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TABLE OF CONTENTS
Issue No. 02 - March/April (vol. 9)
ISSN: 1545-5963
Papers

A New Efficient Algorithm for the Gene-Team Problem on General Sequences (Abstract)

Chung-Chin Kuo , National Tsing Hua University, Hsinchu
Biing-Feng Wang , National Tsing Hua University, Hsinchu
Chien-Hsin Lin , National Tsing Hua University, Hsinchu
Shang-Ju Liu , National Tsing Hua University, Hsinchu
pp. 330-344

A Hybrid EKF and Switching PSO Algorithm for Joint State and Parameter Estimation of Lateral Flow Immunoassay Models (Abstract)

Nianyin Zeng , Fujian Key Lab. of Med. Instrum. & Pharm. Technol., Fuzhou Univ., Fuzhou, China
Zidong Wang , Dept. of Inf. Syst. & Comput., Brunel Univ., Uxbridge, UK
Yurong Li , Fujian Key Lab. of Med. Instrum. & Pharm. Technol., Fuzhou Univ., Fuzhou, China
Min Du , Fujian Key Lab. of Med. Instrum. & Pharm. Technol., Fuzhou Univ., Fuzhou, China
Xiaohui Liu , Dept. of Inf. Syst. & Comput., Brunel Univ., Uxbridge, UK
pp. 321-329

A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences (Abstract)

S. Steinbiss , Center for Bioinf., Univ. of Hamburg, Hamburg, Germany
S. Kurtz , Center for Bioinf., Univ. of Hamburg, Hamburg, Germany
pp. 345-357

A Swarm Intelligence Framework for Reconstructing Gene Networks: Searching for Biologically Plausible Architectures (Abstract)

K. Kentzoglanakis , Div. of Math. Biol., MRC Nat. Inst. of Med. Res., London, UK
M. Poole , Sch. of Comput., Univ. of Portsmouth, Portsmouth, UK
pp. 358-371

Algorithms for Reticulate Networks of Multiple Phylogenetic Trees (Abstract)

Zhi-Zhong Chen , Div. of Inf. Syst. Design, Tokyo Denki Univ., Saitama, Japan
Lusheng Wang , Dept. of Comput. Sci., City Univ. of Hong Kong, Kowloon, China
pp. 372-384

Antilope—A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem (Abstract)

S. Andreotti , Inst. fur Inf., Freie Univ. Berlin, Berlin, Germany
G. W. Klau , Life Sci. Group, CWI, Amsterdam, Netherlands
K. Reinert , Inst. fur Inf., Freie Univ. Berlin, Berlin, Germany
pp. 385-394

Constructing and Drawing Regular Planar Split Networks (Abstract)

A. Spillner , Dept. of Math. & Comput. Sci., Univ. of Greifswald, Greifswald, Germany
B. T. Nguyen , Sch. of Comput. Sci., Univ. of East Anglia, Norwich, UK
V. Moulton , Sch. of Comput. Sci., Univ. of East Anglia, Norwich, UK
pp. 395-407

DICLENS: Divisive Clustering Ensemble with Automatic Cluster Number (Abstract)

S. Mimaroglu , Dept. of Comput. Eng., Bahcesehir Univ., Istanbul, Turkey
E. Aksehirli , Dept. of Comput. Eng., Bahcesehir Univ., Istanbul, Turkey
pp. 408-420

Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree (Abstract)

M. O. Kulekci , Nat. Res. Inst. of Electron. & Cryptology, Gebze, Turkey
J. S. Vitter , Dept. of Electr. Eng. & Comput. Sci., Univ. of Kansas, Lawrence, KS, USA
Bojian Xu , Comput. Sci. Dept., Eastern Washington Univ., Cheney, WA, USA
pp. 421-429

Eigen-Genomic System Dynamic-Pattern Analysis (ESDA): Modeling mRNA Degradation and Self-Regulation (Abstract)

Daifeng Wang , Dept. of Electr. & Comput. Eng., Univ. of Texas, Austin, TX, USA
M. K. Markey , Dept. of Biomed. Eng., Univ. of Texas, Austin, TX, USA
C. O. Wilke , Center for Comput. Biol. & Bioinf., Univ. of Texas, Austin, TX, USA
A. Arapostathis , Dept. of Electr. & Comput. Eng., Univ. of Texas, Austin, TX, USA
pp. 430-437

GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets (Abstract)

