1.   Jintao Meng, Peng Chen, Mingjun Yang, Mohamed Wahib, Liangzhen Zheng, Yanjie Wei*, Shenzhong Feng*, Wei Liu, Junzhou Huang, Boosting the Predictive Performance with Aqueous Solubility Dataset Curation, Scientific Data, accepted.

2.   Haiping Zhang, Tingting Zhang, Konda Mani Saravanan, Linbu Liao, Hao Wu, Haishan Zhang, Huiling Zhang, Yi Pan, Xuli Wu, and Yanjie Wei, A novel virtual drug screening pipeline with deep-leaning as core component identifies inhibitor of pancreatic alpha-amylase, IEEE BIBM 2021（IEEE International Conference on Bioinformatics and Biomedicine 2021）

3.   Md Motiar Rahman *, Md. Tofazzal Hossain, Md. Selim Reza, Ying Peng, Shengzhong Feng, Yanjie Wei *, Identification of potential long non-coding RNA candidates that contribute to triple- negative breast cancer in humans, International Journal of Molecular Sciences, accepted 2021

4.   Zhang, Wenliang*; Zhang, Yan; Min, Zhuochao; Mo, Jing; Ju, Zhen; Guan, Wen; Zeng, Binghui,; Liu, Yang; Chen, Jianliang; Zhang, Qianshen; Li, Hanguang; Zeng, Chunxia; Wei, Yanjie*; Chan, Godfrey Chi Fung*, COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale, accepted by Nucleic Acids Research (2021)

5.   Zhang, Wenliang*; Liu, Yang; Min, Zhuochao; Liang, Guodong; Mo, Jing; Ju, Zhen; Zeng, Binghui,; Guan, Wen; Zhang, Yan; Chen, Jianliang; Zhang, Qianshen; Li, Hanguang; Zeng, Chunxia; Wei, Yanjie*; Chan, Godfrey Chi Fung*, circMine: a comprehensive database to integrate, analyze and visualize human disease related circRNA transcriptome, accepted by Nucleic Acids Research (2021)

6.   Md. Selim Reza, Huiling Zhang, Md. Tofazzal Hossain, Langxi Jin, Shengzhong Feng, Yanjie Wei *, COMTOP: Protein residue–residue contacts prediction through mixed integer linear optimization, Membranes, accepted 2021

7.   Huiling Zhang, Zhendong Bei,Wenhui Xi,Min Hao,Zhen Ju,Konda Mani Saravanan, Haiping Zhang,Ning Guo,Yanjie Wei, Evaluation of residue-residue contact prediction methods: From retrospective to prospective, PLoS Comput Biol 17(5): e1009027, 2021, https://doi.org/10.1371/journal.pcbi.1009027

8.   X Ren, Y Pan, Y Peng, Y Shi, X Wan, Y Liu, Y Wei, A Novel Virtual Screening Procedure Identifies Pralatrexate as Inhibitor of SARS-CoV-2 RdRp and It Reduces Viral Replication in vitro, PloS Computational Biology, 2020 Dec 31;16(12):e1008489

9.   Zekun Yin, Xiaoming Xu, Jinxiao Zhang, Yanjie Wei, Bertil Schmidt, Weiguo Liu, RabbitMash: Accelerating hash-based genome analysis on modern multi-core architectures, Bioinformatics,btaa754, https://doi.org/10.1093/bioinformatics/btaa754, 2020

10.   Haiping Zhang, Konda Mani Saravanan, Yang Yang, Md. Tofazzal Hossain, Junxin Li, Xiaohu Ren, Yanjie Wei, Deep learning based drug screening for novel coronavirus 2019-nCov，Interdisciplinary Sciences-Computational Life Sciences, 2020 Sep;12(3):368-376.

11.   Konda Mani Saravanan, Haiping Zhang, Huiling Zhang, Wenhui Xi, Yanjie Wei, On the conformational dynamics of β-amyloid forming peptides: a computational perspective, Front. Bioeng. Biotechnol. 8:532. (IF=5.89, JCR Q1, CAS Q2)

12.   Haiping Zhang, Konda Mani Saravanan, Jinzhi Lin, Linbu Liao, Jiaxiu Zhou* and Yanjie Wei*, DeepBindPoc: A deep learning method to rank ligand binding pockets using molecular vector representation, PeerJ 2020, 8, e8864

13.   Zhang H, Shao X, Peng Y, Yanning Teng, Konda Mani Saravanan, Huiling Zhang, Hongchang Li, Yanjie Wei. A novel machine learning based approach for iPS progenitor cell identification. PLoS Comput Biol. 2019;15(12):e1007351.

