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TABLE OF CONTENTS
Issue No. 04 - July-Aug. (vol. 9)
ISSN: 1545-5963
Front Covers

[Front cover] (PDF)

pp. c1
Special Section on the IEEE Conference on Bioinformatics and Biomedicine
Special Section on the Seventh International Symposium on Bioinformatics Research and Applications

The Kernel of Maximum Agreement Subtrees (Abstract)

N. D. Pattengale , Sandia Nat. Labs., Albuquerque, NM, USA
E. Chen , Dept. of Biol., Univ. of Ottawa, Ottawa, ON, Canada
K. M. Swenson , Dept. of Math. & Stat., Univ. of Ottawa, Montreal, QC, Canada
D. Sankoff , Dept. of Math. & Stat., Univ. of Ottawa, Ottawa, ON, Canada
pp. 1023-1031
Regular Papers

BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences (Abstract)

R. Marangoni , Dept. of Comput. Sci., Univ. of Pisa, Pisa, Italy
C. Felicioli , Noname Res., Pisa, Italy
pp. 1120-1127
Short Papers

A New Unsupervised Feature Ranking Method for Gene Expression Data Based on Consensus Affinity (Abstract)

Hau-San Wong , Dept. of Comput. Sci., City Univ. of Hong Kong, Kowloon, China
Shaohong Zhang , Dept. of Comput. Sci., Guangzhou Univ., Guangzhou, China
Ying Shen , Dept. of Comput. Sci., City Univ. of Hong Kong, Kowloon, China
Dongqing Xie , Dept. of Comput. Sci., Guangzhou Univ., Guangzhou, China
pp. 1257-1263
Regular Papers

Efficient Genotype Elimination via Adaptive Allele Consolidation (Abstract)

N. De Francesco , Dipt. di Ing. dell'Inf.: Elettron., Inf., Telecomun, Univ. di Pisa, Pisa, Italy
G. Lettieri , Dipt. di Ing. dell'Inf.: Elettron., Inf., Telecomun., Univ. di Pisa, Pisa, Italy
L. Martini , S.p.A., Pisa, Italy
pp. 1180-1189

Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction (Abstract)

Zhihao Yang , Coll. of Comput. Sci., Dalian Univ. of Technol., Dalian, China
Hongfei Lin , Coll. of Comput. Sci., Dalian Univ. of Technol., Dalian, China
Yijia Zhang , Coll. of Comput. Sci., Dalian Univ. of Technol., Dalian, China
Jian Wang , Coll. of Comput. Sci., Dalian Univ. of Technol., Dalian, China
Yanpeng Li , Coll. of Comput. Sci., Dalian Univ. of Technol., Dalian, China
pp. 1190-1202

Detection of Outlier Residues for Improving Interface Prediction in Protein Heterocomplexes (Abstract)

Limsoon Wong , Sch. of Comput., Nat. Univ. of Singapore, Singapore, Singapore
Peng Chen , Inst. of Intell. Machines, Hefei, China
Jinyan Li , Sch. of Comput., Nat. Univ. of Singapore, Singapore, Singapore
pp. 1155-1165
Special Section on the Seventh International Symposium on Bioinformatics Research and Applications

Refining Regulatory Networks through Phylogenetic Transfer of Information (Abstract)

Xiuwei Zhang , Lab. for Comput. Biol. & Bioinf., Ecole Polytech. Fed. de Lausanne, Lausanne, Switzerland
B. M. E. Moret , Lab. for Comput. Biol. & Bioinf., Ecole Polytech. Fed. de Lausanne, Lausanne, Switzerland
pp. 1032-1045
Special Section on the IEEE Conference on Bioinformatics and Biomedicine

A Sparse Regulatory Network of Copy-Number Driven Gene Expression Reveals Putative Breast Cancer Oncogenes (Abstract)

C. Caldas , Li Ka Shing Centre, Cambridge Res. Inst., Cambridge, UK
C. Curtis , Dept. of Preventive Med., Univ. of Southern California, Los Angeles, CA, USA
Yinyin Yuan , Li Ka Shing Centre, Cambridge Res. Inst., Cambridge, UK
F. Markowetz , Li Ka Shing Centre, Cambridge Res. Inst., Cambridge, UK
pp. 947-954
Special Section on the Seventh International Symposium on Bioinformatics Research and Applications

Algorithms to Detect Multiprotein Modularity Conserved during Evolution (Abstract)

R. M. Karp , Div. of Comput. Sci., Univ. of California, Berkeley, CA, USA
L. Hodgkinson , Div. of Comput. Sci., Univ. of California, Berkeley, CA, USA
pp. 1046-1058
Regular Papers

Efficient Approaches for Retrieving Protein Tertiary Structures (Abstract)