L. Acharya , Dept. of Comput. Sci., Univ. of New Orleans, New Orleans, LA, USA
T. Judeh , Dept. of Comput. Sci., Wayne State Univ., Detroit, MI, USA
Zhansheng Duan , Dept. of Comput. Sci., Univ. of New Orleans, New Orleans, LA, USA
M. Rabbat , Dept. of Electr. & Comput. Eng., McGill Univ., Montreal, QC, Canada
Dongxiao Zhu , Dept. of Comput. Sci., Wayne State Univ., Detroit, MI, USA
pp. 438-450

Identification of Differentially Expressed Genes for Time-Course Microarray Data Based on Modified RM ANOVA (Abstract)

O. ElBakry , Dept. of Electr. & Comput. Eng., Concordia Univ., Montreal, QC, Canada
M. O. Ahmad , Dept. of Electr. & Comput. Eng., Concordia Univ., Montreal, QC, Canada
M. N. S. Swamy , Dept. of Electr. & Comput. Eng., Concordia Univ., Montreal, QC, Canada
pp. 451-466

Identifying Bacterial Virulent Proteins by Fusing a Set of Classifiers Based on Variants of Chou's Pseudo Amino Acid Composition and on Evolutionary Information (Abstract)

L. Nanni , Dept. of Inf. Eng., Univ. of Padua, Padova, Italy
A. Lumini , DEIS, Univ. of Bologna, Cesena, Italy
D. Gupta , Struct. & Comput. Biol. Group, Int. Centre for Genetic Eng. & Biotechnol. (ICGEB), New Delhi, India
A. Garg , Struct. & Comput. Biol. Group, Int. Centre for Genetic Eng. & Biotechnol. (ICGEB), New Delhi, India
pp. 467-475

Molecular Dynamics Trajectory Compression with a Coarse-Grained Model (Abstract)

Yi-Ming Cheng , Dept. of Biochem. & Mol. Biol., Michigan State Univ., East Lansing, MI, USA
S. M. Gopal , Dept. of Biochem. & Mol. Biol., Michigan State Univ., East Lansing, MI, USA
S. M. Law , Dept. of Biochem. & Mol. Biol., Michigan State Univ., East Lansing, MI, USA
M. Feig , Dept. of Biochem. & Mol. Biol., Chem., & Comput. Sci. & Eng., Michigan State Univ., East Lansing, MI, USA
pp. 476-486

Multiscale Binarization of Gene Expression Data for Reconstructing Boolean Networks (Abstract)

M. Hopfensitz , Res. Group of Bioinf. & Syst. Biol., Ulm Univ., Ulm, Germany
C. Mussel , Res. Group of Bioinf. & Syst. Biol., Ulm Univ., Ulm, Germany
C. Wawra , Res. Group of Bioinf. & Syst. Biol., Ulm Univ., Ulm, Germany
M. Maucher , Res. Group of Bioinf. & Syst. Biol., Ulm Univ., Ulm, Germany
M. Kuhl , Inst. of Biochem. & Mol. Biol., Ulm Univ., Ulm, Germany
H. Neumann , Inst. of Neural Inf. Process., Ulm Univ., Ulm, Germany
H. A. Kestler , Res. Group of Bioinf. & Syst. Biol., Ulm Univ., Ulm, Germany
pp. 487-498

Mutation Region Detection for Closely Related Individuals without a Known Pedigree (Abstract)

Wenji Ma , Dept. of Comput. Sci., City Univ. of Hong Kong, Hong Kong, China
Yong Yang , Dept. of Comput. Sci., City Univ. of Hong Kong, Hong Kong, China
Zhi-Zhong Chen , Dept. of Inf. Syst. Design, Tokyo Denki Univ., Tokyo, Japan
Lusheng Wang , Dept. of Comput. Sci., City Univ. of Hong Kong, Hong Kong, China
pp. 499-510

On Complexity of Protein Structure Alignment Problem under Distance Constraint (Abstract)

A. Poleksic , Dept. of Comput. Sci., Univ. of Northern Iowa, Cedar Falls, IA, USA
pp. 511-516

On the Elusiveness of Clusters (Abstract)

S. Kelk , Dept. of Knowledge Eng. (DKE), Maastricht Univ., Maastricht, Netherlands
C. Scornavacca , Center for Bioinf. (ZBIT), Tubingen Univ., Tubingen, Germany
L. van Iersel , Dept. of Math. & Stat., Univ. of Canterbury, Christchurch, New Zealand
pp. 517-534

Optimizing Phylogenetic Networks for Circular Split Systems (Abstract)

