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TABLE OF CONTENTS
Issue No. 02 - March-April (vol. 10)
ISSN: 1545-5963

[Front Cover] (PDF)

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[Front inside cover] (PDF)

pp. c2

Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-Dimensional Chain Algorithm (Abstract)

Jikai Lei , Dept. of Comput. Sci. & Eng., Michigan State Univ., East Lansing, MI, USA
Prapaporn Techa-angkoon , Dept. of Comput. Sci. & Eng., Michigan State Univ., East Lansing, MI, USA
Yanni Sun , Dept. of Comput. Sci. & Eng., Michigan State Univ., East Lansing, MI, USA
pp. 274-285

Rough-Fuzzy Clustering for Grouping Functionally Similar Genes from Microarray Data (Abstract)

Pradipta Maji , Machine Intell. Unit, Indian Stat. Inst., Kolkata, India
Sushmita Paul , Machine Intell. Unit, Indian Stat. Inst., Kolkata, India
pp. 286-299

Computational Reconstruction of Transcriptional Relationships from ChIP-Chip Data (Abstract)

Ngoc Tu Le , Sch. of Knowledge Sci., Japan Adv. Inst. of Sci. & Technol., Nomi, Japan
Tu Bao Ho , Sch. of Knowledge Sci., Japan Adv. Inst. of Sci. & Technol., Nomi, Japan
Bich Hai Ho , Inst. of Inf. Technol., Hanoi, Vietnam
pp. 300-307

Guest Editors' Introduction to the Special Section on Computational Methods in Systems Biology (HTML)

Francois Fages , Inria Paris-Rocquencourt, Le Chesnay, France
Sylvain Soliman , Inria Paris-Rocquencourt, Le Chesnay, France
pp. 308-309

The Propagation Approach for Computing Biochemical Reaction Networks (Abstract)

Thomas A. Henzinger , Inst. of Sci. & Technol. Austria (IST Austria), Klosterneuburg, Austria
Maria Mateescu , Inst. of Sci. & Technol. Austria (IST Austria), Klosterneuburg, Austria
pp. 310-322

Curvature Analysis of Cardiac Excitation Wavefronts (Abstract)

Abhishek Murthy , Dept. of Comput. Sci., Stony Brook Univ., Stony Brook, NY, USA
Ezio Bartocci , Fac. of Inf., Vienna Univ. of Technol., Vienna, Austria
Flavio H. Fenton , Dept. of Biomed. Sci., Cornell Univ., Ithaca, NY, USA
James Glimm , Dept. of Comput. Sci., Stony Brook Univ., Stony Brook, NY, USA
Richard A. Gray , Dept. of Appl. Math. & Stat., Stony Brook Univ., Stony Brook, NY, USA
Elizabeth M. Cherry , Office of Sci. & Eng. Labs., Drug Adm., Silver Spring, MD, USA
Scott A. Smolka , Dept. of Comput. Sci., Stony Brook Univ., Stony Brook, NY, USA
Radu Grosu , Dept. of Biomed. Sci., Cornell Univ., Ithaca, NY, USA
pp. 323-336

Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing (Abstract)

Qian Gao , Sch. of Inf. Syst., Comput., & Math., Brunel Univ., Uxbridge, UK
David Gilbert , Sch. of Inf. Syst., Comput., & Math., Brunel Univ., Uxbridge, UK
Monika Heiner , Fac. of Math., Natural Sci. & Comput. Sci., Brandenburg Univ. of Technol. Cottbus, Cottbus, Germany
Fei Liu , Control & Simulation Center, Harbin Inst. of Technol. Sci. Park, Harbin, China
Daniele Maccagnola , Dept. of Comput. Sci. (DISCo), Univ. of Milano-Bicocca, Milano, Italy
David Tree , Sch. of Health Sci. & Social Care, Brunel Univ., Uxbridge, UK
pp. 337-351

A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map (Abstract)

Serdar Bozdag , Dept. of Math., Stat. & Comput. Sci., Marquette Univ., Milwaukee, WI, USA
Timothy J. Close , Dept. of Botany & Plant Sci., Univ. of California, Riverside, Riverside, CA, USA
Stefano Lonardi , Dept. of Comput. Sci. & Eng., Univ. of California, Riverside, Riverside, CA, USA
pp. 352-360

Evaluation of Breast Cancer Susceptibility Using Improved Genetic Algorithms to Generate Genotype SNP Barcodes (Abstract)

