A statistical framework for the design of microarray experiments and effective detection of differential gene expression. - Shu-Dong Zhang; Timothy W. Gant (Bioinform., 2004)

Effect of pooling samples on the efficiency of comparative studies using microarrays. - Shu-Dong Zhang; Timothy W. Gant (Bioinform., 2005)

A simple and robust method for connecting small-molecule drugs using gene-expression signatures. - Shu-Dong Zhang; Timothy W. Gant (BMC Bioinform., 2008)

sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures. - Shu-Dong Zhang; Timothy W. Gant (BMC Bioinform., 2009)

cudaMap: a GPU accelerated program for gene expression connectivity mapping. - Darragh G. McArt; Peter Bankhead; Philip D. Dunne; Manuel Salto-Tellez; Peter Hamilton; Shu-Dong Zhang (BMC Bioinform., 2013)

RMA with quantile normalization mixes biological signals between different sample groups in microarray data analysis. - Chang Sik Kim; Seungwoo Hwang; Shu-Dong Zhang (BIBM, 2014)

Integrative analysis of chemo-transcriptomic profiles for drug-feature specific gene expression signatures. - Chang Sik Kim; Qing Wen; Shu-Dong Zhang (BIBM, 2014)

QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics. - Paul G. O'Reilly; Qing Wen; Peter Bankhead; Philip D. Dunne; Darragh G. McArt; Suzanne McPherson; Peter Hamilton; Ken I. Mills; Shu-Dong Zhang (BMC Bioinform., 2016)

A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping. - Qing Wen; Chang Sik Kim; Peter Hamilton; Shu-Dong Zhang (BMC Bioinform., 2016)

A review of connectivity map and computational approaches in pharmacogenomics. - Aliyu Musa; Laleh Soltan Ghoraie; Shu-Dong Zhang; Galina V. Glazko; Olli Yli-Harja; Matthias Dehmer; Benjamin Haibe-Kains; Frank Emmert-Streib (Briefings Bioinform., 2017)

An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping. - Gayathri Thillaiyampalam; Fabio Liberante; Liam Murray; Chris Cardwell; Ken I. Mills; Shu-Dong Zhang (BMC Bioinform., 2017)