ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome. - Yan Kou; Edward Y. Chen; Neil R. Clark; Qiaonan Duan; Christopher M. Tan; Avi Ma'ayan (CD-ARES, 2013)

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. - Edward Y. Chen; Christopher M. Tan; Yan Kou; Qiaonan Duan; Zichen Wang 002; Gabriela Vaz Meirelles; Neil R. Clark; Avi Ma'ayan (BMC Bioinform., 2013)

Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. - Qiaonan Duan; Zichen Wang 002; Nicolas F. Fernandez; Andrew D. Rouillard; Christopher M. Tan; Cyril H. Benes; Avi Ma'ayan (Bioinform., 2014)

The characteristic direction: a geometrical approach to identify differentially expressed genes. - Neil R. Clark; Kevin S. Hu; Axel S. Feldmann; Yan Kou; Edward Y. Chen; Qiaonan Duan; Avi Ma'ayan (BMC Bioinform., 2014)

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. - Qiaonan Duan; Corey Flynn; Mario Niepel; Marc Hafner; Jeremy Muhlich; Nicolas F. Fernandez; Andrew D. Rouillard; Christopher M. Tan; Edward Y. Chen; Todd R. Golub; Peter K. Sorger; Aravind Subramanian; et al. (Nucleic Acids Res., 2014)

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. - Maxim V. Kuleshov; Matthew R. Jones; Andrew D. Rouillard; Nicolas F. Fernandez; Qiaonan Duan; Zichen Wang 002; Simon Koplev; Sherry L. Jenkins; Kathleen M. Jagodnik; Alexander Lachmann; Michael G. McDermott; Caroline D. Monteiro; et al. (Nucleic Acids Res., 2016)

Cell-specific prediction and application of drug-induced gene expression . - Rachel Hodos; Ping Zhang 016; Hao-Chih Lee; Qiaonan Duan; Zichen Wang 002; Neil R. Clark; Avi Ma'ayan; Fei Wang 001; Brian A. Kidd; Jianying Hu; David A. Sontag; Joel Dudley (PSB, 2018)

Accelerating Drug Discovery in Rare and Complex Diseases. - Shima Dastgheib; Craig Webb; Qiaonan Duan; Rowan Copley; Gini Deshpande; Asim Siddiqui (ISWC (P&D/Industry/BlueSky), 2018)

Comut-viz: efficiently creating and browsing comutation plots online. - Qiaonan Duan; Weiyi Wang; Feiling Feng; Xiaoqing Jiang; Hao Chen; Dadong Zhang; Tongyi Zhang (BMC Bioinform., 2023)