Cheng-Hong Yang , Dept. of Electron. Eng., Nat. Kaohsiung Univ. of Appl. Sci., Kaohsiung, Taiwan
Yu-Da Lin , Dept. of Electron. Eng., Nat. Kaohsiung Univ. of Appl. Sci., Kaohsiung, Taiwan
Li-Yeh Chuang , Dept. of Chem. Eng., I-Shou Univ., Kaohsiung, Taiwan
Hsueh-Wei Chang , Dept. of Biomed. Sci. & Environ. Biol., Kaohsiung Med. Univ. Cancer Center, Kaohsiung, Taiwan
pp. 361-371

FNphasing: A Novel Fast Heuristic Algorithm for Haplotype Phasing Based on Flow Network Model (Abstract)

Jiaoyun Yang , Anhui Province & the Sch. of Comput. Sci., Univ. of Sci. & Technol. of China, Hefei, China
Yun Xu , Anhui Province & the Sch. of Comput. Sci., Univ. of Sci. & Technol. of China, Hefei, China
Xiaohui Yao , Anhui Province & the Sch. of Comput. Sci., Univ. of Sci. & Technol. of China, Hefei, China
Guoliang Chen , Anhui Province & the Sch. of Comput. Sci., Univ. of Sci. & Technol. of China, Hefei, China
pp. 372-382

GENESHIFT: A Nonparametric Approach for Integrating Microarray Gene Expression Data Based on the Inner Product as a Distance Measure between the Distributions of Genes (Abstract)

Cosmin Lazar , Dept. of Comput. Sci., Vrije Univ. Brussel, Brussels, Belgium
Jonatan Taminau , Dept. of Comput. Sci., Vrije Univ. Brussel, Brussels, Belgium
Stijn Meganck , Dept. of Comput. Sci., Vrije Univ. Brussel, Brussels, Belgium
David Steenhoff , Dept. of Comput. Sci., Vrije Univ. Brussel, Brussels, Belgium
Alain Coletta , IRIDIA, Univ. Libre de Bruxelles, Brussels, Belgium
David Y. Weiss Solis , IRIDIA, Univ. Libre de Bruxelles, Brussels, Belgium
Colin Molter , IRIDIA, Univ. Libre de Bruxelles, Brussels, Belgium
Robin Duque , IRIDIA, Univ. Libre de Bruxelles, Brussels, Belgium
Hugues Bersini , IRIDIA, Univ. Libre de Bruxelles, Brussels, Belgium
Ann Nowe , Dept. of Comput. Sci., Vrije Univ. Brussel, Brussels, Belgium
pp. 383-392

Gene Regulation Networks in Early Phase of Duchenne Muscular Dystrophy (Abstract)

Camilla Bernardini , Inst. of Anatomy & Cell Biol., Univ. Cattolica del Sacro Cuore, Rome, Italy
Federica Censi , Dept. of Technol. & Health, Ist. Superiore di Sanita, Rome, Italy
Wanda Lattanzi , Inst. of Anatomy & Cell Biol., Univ. Cattolica del Sacro Cuore, Rome, Italy
Giovanni Calcagnini , Dept. of Technol. & Health, Ist. Superiore di Sanita, Rome, Italy
Alessandro Giuliani , Dept. of Environ. & Health, Ist. Superiore di Sanita, Rome, Italy
pp. 393-400

How Many Clusters: A Validation Index for Arbitrary-Shaped Clusters (Abstract)

Ariel E. Baya , French Argentine Int. Center for Inf. & Syst. Sci., UPCAM, France
Pablo M. Granitto , French Argentine Int. Center for Inf. & Syst. Sci., UPCAM, France
pp. 401-414

Mining Featured Patterns of MiRNA Interaction Based on Sequence and Structure Similarity (Abstract)

Qingfeng Chen , State Key Lab. for Conservation & Utilization of Subtropical Agro-bioresources, Guangxi Univ., Nanning, China
Wei Lan , Sch. of Comput., Electron. & Inf., Guangxi Univ., Nanning, China
Jianxin Wang , Sch. of Inf. Sci. & Eng., Central South Univ., Changsha, China
pp. 415-422

Mining Quasi-Bicliques from HIV-1-Human Protein Interaction Network: A Multiobjective Biclustering Approach (Abstract)

Ujjwal Maulik , Dept. of Comput. Sci. & Eng., Jadavpur Univ., Kolkata, India
Anirban Mukhopadhyay , Dept. of Comput. Sci. & Eng., Univ. of Kalyani, Kalyani, India
Malay Bhattacharyya , Dept. of Comput. Sci. & Eng., Univ. of Kalyani, Kalyani, India
Lars Kaderali , Inst. for Med. Inf. & Biometry, Dresden Univ. of Technol., Dresden, Germany
Benedikt Brors , Dept. of Theor. Bioinf., Univ. of Heidelberg, Heidelberg, Germany
Sanghamitra Bandyopadhyay , Machine Intell. Unit, Indian Stat. Inst., Kolkata, India
Roland Eils , Dept. of Theor. Bioinf., Univ. of Heidelberg, Heidelberg, Germany
pp. 423-435

