基本信息

魏彦杰  男  博导  中国科学院深圳先进技术研究院
电子邮件: yj.wei@siat.ac.cn
电话:0086-755-26907048

通信地址: 广东深圳市南山区西丽深圳大学城学苑大道1068号
邮政编码: 518055



个人主页:http://hpcc.siat.ac.cn/cbb-lab/index.html

研究领域及简介

魏彦杰研究员现担任中国科学院深圳先进技术研究院高性能计算研究中心执行主任,深圳市高性能大数据处理平台主任。他的研究领域为生物信息学与高性能计算交叉领域,聚焦蛋白质折叠、基因大数据分析等研究。曾获2020年中国科学院必和比拓导师科研奖,2021年中国科学院青年促进会优秀会员,深圳市优青(2020)。他曾担任2018年国际计算生物学和系统生物学大会(CBSB2018)主席,2021年生物信息学研究与应用国际研讨会(ISBRA2021)/第四届CCF生物信息学会议(CBC2019)程序委员会主席,世界超算大会(SC2019BoFs主席,CNCC2021论坛委员会委员,Interdisciplinary Sciences: Computational Life SciencesFuture Generation Computer Systems期刊编委CCF 高性能专委委员/生物信息学专委委员。目前已发表学术论文100多篇,包括Nucleic Acids Research, PloS Computational BiologyBioinformatics, Cell Research, Molecular Cancer, ProteinsJ of Chemical Theory and ComputationJournal of Physical Chemistry B, ICPP2016, ICPP2018, PPoPP2015等,授权专利近20项。主持多项研究课题,包括科技部重点研发计划课题、国家自然科学基金、国家发改委项目、广东省重点研发计划、广东省产学研项目以及深圳市孔雀计划项目等。

教育背景和工作经历


教育背景

2004-08--2007-12   密歇根理工大学   理学博士 


2000-09--2004-07   四川大学   理学学士

工作经历

2020.12-现在,        中国科学院深圳先进技术研究院数字所,所长助理;


2018.12-现在,        中国科学院深圳先进技术研究院高性能研究中心,执行主任;


2016.11-现在,        中国科学院深圳先进技术研究院,研究员;


2011.08-2016.11,    中国科学院深圳先进技术研究院,副研究员;


2008.03-2011.07,  普林斯顿大学, 博士后研究员;

2013.11/2015.10 /2018.07,  美国阿贡国家实验室,访问学者;

2007.05-2007.08/2006.06-2006.08/2005.07-2005.08,   德国Julich冯诺依曼研究中心,访问学生

招生信息

   
博士招生

中国科学院深圳先进技术研究院全日制博士

招生专业:081203-计算机应用技术

招生信息查询:https://www.siat.ac.cn/yjsjy2016/zsjs2016/

2022年度信息参考:导师查询报名公告


中国科学院深圳先进技术研究院-澳门大学联合培养博士

招生专业:计算机科学、计算生物学、生物信息学等

参考申请时间:2022年度申请截止时间2月28日

2022年度招生简章参考:网页查询


中国科学院深圳理工大学-宁波诺丁汉大学联合培养博士

招生领域:电器与电子工程、计算机科学、生物信息学、人工智能与优化、大数据分析与信息系统、生物医学工程等

参考申请时间:2022年度申请截止时间10月15日

2022年度招生简章参考:网页查询


如有疑问,可以邮件联系魏彦杰:yj.wei@siat.ac.cn。

硕士招生

081203-计算机科学与技术(中国科学院深圳先进技术研究院,全日制) 

2022年度参考信息:招生简章更多


085400-电子信息(中国科学院深圳先进技术研究院,全日制、非全日制)

2022年度参考信息:招生简章更多


080900-电子科学与技术(深圳理工大学-南方科技大学联合培养,全日制)

2022年度参考信息:调剂信息更多


如有疑问,可以邮件联系魏彦杰:yj.wei@siat.ac.cn。


代表论文

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


指导学生

已指导学生

郑志春  硕士研究生  085211-计算机技术  

程博  硕士研究生  085211-计算机技术  

张海山  硕士研究生  085211-计算机技术  

任倩茹  硕士研究生  085211-计算机技术  

张玉楼  硕士研究生  085211-计算机技术  

刘树珍  硕士研究生  085212-软件工程  

现指导学生

张慧玲  博士研究生  081203-计算机应用技术  

鞠震  博士研究生  081203-计算机应用技术  

庄晨  硕士研究生  085211-计算机技术  

张静静  博士研究生  081203-计算机应用技术  

黄莹  硕士研究生  085400-电子信息  

刘祖权  博士研究生  081203-计算机应用技术  

张玉兰  博士研究生  081203-计算机应用技术  

李兴昊  硕士研究生  085400-电子信息