14.   Zhang H, Liao L, Saravanan KM, Yin P, Wei Y. DeepBindRG: a deep learning based method for estimating effective protein–ligand affinity. PeerJ 2019, 7:e7362.

15.   Jianqiu Ge, Jintao Meng, Ning Guo, Yanjie Wei, Pavan Balaji, Shengzhong Feng, Counting Kmers for Biological Sequences at Scale, Interdisciplinary Sciences: Computational Life Sciences, 1-10, 2019.

16.   Haiping Zhang, Jianbo Pan, Xuli Wu, Ai-Ren Zuo, Yanjie Wei, Zhi-Liang Ji, Large-Scale Target Identification of Herbal Medicine Using a Reverse Docking Approach, ACS Omega, 4(6), 9710-9719, 2019.

17.   Qingsheng Huang, Yin Peng, Yuefeng Peng, Dan Wei, Yanjie Wei, Shengzhong Feng, The TwistDock workflow for evaluation of bivalent Smac mimetics targeting XIAP, Drug Design Development and Therapy (2019), 13,1373.

18.   JT Meng, N Guo, JQ Ge, YJ Wei , P Balaji, BQ Wang, Scalable Assembly for Massive Genomic Graphs. CCGrid 2017: 665-670.

19.   K Xu, R Kobus, YD Chan, P Gao, XX Meng, YJ Wei, B Schmidt, WG Liu, SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures, 47th International Conference on Parallel Processing (ICPP 2018), Eugene, Oregon, USA, Aug 13 to 16th. 2018

20.   HL Zhang, WH Xi, UHE Hansmann, YJ Wei, Fibril-Barrel Transitions in Cylindrin Amyloids, J of Chemical Theory and Computation. 2017 Aug 8;13(8):3936-3944

21.   Jintao Meng, Sangmin Seo, Pavan Balaji, Yanjie Wei, Bingqiang Wang, and Shenzhong Feng, SWAP-Assembler 2: Optimization of De Novo Genome Assembler at Extreme Scale, The 45th International Conference on Parallel Processing (ICPP-2016), Philadelphia, USA, Aug 2016.

22.   Huiling Zhang, Qingsheng Huang, Zhendong Bei, Yanjie Wei, Chris Floudas, COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming, Proteins-Structure, Function and Bioinformatics, 2016, 84:332–348

23.   Jintao Meng, Bingqiang Wang, Yanjie Wei, Shengzhong Feng, and Pavan Balaji. SWAP-Assembler: Scalable and Efficient Genome Assembly Towards Thousands of Cores. BMC Bioinformatics. Vol. 15 (S9), 2014

24.   D.Wei, QS Jiang and YJ Wei, SR Wang，A Novel Hierarchical Clustering Algorithm for Gene Sequences, BMC Bioinformatics, 2012, 13:174 25.   Y. Wei, J. Thompson, C.A. Floudas, CONCORD: A consensus method for protein secondary structure prediction via Mixed Integer Linear Optimization, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Science 2012, 468 (2139), 831-850.

26.   Wei, Y.; Floudas, C..A. Enhanced inter-helical residue contact prediction in transmembrane proteins. Chemical Engineering Science, 66(2011), 4356-4369.

27.   Y. Wei, W. Nadler and U.H.E. Hansmann, Backbone and Sidechain Ordering in a Small Protein, J. Chem. Phys., 128 (2008) 025105.

28.   Y. Wei, W. Nadler and U.H.E. Hansmann, On the Helix-coil Transition in Alanine-based Polypeptides in Gas Phase, J. Chem. Phys., 126 (2007) 204307.

29.   Y. Wei, W. Nadler and U.H.E. Hansmann, Side chain and backbone ordering in a polypeptide, J. Chem. Phys., 125 (2006) 164902