Yanjie Wei
Ph.D, Professor

Center for High Performance Computing

Address: Room 1108, Building F, 1068 Xueyuan Rd, Shenzhen, Guangdong, China
E-mail: yj.wei@siat.ac.cn
Phone: 0086-755-26907048

Executive Director     Dec. 2018 to present
Professor     Dec. 2016 to present
Associate Professor     Aug. 2011-Nov 2016
Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

Post-doctoral Research Associate
Mar. 2008 to Jun. 2011
Advisor: Dr. Christodoulos A. Floudas
Department of Chemical and Biological Engineering, Princeton University

Graduate Research Assistant
Aug. 2004 to Dec. 2007
Advisor: Dr. Ulrich Hansmann
Department of Physics, Michigan Technological University

Visiting scientist
Nov. 2013, Oct 2015, Aug 2018
Argonne National Lab

Visiting scientist
Jul. to Aug. 2005, Jun. to Jul. 2006, May. to Aug. 2007
John Von Neumann Institute for Computing at Juelich, Germany

PHD in Computational Biophysics
Michigan Technological University

MS in Computational Biophysics
Michigan Technological University

B.S in Applied Physics
Sichuan University

1.   Jintao Meng, Chen Zhuang, Peng Chen, Mohamed Wahib, Bertil Schmidt, Xiao Wang, Haidong Lan, Dou Wu, Minwen Deng, Yanjie Wei, Shenzhong Feng, Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning, in IEEE Transactions on Parallel and Distributed Systems, doi: 10.1109/TPDS.2022.3146257.

2.   Liangzhen Zheng, Jintao Meng, Kai Jiang, Haidong Lan, Zechen Wang, Mingzhi Lin, Weifeng Li, Hongwei Guo, Yanjie Wei*, Yuguang Mu, Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term, Briefings in Bioinformatics, 2022; bbac051

3.  Zhang, J.; Hossain, M.T.; Liu, W.; Peng, Y.; Pan, Y.; Wei, Y*. Evaluation of CircRNA Sequence Assembly Methods Using Long Reads. Front. Genet. 2022, 13, 1–12, doi:10.3389/fgene.2022.816825

4.   Hossain, M.T.; Li, S.; Reza, M.S.; Feng, S.; Zhang, X.; Jin, Z.; Wei, Y.; Peng, Y. Identification of circRNA Biomarker for Gastric Cancer through Integrated Analysis. Front. Mol. Biosci. 2022, 9:857320. doi: 10.3389/fmolb.2022.857320

5.   Reza, M.S.; Harun-Or-Roshid M.; Islam M.A.; et al. Bioinformatics screening of potential biomarkers from mRNA expression profiles to discover drug targets and agents for cervical cancer. Int. J. Mol. Sci. 2022 (accepted)

6.   Zhang Haiping, Li Junxin, Saravanan Konda Mani, Wu Hao, Wang Zhichao, Wu Du, Wei Yanjie, Lu Zhen, Chen Youhai H., Wan Xiaochun, Pan Yi, An Integrated Deep Learning and Molecular Dynamics Simulation-Based Screening Pipeline Identifies Inhibitors of a New Cancer Drug Target TIPE2, Frontiers in Pharmacology, 2021, vol 12, 3297

7.   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, 9 (1), 1-13.

8.   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)

9.   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, 2021, 22(22),12359

10.   Reza MS, Cai Y, Zhang L, Zhang X and Wei Y (2021) Computational Solutions for Microbiome and Metagenomics Sequencing Analyses. Front. Mol. Biosci. 8:698384. doi: 10.3389/fmolb.2021.698384

11.   Zhen Ju, Huiling Zhang, Jingtao Meng, Jingjing Zhang, Xuelei Li, Jianping Fan, Yi Pan, Weiguo Liu, and Yanjie Wei, An Efficient Greedy Incremental Sequence Clustering Algorithm, ISBRA 2021, Nov 26-28, Shenzhen, China.

12.   Zhongyang Dai, Haishan Zhang, Feifei Lin, Shengzhong Feng, Yanjie Wei, Jiaxiu Zhou, The classification system and biomarkers for autism spectrum disorder: A machine learning approach, ISBRA 2021, Nov 26-28, Shenzhen, China

13.   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, Nucleic Acids Research, 2021 50(D1), D747-757

14.   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, Nucleic Acids Research 2022,50 (D1), D83-D92

15.   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, 2021,11(7),503

16.   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

17.   Wenliang Zhang, Binhui Zeng, Huancai Lin, Wen Guan, Jing Mo, Song Wu, Yanjie Wei, Qianshen Zhang, Dongsheng Yu, Weizhong Li, and Godfrey Chi-Fung Chan, CanImmunother: a manually curated database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects, OncoImmunology 2021, 10(1), 1944553

18.   Konda Mani Saravanan, Haiping Zhang, Md. Tofazzal Hossain, Md. Selim Reza & Yanjie Wei, Deep Learning Based Drug Screening For COVID-19 and Case Studies, in the Book series entitled SpringerProtocols: In Silico Modeling of Drugs Against Coronaviruses - Computational Tools and Protocols, 2020, Methods in Pharmacology and Toxicology, DOI 10.1007/7653_2020_58

19.   Huiling Zhang, Hao Wu, Hing-Fung Ting and Yanjie Wei, Protein interresidue contact prediction based on deep learning and massive features from multi-sequence alignment, PDCAT2020, Dec 28-30 Shenzhen, China.

