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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
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)

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