电子邮件： yj.wei@siat.ac.cn
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主任，深圳市高性能大数据处理平台主任。研究领域为生物信息学与高性能计算交叉领域，聚焦蛋白质折叠和药物筛选、基因大数据分析等领域研究。曾获2020年中国科学院必和比拓导师科研奖，2021年中国科学院青年人才，深圳市高层次人才。他曾担任2024年ACM BCB24大会程序委员会主席，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（SC2019）BoFs主席，CNCC2021论坛委员会委员，Big Data Mining and Analytics副主编, Innovation, Scientific Data,Interdisciplinary Sciences: Computational Life Sciences和Future Generation Computer Systems期刊编委，CCF 高性能专委委员／生物信息学专委委员。发表学术论文130多篇，包括Nucleic Acids Research, PloS Computational Biology，Bioinformatics, Cell Research, Molecular Cancer, Proteins，J of Chemical Theory and Computation，Journal 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
2016.11-现在, 中国科学院深圳先进技术研究院,研究员；
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；
2023.06-现在, 中国科学院深圳先进技术研究院高性能研究中心,主任；
2018.12-2023.06, 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；
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
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/
如有疑问，可以联系：yj.wei@siat.ac.cn。
代表论文
1. OpenDock: a pytorch-based open-source framework for protein-ligand docking and modelling, Qiuyue Hu, Zechen Wang, Jintao Meng, Weifeng Li, Jingjing Guo, Yuguang Mu, Sheng Wang, Liangzhen Zheng∗ and Yanjie Wei∗ Bioinformatics 2024
2. autoGEMM: Pushing the Limits of Irregular Matrix Multiplication on Arm Architectures, Du Wu.Jintao Meng,Peng Chen,Mohamed Wahib,Xiao Wang,Minwen Deng, Wenxi Zhu,Luo Tao, Yanjie Wei, SC24: The International Conference for High Performance Computing, Networking, Storage and Analysis, Atlanta, GA, USA, November 17–22, 2024(CCF A)
3. Yang Liu, Zhuochao Min, Jing Mo, Zhen Ju, Jianliang Chen, Weiling Liang, Lantian Zhang, Hanguang Li, Godfrey Chi-Fung Chan*, Yanjie Wei*, Wenliang Zhang*, ExomiRHub:a comprehensive database for hosting and analyzing human disease-related extracellular microRNA transcriptomics data, Computational and Structural Biotechnology Journal, (2024) doi:https://doi.org/10.1016/j.csbj.2024.07.02
4. Zhen Ju, Mingyu Wang, Xuelei Li, Jintao Meng, Wenhui Xi, Yanjie Wei*, An In-depth Assessment of Sequence Clustering softares in bioinformatics, 20th International Symposium, ISBRA 2024, Kunming, China, July 19–21, 2024 (best paper award)
5. Xijian Li, Ying Huang, Runxuan Tang, Guangcheng Xiao, Xiaochuan Chen, Ruilin He, Zhaolei Zhang, Jiana Luo, Yanjie Wei*, Yijun Mao*, Huiling Zhang*, PmmNDD: Predicting the Pathogenicity of Missense Mutations in Neurodegenerative Diseases via Ensemble Learning, 20th International Symposium, ISBRA 2024, Kunming, China, July 19–21, 2024
6. Huang Y, Zhang H, Lin Z, Wei Y*, Xi W*. RevGraphVAMP: A protein molecular simulation analysis model combining graph convolutional neural networks and physical constraints. Methods. 2024 Jul 6;229:163-174
7. Qingsheng Huang, Yin Peng, Yuefeng Peng, Huijuan Lin, Shiqi Deng, Shengzhong Feng, Yanjie Wei, Design, in silico evaluation, and in vitro verification of new bivalent Smac mimetics with pro-apoptotic activity, Methods, 2024/2/17
8. Z. Cai, M. Li, P. Skums and Y. Wei, Introduction to the Special Section on Bioinformatics Research and Applications," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 20, no. 6, pp. 3329-3331, Nov.-Dec. 2023, doi: 10.1109/TCBB.2023.3325032
