Lijun Cheng

Lijun Cheng, PhD

Assistant Research Professor of Medical & Molecular Genetics


Dr. Lijun Cheng works in the Center for Computational Biology and Bioinformatics (CCBB), Indiana University School of Medicine (IUSM). Dr. Cheng’s computational research expertise includes kernel based nonlinear methods, machine learning, and database development for big data. In particular, her computational research is in the scope of system pharmacology. Her research application includes cancer genomics, precision medicine, system pharmacology, and drug discovery. Her current research interest is to develop system pharmacology models to predict drug response for either single drug or drug combinations in both in vitro and clinical settings.

Center for Computational Biology and Bioinformatics Website:

Key Publications

Guanglong Jiang, Shijun Zhang, Aida Yazdanparast, Meng Li, Aniruddha Vikram Pawar, Yunlong Liu, Sai Mounika Inavolu, and Lijun Cheng*. Comprehensive comparison of molecular portraits between cell lines and tumor in breast cancer, BMC Genomics, 2016, (in press).

Lijun Cheng, Bryan P. Schneider and Lang Li. A bioinformatics approach for the precision medicine off-label drug usage among triple negative breast cancer patients, Journal of the American Medical Informatics Association, 2016, pii: ocw004. (PMID: 27107440)

Lijun Cheng, Guanglong Jiang, Ao Zhou, Lang Li. Challenges and strategies for differential transcriptome analysis from microarray to deep sequencing in statistics, Annals of Biometrics & Biostatistics, 2015, 2(1): 1014.

Yongsheng Ding, Lijun Cheng, Witold Pedrycz, and Kuangrong Hao, Global nonlinear kernel prediction for large dataset with a particle swarm optimized interval support vector regression, IEEE Transaction on neural network and learning systems, 2015, 26(10), 2521-2534. (PMID: 25974954)

Chirayu Pankaj Goswami, Lijun Cheng, Phillip Scott Alexander, Aditya Singal, Lang Li, A new drug combinatory effect prediction algorithm on the cancer cell based on gene expression and dose responsive curve, CPT: Pharmacometrics & Systems Pharmacology, 2015 Feb, 4(2: e9.(PMID: PMC4360667)

Lei Du, A. Chakraborty, Penyue Zhang, Wei Chiang, Lijun Cheng, Sara Kay Quinney, Lang Li, Li Shen. Graphic mining of high-order drug interactions and their directional effects on myopathy using electronic medical records,Pharmacometrics & Systems Pharmacology, 2015; 4(8): 481-82.(PMID: 26380157)

Penyue Zhang, Lei Du, Lei Wang, Meng Liu, Lijun Cheng, Wei Hsin Chiang, Huanmei Wu, Sara Kay Quinney, Li Shen, Lang Li. A mixture dose-response model for identifying high-dimensional drug interaction effects on myopathy using electronic medical record databases,Pharmacometrics & Systems Pharmacology, 2015; 4(8): 474-80.(PMID: 26380156)

Yongsheng Ding, Yifan Hu, Kuangrong Hao, Lijun Cheng. An intelligent routing recovery scheme for heterogeneous wireless sensor networks,Information Sciences, Volume 308, 2015; 49-60.(SCI)

Lijun Cheng, K. Khorasani, Yongsheng Ding and Xihong Guo. Gene interaction networks based on kernel correlation metrics, Int. J. Computational Biology and Drug Design2013,6(1-2):72-92. (SCI: PREV201300364952, PMID: 23428475)

Rongfang Li, Lijun Cheng, Yongsheng Ding, Yunxiang Chen and Wei Wang, An operational drought risk management framework based on stream-flow intelligent internet control, Journal of Risk Analysis and Crisis Response,2013,3(1):34-43.

Lijun Cheng, Yongsheng Ding, Kuangrong Hao, Yifan Hu, An ensemble kernel classifier with immune clonal selection algorithm for automatic discriminant of primary open-angle glaucoma, Neurocomputing, 2012, 83(15): 1-11.(SCI: 000301613800001, EI: 20120614753592)

Yongsheng Ding, Yizhen Shen, Lihong Ren, and Lijun Cheng, Dynamic and collective analysis of membrane protein interaction network based on gene regulatory network model, Neurocomputing, 2012, 98(3): 151-158. SCI: 000310864900016, EI: 20124115555972)

Yongsheng Ding, Yizhen Shen, Lijun Cheng, and Jinjin Xu, Study on Membrane Protein Interaction Networks by Constructing Gene Regulatory Network Model, Life System Modeling and Intelligent Computing, Communications in Computer and Information Science, 2010, Vol. 98, Part 5, 244-252. EI: 20104513368907)

Lijun Cheng, Yongsheng Ding, K. Khorasani, Rongfang Li and YunXiang Cheng, Long-term stream-flow prediction and water risk identification by the data-driven support vector regression with a dynamic stream deficit index, Intelligent Systems and Decision Making for Risk Analysis and Crisis Response, Proceedings of the 4th International Conference on Risk Analysis and Crisis Response, Istanbul, Turkey, 27-29 August 2013, EI 20134817021455

Lijun Cheng, Yongsheng Ding, SVM and statistical technique method applying in primary open angle glaucoma diagnosis, Intelligent Control and Automation (WCICA), 2010 8th World Congress, July 6, 2010, Jinan, China, 2973-2978. (EI: 20104313325034)


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