P. Phipps , Univ. of Texas at Dallas, Plano, TX, USA
S. Bereg , Dept. of Comput. Sci., Univ. of Texas at Dallas, Richardson, TX, USA
pp. 535-547

Output-Sensitive Algorithms for Finding the Nested Common Intervals of Two General Sequences (Abstract)

Biing-Feng Wang , Dept. of Comput. Sci., Nat. Tsing Hua Univ., Hsinchu, Taiwan
pp. 548-559

Parallelized Evolutionary Learning for Detection of Biclusters in Gene Expression Data (Abstract)

Qinghua Huang , Sch. of Electron. & Inf. Eng., South China Univ. of Technol., Guangzhou, China
Dacheng Tao , Centre for Quantum Comput. & Intell. Syst., Univ. of Technol., Sydney, NSW, Australia
Xuelong Li , State Key Lab. of Transient Opt. & Photonics, Xi'an Inst. of Opt. & Precision Mech., Xi'an, China
A. Liew , Sch. of Inf. & Commun. Technol., Griffith Univ., Griffith, QLD, Australia
pp. 560-570

Quantum Gate Circuit Model of Signal Integration in Bacterial Quorum Sensing (Abstract)

I. G. Karafyllidis , Dept. of Electr. & Comput. Eng., Democritus Univ. of Thrace, Xanthi, Greece
pp. 571-579

Robust Classification Method of Tumor Subtype by Using Correlation Filters (Abstract)

Shu-Lin Wang , Coll. of Inf. Sci. & Eng., Hunan Univ., Changsha, China
Yi-Hai Zhu , Intell. Comput. Lab., Hefei Inst. of Intell. Machines, Hefei, China
Wei Jia , Intell. Comput. Lab., Hefei Inst. of Intell. Machines, Hefei, China
De-Shuang Huang , Sch. of Electron. & Inf. Eng., Tongji Univ., Shanghai, China
pp. 580-591

SimBioNeT: A Simulator of Biological Network Topology (Abstract)

B. Di Camillo , Inf. Eng. Dept., Univ. of Padova, Padova, Italy
M. Falda , Biol. Chem. Dept., Univ. of Padova, Padova, Italy
G. Toffolo , Inf. Eng. Dept., Univ. of Padova, Padova, Italy
C. Cobelli , Inf. Eng. Dept., Univ. of Padova, Padova, Italy
pp. 592-600

Structural SCOP Superfamily Level Classification Using Unsupervised Machine Learning (Abstract)

U. B. Angadi , Nat. Inst. of Animal Nutrition & Physiol., Kalasalingam Univ., Bangalore, India
M. Venkatesulu , Dept. of Comput. Applic., Kalasalingam Univ., Srivilliputtur, India
pp. 601-608

Subcellular Localization Prediction through Boosting Association Rules (Abstract)

Yongwook Yoon , Dept. of Comput. Sci. & Eng., Pohang Univ. of Sci. & Technol. (POSTECH), Pohang, South Korea
G. G. Lee , Dept. of Comput. Sci. & Eng., Pohang Univ. of Sci. & Technol. (POSTECH), Pohang, South Korea
pp. 609-618

The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes (Abstract)

Chien-Hao Su , Inst. of Inf. Sci., Acad. Sinica, Taipei, Taiwan
Tse-Yi Wang , Inst. of Inf. Sci., Acad. Sinica, Taipei, Taiwan
Ming-Tsung Hsu , Inst. of Inf. Sci., Acad. Sinica, Taipei, Taiwan
F. C-H Weng , Biodiversity Res. Center, Acad. Sinica, Taipei, Taiwan
Cheng-Yan Kao , Dept. of Comput. Sci. & Inf. Eng., Nat. Taiwan Univ., Taipei, Taiwan
Daryi Wang , Biodiversity Res. Center, Acad. Sinica, Taipei, Taiwan
Huai-Kuang Tsai , Inst. of Inf. Sci., Acad. Sinica, Taipei, Taiwan
pp. 619-628

The LASSO and Sparse Least Squares Regression Methods for SNP Selection in Predicting Quantitative Traits (Abstract)

Z. Z. Feng , Dept. of Math. & Stat., Univ. of Guelph, Guelph, ON, Canada
Xiaojian Yang , Dept. of Animal & Poultry Sci., Univ. of Guelph, Guelph, ON, Canada
S. Subedi , Dept. of Math. & Stat., Univ. of Guelph, Guelph, ON, Canada
P. D. McNicholas , Dept. of Math. & Stat., Univ. of Guelph, Guelph, ON, Canada
pp. 629-636
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