Research Ability Oral Examination Waive Application
Applicant: Lin Chen
Data of enter Ph.D. program: 09/2010
Application reason
I passed the broad exam in May, 2011. I would like to waive the research ability oral
examination. I have published one paper and have been reading over 50 research literatures
while working on my research and during the course work.
Publication
Chen, L., He, J. "A distance and orientation dependent potential energy function with cluster
energy" The Proceeding of the 2011 IEEE International Conference on Bioinformatics and
Biomedicine Workshops, p405-9, Nov 12-15, 2011
In our paper, a novel protein potential energy function has been proposed and has been applied
to several decoy sets. By comparing results with energy functions, our energy function has overall
better accuracy than Multi-well (our group’s previous energy function), OPUS-PSP (Dr. Jiangpneg
Ma’s energy function) in protein structure predication.
Literatures
M. Lu, A.D. Dousis and J. Ma. J. Mol. Biol. 376, 288-301, 2008.
S.Miyazawa, R.L. Jernigan. J. Mol. Biol. 256, 623-644, 1996.
I. Bahar, R.L. Jernigan. J. Mol. Biol. 266, 195-214, 1997.
S. Miyazawa and R.J. Jernigan, J. Chem. Phys. 122(2), 024901, 2005.
W. Sun and J. He Proteins: Structure, Function, and Bioinformatics, 77, 159-73, 2009.
G. Wang and R.L. Dunbrack. Bioinformatics, 19, 1589-1591, 2003.
B. Jone, A. Sali. Nucleic Acids Research, 31, 3982-3992, 2003.
H.Y. Zhou, Y.Q. Zhou. Protein Science, 11, 2714-2726, 2002.
M.J. Sippl. J. Mol. Biol. 213, 859-883, 1990.
M.J. Sippl. Current Opinion in Structural Biology, 5, 229-235, 1995.
J. Zhang, Y. Zhang. PlosOne, 5(10), e15386, 2010.
Presentations
1.
2.
Secure E-mail CS555 Introduction of Networks and Communication
Analysis and Network Representation of Hotspots in Protein Interfaces Using Minimum Cut
3.
Trees CS795 Application of Graph in Bioinformatics
The Signature Molecular Descriptor: 1. Using Extended Valence Sequences in QSAR and
4.
5.
6.
QSPR Studies CS795 Application of Graph in Bioinformatics
A Configuration Bias Monte Carlo Method for Water CS795 Monte Carlo Method
Hadoop High Availability through Metadata Replication CS875 Distributed System
A Minimal Sequence Code for Switching Protein Structure and Function CS895
Computational Structural Bioinformatics
7.
Gapped BLAST and PSI-BLAST Iterated Application of BLAST to Position-Specific Score
8.
Matrices CS895 Bioinformatics I
Prediction of Protein Secondary Structure at Better than 70% Accuracy(2e, 2f) CS895
Bioinformatics I
Projects
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2.
3.
4.
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6.
7.
8.
9.
10.
11.
Score board simulation CS665 Computer Achitecture
Looking for the hotspot of protein CS795 Application of Graph in Bioinformatics
Buffon’s needle CS795 Monte Carlo Method
Hit-or-miss and crude Monte Carlo CS795 Monte Carlo Method
Random walks CS795 Monte Carlo Method
Neutron transport simulation CS795 Monte Carlo Method
Ising model and Metropolis method CS795 Monte Carlo Method
Ad-hoc Coalition System CS875 Distributed System
Structure optimization CS895 Computational Structural Bioinformatics
Sequence Analysis CS895 Bioinformatics I
Secondary structure alignment CS895 Bioinformatics I
Reference papers in presentations and projects
N. Tuncbag, F.S. Salman, O. Keskin, A. Gursoy. Proteins. 2010, 78, 2283.
K.S. Thorn, A.A. Bogan. Bioinformatics, 2001, 17, 284.
I.S. Moreira, P.A. Fernandes, M.J. Ramos. Proteins, structure, function and bioinformatics, 2007,
68, 803.
O. Keskin, I. Bahar, A.Y. Badretdionov, O.B. Ptitsyn, R.L. Jernigan. Protein Sci, 1998, 7, 2578.
A.V. Goldberg, R.E. Tarjan. JACM. 1988, 35, 921.
J.L. Faulon, D.P. Visco and R.S. Pophale, J. Chem. Inf. Comput. Sci. 2003, 43, 707
D.P. Visco , R.S. Pophale, M.D. Rintourl and J.L. Faulon, J. Chem. Inf. Comput. Sci. 2003, 43, 707
J.C. Shelley and G.N. Patey. J. Chem. Phys. 1995, 102(19), 7656
F. Wang, et. al. CloudDB ‘09 Proceeding of the first international workshop on Cloud data
management, 2009
P.A. Alexander, et. al. Proc. Natl. Acad. Sci., 2009, 106(50), 21149-54
S.F. Altschul et al. Nucleic Acids Research 1997, 25(17) 3389-3402)
B. Rost, C. Sander. J. Mol. Biol. (1993) 232, 584-599