共 14 条
APCluster: an R package for affinity propagation clustering
被引:333
作者:

Bodenhofer, Ulrich
论文数: 0 引用数: 0
h-index: 0
机构:
Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria

Kothmeier, Andreas
论文数: 0 引用数: 0
h-index: 0
机构:
Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria

Hochreiter, Sepp
论文数: 0 引用数: 0
h-index: 0
机构:
Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria
机构:
[1] Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria
关键词:
NETWORKS;
D O I:
10.1093/bioinformatics/btr406
中图分类号:
Q5 [生物化学];
学科分类号:
071010 ;
081704 ;
摘要:
Affinity propagation (AP) clustering has recently gained increasing popularity in bioinformatics. AP clustering has the advantage that it allows for determining typical cluster members, the so-called exemplars. We provide an R implementation of this promising new clustering technique to account for the ubiquity of R in bioinformatics. This article introduces the package and presents an application from structural biology.
引用
收藏
页码:2463 / 2464
页数:2
相关论文
共 14 条
[1]
Clustering by passing messages between data points
[J].
Frey, Brendan J.
;
Dueck, Delbert
.
SCIENCE,
2007, 315 (5814)
:972-976

Frey, Brendan J.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Toronto, Dept Elect & Comp Engn, Toronto, ON M5S 3G4, Canada Univ Toronto, Dept Elect & Comp Engn, Toronto, ON M5S 3G4, Canada

Dueck, Delbert
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Toronto, Dept Elect & Comp Engn, Toronto, ON M5S 3G4, Canada Univ Toronto, Dept Elect & Comp Engn, Toronto, ON M5S 3G4, Canada
[2]
Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana
[J].
Kiddle, Steven J.
;
Windram, Oliver P. F.
;
McHattie, Stuart
;
Mead, Andrew
;
Beynon, Jim
;
Buchanan-Wollaston, Vicky
;
Denby, Katherine J.
;
Mukherjee, Sach
.
BIOINFORMATICS,
2010, 26 (03)
:355-362

Kiddle, Steven J.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England
Univ Warwick, Warwick HRI, Wellesbourne CV35 9EF, Warwick, England Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England

Windram, Oliver P. F.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Warwick, Warwick HRI, Wellesbourne CV35 9EF, Warwick, England Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England

McHattie, Stuart
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England
Univ Warwick, Warwick HRI, Wellesbourne CV35 9EF, Warwick, England Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England

论文数: 引用数:
h-index:
机构:

Beynon, Jim
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England
Univ Warwick, Warwick HRI, Wellesbourne CV35 9EF, Warwick, England Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England

Buchanan-Wollaston, Vicky
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England
Univ Warwick, Warwick HRI, Wellesbourne CV35 9EF, Warwick, England Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England

Denby, Katherine J.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England
Univ Warwick, Warwick HRI, Wellesbourne CV35 9EF, Warwick, England Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England

Mukherjee, Sach
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Warwick, Dept Stat, Coventry CV4 7AL, W Midlands, England
Univ Warwick, Ctr Complex Sci, Coventry CV4 7AL, W Midlands, England Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England
[3]
Clustering by soft-constraint affinity propagation: applications to gene-expression data
[J].
Leone, Michele
;
Sumedha
;
Weigt, Martin
.
BIOINFORMATICS,
2007, 23 (20)
:2708-2715

Leone, Michele
论文数: 0 引用数: 0
h-index: 0
机构:
Inst Sci Interchange, I-10133 Turin, Italy Inst Sci Interchange, I-10133 Turin, Italy

Sumedha
论文数: 0 引用数: 0
h-index: 0
机构:
Inst Sci Interchange, I-10133 Turin, Italy Inst Sci Interchange, I-10133 Turin, Italy

