Bioinformatics: from Informatics to Biology

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Oct 16, 2013 (3 years and 10 months ago)

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講題

Bioinformatics: from Informatics to Biology


摘要

Recently, the government gets “Two Trillion & Twin Star” moving enthusiastically;
one of twin star is the industry of biological technology. With the
high
-
throughput
of
biological
technology, the

number of

biological data

is increasing extensively.
T
herefore,
the technology of bioinformatics and statistics
could

efficiently
promote

the development of biological research.
For instance,
you can

apply
data mining to
identify carcinogenic gene
,
adopt database s
ystem to
construct

the biological data

warehouse
, utiliz
e

machine learning to construct the predictive model for biological
functional sit
es, employ the algorithm to design a useful program for biological
analysis, and us
e

statistical method to discover ge
ne regulatory network.


Prote
in phosphorylation catalyzed by kinases
plays crucial role in signaling

transduction.
Due to the difficulty of detecting the conserved motifs for all data with a
larger size, this work applies maximal dependence decomposition (
MDD) to cluster
all sequences of
phosphorylation
site
s

into subgroups, which have obvious motifs.
MDD is a methodology to group a set of aligned signal sequences to moderate a large
group into subgroups that capture the most significant dependencies betwee
n
positions, based on chi
-
square test.
T
he MDD
-
clustered subgroups can be
used to
learn profile hidden Markov models (HMMs) for identifying phosphorylation sites.
According to five
-
fold cross
-
validation, t
he models trained with
MDD
-
clustered
subgroups coul
d improve
the predictive

accuracy, when compare to the model without
the application of MDD clustering.

MDD also can be widely applied to the
investigation

of protein functional sites.


李宗夷

Tzong
-
Yi Lee


元智資工系

助理教授

(2009.08 ~ )


主要研究領域



生 物 資 訊 、 計 算 蛋 白 質 體 學 、 基 因 調 控 網 路 、 生 物 資 料 庫 、 資 料 探 勘 與 機 器 學 習


研 究 成 果




T z o n g
-
Y i L e e
, J u s t i n B o
-
K a i H s u, W e n
-
C h i C h a n g, a n d H s i e n
-
D a H u a n g * , 2 0 1 0, "R e g P h o s: a s y s t e m t o e x p l o r e t h e p r o t e i n
k i n a s e
-
s u b s t r a t e p h o s p h o r y l a t i o n n e t w
o r k i n h u m a n s,"
N u c l e i c A c i d s R e s e a r c h.
( i n p r e s s ). ( S C I, I F:7.4 7 9 )

S h u
-
A n C h e n †,
T z o n g
-
Y i L e e
† ( † j o i n t f i r s t a u t h o r s h i p ), a n d Y u
-
Y e n O u *, 2 0 1 0, "I n c o r p o r a t i n g s i g n i f i c a n t a m i n o a c i d p a i r s t o
i d e n t i f y O
-
l i n k e d g l y c o s y l a t i o n s i t e s o n t r a n s m e m b r a n e p r o t e i n s

a n d n o n
-
t r a n s m e m b r a n e p r o t e i n s,"
B M C B i o i n f o r m a t i c s.
1 1:5 3 6. ( S C I, I F: 3.4 3 )

T z o n g
-
Y i L e e
, J u s t i n B o
-
K a i H s u, F e n g
-
M a o L i n, W e n
-
C h i C h a n g, P o
-
C h i a n g H s u, a n d H s i e n
-
D a H u a n g, 2 0 1 0, "N
-
A c e: u s i n g
s o l v e n t a c c e s s i b i l i t y a n d p h y s i c o c h e m i c a l p r o p e r t i e s t o i d e n t
i f y p r o t e i n N
-
A c e t y l a t i o n s i t e s,"
J o u r n a l o f C o m p u t a t i o n a l
C h e m i s t r y.
V o l. 3 1 ( 1 5 ), 2 7 5 9
-
2 7 7 1. ( S C I, I F: 3.7 6 9 )

T z o n g
-
Y i L e e
, J.B.K. H s u, W.C. C h a n g, T.Y. W a n g, P.C. H s u, a n d H.D. H u a n g *, 2 0 0 9, "A C o m p r e h e n s i v e R e s o u r c e f o r
I n t e g r a t i n g a n d D i s p l a y i n g P r o t e
i n P o s t
-
T r a n s l a t i o n a l M o d i f i c a t i o n s,"
B M C R e s e a r c h N o t e s.
2 ( 1 ):1 1 1.