9. Fangyu Zhang, Yi Pan, Yanjie Wei, Jin Liu, Zhenli Lin, A Heuristic Sparsification Method to Improve the Performance of Neural Networks on Autism Spectrum Disorder Identification Tasks, 2023 13th International Conference on Information Science and Technology (ICIST), 2023/12/08, Hongkong, China
10. Keliang Zhao, Jovial Niyogisubizo, Linxia Xiao, Yi Pan, Dongqing Wei, Didi Rosiyadi, Yanjie Wei, A Novel Deep Learning Approach Featuring Graph-Based Algorithm for Cell Segmentation and Tracking, 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 1752-1757,Dec 5th, 2023
11. Tao Shen, Fuxu Liu, Zechen Wang, Jinyuan Sun, Yifan Bu, Jintao Meng, Weihua Chen, Keyi Yao, Yuguang Mu, Weifeng Li, Guoping Zhao, Sheng Wang, Yanjie Wei, Liangzhen Zheng, zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15, Proteins: Structure, Function, and Bioinformatics, 91,12: 1837-1849 (2023)
12. Hao Wu, Jovial Niyogisubizo, Keliang Zhao, Jintao Meng, Wenhui Xi, Hongchang Li, Yi Pan, Yanjie Wei, A Weakly Supervised Learning Method for Cell Detection and Tracking Using Incomplete Initial Annotations, International Journal of Molecular Sciences, 24,22:16028 (2023)
13. Jingjing Zhang, Md Tofazzal Hossain, Zhen Ju, Wenhui Xi, Yanjie Wei, Identification and Functional Annotation of circRNAs in Neuroblastoma Based on Bioinformatics, International Symposium on Bioinformatics Research and Applications, ISBRA 2023. Lecture Notes in Computer Science, vol 14248. Springer, Singapore.
14. Md Tofazzal Hossain, Song Li, Md Selim Reza, Shengzhong Feng, Xiaojing Zhang, Zhe Jin, Yanjie Wei, Yin Peng, Corrigendum: Identification of circRNA biomarker for gastric cancer through integrated analysis, Frontiers in Molecular Biosciences, 1249019, 2023/7/4
15. Jovial Niyogisubizo, Yunpeng Cai, Lu Zhang, Xingyu Zhang, Yanjie Wei, Editorial: Computational solutions for microbiome and metagenomics sequencing analyses Volume II, Frontiers in Molecular Biosciences, 2023/7
16. Jingjing Zhang, Huiling Zhang, Zhen Ju, Yin Peng, Yi Pan, Wenhui Xi, Yanjie Wei, JCcirc: circRNA full-length sequence assembly through integrated junction contigs, Briefings in Bioinformatics, Volume 24, Issue 6, November 2023, bbad363
17. Hossain, M., Reza, M., Li, X., Peng, Y., Feng, S., Wei, Y. (2023). PCPI: Prediction of circRNA and Protein Interaction Using Machine Learning Method. In: Guo, X., Mangul, S., Patterson, M., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Computer Science, vol 14248. Springer, Singapore.
18. Jingjing Zhang, Md. Tofazzal Hossain, Weiguo Liu, Yin Peng, Yi Pan, Yanjie Wei, Corrigendum: Evaluation of CircRNA Sequence Assembly Methods Using Long Reads, Front. Genet. 2023,14:1248519.
19. Zhang, J., Hossain, M.T., Ju, Z., Xi, W., Wei, Y. (2023). Identification and Functional Annotation of circRNAs in Neuroblastoma Based on Bioinformatics. In: Guo, X., Mangul, S., Patterson, M., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Computer Science, vol 14248. Springer, Singapore.
20. Zhichao Wang, Xuelei Li, Jianping Fan, Jintao Meng, Zhenli Lin, Yi Pan, and Yanjie Wei. SWsnn: A Novel Simulator for Spiking Neural Networks. Journal of Computational Biology. 2023.951-960.
