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TABLE OF CONTENTS
Issue No. 04 - July-Aug. (vol. 10)
ISSN: 1545-5963

[Front Cover] (PDF)

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[front inside cover] (PDF)

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Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes (Abstract)

Pedro Feijao , Inst. of Comput., Univ. of Campinas, Campinas, Brazil
Joao Meidanis , Inst. of Comput., Univ. of Campinas, Campinas, Brazil
pp. 819-831

2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction (Abstract)

Ronny Lorenz , Dept. of Theor. Chem., Univ. of Vienna, Vienna, Austria
Stephan H. Bernhart , Dept. of Comput. Sci., Univ. of Leipzig, Leipzig, Germany
Jing Qin , Max Planck Inst. for Math. in the Sci., Leipzig, Germany
Christian Honer Zu Siederdissen , Dept. of Theor. Chem., Univ. of Vienna, Vienna, Austria
Andrea Tanzer , Dept. of Theor. Chem., Univ. of Vienna, Vienna, Austria
Fabian Amman , Dept. of Theor. Chem., Univ. of Vienna, Vienna, Austria
Ivo L. Hofacker , Dept. of Theor. Chem., Univ. of Vienna, Vienna, Austria
Peter F. Stadler , Dept. of Comput. Sci., Univ. of Leipzig, Leipzig, Germany
pp. 832-844

Proximity Measures for Clustering Gene Expression Microarray Data: A Validation Methodology and a Comparative Analysis (Abstract)

Pablo A. Jaskowiak , Inst. of Math. & Comput. Sci., Univ. of Sao Paulo, Sao Carlos, Brazil
Ricardo J. G. B. Campello , Inst. of Math. & Comput. Sci., Univ. of Sao Paulo, Sao Carlos, Brazil
Ivan G. Costa , Center of Inf., Fed. Univ. of Pernambuco, Recife, Brazil
pp. 845-857

A Closed-Loop Control Scheme for Steering Steady States of Glycolysis and Glycogenolysis Pathway (Abstract)

Surajit Panja , Dept. of Electr. Eng., Indian Inst. of Technol. Kharagpur, Kharagpur, India
Sourav Patra , Dept. of Electr. Eng., Indian Inst. of Technol. Kharagpur, Kharagpur, India
Anirban Mukherjee , Dept. of Electr. Eng., Indian Inst. of Technol. Kharagpur, Kharagpur, India
Madhumita Basu , Dept. of Biochem., Univ. of Calcutta, Kolkata, India
Sanghamitra Sengupta , Dept. of Biochem., Univ. of Calcutta, Kolkata, India
Pranab K. Dutta , Dept. of Electr. Eng., Indian Inst. of Technol. Kharagpur, Kharagpur, India
pp. 858-868

A Divide and Conquer Approach for Construction of Large-Scale Signaling Networks from PPI and RNAi Data Using Linear Programming (Abstract)

Oyku Eren Ozsoy , Inf. Inst., Middle East Tech. Univ., Ankara, Turkey
Tolga Can , Dept. of Comput. Eng., Middle East Tech. Univ., Ankara, Turkey
pp. 869-883

A Knowledge-Based Multiple-Sequence Alignment Algorithm (Abstract)

Ken D. Nguyen , Dept. of Comput. Sci. & Inf. Technol., Clayton State Univ., Morrow, GA, USA
Yi Pan , Dept. of Comput. Sci., Georgia State Univ., Atlanta, GA, USA
pp. 884-896

A Two-Phase Bio-NER System Based on Integrated Classifiers and Multiagent Strategy (Abstract)

Lishuang Li , Coll. of Comput. Sci. & Technol., Dalian Univ. of Technol., Dalian, China
Wenting Fan , Coll. of Comput. Sci. & Technol., Dalian Univ. of Technol., Dalian, China
Degen Huang , Coll. of Comput. Sci. & Technol., Dalian Univ. of Technol., Dalian, China
pp. 897-904

An Improved Approximation Algorithm for Scaffold Filling to Maximize the Common Adjacencies (Abstract)