W.C. C h a n g †,
T z o n g
-
Y i L e e
† ( † j o i n t f i r s t a u t h o r s h i p ), D.M. S h i e n, J. B.K. H s u, P.C. H s u, T.Y. W a n g, J.T. H o r n g, H.D. H u a n g *
a n d R.L. P a n *, 2 0 0 9, N o v 3 0 "I n c o r p o r a t i n g s u p p o r t v e c t o r m a c h
i n e f o r i d e n t i f y i n g p r o t e i n t y r o s i n e s u l f a t i o n s i t e s,"
J o u r n a l
o f C o m p u t a t i o n a l C h e m i s t r y.
. ( S C I, I F: 3.7 6 9 ) ( C i t a t i o n s:3 )

D.M. S h i e n †,
T z o n g
-
Y i L e e
† ( † j o i n t f i r s t a u t h o r s h i p ), W.C. C h a n g, J.B.K. H s u, J.T. H o r n g, P.C. H s u, T.Y. W a n g a n d H.D.
H u a n g *, 2 0 0 9
, J u l 1 5 "I n c o r p o r a t i n g S t r u c t u r a l C h a r a c t e r i s t i c s f o r I d e n t i f i c a t i o n o f P r o t e i n M e t h y l a t i o n S i t e s,"
J o u r n a l o f
C o m p u t a t i o n a l C h e m i s t r y.
V o l. 3 0, N o. 9, p p.1 5 3 2
-
1 5 4 3. ( S C I, I F: 3.7 6 9 ) ( C i t a t i o n s:2 )

W.C. C h a n g,
T z o n g
-
Y i L e e
, H.D. H u a n g *, H.Y. H u a n g, R.L. P a
n *, 2 0 0 8, "P l a n t P A N: P l a n t P r o m o t e r A n a l y s i s N a v i g a t o r, f o r
i d e n t i f y i n g c o m b i n a t o r i a l c i s
-
r e g u l a t o r y e l e m e n t s w i t h d i s t a n c e c o n s t r a i n t i n p l a n t g e n e g r o u p,"
B M C G e n o m i c s.
9:5 6 1. ( S C I,
I F: 4.1 8 ) (
C i t a t i o n s:7
)

Y.H. W o n g †,
T z o n g
-
Y i L e e
† ( † j o i n t f i r s t a u t h o r s h
i p ), H.K. L i a n g, C.M. H u a n g, Y.H. Y a n g, C.H. C h u, H.D. H u a n g * , M.T. K o, a n d
J.K. H w a n g, 2 0 0 7, "K i n a s e P h o s 2.0: a w e b s e r v e r f o r i d e n t i f y i n g p r o t e i n k i n a s e
-
s p e c i f i c p h o s p h o r y l a t i o n s i t e s b a s e d o n
s e q u e n c e s a n d c o u p l i n g p a t t e r n s,"
N u c l e i c A c i d s R e s e a r c h.
Vo
l 35, W588
-
594. (SCI, IF: 7.479) (
Citations:30
)

J.H. Hung†, H.D. Huang†,* († joint first authorship), and
Tzong
-
Yi Lee
, 2006, "ProKware: an integrated software for
presenting protein structural properties in protein tertiary structures,"
Nucleic Acids Rese
arch.
Vol 34, W89
-
W94. (SCI,
impact factor: 7.479)

Tzong
-
Yi Lee
, H.D. Huang*, J.H. Hung, Y.S. Yang, and T.H. Wang*, 2006, "dbPTM: An information repository of protein
post
-
translational modification,"
Nucleic Acids Research.
Vol. 34, D622
-
D627. (SCI, IF: 7
.479) (
Citations:33
)

Tzong
-
Yi Lee
, J.T. Horng, H.F. Juan, H.D. Huang, L.C. Wu, and F.M. Lin, 2006, "An agent
-
based system to discover
protein
-
protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints,"
Journal of

Computational Chemistry.
Vol. 27, No. 9, 1020
-
32. (SCI, impact factor: 4.297)

H.D. Huang*,
Tzong
-
Yi Lee
, S.W. Tseng, and J.T. Horng, 2005, "KinasePhos: a web tool for identifying protein kinase
-
specific
phosphorylation sites,"
Nucleic Acids Research.
Vol.

33, W226
-
229. (SCI, IF: 7.479) (
Citations:45
)

H.D. Huang,
Tzong
-
Yi Lee
, L.C. Wu, F.M. Lin, J.T. Horng, and A.P. Tsou, 2005, "MultiProtIdent: identifying proteins using
database search and protein
-
protein interactions,"
Journal of Proteome Research.
Vol. 4
(3), 690
-
697. (SCI, impact factor:
6.917)

H.D. Huang*,
Tzong
-
Yi Lee
, S.W. Tseng, L.C. Wu, J.T. Horng, and A.P. Tsou, 2005, "Incorporating Hidden Markov Model for
identifying protein kinase
-
specific phosphorylation sites,"
Journal of Computational Chemistry.
Vol. 26, pp.1032
-
1041. (SCI,
IF: 4.297) (
Citations:15
)