近期代表性论文：
期刊论文：
2012
1.Kui Wang , Wei Cui , Gang Hu , Jianzhao Gao , Zhonghua Wu , Xingye Qiu , Jishou Ruan , Yi Feng , Zhi Qi , Yiming Shao and Jack A. Tuszynski, Computable features required to evaluate the efficacy of drugs and a universal algorithm to find optimally effective drug in a drug complex. Plos One， 2012
2011
1.Ning Zhang; Shan Gao; Lei Chen; Jishou Ruan; Yudong Cai. Using multitask learning methods to investigate signal peptides and signal anchors. Amino Acids. 2011 Under Review
2.Lei Zhang, Ning Zhang, Ji-Shou Ruan, Tao Zhang. Studies on the Rules of β-Strand Alignment in a Protein β-Sheet Structure. Journal of Theoretical Biology. 2011,DOI: 10.1016/j.jtbi.2011.06.030
3.Ning Zhang, Yutao Tian, Lei Zhang, Zhuo Yang, Tao Zhang, and Jishou Ruan, 'Desktop Software for Patch-Clamp Raw Binary Data Conversion and Preprocessing,' Journal of Electrical and Computer Engineering, vol. 2011, Article ID 251215, 7 pages, 2011. doi:10.1155/2011/251215
2010
1.Hua Zhang, Tuo Zhang, Jianzhao Gao, Jishou Ruan, Shiyi Shen, Lukasz A. Kurgan, Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility, Amino Acids,2010.(in press)
2.Gao J, Zhang T, Zhang H, Shen S, Ruan J, Kurgan L.Accurate prediction of protein folding rates from sequence and sequence-derived residue flexibility and solvent accessibility. Proteins. 2010 Jul; 78(9):2114-30.
2009
1.Zhang, Hua, Zhang, Tuo, Chen, Ke, Shen, Shiyi, Ruan, Jishou, Kurgan, Lukasz (2009): On the relation between residue flexibility and local solvent accessibility in proteins, Proteins-Structure Function and Bioinformatics, vol 76, no3. 617 - 636. impact factor 4.019
2.Zhang Ning; Ruan Jishou; Duan Guangyou; Gao Shan; Zhang Tao (2009): The interstrand amino acid pairs play a significant role in determining the parallel or antiparallel orientation of beta-strands, Biochemical and biophysical research communications, 386(3):537-43，影响因子2.823。
3.Shan Gao, Ning Zhang, You G Duan, Zhuo Yang, JS Ruan, Tao Zhang* (2009): Prediction of function changes associated with single-point protein mutations using support vector machines (SVMs). Human Mutation, 30(8):1161-1166, 2008 年影响因子7.033。
2008
1.Ruan J, Chen H, Kurgan LA, Chen K, Kang C, Pu P, 2008. HuMiTar: A sequence-based Method for Prediction of Human microRNA Targets. Algorithms for Molecular Biology, 3:16， 影响因子2.08 Y
2.Zhang T, Zhang H, Chen K, Shen S, Ruan J, Kurgan LA, 2008. Accurate Sequence-based Prediction of Catalytic Residues. Bioinformatics, 24(20):2329-2338 ，影响因子5.039 Y
3.Zhang H, Zhang T, Chen K, Shen S, Ruan J, Kurgan LA, 2008. Sequence Based Residue Depth Prediction Using Evolutionary Information and Predicted Secondary Structure. BMC Bioinformatics, 9:388， 影响因子3.78 Y
4.Kurgan LA, Cios KJ, Zhang H, Zhang T, Chen K, Shen S, Ruan J. 2008. Sequence-based Methods for Real Value Predictions of Protein Structure. Current Bioinformatics, 3(3):183-196，影响因子4.7 X
5.Kurgan LA, Zhang T, Zhang H, Shen S, Ruan J, 2008. Secondary Structure Based Assignment of the Protein Structural Classes. Amino Acids, 35(3):551-564 ， 影响因子2.78 Y
6.Chen K, Kurgan LA, Ruan J, 2008. Prediction of Protein Structural Class Using Novel Evolutionary Collocation Based Sequence Representation. Journal of Computational Chemistry, 29(10):1596-1604 ，影响因子2.86 Y
2007
1.Chen K, Kurgan LA, Ruan J, 2007. Prediction of Flexible/Rigid Regions in Proteins from Sequences Using Collocated Amino Acid Pairs. BMC Structural Biology, 7:25， 影响因子3.06X
2.Homaeian L, Kurgan LA, Cios KJ, Ruan J, Chen K, 2007. Prediction of Protein Secondary Structure Content for the Twilight Zone Sequences. Proteins: Structure, Function, and Bioinformatics, 69(3):486-498， 影响因子3.73X
3.Kurgan LA, Stach W, Ruan J, 2007. Novel Scales Based on Hydrophobicity Indices for Secondary Protein Structure. Journal of Theoretical Biology, 248(2):354-366 ， 影响因子2.6 X
4.Guangyue Hu, Shiyi Shen, Jishou Ruan: SGA: A Grammar-Based Alignment Algorithm, Computer Methods and Programs in Biomedicine, 86(2007) pp17-20， （impact factor 0.788）影响因子0.85 X
5.Ning Zhang, Jishou Ruan, Jie Wu, Tao Zhang*. SheetsPair: a database of amino acids pairs in protein sheet structures, Data science journal, 2007，6：s589－s595. ，[查看 168 次X
2006
1.Ruan J, Chen K, Tuszynski J, Kurgan LA, 2006. Quantitative Analysis of the Conservation of the Tertiary Structure of Protein Segments. Protein Journal, 25(5):301-315 ，影响因子1.3
2.Chen K, Ruan J, Kurgan LA, 2006. Prediction of Three Dimensional Structure of Calmodulin. Protein Journal, 25(1):57-70 ，影响因子1.3
3.Shiyi Shen, Bo Kai, Jishou Ruan? J. Torin Huzil, Eric Carpenter, Jack A. Tuszynski， Probabilistic Analysis of The Frequencies of Amino Acid Pairs within Characterized Protein Sequences, Physica A：Statistical and Theoretical Physics，Volume 370, Issue 2, 15 October 2006, Pages 651-662. (impact factor 1. 311)
2005
1.Ruan J, Wang K, Yang J, Kurgan LA, Cios KJ, 2005. Highly Accurate and Consistent Method for Prediction of Helix and Strand Content from Primary Protein Sequences. Artificial Intelligence in Medicine, special issue on Computational Intelligence Techniques in Bioinformatics, 35(1-2):19-35，影响因子1.825
2004
1.沈世镒，余涛，开波，阮吉寿（2004）：生物序列的语义分析与第二密码规则，工程数学学报，第21卷，第6期 pp862-870。
2003
2.沈世镒，阮吉寿（2003）：蛋白质二级结构的条件隐Markov性及其预测问题，工程数学学报， 第20卷，第3期，pp117－124。
2002
3.阮吉寿，沈世镒（2002）：弱Takens嵌入定理，高校应用数学学报，第17卷，A 第4期，pp419－424。
教材
[1] 阮吉寿、张华 （译），沈世镒（审校）（原著：（美）Thomas M. Cover & Joy A. Thomas）：《信息论基础》（第一版），机械工业出版社，2005.5.
[2] 阮吉寿、张华 （译），沈世镒（审校）（原著：（美）Thomas M. Cover & Joy A. Thomas）：《信息论基础》（第二版），机械工业出版社，2007.7.