Research Ability Oral Examination Waive Application

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2 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

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Research Ability

Oral Examination Waive Application


Applicant:

Lin Chen


Data of e
nter 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 pote
ntial energy function has been proposed and has been applied
to several decoy sets. By comparing results with energy function
s
, 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.


L
iteratures

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.


Presentation
s

1.

Secure E
-
mail
CS555

Introduction of Networks and Communication

2.

Analysis and Network Representation of Hotspots in Protein Interfaces Using Minimum Cut
Trees
CS795

Application of Graph in Bioinformatics

3.

The Signature Molecular Descriptor: 1. Using Extended Valence Sequences in QSAR and
QSPR Studies
CS795

Application of Graph in Bioinformatics

4.

A Configuration Bias Monte Carlo Method for Water
CS795

Monte Carlo Method

5.

Hadoop High Availabi
lity through Metadata Replication
CS875

Distributed System

6.

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
Matrices
CS895

Bioinformatics I

8.

Prediction of Protein Secondary Struct
ure at Better than 70% Accuracy
(2e, 2f)
CS895

Bioinformatics I



Project
s

1.

Score board simulation
CS665

Computer Achitecture

2.

Looking for the hotspot of protein
CS795

Application of
Graph in Bioinformatics

3.

Buffon’s needle
CS795

Monte Carlo Method

4.

Hit
-
or
-
miss and crude Monte Carlo
CS795

Monte Carlo Method

5.

Random walks
CS795

Monte Carlo Method

6.

Neutron transport simulation
CS795

Monte Carlo Method

7.

Ising model and Metropolis method
CS795
Monte Carlo Method

8.

Ad
-
hoc Coalition System
CS875

Distributed System

9.

Structure optimization
CS895

Computational Structural
Bioinformatics

10.

Sequence Analysis
CS895
Bioinformatics I

11.

Secondary structure alignment

CS895
Bioinformati
cs I


Reference paper
s

in presentation
s

and project
s

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