Nan Liu , Sch. of Comput. Sci. & Technol., Shandong Univ., Jinan, China
Haitao Jiang , Sch. of Comput. Sci. & Technol., Shandong Univ., Jinan, China
Daming Zhu , Sch. of Comput. Sci. & Technol., Shandong Univ., Jinan, China
Binhai Zhu , Dept. of Comput. Sci., Montana State Univ., Bozeman, MT, USA
pp. 905-913

An Optimization Rule for In Silico Identification of Targeted Overproduction in Metabolic Pathways (Abstract)

Mouli Das , Machine Intell. Unit, Indian Stat. Inst., Kolkata, India
C. A. Murthy , Machine Intell. Unit, Indian Stat. Inst., Kolkata, India
Rajat K. De , Machine Intell. Unit, Indian Stat. Inst., Kolkata, India
pp. 914-926

Algebraic Representation of Asynchronous Multiple-Valued Networks and Its Dynamics (Abstract)

Chao Luo , Fac. of Electron. Inf. & Electr. Eng., Dalian Univ. of Technol., Dalian, China
Xingyuan Wang , Fac. of Electron. Inf. & Electr. Eng., Dalian Univ. of Technol., Dalian, China
pp. 927-938

Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony (Abstract)

Mukul S. Bansal , Comput. Sci. & Artificial Intell. Lab., Massachusetts Inst. of Technol., Cambridge, MA, USA
Oliver Eulenstein , Dept. of Comput. Sci., Iowa State Univ., Ames, IA, USA
pp. 939-956

Analytical Solution of Steady-State Equations for Chemical Reaction Networks with Bilinear Rate Laws (Abstract)

Adam M. Halasz , Dept. of Math., West Virginia Univ., Morgantown, WV, USA
Hong-Jian Lai , Dept. of Math., West Virginia Univ., Morgantown, WV, USA
Meghan McCabe Pryor , Dept. of Chem. & Nucl. Eng., Univ. of New Mexico, Albuquerque, NM, USA
Krishnan Radhakrishnan , Dept. of Preventive Med. & Environ. Health, Univ. of Kentucky, Lexington, KY, USA
Jeremy S. Edwards , Dept. of Mol. Genetics & Microbiol., Univ. of New Mexico Health Sci. Center, NM, USA
pp. 957-969

Characterizing the Topology of Probabilistic Biological Networks (Abstract)

Andrei Todor , Dept. of Comput. & Inf. Sci. & Eng., Univ. of Florida, Gainesville, FL, USA
Alin Dobra , Dept. of Comput. & Inf. Sci. & Eng., Univ. of Florida, Gainesville, FL, USA
Tamer Kahveci , Dept. of Comput. & Inf. Sci. & Eng., Univ. of Florida, Gainesville, FL, USA
pp. 970-983

Decomposition of Flux Distributions into Metabolic Pathways (Abstract)

Onur Seref , Dept. of Bus. Inf. Technol., Virginia Polytech. Inst. & State Univ., Blacksburg, VA, USA
J. Paul Brooks , Dept. of Stat. Sci. & Oper. Res., Virginia Commonwealth Univ., Richmond, VA, USA
Stephen S. Fong , Dept. of Chem. & Life Sci. Eng., Virginia Commonwealth Univ., Richmond, VA, USA
pp. 984-993

Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering (Abstract)

Dong-Jun Yu , Sch. of Comput. Sci. & Eng., Nanjing Univ. of Sci. & Technol., Nanjing, China
Jun Hu , Sch. of Comput. Sci. & Eng., Nanjing Univ. of Sci. & Technol., Nanjing, China
Jing Yang , Key Lab. of Syst. Control & Inf. Process., Shanghai Jiao Tong Univ., Shanghai, China
Hong-Bin Shen , Key Lab. of Syst. Control & Inf. Process., Shanghai Jiao Tong Univ., Shanghai, China
Jinhui Tang , Sch. of Comput. Sci. & Eng., Nanjing Univ. of Sci. & Technol., Nanjing, China
Jing-Yu Yang , Sch. of Comput. Sci. & Eng., Nanjing Univ. of Sci. & Technol., Nanjing, China
pp. 994-1008

GeneOnEarth: Fitting Genetic PC Plots on the Globe (Abstract)

