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
所在单元
魏彦杰
性别
男
计算生物/生物信息
高性能计算
职称
副研究员
导师类别
□博导 □硕导
是否兼职
□是
□否
照片
□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（蛋白质结构预测；蛋白质折叠与折叠病；基因拼接算
法）
主持国家自然科学基金青年基金，“蛋白质折叠高效模拟方法及折叠病致
在研课题
病机理研究“（项目批准号：11204342，2013-2015 年, 25 万, 项目负责人）
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，
深圳市海外高层次人才“孔雀计划”B 类人才。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
个人简历
研究蛋白质的热动力学和结构特性；分别于 2006 年和 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。今年来发表文章近 20 篇。
主要科研
成果及所
获荣誉
发表高质量学术论文近 20 余篇，包括 Proteins，BMC Bioinformatics,
Journal of Physical 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。
其他
联系方式
邮箱
yj.wei@siat.ac.cn
电话
0755-86392359
个人主页
备注
Name
Academic
title
Phone
Yanjie Wei
Positions
Associate Professor
E-mail
0086-755-86392359
Personal
Associate Professor
yj.wei@siat.ac.cn
照片
Website
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
classification
Resume
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 poster at 5th Chinese Conference on Bioinformatics and
Systems Biology, Harbin, China, Aug 2012
Attending ICiS ‘Next Generation Sequencing Analysis’ workshop, Park
City, UT, Aug 2012
Presented an invited talk at Argonne National Lab, Jul. 2012
Presented an invited talk ‘Protein Folding and Structure Prediction’ at
Shenzhen Graduate School, Peking University, Shenzhen, China, Apr
27th. 2012
Organizer of Computational and Experimental Biology workshop,
Shenzhen, China, Apr 11th. 2012
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（Protein folding and structure prediction,
gene assembly and classification）
Dr. Wei has been published nearly 20 papers in peer-reviewed journals, such as
Proteins, Journal of Chemical Physics, Journal of Physical Chemistry B,
Achievements
Chemical 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.
D.Wei, QS Jiang and YJ Wei, SR Wang， A Novel Hierarchical
Clustering Algorithm for Gene Sequences, BMC Bioinformatics,
2012, 13:174 ( corresponding author)
JT Meng, JR Yuan, JF Cheng, YJ Wei, SZ Feng, Small World
Asynchronous Parallel Model for Genome Assembly, Accepted by IFIP
International Conference on Network and Parallel Computing (NPC2012)
Gwangju, South Korea. (Corresponding author)
YJ Zhang, SZ Feng, JP Fan, YJ Wei, A Parallel Wang-Landau Algorithm
for Protein Folding, Accepted by 2012 International Conference on
Electrical Engineering and Computer Science, August, 2012, Shanghai,
China (corresponding author)
Article
JT Meng, JR Yuan, JF Cheng, YJ Wei, SZ Feng, DGraph: Algorithms for
shortgun reads assembly using De Bruijn Graph, Accepted by IFIP
International Conference on Network and Parallel Computing (NPC2012)
Gwangju, South Korea. (Corresponding author)
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
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, Y.; 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), 1825-1846
Y. Wei, W. Nadler and U.H.E. Hansmann, Backbone and Sidechain
Ordering in a Small Protein, J. Chem. Phys., 128 (2008) 025105.
Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain and backbone
ordering in homopolymers, J. Phys. Chem. B, 111 (2007) 4244.
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.
P. Kar, Y. Wei, U.H.E. Hansmann and S. Höfinger, Systematic Study of
the Boundary Composition in Poisson Boltzmann Calculations, J. Comp.
Chem., 28 (2007) 2538.
Y. Wei, W. Nadler and U.H.E. Hansmann, Side chain and backbone
ordering in a polypeptide, J. Chem. Phys., 125 (2006) 164902
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.
P. Kar, Y. Wei, U.H.E. Hansmann and S. Höfinger, 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.
Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain Ordering in
PolyGlutamic Acid, 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. 205 - 209.