Multilabel Learning via Random Label Selection for Protein Subcellular Multilocations Prediction (Abstract)

Xiao Wang , Dept. of Control Sci. & Eng., Tongji Univ., Shanghai, China
Guo-Zheng Li , Dept. of Control Sci. & Eng., Tongji Univ., Shanghai, China
pp. 436-446

Nonnegative Least-Squares Methods for the Classification of High-Dimensional Biological Data (Abstract)

Yifeng Li , Sch. of Comput. Sci., Univ. of Windsor, Windsor, ON, Canada
Alioune Ngom , Sch. of Comput. Sci., Univ. of Windsor, Windsor, ON, Canada
pp. 447-456

Normalized Feature Vectors: A Novel Alignment-Free Sequence Comparison Method Based on the Numbers of Adjacent Amino Acids (Abstract)

De-Shuang Huang , Sch. of Electron. & Inf. Eng., Tongji Univ., Shanghai, China
Hong-Jie Yu , Dept. of Math., Anhui Sci. & Technol. Univ., Fengyang, China
pp. 457-467

On the Increase in Network Robustness and Decrease in Network Response Ability during the Aging Process: A Systems Biology Approach via Microarray Data (Abstract)

Chien-Ta Tu , Dept. of Electr. Eng., Nat. Tsing Hua Univ., Hsinchu, Taiwan
Bor-Sen Chen , Dept. of Electr. Eng., Nat. Tsing Hua Univ., Hsinchu, Taiwan
pp. 468-480

Pareto Optimal Pairwise Sequence Alignment (Abstract)

Kevin W. DeRonne , Dept. of Comput. Sci. & Eng., Univ. of Minnesota, Minneapolis, MN, USA
George Karypis , Dept. of Comput. Sci. & Eng., Univ. of Minnesota, Minneapolis, MN, USA
pp. 481-493

Profile-Based LC-MS Data Alignment - A Bayesian Approach (Abstract)

Tsung-Heng Tsai , Dept. of Electr. & Comput. Eng., Georgetown Univ., Washington, DC, USA
Mahlet G. Tadesse , Dept. of Math. & Stat., Georgetown Univ., Washington, DC, USA
Yue Wang , Dept. of Electr. & Comput. Eng., Virginia Tech, Arlington, VA, USA
Habtom W. Ressom , Dept. of Oncology, Georgetown Univ., Washington, DC, USA
pp. 494-503

RANGI: A Fast List-Colored Graph Motif Finding Algorithm (Abstract)

Ali Gholami Rudi , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
Saeed Shahrivari , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
Saeed Jalili , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
Zahra Razaghi Moghadam Kashani , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
pp. 504-513

Reconstruction of Signaling Network from Protein Interactions Based on Function Annotations (Abstract)

Wei Liu , Dept. of Autom. Control, Nat. Univ. of Defense Technol., Changsha, China
Dong Li , Beijing Proteome Res. Center, Beijing Inst. of Radiat. Med., Beijing, China
Yunping Zhu , Beijing Proteome Res. Center, Beijing Inst. of Radiat. Med., Beijing, China
Hongwei Xie , Dept. of Autom. Control, Nat. Univ. of Defense Technol., Changsha, China
Fuchu He , Beijing Proteome Res. Center, Beijing Inst. of Radiat. Med., Beijing, China
pp. 514-521

Unrooted Tree Reconciliation: A Unified Approach (Abstract)

Pawel Gorecki , Dept. of Math., Inf. & Mech., Univ. of Warsaw, Warsaw, Poland
Oliver Eulenstein , Dept. of Comput. Sci., Iowa State Univ., Ames, IA, USA
Jerzy Tiuryn , Dept. of Math., Inf. & Mech., Univ. of Warsaw, Warsaw, Poland
pp. 522-536

Parameter Estimation of Biological Phenomena: An Unscented Kalman Filter Approach (Abstract)

N. Meskin , Electr. Eng. Dept., Qatar Univ., Doha, Qatar
H. Nounou , Electr. & Comput. Eng. Program, Texas A&M Univ. at Qatar, Doha, Qatar
M. Nounou , Chem. Eng. Program, Texas A&M Univ. at Qatar, Doha, Qatar
A. Datta , Dept. of Electr. & Comput. Eng., Texas A&M Univ., College Station, TX, USA
pp. 537-543
Call For Papers

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