Georgina Mirceva , Dept. of Comput. Sci. & Comput. Eng., Ss. Cyril & Methodius Univ. in Skopje, Macedonia, Skopje, Macedonia
Ivana Cingovska , Dept. of Comput. Sci. & Comput. Eng., Ss. Cyril & Methodius Univ. in Skopje, Macedonia, Skopje, Macedonia
Zoran Dimov , Microsoft Corp., Seattle, WA, USA
Danco Davcev , Dept. of Comput. Sci. & Comput. Eng., Ss. Cyril & Methodius Univ. in Skopje, Macedonia, Skopje, Macedonia
pp. 1166-1179

Peptide Reranking with Protein-Peptide Correspondence and Precursor Peak Intensity Information (Abstract)

Can Yang , Yale Sch. of Public Health, Yale Univ., New Haven, CT, USA
Zengyou He , Sch. of Software, Dalian Univ. of Technol., Dalian, China
Chao Yang , Hong Kong Univ. of Sci. & Technol., Kowloon, China
Weichuan Yu , Dept. of Electron. & Comput. Eng., Hong Kong Univ. of Sci. & Technol., Kowloon, China
pp. 1212-1219

A Survey on Filter Techniques for Feature Selection in Gene Expression Microarray Analysis (Abstract)

V. de Schaetzen , Univ. Libre de Bruxelles, Brussels, Belgium
C. Molter , Univ. Libre de Bruxelles, Brussels, Belgium
A. Coletta , Univ. Libre de Bruxelles, Brussels, Belgium
D. Steenhoff , Dept. of Comput. Sci., Vrije Univ. Brussel, Brussels, Belgium
S. Meganck , Dept. of Comput. Sci., Vrije Univ. Brussel, Brussels, Belgium
J. Taminau , Dept. of Comput. Sci., Vrije Univ. Brussel, Brussels, Belgium
C. Lazar , Dept. of Comput. Sci., Vrije Univ. Brussel, Brussels, Belgium
R. Duque , Univ. Libre de Bruxelles, Brussels, Belgium
H. Bersini , IRIDIA, Univ. Libre de Bruxelles, Bruxelles, Belgium
A. Nowe , Dept. of Comput. Sci., Vrije Univ. Brussel, Brussels, Belgium
pp. 1106-1119

Transient Dynamics of Reduced-Order Models of Genetic Regulatory Networks (Abstract)

R. Pal , Dept. of Electr. & Comput. Eng., Texas Tech Univ., Lubbock, TX, USA
S. Bhattacharya , Dept. of Electr. & Comput. Eng., Texas Tech Univ., Lubbock, TX, USA
pp. 1230-1244

Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform (Abstract)

J. Dopazo Blazquez , Bioinf. & Genomics Dept., CIPF, Valencia, Spain
J. Terraga Gimenez , Bioinf. & Genomics Dept., CIPF, Valencia, Spain
I. Medina Castello , Bioinf. & Genomics Dept., CIPF, Valencia, Spain
V. Hernendez Garcia , Centro Mixto CSIC, Univ. Politec. de Valencia-CIEMAT, Valencia, Spain
I. B. Espert , Centro Mixto CSIC, Univ. Politec. de Valencia-CIEMAT, Valencia, Spain
A. T. Dominguez , Centro Mixto CSIC, Univ. Politec. de Valencia-CIEMAT, Valencia, Spain
J. S. Torres , Centro Mixto CSIC, Univ. Politec. de Valencia-CIEMAT, Valencia, Spain
pp. 1245-1256

Scaffold Filling under the Breakpoint and Related Distances (Abstract)

Chunfang Zheng , Dept. d'Inf. et de Rech. Operationnelle, Univ. de Montreal, Montreal, QC, Canada
Haitao Jiang , Sch. of Comput. Sci. & Technol., Shandong Univ., Jinan, China
D. Sankoff , Dept. of Math. & Stat., Univ. of Ottawa, Ottawa, ON, Canada
Binhai Zhu , Dept. of Comput. Sci., Montana State Univ., Bozeman, MT, USA
pp. 1220-1229
Special Section on the IEEE Conference on Bioinformatics and Biomedicine

Exploiting the Functional and Taxonomic Structure of Genomic Data by Probabilistic Topic Modeling (Abstract)

T. Y. Lim , Coll. of Comput. & Inf. Eng., Henan Univ., Kaifeng, China
Xiaohua Hu , Coll. of Inf. Sci. & Technol., Drexel Univ., Philadelphia, PA, USA
Xin Chen , Coll. of Inf. Sci. & Technol., Drexel Univ., Philadelphia, PA, USA
Xiajiong Shen , California State Univ. - Chico, Chico, CA, USA
E. K. Park , Dept. of Electr. & Comput. Eng., Drexel Univ., Philadelphia, PA, USA
G. L. Rosen , Dept. of Electr. & Comput. Eng., Drexel Univ., Philadelphia, PA, USA
pp. 980-991

Predicting Ligand Binding Residues and Functional Sites Using Multipositional Correlations with Graph Theoretic Clustering and Kernel CCA (Abstract)

Li Liao , Comput. & Inf. Sci. Dept., Univ. of Delaware, Newark, DE, USA
A. J. Gonzalez , Comput. & Inf. Sci. Dept., Univ. of Delaware, Newark, DE, USA
C. H. Wu , Center for Bioinf. & Comput. Biol., Univ. of Delaware, Newark, DE, USA
pp. 992-1001