20.   Lei Zhu, Hongmin Cai, Fa Zhang, Quan Zou, Yanjie Wei, Huiru Zhen, Computational Learning Models and Methods Driven by Omics for Precision Medicine, Frontiers in Genetics, 2020 Dec 23;11:620976. doi:10.3389/fgene.2020.620976.

21.   Konda Mani Saravanan, Haiping Zhang, Renganathan Senthil, Kevin Kumar Vijayakumar, Vignesh Sounderrajan, Yanjie Wei, Harshavardhan Shakila, Structural basis for the inhibition of SARS-CoV2 main protease by Indian medicinal plant-derived antiviral compounds, J Biomol Struct Dyn, 2020 Oct 19;1-9

22.   H Zhang, Y Yang, J Li, M Wang, KM Saravanan, J Wei, JT Ng, MT Hossain, M Liu, 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

23.   Zekun Yin, Xiaoming Xu, Jinxiao Zhang, Yanjie Wei, Bertil Schmidt, Weiguo Liu, RabbitMash: Accelerating hash-based genome analysis on modern multi-core architectures, Bioinformatics, Volume 37, Issue 6, 2021, Pages 873–875

24.   Zekun Yin, Hao Zhang, Meiyang Liu, Wen Zhang, Honglei Song, Haidong Lan, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu, RabbitQC: High-speed scalable quality control for sequencing data, Bioinformatics, btaa719, https://doi.org/10.1093/bioinformatics/btaa719, 2020

25.   Konda Mani Saravanan, Haiping Zhang, Yanjie Wei*, Identifying Native and Non-native Membrane Protein Loops by Using Stabilizing Energetic Terms of Three Popular Force Fields, Current Chinese Science, Vol 1, 2021.

26.   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.

27.   Xuelei Li, Xiaomin Zhu, Yanjie Wei, Shengzhong Feng, Application of Sunway TaihuLight Accelerating in Brain Neural Network Simulation, Chinese Journal of Computers, 43(6), 1025-1037

28.   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.

29.   Md. Tofazzal Hossain, Yin Peng, Shengzhong Feng, Yanjie Wei, FcircSEC: An R Package for Full Length circRNA Sequence Extraction and Classification, International Journal of Genomics, vol. 2020, Article ID 9084901, 11 pages, 2020

30.   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

31.   Xiaomin Zhu, Yunhui Zeng, Yanjie Wei, Shengzhong Feng, Weiguo Liu, Pavan Balaji,An Auto Code Generator for Stencil on SW26010, IEEE 21st International Conference on High Performance Computing and Communications (HPCC2019), Aug 10-12, 2019, Zhangjiajie, China. 

32.   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.

33.   Zhichun Zheng, Ning Guo, Konda Mani Saravanan, Yanjie Wei, Efficient gene assembly and identification for many genome samples, 2019 International Conference on Cognitive Computing (ICCC2019), June 25-June 30, 2019, San Diego, USA.

34.   Zekun Yin, Tianyu Zhang, André Müller, Hui Liu, Yanjie Wei, Bertil Schmidt, and Weiguo Liu, Efficient Parallel Sort on AVX-512-based Multi-core and Many-core Architectures, IEEE 21st International Conference on High Performance Computing and Communications (HPCC2019), Aug 10-12, 2019, Zhangjiajie, China.

35.   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.

36.   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.

37.   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.

38.   KM Saravanan, Y Peng, YJ Wei, Systematic Analysis of No Regular Secondary Structural Regions (NORS) In Membrane and Non-Membrane Proteins,Journal of Biomolecular Structure & Dynamics, 1-7, 2019.

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

41.   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 (TOPC), 5(3), 12.

42.   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

43.   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.

44.   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.

45.   Tao Gao, Yanfei Guo, Yanjie Wei, Bingqiang Wang, Yutong Lu, Pietro Cicotti, Pavan Balaji and Michela 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.

46.   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,2018 (2) :1-14

47.   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

48.   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.

49.   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

50.   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

51.   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

52.   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

53.   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

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

55.   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.

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

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

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

59.   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.

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