Yanjie Wei 
Ph.D, Professor

Shenzhen Institutes of Advanced Tech., CAS
Email: yj.wei@siat.ac.cn
P: +86-755-86392336
F: +86-755-86392299
Office: Rm. 1107, Bldg F
Address: 1068 Xueyuan Blvd., Shenzhen, Guangdong, China
Postcode: 518055

News:
The Workshop on Extreme Scale Genome Analytics is going to be held in Shenzhen from March 31 to Apr 1st.
Summary
    Relying on the world class supercomputers, such as Tianhe-2 at NSCC-Guangzhou, Mira at Argonne National Lab, the lab develops computational techniques to study biologically important problems, such as protein folding and structure prediction, gene assembly and classification etc. The aim is, through developing more efficient computational algorithms, to provide fundamental understanding of several key issues in these areas.
     

    Research is funded by The National Key Research and Development Program of China, National Natural Science Foundation of China, National High Technology Research and Development Program of China(863), Guangdong Provincial Department of Science and Technology, Science & Technology Innovation Commission of Shenzhen.


About Me
    EDUCATION
    Ph.D. in Computational Biophysics, Michigan Technological University, Dec. 2007, Advisor: Ulrich HE Hansmann
    M.S. in Computational Biophysics, Michigan Technological University, Oct. 2006,  Advisor: Ulrich HE Hansmann
    B.S. in Applied Physics, Sichuan University, July 2004, Chengdu, P.R. China
    WORK EXPERIENCE
    2016.12-present, Professor., Shenzhen Institues of Advanced Tech., Chinese Academy of Sciences
    2011.8-2016.11, Associate Professor., Shenzhen Institues of Advanced Tech., Chinese Academy of Sciences
    2008.3-2011.6, Postdoctoral Research Associate, Princeton University   (Supervisor: Christodoulos A. Floudas)
    2005.5-2007.12, Research Assistant, Michigan Tech University, (Advisor: Ulrich H.E. Hansmann)
    2004.8-2005.5, Teaching Assistant, Department of Physics, Michigan Tech University   
    2013.11, 2015.10, Visitor, Argonne National Lab at Argonne, IL
      
    2005.7-8, 2006.6-7, 2007.5-8, Visitor, John Von Neumann Institute for Computing at Juelich, Germany

Research Projects
    1. Genome Assembly
     
    Next Generation Sequencing techniques generate vast amount of genetic data that requires highly scalable and efficient tools for analyzing these data. Sequencing reads from the machines can be in the range of TB-PB range, sequential algorithms can no longer meet the needs. In our lab, we focus on developing De Bruijn graph based approach for assembling the raw reads. Through mathematical abstraction and building an asynchronous computing modelwe have developed SWAP-Assembler for large scale genome assembly. We have demonstrated that SWAp-Assembler can scale to tens of thousands cores on Mira@Argonne National Lab, and Tianhe-1A@National Supercomputing Center in Tianjin. This is an open source project, and the software can be download from http://sourceforge.net/projects/swapassembler/.
              Above: De Bruijn Graph based Genome Assembly and its High Scalability on Tianhe 1A

    2. Contact Prediction for Membrane Proteins
    About 60% of the drug targets locate on the surface of the membrane proteins, thus it is of high significance for membrane protein structure determination. However, membrane structure determination in experiments is very hard and costly, membrane protein structure prediction using computational techniques provide an alternative.  We use machine learning techniques and deterministic  optimizaiton techniques for residue-residue contact predictions of membrane proteins, which can be used as distance constraints to reduce the search space during membrane protein structure prediction.

    Above: Hybrid Method of Residue Contact Prediciton for Membrane Proteins (http://hpcc.siat.ac.cn/COMSAT/)


Publications (Selective)
  • HL Zhang, WH Xi, UHE Hansmann, YJ Wei, Fibril-Barrel Transitions in Cylindrin Amyloids, accepted by J of Chemical Theory and Computing.

    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

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

    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

    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.

    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

    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 May;26(5):593-612

    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

    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, 6(32):32878-89.

    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. 2015, 61:161-162

    JT Meng, YJ Wei, S Seo, P Balaji, SWAP-Assembler 2: Scalable Genome Assembler towards Millions of Cores - Practice and Experience, 15th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid Doctoral Symposium), May 4-7, 2015, Shenzhen, China
     
    Abdelhalim Amer, Huiwei Lu, Yanjie Wei, Pavan Balaji and Satoshi Matsuoka. MPI+Threads: Runtime Contention and Remedies. the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPoPP 2015, San Francisco, CA, USA, Feb 7-11, 2015  

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

    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  

    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 (abstract) 8492, P376  

    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  

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

    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.  

    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.  

    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.  

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

    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

    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

    Kar P, Wei Y, Hansmann U H, et al. Systematic study of the boundary composition in Poisson Boltzmann calculations[J]. Journal of Computational Chemistry, 2007, 28(16): 2538-2544.  

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

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

    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.

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

Group Members
    Current:  
    Huiling Zhang (M.S., Research Assistant, 2011.8-now)
    Ning Guo(M.S., Research Assistant, 2015.12-now)
    Runyu Jing (Postdoc, 2016.7-now, PhD from Sichuan Univ)
    Jianqiu Ge (M.S. student, 2016.8-now )
    Zhichun Zheng (M.S. Student, 2016.9-now )
    Zhaiqi Li (M.S. Student, 2017.8-now )
    Shuzhen Liu (M.S. Student, 2017.8-now )
    Haishan Zhang (M.S. Student, 2017.8-now )
    Tofazzal Hossain (PhD Student, 2017.8-now )
    Selim Reza (PhD Student, 2017.8-now )

    Former:
    Yanning Teng (M.S.,2017.9)
    Yuhuan Zhu (M.S., 2017.8)
    Jintao Meng (PhD, 2016.7), Current Position: Analyst at WeBank (微众银行).
    Qingsheng Huang(Postdoc, 2013.10-2015.12), Current Position: Associate Professor at Sun Yat-Sen Univ;
    Mingyang Chen (M.S. 2015), Current position: Enginneer at PingAn Technology (Shenzhen) (平安科技)

    Linfei Gui (M.S. 2015)
    Qingfen Yu, (Research assistant, 2014), Current Position: PhD at Forschungszentrum Julich, Germany
    Fengbin Peng(M.S. 2014), Current Position: Engineer at GTA(国泰安)
    Dan Wei(Ph.D 2013) ,Current Position: Lecture at Hangzhou Dianzi University(杭州电子科技大学)
    Yongjian Zhan(M.S. 2012), Current position: Enginneer at Tencent(腾讯)
    Jianrui Yuan(M.S. 2012), Current position: Analyst at China Merchants Bank(招商银行)

Collaborators

Software/Tools

Opennings
    We are looking for Postdocs, PHD students, guest/intern students in the areas of computational biology/bioinformatics, high performance computing. If you are interested, please send me your CV to yj.wei@siat.ac.cn.