魏彦杰- 中国科学院深圳先进技术研究院

中国科学院深圳先进技术研究院导师简况表

导师姓名 专业名称 魏彦杰 性别 男 职称 副研究员 计算生物/生物信息 导师类别 □博导 □硕导 是否兼职 □是 □否 所在单元 高性能计算 □物理化学（含化学物理）□生物化学与分子生物学□信号招生专业 与信息处理□模式识别与智能系统□计算机应用技术□材料工程□电子与通信工程□控制工程□计算机技术□生物工程 研究方向 计算生物/生物信息学 在研课题 蛋白质结构预测；蛋白质折叠与折叠病；基因拼接算法。 魏彦杰，博士，副研究员，2011年8月中科院深圳先进技术研究院引进人才。魏彦杰于2004年7月毕业于四川大学应用物理系，同年8月赴美国密歇根理工大学攻读生物物理学博士学位。他师从随机优化领域专家Ulrich Hansmann教授，利用蒙特卡洛随机优化方法研究蛋白质的热动力学和结构特性；分别于2006年和个人简历 2007年获得理学硕士和博士学位。 他在2008年3月到2011年7月期间任美国普林斯顿大学化学与生物工程系博士后研究员，师从美国工程院院士，世界著名全局优化领域专家Christodoulos A. Floudas教授，用全局优化知识以及数学建模方法预测蛋白质的三维结构。 发表高质量学术论文10余篇，包括Proteins， Journal of Physical 主要科研成果及所获荣誉 其他 Chemistry B等著名期刊。在美国期间曾参与了美国自然科学基金，美国健康研究院, 美国环境保护机构EPA等若干科研项目。担任Journal of Chemical Physics期刊, ICPADS2012, ICIC2012等审稿人。 邮箱 yj.wei@siat.ac.cn 0755-86392359 联系方式 电话 个人主页 备注

Name Academic title Phone Yanjie Wei Associate Professor 0086-755-86392359 Positions Associate Professor E-mail Personal Website Yj.wei@siat.ac.cn EDUCATION： PHD in Computational Biophysics 8/2004-12/2007 Depart. of Phy., Michigan Technological University, Houghton, MI USA Overall GPA: 4 B.S in Applied Physics 09/2000-07/2004 College of Physical Science/Technology Sichuan University, Chengdu, Sichuan Province, P.R.China Overall GPA: 3.8/4 RESEARCH INTERESTS: Protein Folding and structure prediction; Bioinformatics; deterministic and stochastic optimization; PROFESSIONAL EXPERIENCE: Associate Professor Aug. 2011 to present Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China Focus: protein structure prediction, protein folding, gene assembly, gene Resume classification Post-doctoral Research Associate Mar. 2008 to Jun. 2011 Advisor: Dr. Christodoulos A. Floudas Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ USA Focus: protein structure prediction using deterministic optimization method. Graduate Research Assistant Aug. 2004 to Dec. 2007 Advisor: Dr. Ulrich Hansmann Depart. of Phy., Michigan Technological University, Houghton, MI USA Focus: protein folding problems using multicanonical Monte Carlo sampling algorithm. Visiting scientist--- Jul. 2005 to Aug. 2005,Jun. 2006 to Jul. 2006, May. 2007 to Aug. 2007 John Von Neumann Institute for Computing at Juelich, Germany CONFERENCES/MEETINGS: Presented a talk ‘Computational Optimization and Protein Folding’ at CUHK-SIAT workshop, Shenzhen, China, Dec 6th. 2011 Participated in HPC China 2011, Jinan, Shangdong, China, Oct 26th to Oct 29th, 2011 Participated in conference SCA2011(Super Computer Application，Chinese Academy of Sciences)，Qingdao,Shandong, China, Nov 6th to Nov 9th, 2011 Presented a talk ‘New Advances in the First Principles Protein 3D Structure Prediction Method ASTRO-FOLD’ at AICHE annual meeting, Salt Lake City, Utah, Nov. 7-12, 2010. Presented an invited talk ‘Residue Contact Prediction and its Impact on Protein 3D Structure Prediction’ at American Chemical Society annual meeting in San Francisco, CA, Mar. 21th to 25th, 2010. Presented a poster Side-chain Ordering in Homopolymers at From Computational Biology to System Biology (CBSB07) Workshop held in Juelich, Germany, May. 2nd to 4th, 2007. Presented a poster at Quantitative Computational Biophysics Workshop hold in Tallahassee, Florida, Feb 18th to 21th, 2007 Presented a poster at The fifth Asia-Pacific Bioinformatics Conference hold in Hong Kong, China, Jan 14th to 17th, 2007 Presented a poster at From Computational Biology to System Biology Workshop hold in Juelich, Germany, July 6th to 9th, 2006 Participated in Midwest Computational Structural Biology Workshop, Augusta, Michigan, USA, Apr 30th to May 1st, 2005 Direction Computational Biology/Bioinformatics Dr. Wei has been published 12 papers in peer-reviewed journals, such as Proteins, Journal of Chemical Physics, Journal of Physical Chemistry B, Chemical Achievements Engineering Sci., etc. He has presented his works at various conferences and workshops, such as an invited talk at ACS 2010 annual conference. He also serves as a reviewer for several journals and conferences, including Journal of Chem. Phy., ICIC2012, ICPADS2012 etc. ? [1] Y. Wei, W. Nadler and U.H.E. Hansmann, Backbone and Sidechain Ordering in a small Protein, J. Chem. Phys. 2008, 128:025105. Article ? [2]Y. Wei, W. Nadler and U.H.E. Hansmann, On the Helix-coil Transition in Alanine-based Polypeptides in Gas Phase, J. Chem. Phys. 2007, 126:204307 [3]P. Kar, Y. Wei, U.H.E. Hansmann and S. H?finger, Systematic Study of the Boundary Composition in Poisson Boltzmann Calculations, J. Comp. Chem. 2007, 28:2538 [4]Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain and backbone ordering in homopolymers, J. Phys. Chem. B 2007, 111:4244 [5]Y. Wei, W. Nadler and U.H.E. Hansmann, Side chain and backbone ordering in a polypeptide, J. Chem. Phys. 2006, 125:164902. [6]Rajgaria R, Wei Y, Floudas CA, 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: Structure Function and Bioinformatics 2011, 78(8): 1825-1846 [7]Y. Wei, J. Thompson and C. A. Floudas, CONCORD: A consensus method for protein secondary structure prediction via Mixed Integer Linear Optimization, Proc. R. Soc. A, 2012, 468 (2139): 831-850. [8]Wei, Y.; Floudas, C. A. Enhanced inter-helical residue contact prediction in transmembrane proteins. Chemical Engineering Science 2011, 66, 4356-4369 [9]A. Subramani, Y. Wei, C. A. Floudas，ASTRO-FOLD 2.0: An enhanced framework for protein structure prediction，AICHE Journal， published online May 31,2011. DOI: 10.1002/aic.12669 [10]Y. Wei, W. Nadler and U. H. E. Hansmann, Side-Chain Ordering in Homopolymers, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 297-300 [11]Y. Wei, W. Nadler and U. H. E. Hansmann, Side-Chain Ordering in Homopolymers, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 297-300. [12]Parimal Kar, Yanjie Wei,Ulrich H.E. Hansmann and Siegfried H?finger, The Influence of Molecular Surface Composition on the Outcome of Poisson Boltzmann Calculations Performed to Obtain Solvation Free Energies, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 161 - 164 ? ? ? ? ? ? ? ? ? ?

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