Publications

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

2. D Wei, Y Peng, YJ Wei , QS jiang, JL Fang, A hybrid method for splice site prediction based on Markov model and codon information. International J. of Data Mining and Bioinformatics, 2016; 16(4):345-362

3. JQ Ge , JT Meng, N Guo,YJ Wei, BQ Wang,Genome Profiling at Extreme Scale， HPC-China 2017, Hefei, China

4. Runyu Jing, Yu Liang, Yi Ran, Sheng-Zhong Feng, Yanjie Wei and Li He，Ensemble methods with voting protocols exhibit superior performance for predicting cancer clinical endpoints and providing more complete coverage of disease-related genes，International Journal of Genomics， accepted

5. X Zhang; … Yanjie Wei; Zhendan He; Xinmin Fan; Stephen J. Meltzer; Song Li; Zhe Jin, SMG-1 inhibition by miR -192/ -215 causes epithelial-mesenchymal transition in gastric, Cancer Medicine, Accepted.

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

7. Y Peng, XJ Zhang, Q Ma, R Yan, Y Qin, YQ Zhao, YL Cheng, MT Yang, QX Wang, XL Feng, Y Huang, WL Huang, ZF Zhao, L Wang, YJ Wei , ZD He, XM Fan, S Li, Z Jin, SJ. Meltzer, MiRNA-194 activates the Wnt/beta-catenin signaling pathway in gastric cancer by targeting the negative Wnt regulator, SUFU, Cancer Letters, 2017 Jan 28; 385:117-127

8. 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.

9. Xiang Gu, Xiangke Liao, Chengkun Wu, Lin Fang, Yanjie Wei and Shaoliang Peng, Locality Sensitive Hashing Method to Speedup All Pairs Similarity Search in Metagenomics, HPCChina 2016, Xian, China

10. Huashun Li, Ximing Shao, Yi Liu, Qian Yu, Zhihao Ding, Wenyu Qian, Lei Zhang, Jianchao Zhang, Nan Jiang, Linfei Gui, Zhiheng Xu, Yang Hong, Yifan Ma, Yanjie Wei, Xiaoqing Liu, Changan Jiang, Minyan Zhu, and Hongchang Li, Numb Regulates Vesicular Docking for Homotypic Fusion of Early Endosomes via Membrane Recruitment of Mon1b, Cell Research 2016, doi:10.1038/cr.2016.34

11. 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(IF = 3)

12. Zhang X, Peng Y, Jin Z, Huang W, Cheng Y, Liu Y, Feng X, Yang M, Huang Y, Zhao Z, Wang L, Wei Y, Fan X, Zheng D, Meltzer SJ. Integrated miRNA profiling and bioinformatics analyses reveal potential causative miRNAs in gastric adenocarcinoma, Oncotarget, 2015 Oct 20;6(32):32878-89.

13. Miaomiao Zhao, Yunpeng Cai, Jiankui He, Guanyu Wang, Dongqing Wei, Yanjie Wei, Caiwan Zhang, Fengfeng Zhou: Personalized clinical data screening: Special issue on health informatics. Comp. in Bio. and Med. 61: 161-162 (2015)

14. JT Meng, YJ Wei, S Seo, P Balaji, SWAP-Assembler 2: Scalable Genome Assembler towards Millions of Cores - Practice and Experience, CCgrid 2015:769-772

15. Abdelhalim Amer, Huiwei Lu, Yanjie Wei, Pavan Balaji and Satoshi Matsuoka. MPI+Threads: Runtime Contention and Remedies. ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPoPP 2015

16. 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

17. Shuqiang Wang, Jinxing Hu, Yanyan Shen, Ling Yin, Yanjie Wei, Modeling and analysis of gene regulatory networks with a Bayesian-driven approach, 14th International Symposium on Communications and Information Technologies (ISCIT), 24-26 Sept. 2014, P289-293, Incheon, South Korea

18. Meng Jintao, Guo Guixin, Ye Zhiqiang, Qiu Shuang, Li Shengkang, Wei Yanjie, Wang Bingqiang, Cheng Jiefeng, Feng Shengzhong, An Ultra-fast Memory Efficient Parallel List Ranking Algorithm for BSP Based Graph Processing Systems, HPCChina 2014, Guangzhou, China, 2014, Nov.

