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.
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
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
1. Genome Assembly
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 model, we 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
Above: De Bruijn Graph based Genome Assembly and its High Scalability on Tianhe 1A
2. Contact Prediction for Membrane Proteins
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/)
RY Jing, Y Liang, Y Ran, SZ Feng, YJ Wei and L 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，2018(2):1-14.
A Amer, HW Lu, P Balaji, M Chabbi, YJ Wei, J Hammond, S Matsuoka, Lock Contention Management in Multithreaded MPI, ACM Transactions on Parallel Computing, accepted.
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
JQ Ge, YJ Wei, JT Meng, N Guo, BQ Wang, P Balaji, SZ Feng, JX Zhou, K-mer Counting for Genomic Big Data, International Congress on Bigdata, Seattle, USA, June 25 to 30 2018.
HL Zhang, YJ Wei, N Guo, GY Liu, JH Hu, JX Zhou, SZ Feng, Ensemble Learning Based Gender Recognition from Physiological Signals, International Congress on Bigdata, Seattle, USA, June 25 to 30 2018.
XJ Zhang, Y Peng, Y Huang, MT Yang, RB Yan, YQ Zhao, YL Cheng, X Liu, SQ Deng, XL Feng, HJ Lin, HM Yu, S Chen, ZF Zhao, SN Li, KL Li, L Wang, YJ Wei, ZD He, XM Fan, SJ. Meltzer, S Li, and Z Jin, SMG-1 inhibition by miR-192/-215 causes epithelial-mesenchymal transition in gastric carcinogenesis via activation of Wnt signaling, Cancer Medicine, Cancer Medicine 2018; 7(1):146–156
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.
T Gao, YF Guo, YJ Wei, BQ Wang, YT Lu, P Cicotti, P Balaji and M Taufer. Bloomfish: A Highly Scalable Distributed K-mer Counting Framework. IEEE International Conference on Parallel and Distributed Systems (ICPADS). Dec. 15–17, 2017, Shenzhen, China
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,
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,
D.Wei, QS Jiang and YJ Wei, SR Wang，A 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,
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),
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.
Wei, W. Nadler and U.H.E. Hansmann, Backbone and Sidechain
Ordering in a Small Protein, J. Chem. Phys., 128 (2008) 025105.
Wei, W. Nadler and U.H.E. Hansmann, Side-chain and backbone ordering in
homopolymers, J. Phys. Chem. B, 111 (2007) 4244.
Wei, W. Nadler and U.H.E. Hansmann, On the Helix-coil
Transition in Alanine-based Polypeptides in Gas Phase, J. Chem. Phys., 126
Wei, W. Nadler and U.H.E. Hansmann, Side chain and backbone ordering in a polypeptide, J. Chem. Phys., 125
Runyu Jing (Postdoc, 2016.7-now, PhD from Sichuan Univ)
Haiping Zhang (Postdoc, 2018.7-now, PhD from Nanyang Tech Univ)
Konda Mani Saravanan (Postdoc, 2018.7-now, PhD from Bharathidasan Univ)
Xuelei Li (Joint Postdoc with NSCC-Shenzhen, 2018.5-now, PhD from Institute of Geodesy and Geophysics. CAS)
Huiling Zhang (M.S., Research Assistant, 2011.8-now)
Ning Guo(M.S., Research Assistant, 2015.12-now)
Zhichun Zheng (M.S. Student, 2016.9-now )
Zhaoqi 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 )
Jianqiu Ge (M.S., 2018.7), Current position: Engineer at Huawei Tech. Co.(华为上海)
Yanning Teng (M.S.,2017.9), Current position: Engineer at CMB Network Tech.(招商网银科技)
Yuhuan Zhu (M.S., 2017.8), Current position: Engineer at Tencent(腾讯)
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: Engineer at PingAn Technology (Shenzhen) (平安科技)
Linfei Gui (M.S. 2015), Current position: Engineer at 爱立信;
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: Engineer at Tencent(腾讯)
Jianrui Yuan(M.S. 2012), Current position: Analyst at China Merchants Bank(招商银行)
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 email@example.com.