21. Hossain MT, Li S, Reza MS, Feng S, Zhang X, Jin Z, Wei Y and Peng Y (2023) Corrigendum: Identification of circRNA biomarker for gastric cancer through integrated analysis. Front. Mol. Biosci. 10:1249019
22. Hilbert Yuen In Lam, Robbe Pincket, Hao Han, Xing Er Ong, Zechen Wang, Jamie Hinks, Yanjie Wei, Weifeng Li, Liangzhen Zheng, Yuguang Mu, Application of variational graph encoders as an effective generalist algorithm in computer-aided drug design, Nature Machine Intelligence, 1-11, 2023(IF 23.8, CAS Q1)
23. Xiaoming Xu, Zekun Yin, Lifeng Yan, Hao Zhang, Borui Xu, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu. RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches. Genome Biol 24, 121 (2023).
24. Haiping Zhang, Konda Mani Saravanan, Yanjie Wei, Yang Jiao, Yang Yang, Yi Pan, Xuli Wu, John ZH Zhang, Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening, Journal of Chemical Information and Modeling, 2023, 63, 3, 835–845
25. Lifeng Yan, Zekun Yin, Hao Zhang, Zhan Zhao, Mingkai Wang, André Müller, Robin Kobus, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu, RabbitQCPlus: More Efficient Quality Control for Sequencing Data," 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Las Vegas, NV, USA, 2022, pp. 619-626
26. Zechen Wang, Liangzhen Zheng, Sheng Wang, Mingzhi Lin, Zhihao Wang, Adams Wai-Kin Kong, Yuguang Mu, Yanjie Wei, Weifeng Li, A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function, Briefings in Bioinformatics, 24,1, bbac520
27. M. T. Hossain, M. S. Reza, Y. Peng, S. Feng and Y. Wei, "Identification of Key Genes as Potential Drug Targets for Gastric Cancer," in Tsinghua Science and Technology, vol. 28, no. 4, pp. 649-664, August 2023
28. H. Zhang, Z. Yin, Y. Wei, B. Schmidt and W. Liu, "DeepFilter: A Deep Learning Based Variant Filter for VarDict," in Tsinghua Science and Technology, vol. 28, no. 4, pp. 665-672, August 2023
29. Haiping Zhang, Xiao Lin, Yanjie Wei, Huiling Zhang, Linbu Liao, Hao Wu, Yi Pan, Xuli Wu, Validation of Deep Learning-Based DFCNN in Extremely Large-Scale Virtual Screening and Application in Trypsin I Protease Inhibitor Discovery, Front. Mol. Biosci. 01 June 2022
30. Haiping Zhang, Xiaohua Gong, Yun Peng, Konda Mani Saravanan, Hengwei Bian, John ZH Zhang, Yanjie Wei, Yi Pan, Yang Yang, An efficient modern strategy to screen drug candidates targeting RdRp of SARS-CoV-2 with potentially high selectivity and specificity, Frontiers in chemistry 10, 933102
31. Fangyu Zhang, Yanjie Wei, Jin Liu, Yanlin Wang, Wenhui Xi, Yi Pan, Identification of Autism spectrum disorder based on a novel feature selection method and Variational Autoencoder, Computers in Biology and Medicine, 2022, 148:105854
32. Hao Zhang, Honglei Song, Xiaoming Xu, Qixin Chang, Mingkai Wang, Yanjie Wei, Zekun Yin, Bertil Schmidt, Weiguo Liu, "RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 20, no. 3, pp. 2341-2348, 1 May-June 2023
33. Yanlin Wang, Shi Tang, Ruimin Ma, Ibrahim Zamit, Yanjie Wei, Yi Pan, Multi-modal intermediate integrative methods in neuropsychiatric disorders: A review, Computational and Structural Biotechnology Journal, 2022
34. Wang, Z., Li, X., Meng, J., Pan, Y., Wei, Y. (2022). Simulating Spiking Neural Networks Based on SW26010pro. In: Bansal, M.S., Cai, Z., Mangul, S. (eds) Bioinformatics Research and Applications. ISBRA 2022. Lecture Notes in Computer Science, vol 13760