19. HUANG Qingsheng, XIAO Tianxia, ZHANG Jian, WEI Yanjie, Molecular Dynamics Simulation of Endothelin-1 Conformational Change within Uniform Flow, Journal of Integration Technology, 2014, 3(2):17-26 (In Chinese)

20. Dan Wei, Yin Peng, Yanjie Wei and Qingshan Jiang, Splice Site Prediction using Support Vector Machine with Markov Model and Codon Information, M. Basu, Y. Pan and J. Wang (Eds): ISBRA 2014, Lecture Notes in Bioinformatics 8492, P376

21. Jintao Meng, Yanjie Wei, Gene and Disease Association Study with Metagenomics Assembling Tool: SWAP-Meta, e-Science Technology & Application, 5(3), 30-37, 2014 ( in Chinese)

22. Yanjie Wei, Huiling Zhang, Qingsheng Huang, Advances on Computer Simulations of Protein Folding, Journal of Integration Technology, 2014,3(4):58-66 (In Chinese)

23. Huiling Zhang, Li Ning, Jintao Meng, Yanjie Wei, Shengzhong Feng, On Large Scale Graph Processing, Network New Media, 2014(1):26-30 ( In Chinese)

24. Dan Wei, HL Zhang, YJ Wei, QS Jiang, A Novel Splice Site Prediction Method using Support Vector Machine, Journal of Computational Information Systems, 2013, 9: 20

25. Jintao Meng, Jianrui Yuan, Shengzhong Feng, Yanjie Wei. An Energy Efficient Clustering Scheme for Data Aggregation in Wireless Sensor Networks, Journal of Computer Science and Technology, 2013, Vol. 28:564-573

26. D.Wei, QS Jiang and YJ Wei, SR Wang，A Novel Hierarchical Clustering Algorithm for Gene Sequences, BMC Bioinformatics, 2012, 13:174

27. FB Peng, HL Zhang, YJ Wei, SZ Feng, ZX Yin, Protein Folding Study Based on Parallel Group Annealing Algorithms, e-Science Technology & Application, 2 0 1 3 , 4(5) : 2 6 – 3 4 ( In Chinese, SCA 2013 conference, Aug 2013, Huangshan, China )

28. JT Meng, JR Yuan, YJ Wei, SZ Feng, The Analysis of De Novo Genome Assembly Software Based on De Bruijn Graph, e-Science Technology & Application, 2013,4(5) : 58-69 (In Chinese, SCA 2013, Aug 16-17, 2013, Huangshan, China)

29. JT Meng, JR Yuan, JF Cheng, YJ Wei, SZ Feng, Small World Asynchronous Parallel Model for Genome Assembly, IFIP International Conference on Network and Parallel Computing (NPC2012) Gwangju, South Korea.

30. JT Meng, JR Yuan, JF Cheng, YJ Wei, SZ Feng, DGraph: Algorithms for shortgun reads assembly using De Bruijn Graph, IFIP International Conference on Network and Parallel Computing (NPC2012) Gwangju, South Korea.

31. D.Wei, WW Zhuang, QS Jiang, YJ Wei, A New Classification Method for Human Gene Splice Sites Prediction, proceedings of The 1st International Conference on Health Information Science (HIS 2012), Beijing, China, 8-10 April 2012

32. 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.

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

34. Subramani, A., Wei, Y. and Floudas, C. A., ASTRO-FOLD 2.0: An enhanced framework for protein structure prediction. AIChE Journal. 2012, 58 (5), 1619-1637

35. Rajgaria R., Wei Y. and C.A. Floudas, Contact Prediction for Beta and Alpha-Beta Proteins Using Integer Linear Optimization and its Impact on the First Principles 3D Structure Prediction Method ASTRO-FOLD, Proteins, 78(2010), 1825-1846

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

37. Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain and backbone ordering in homopolymers, J. Phys. Chem. B, 111 (2007) 4244.

38. 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.

39. P. Kar, Y. Wei, U.H.E. Hansmann and S. Höfinger, Systematic Study of the Boundary Composition in Poisson Boltzmann Calculations, J. Comp. Chem., 28 (2007) 2538.

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

41. Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain Ordering in Homopolymers, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 297-300.

42. P. Kar, Y. Wei, U.H.E. Hansmann and S. Höfinger, The Influence of Molecular Surface Composition on the Outcome of Poisson Boltzmann Calculations Performed to Obtain Solvation Free Energies, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 161 - 164.

43. Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain Ordering in PolyGlutamic Acid, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 205 - 209.