick; Kenneth B. Tomer; Pierre R. Bushel; Richard S. Paules; Nancy Stegman; Gerald Nehls; Kenneth J. Yost III; C. Harris Johnson; Scott F. Gustafson; Sandhya Xirasagar; et al. (Nucleic Acids Res., 2008)

Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle. - Pierre R. Bushel; Nicholas A. Heard; Roee Gutman; Liwen Liu; Shyamal D. Peddada; Saumyadipta Pyne (BMC Syst. Biol., 2009)

Clustering of Gene Expression Data and End-Point Measurements by Simulated Annealing. - Pierre R. Bushel (J. Bioinform. Comput. Biol., 2009)

Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes. - ClarLynda R. Williams-DeVane; David M. Reif; Elaine Cohen Hubal; Pierre R. Bushel; Edward E. Hudgens; Jane E. Gallagher; Stephen W. Edwards (BMC Syst. Biol., 2013)

goSTAG: gene ontology subtrees to tag and annotate genes within a set. - Brian D. Bennett; Pierre R. Bushel (Source Code Biol. Medicine, 2017)