Weigt, Martin
论文数: 0 引用数: 0
h-index: 0
机构:
Inst Sci Interchange, I-10133 Turin, Italy Inst Sci Interchange, I-10133 Turin, Italy
[4]
Detecting microarray data supported microRNA-mRNA interactions
[J].
Liu, Hui
;
Zhou, Shuigeng
;
Guan, Jihong
.
INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS,
2010, 4 (06)
:639-655

Liu, Hui
论文数: 0 引用数: 0
h-index: 0
机构:
Fudan Univ, Sch Comp Sci, Shanghai 200433, Peoples R China
Jiangsu Polytech Inst, Sch Informat Sci & Engn, Jiangsu, Peoples R China Fudan Univ, Sch Comp Sci, Shanghai 200433, Peoples R China

Zhou, Shuigeng
论文数: 0 引用数: 0
h-index: 0
机构:
Fudan Univ, Sch Comp Sci, Shanghai 200433, Peoples R China
Fudan Univ, Shanghai Key Lab Intelligent Informat Proc, Shanghai 200433, Peoples R China Fudan Univ, Sch Comp Sci, Shanghai 200433, Peoples R China

Guan, Jihong
论文数: 0 引用数: 0
h-index: 0
机构:
Tongji Univ, Dept Comp Sci & Technol, Shanghai 200092, Peoples R China Fudan Univ, Sch Comp Sci, Shanghai 200433, Peoples R China
[5]
Complex Networks Govern Coiled-Coil Oligomerization - Predicting and Profiling by Means of a Machine Learning Approach
[J].
Mahrenholz, Carsten C.
;
Abfalter, Ingrid G.
;
Bodenhofer, Ulrich
;
Volkmer, Rudolf
;
Hochreiter, Sepp
.
MOLECULAR & CELLULAR PROTEOMICS,
2011, 10 (05)

Mahrenholz, Carsten C.
论文数: 0 引用数: 0
h-index: 0
机构:
Charite, Inst Med Immunol, D-10117 Berlin, Germany Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria

Abfalter, Ingrid G.
论文数: 0 引用数: 0
h-index: 0
机构:
Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria

Bodenhofer, Ulrich
论文数: 0 引用数: 0
h-index: 0
机构:
Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria

Volkmer, Rudolf
论文数: 0 引用数: 0
h-index: 0
机构:
Charite, Inst Med Immunol, D-10117 Berlin, Germany Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria

Hochreiter, Sepp
论文数: 0 引用数: 0
h-index: 0
机构:
Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria
[6]
Coiled coil domains: Stability, specificity, and biological implications
[J].
Mason, JM
;
Arndt, KM
.
CHEMBIOCHEM,
2004, 5 (02)
:170-176

Mason, JM
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Freiburg, Inst Biol 3, D-79104 Freiburg, Germany Univ Freiburg, Inst Biol 3, D-79104 Freiburg, Germany

Arndt, KM
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Freiburg, Inst Biol 3, D-79104 Freiburg, Germany Univ Freiburg, Inst Biol 3, D-79104 Freiburg, Germany
[7]
A New Clustering of Antibody CDR Loop Conformations
[J].
North, Benjamin
;
Lehmann, Andreas
;
Dunbrack, Roland L., Jr.
.
JOURNAL OF MOLECULAR BIOLOGY,
2011, 406 (02)
:228-256

North, Benjamin
论文数: 0 引用数: 0
h-index: 0
机构:
Fox Chase Canc Ctr, Inst Canc Res, Philadelphia, PA 19111 USA Fox Chase Canc Ctr, Inst Canc Res, Philadelphia, PA 19111 USA

Lehmann, Andreas
论文数: 0 引用数: 0
h-index: 0
机构:
Fox Chase Canc Ctr, Inst Canc Res, Philadelphia, PA 19111 USA Fox Chase Canc Ctr, Inst Canc Res, Philadelphia, PA 19111 USA