35. Ruiquan Ge, Chuan Dong, Juexin Wang, Yanjie Wei, Editorial: Machine learning for peptide structure, function, and design, Front. Genet., 20 September 2022，Volume 13 - 2022 | https://doi.org/10.3389/fgene.2022.1007635
36. Fan Hu, Yin Peng, Shanshan Chang, Xiaonuan Luo, Yuan Yuan, Xiaohui Zhu, Yidan Xu, Kaining Du, Yang Chen, Shiqi Deng, Fan Yu, Xianling Feng, Xinmin Fan, Hassan Ashktorab, Duane Smoot, Stephen J Meltzer, Song Li, Yanjie Wei, Xiaojing Zhang, Zhe Jin, Vimentin binds to a novel tumor suppressor protein, GSPT1-238aa, encoded by circGSPT1 with a selective encoding priority to halt autophagy in gastric carcinoma, Cancer Letters, 2022, 545, 215826
37. Yuan Yuan, Xiaojing Zhang, Kaining Du, Xiaohui Zhu, Shanshan Chang, Yang Chen, Yidan Xu, Jiachun Sun, Xiaonuan Luo, Shiqi Deng, Ying Qin, Xianling Feng, Yanjie Wei, Xinmin Fan, Ziyang Liu, Baixin Zheng, Hassan Ashktorab, Duane Smoot, Song Li, Xiaoxun Xie, Zhe Jin, Yin Peng. Circ_CEA promotes the interaction between the p53 and cyclin-dependent kinases 1 as a scaffold to inhibit the apoptosis of gastric cancer. Cell Death Dis 13, 827 (2022).
38. Zhen Ju, Huiling Zhang, Jintao Meng, Jingjing Zhang, Jianping Fan, Yi Pan, Weiguo Liu, Xuelei Li, Yanjie Wei, nGIA: A novel Greedy Incremental Alignment based algorithm for gene sequence clustering, Future Generation Computer Systems, Volume 136, 2022,Pages 221-230
39. Haiping Zhang, Tingting Zhang, Konda Mani Saravanan, Linbu Liao, Hao Wu, Haishan Zhang, Huiling Zhang, Yi Pan, Xuli Wu, Yanjie Wei, DeepBindBC: A practical deep learning method for identifying native-like protein-ligand complexes in virtual screening, Methods 205, 247-262
40. Haiping Zhang, Konda Mani Saravanan, Yang Yang, Yanjie Wei, Pan Yi, John ZH Zhang, Generating and screening de novo compounds against given targets using ultrafast deep learning models as core components, Briefings in Bioinformatics, 23,4 bbac226
41. Md Tofazzal Hossain, Jingjing Zhang, Md Selim Reza, Yin Peng, Shengzhong Feng, Yanjie We, Reconstruction of Full-Length circRNA Sequences Using Chimeric Alignment Information, International Journal of Molecular Sciences, 23, 12, 67-76
42. Hao Zhang, Qixin Chang, Zekun Yin, Xiaoming Xu, Yanjie Wei, Bertil Schmidt, Weiguo Liu, RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures, Bioinformatics, 38,10,2932-2933
43. Yin Peng, Yidan Xu, Xiaojing Zhang, Shiqi Deng, Yuan Yuan, Xiaonuan Luo, Md Tofazzal Hossain, Xiaohui Zhu, Kaining Du, Fan Hu, Yang Chen, Shanshan Chang, Xianling Feng, Xinmin Fan, Hassan Ashktorab, Duane Smoot, Stephen J. Meltzer, Gangqiang Hou, Yanjie Wei, Song Li, Ying Qin & Zhe Jin，A novel protein AXIN1-295aa encoded by circAXIN1 activates the Wnt/β-catenin signaling pathway to promote gastric cancer progression，Molecular Cancer (2021) 20:158
44. 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, IEEE Transactions on Parallel and Distributed Systems, doi: 10.1109/TPDS.2022.3146257.
45. 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
46. 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
47. 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
48. †Hossain, M.T; †Reza, M.S.; Peng, Y.; Feng, S.; Wei, Y. (2022) Identification of key genes as potential drug targets and drugs for gastric cancer. Tsinghua Science and Technology (accepted) (IF=2.02).
49. Reza MS, Harun-Or-Roshid M, Islam MA, Hossen MA, Hossain MT, Feng S, Xi W, Mollah MNH*, Wei Y*. Bioinformatics Screening of Potential Biomarkers from mRNA Expression Profiles to Discover Drug Targets and Agents for Cervical Cancer. Int J Mol Sci. 2022 Apr 2;23(7):3968.