Stochastic Gene Expression Modeling with Hill Function for Switch-Like Gene Responses (Abstract)

Haseong Kim , Dept. of Electr. & Electron. Eng., Imperial Coll. London, London, UK
E. Gelenbe , Dept. of Electr. & Electron. Eng., Imperial Coll. London, London, UK
pp. 973-979
Special Section on the Seventh International Symposium on Bioinformatics Research and Applications

A Metric for Phylogenetic Trees Based on Matching (Abstract)

Yu Lin , Lab. for Comput. Biol. & Bioinf., Swiss Fed. Inst. of Technol. (EPFL), Lausanne, Switzerland
V. Rajan , Lab. for Comput. Biol. & Bioinf., Swiss Fed. Inst. of Technol. (EPFL), Lausanne, Switzerland
B. M. E. Moret , Lab. for Comput. Biol. & Bioinf., Swiss Fed. Inst. of Technol. (EPFL), Lausanne, Switzerland
pp. 1014-1022
Regular Papers

Inferring Gene Regulatory Networks via Nonlinear State-Space Models and Exploiting Sparsity (Abstract)

E. Serpedin , Dept. of Electr. & Comput. Eng., Texas A& M Univ., College Station, TX, USA
A. Noor , Dept. of Electr. & Comput. Eng., Texas A& M Univ., College Station, TX, USA
M. Nounou , Chem. Eng. Dept., Texas A&M Univ. at Qatar, Doha, Qatar
Hazem N. Nounou , Electr. Eng. Dept., Texas A&M Univ. at Qatar, Doha, Qatar
pp. 1203-1211

CSD Homomorphisms between Phylogenetic Networks (Abstract)

S. J. Willson , Dept. of Math., Iowa State Univ., Ames, IA, USA
pp. 1128-1138
Special Section on the Seventh International Symposium on Bioinformatics Research and Applications

Identification of Essential Proteins Based on Edge Clustering Coefficient (Abstract)

Min Li , Sch. of Inf. Sci. & Eng., Central South Univ., Changsha, China
Jianxin Wang , Sch. of Inf. Sci. & Eng., Central South Univ., Changsha, China
Huan Wang , Sch. of Inf. Sci. & Eng., Central South Univ., Changsha, China
Yi Pan , Dept. of Comput. Sci., Georgia State Univ., Atlanta, GA, USA
pp. 1070-1080

Predicting Protein Function by Multi-Label Correlated Semi-Supervised Learning (Abstract)

L. J. McQuay , Pharmacoepidemiology & Risk Manage. Div., RTI Health Solutions, Research Triangle Park, NC, USA
J. Q. Jiang , Dept. of Inf. Syst., City Univ. of Hong Kong, Kowloon, China
pp. 1059-1069
Regular Papers

A Hybrid Approach to Survival Model Building Using Integration of Clinical and Molecular Information in Censored Data (Abstract)

M. W. Kattan , Dept. of Quantitative Health Sci., Cleveland Clinic Found., Cleveland, OH, USA
Ickwon Choi , Dept. of Electr. Eng. & Comput. Sci., Case Western Reserve Univ., Cleveland, OH, USA
B. J. Wells , Dept. of Quantitative Health Sci., Cleveland Clinic Found., Cleveland, OH, USA
Changhong Yu , Dept. of Quantitative Health Sci., Cleveland Clinic Found., Cleveland, OH, USA
pp. 1091-1105

De Novo Design of Potential RecA Inhibitors Using MultiObjective Optimization (Abstract)

S. Bandyopadhyay , Machine Intell. Unit, Indian Stat. Inst., Kolkata, India
S. Sengupta , Machine Intell. Unit, Indian Stat. Inst., Kolkata, India
pp. 1139-1154
Special Section on the Seventh International Symposium on Bioinformatics Research and Applications

Fast Local Search for Unrooted Robinson-Foulds Supertrees (Abstract)

J. G. Burleigh , Dept. of Biol., Univ. of Florida, Gainesville, FL, USA
R. Chaudhary , Dept. of Comput. Sci., Iowa State Univ., Ames, IA, USA
D. Fernandez-Baca , Dept. of Comput. Sci., Iowa State Univ., Ames, IA, USA
pp. 1004-1013
Regular Papers

A Computational Model for Predicting Protein Interactions Based on Multidomain Collaboration (Abstract)

Suk-Hoon Jung , Dept. of Inf. & Commun. Eng., Korea Adv. Inst. of Sci. & Technol., Daejeon, South Korea
Woo-Hyuk Jang , Dept. of Inf. & Commun. Eng., Korea Adv. Inst. of Sci. & Technol., Daejeon, South Korea
Dong-Soo Han , Dept. of Inf. & Commun. Eng., Korea Adv. Inst. of Sci. & Technol., Daejeon, South Korea
pp. 1081-1090
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