Dunbrack, Roland L., Jr.
论文数: 0 引用数: 0
h-index: 0
机构:
Fox Chase Canc Ctr, Inst Canc Res, Philadelphia, PA 19111 USA Fox Chase Canc Ctr, Inst Canc Res, Philadelphia, PA 19111 USA
[8]
TASSER_low-zsc: An approach to improve structure prediction using low z-score-ranked templates
[J].
Pandit, Shashi B.
;
Skolnick, Jeffrey
.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,
2010, 78 (13)
:2769-2780

Pandit, Shashi B.
论文数: 0 引用数: 0
h-index: 0
机构:
Georgia Inst Technol, Sch Biol, Ctr Study Syst Biol, Atlanta, GA 30318 USA Georgia Inst Technol, Sch Biol, Ctr Study Syst Biol, Atlanta, GA 30318 USA

Skolnick, Jeffrey
论文数: 0 引用数: 0
h-index: 0
机构:
Georgia Inst Technol, Sch Biol, Ctr Study Syst Biol, Atlanta, GA 30318 USA Georgia Inst Technol, Sch Biol, Ctr Study Syst Biol, Atlanta, GA 30318 USA
[9]
Arena3D: visualization of biological networks in 3D
[J].
Pavlopoulos, Georgios A.
;
O'Donoghue, Sean I.
;
Satagopam, Venkata P.
;
Soldatos, Theodoros G.
;
Pafilis, Evangelos
;
Schneider, Reinhard
.
BMC SYSTEMS BIOLOGY,
2008, 2

Pavlopoulos, Georgios A.
论文数: 0 引用数: 0
h-index: 0
机构:
EMBL, Struct & Computat Biol Unit, Heidelberg, Germany EMBL, Struct & Computat Biol Unit, Heidelberg, Germany

O'Donoghue, Sean I.
论文数: 0 引用数: 0
h-index: 0
机构:
EMBL, Struct & Computat Biol Unit, Heidelberg, Germany EMBL, Struct & Computat Biol Unit, Heidelberg, Germany

Satagopam, Venkata P.
论文数: 0 引用数: 0
h-index: 0
机构:
EMBL, Struct & Computat Biol Unit, Heidelberg, Germany EMBL, Struct & Computat Biol Unit, Heidelberg, Germany

Soldatos, Theodoros G.
论文数: 0 引用数: 0
h-index: 0
机构:
EMBL, Struct & Computat Biol Unit, Heidelberg, Germany EMBL, Struct & Computat Biol Unit, Heidelberg, Germany

Pafilis, Evangelos
论文数: 0 引用数: 0
h-index: 0
机构:
EMBL, Struct & Computat Biol Unit, Heidelberg, Germany EMBL, Struct & Computat Biol Unit, Heidelberg, Germany

Schneider, Reinhard
论文数: 0 引用数: 0
h-index: 0
机构:
EMBL, Struct & Computat Biol Unit, Heidelberg, Germany EMBL, Struct & Computat Biol Unit, Heidelberg, Germany
[10]
A Poisson-based adaptive affinity propagation clustering for SAGE data
[J].
Tang, DongMing
;
Zhu, QingXin
;
Yang, Fan
.
COMPUTATIONAL BIOLOGY AND CHEMISTRY,
2010, 34 (01)
:63-70

Tang, DongMing
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Elect Sci & Technol China, Sch Comp Sci & Engn, Chengdu 610054, Peoples R China Univ Elect Sci & Technol China, Sch Comp Sci & Engn, Chengdu 610054, Peoples R China

Zhu, QingXin
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Elect Sci & Technol China, Sch Comp Sci & Engn, Chengdu 610054, Peoples R China Univ Elect Sci & Technol China, Sch Comp Sci & Engn, Chengdu 610054, Peoples R China

Yang, Fan
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Elect Sci & Technol China, Sch Comp Sci & Engn, Chengdu 610054, Peoples R China Univ Elect Sci & Technol China, Sch Comp Sci & Engn, Chengdu 610054, Peoples R China