Logical transformation of genome-scale metabolic models for gene level applications and analysis. - Cheng Zhang 002; Boyang Ji; Adil Mardinoglu; Jens Nielsen; Qiang Hua (Bioinform., 2015)

In silico identification of gene amplification targets based on analysis of production and growth coupling. - Xingxing Jian; Shengguo Zhou; Cheng Zhang 002; Qiang Hua (Biosyst., 2016)

IdealKnock: A framework for efficiently identifying knockout strategies leading to targeted overproduction. - Deqing Gu; Cheng Zhang 002; Shengguo Zhou; Liujing Wei; Qiang Hua (Comput. Biol. Chem., 2016)

Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data. - Deqing Gu; Xingxing Jian; Cheng Zhang 002; Qiang Hua (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

TCSBN: a database of tissue and cancer specific biological networks. - Sunjae Lee; Cheng Zhang 002; Muhammad Arif 007; Zhengtao Liu; Rui Benfeitas; Gholamreza Bidkhori; Sumit Deshmukh; Mohamed Al Shobky; Alen Lovric; Jan Boren; Jens Nielsen; Mathias Uhlen; et al. (Nucleic Acids Res., 2018)

iNetModels 2.0: an interactive visualization and database of multi-omics data. - Muhammad Arif 007; Cheng Zhang 002; Xiangyu Li; Cem Güngör; Bugra Çakmak; Metin Arslantürk; Abdellah Tebani; Berkay Özcan; Oguzhan Subas; Wenyu Zhou; Brian Piening; Hasan Turkez; et al. (Nucleic Acids Res., 2021)

Open MoA: revealing the mechanism of action (MoA) based on network topology and hierarchy. - Xinmeng Liao; Mehmet Ozcan; Mengnan Shi; Woonghee Kim; Han Jin; Xiangyu Li; Hasan Turkez; Adnane Achour; Mathias Uhlén; Adil Mardinoglu; Cheng Zhang 002 (Bioinform., 2023)