Sergio Torres-Sanchez , Dept. de Lenguajes y Sist. Informaticos, Univ. de Granada, Granada, Spain
Nuria Medina-Medina , Dept. de Lenguajes y Sist. Informaticos, Univ. de Granada, Granada, Spain
Chris Gignoux , Dept. of Med., Univ. of California San Francisco, San Francisco, CA, USA
Maria M. Abad-Grau , Dept. de Lenguajes y Sist. Informaticos, Univ. de Granada, Granada, Spain
Esteban Gonzalez-Burchard , Dept. of Med., Univ. of California San Francisco, San Francisco, CA, USA
pp. 1009-1016

Identification of DNA-Binding and Protein-Binding Proteins Using Enhanced Graph Wavelet Features (Abstract)

Yuan Zhu , Dept. of Math., Guangdong Univ. of Finance & Econ., Guangzhou, China
Weiqiang Zhou , Dept. of Electron. Eng., City Univ. of Hong Kong, Kowloon, China
Dao-Qing Dai , Dept. of Math., Sun Yat-Sen Univ., Guangzhou, China
Hong Yan , Dept. of Electron. Eng., City Univ. of Hong Kong, Kowloon, China
pp. 1017-1031

Pareto Optimality in Organelle Energy Metabolism Analysis (Abstract)

Claudio Angione , Comput. Lab., Univ. of Cambridge, Cambridge, UK
Giovanni Carapezza , Dept. of Math. & Comput. Sci., Univ. of Catania, Catania, Italy
Jole Costanza , Dept. of Math. & Comput. Sci., Univ. of Catania, Catania, Italy
Pietro Lio , Comput. Lab., Univ. of Cambridge, Cambridge, UK
Giuseppe Nicosia , Dept. of Math. & Comput. Sci., Univ. of Catania, Catania, Italy
pp. 1032-1044

Protein Function Prediction Using Multilabel Ensemble Classification (Abstract)

Guoxian Yu , Coll. of Comput. & Inf. Sci., Southwest Univ., Beibei, China
Huzefa Rangwala , Dept. of Comput. Sci., George Mason Univ., Fairfax, VA, USA
Carlotta Domeniconi , Dept. of Comput. Sci., George Mason Univ., Fairfax, VA, USA
Guoji Zhang , Sch. of Sci., South China Univ. of Technol., Guangzhou, China
Zhiwen Yu , Sch. of Comput. Sci. & Eng., South China Univ. of Technol., Guangzhou, China
pp. 1045-1057

Temporal Logics for Phylogenetic Analysis via Model Checking (Abstract)

Jose Ignacio Requeno , Dept. Inf. e Ing. de Sist., Univ. de Zaragoza, Zaragoza, Spain
Gregorio De Miguel Casado , Dept. Inf. e Ing. de Sist., Univ. de Zaragoza, Zaragoza, Spain
Roberto Blanco , Dept. Inf. e Ing. de Sist., Univ. de Zaragoza, Zaragoza, Spain
Jose Manuel Colom , Dept. Inf. e Ing. de Sist., Univ. de Zaragoza, Zaragoza, Spain
pp. 1058-1070

Application of Dempster-Schafer Method in Family-Based Association Studies (Abstract)

Farid Rajabli , Dept. of Electr. & Electron. Eng., Turgut Ozal Univ., Ankara, Turkey
Unal Goktas , Dept. of Comput. Eng., Turgut Ozal Univ., Ankara, Turkey
Gul Inan , Dept. of Stat., Middle East Tech. Univ., Ankara, Turkey
pp. 1071-1075

Hamiltonian Walks of Phylogenetic Treespaces (Abstract)

Kevaughn Gordon , Dept. of Math. & Comput. Sci., City Univ. of New York, New York, NY, USA
Eric Ford , Dept. of Comput. Sci., City Univ. of New York, New York, NY, USA
Katherine St. John , Dept. of Math. & Comput. Sci., City Univ. of New York, New York, NY, USA
pp. 1076-1079

Hierarchical Clustering of High- Throughput Expression Data Based on General Dependences (Abstract)

Tianwei Yu , Dept. of Biostat. & Bioinf., Emory Univ., Atlanta, GA, USA
Hesen Peng , Dept. of Biostat. & Bioinf., Emory Univ., Atlanta, GA, USA
pp. 1080-1085

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