50. Huiling Zhang, Min Hao, Hao Wu, Wenhui Xi，Yanjie Wei. Protein residue contact prediction based on deep learning and massive statistical features from multi-sequence alignment, Tsinghua Science and Technology, 2022, 27, 5:843=854
51. 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
52. 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.
53. 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）
54. 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
55. 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
56. 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.
57. 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
58. 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
59. 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
60. 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
61. 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
62. 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
63. 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
64. 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.
65. 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.
66. 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
67. 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
68. 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
69. Xiaojing Zhang, Yin Peng, Yuan Yuan, Yuli Gao, fan hu, Jian Wang, Xiaohui Zhu, Ruibin Yan, Yulan Cheng, yanjie wei, Xinmin Fan, Yaohong Xie, Hassan Ashktorab, Duane Smoot, Song Li, Stephen Meltzer, Gangqiang Hou, and Zhe Jin, Histone Methyltransferase SET8 is Regulated by miR-192/-215 and Induces Oncogene-Induced Senescence via p53-Dependent DNA Damage in Human Gastric Carcinoma Cells, Cell Death & Disease, 2020 Oct 30;11(10):937.
70. 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
71. 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.
72. 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.
73. 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
74. 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.
75. 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
76. 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
77. 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.
78. 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.
79. 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.
80. 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.
81. J Zhu, Z Yang, M Mourshed, Y Guo, Y Zhou, Y Chang, Y Wei, S Feng, Electric Vehicle Charging Load Forecasting: A Comparative Study of Deep Learning Approaches, Energies 12 (14), 2692.
82. 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. (IF=2.98)
83. 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.
84. 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.
85. 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.
86. 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.
87. Yin Peng, Xiaojing Zhang, Huijuan Lin, Shiqi Deng, Yong Huang, Ying Qin, Xianling Feng, Ruibin Yan, Yanqiu Zhao, Yulan Cheng, Yanjie Wei, Jian Wang, Wangchun Chen, Xinmin Fan, Hassan Ashktorab, Duane Smoot, Stephen Meltzer, Song Li, Zhong Zhang, Zhe Jin, (2018). Inhibition of miR-194 suppresses the Wnt/β-catenin signalling pathway in gastric cancer. Oncology Reports, 40(6), 3323-3334.
88. JT Meng, N Guo, JQ Ge, YJ Wei , P Balaji, BQ Wang, Scalable Assembly for Massive Genomic Graphs. CCGrid 2017: 665-670.
89. 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.
90. 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
91. 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.
92. 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.
93. 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.
94. JQ Ge , JT Meng, N Guo,YJ Wei , BQ Wang,Genome Profiling at Extreme Scale， HPC-China 2017, Hefei, China
95. 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
96. 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, 2018; 7(1):146–156
97. 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(IF=6)
98. 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.
99. 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
100. 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
101. 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.
102. 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)
103. 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
104. 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
105. 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
106. 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
107. 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.
108. 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
109. 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
110. Jintao Meng, Yanjie Wei, Gene and Disease Association Study with Metagenomics Assembling Tool: SWAP-Meta, e-Science Technology & Application, 5(3), 30-37, 2014
111. Yanjie Wei, Huiling Zhang, Qingsheng Huang, Advances on Computer Simulations of Protein Folding, Journal of Integration Technology, 2014,3(4):58-66
112. 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
113. 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
114. D.Wei, QS Jiang and YJ Wei, SR Wang，A Novel Hierarchical Clustering Algorithm for Gene Sequences, BMC Bioinformatics, 2012, 13:174
115. 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.
116. 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.
117. 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
118. 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.
119. Wei, Y.; Floudas, C..A. Enhanced inter-helical residue contact prediction in transmembrane proteins. Chemical Engineering Science, 66(2011), 4356-4369.
120. 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
121. Y. Wei, W. Nadler and U.H.E. Hansmann, Backbone and Sidechain Ordering in a Small Protein, J. Chem. Phys., 128 (2008) 025105.
122. Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain and backbone ordering in homopolymers, J. Phys. Chem. B, 111 (2007) 4244.
123. 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
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