IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 9, No. 2, March/April 2012

PAPERS
A Hybrid EKF and Switching PSO Algorithm for Joint State and Parameter Estimation of Lateral Flow Immunoassay Models
Nianyin Zeng, Zidong Wang, Yurong Li, Min Du, Xiaohui Liu
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.140

A New Efficient Algorithm for the Gene-Team Problem on General Sequences
Biing-Feng Wang, Chung-Chin Kuo, Shang-Ju Liu, Chien-Hsin Lin
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.96

A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences
Sascha Steinbiss, Stefan Kurtz
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.146

A Swarm Intelligence Framework for Reconstructing Gene Networks: Searching for Biologically Plausible Architectures
Kyriakos Kentzoglanakis, Matthew Poole
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.87

Algorithms for Reticulate Networks of Multiple Phylogenetic Trees
Zhi-Zhong Chen, Lusheng Wang
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.137

Antilope?A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem
Sandro Andreotti, Gunnar W. Klau, Knut Reinert
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.59

Constructing and Drawing Regular Planar Split Networks
Andreas Spillner, Binh T. Nguyen, Vincent Moulton
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.115

DICLENS: Divisive Clustering Ensemble with Automatic Cluster Number
Selim Mimaroglu, Emin Aksehirli
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.129

Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree
M. Oguzhan Kulekci, Jeffrey Scott Vitter, Bojian Xu
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.127

Eigen-Genomic System Dynamic-Pattern Analysis (ESDA): Modeling mRNA Degradation and Self-Regulation
Daifeng Wang, Mia K. Markey, Claus O. Wilke, Ari Arapostathis
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.150

GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets
Lipi R. Acharya, Thair Judeh, Zhansheng Duan, Michael G. Rabbat, Dongxiao Zhu
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.143

Identification of Differentially Expressed Genes for Time-Course Microarray Data Based on Modified RM ANOVA
Ola ElBakry, M. Omair Ahmad, M.N.S. Swamy
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.65

Identifying Bacterial Virulent Proteins by Fusing a Set of Classifiers Based on Variants of Chou's Pseudo Amino Acid Composition and on Evolutionary Information
Loris Nanni, Alessandra Lumini, Dinesh Gupta, Aarti Garg
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.117

Molecular Dynamics Trajectory Compression with a Coarse-Grained Model
Yi-Ming Cheng, Srinivasa Murthy Gopal, Sean M. Law, Michael Feig
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.141

Multiscale Binarization of Gene Expression Data for Reconstructing Boolean Networks
Martin Hopfensitz, Christoph Mussel, Christian Wawra, Markus Maucher, Michael Kuhl, Heiko Neumann, Hans A. Kestler
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.62

Mutation Region Detection for Closely Related Individuals without a Known Pedigree
Wenji Ma, Yong Yang, Zhi-Zhong Chen, Lusheng Wang
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.134

On Complexity of Protein Structure Alignment Problem under Distance Constraint
Aleksandar Poleksic
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.133

On the Elusiveness of Clusters
Steven M. Kelk, Celine Scornavacca, Leo van Iersel
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.128

Optimizing Phylogenetic Networks for Circular Split Systems
Paul Phipps, Sergey Bereg
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.109

Output-Sensitive Algorithms for Finding the Nested Common Intervals of Two General Sequences
Biing-Feng Wang
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.112

Parallelized Evolutionary Learning for Detection of Biclusters in Gene Expression Data
Qinghua Huang, Dacheng Tao, Xuelong Li, Alan Wee-Chung Liew
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.53

Quantum Gate Circuit Model of Signal Integration in Bacterial Quorum Sensing
Ioannis G. Karafyllidis
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.104

Robust Classification Method of Tumor Subtype by Using Correlation Filters
Shu-Lin Wang, Yi-Hai Zhu, Wei Jia, De-Shuang Huang
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.135

SimBioNeT: A Simulator of Biological Network Topology
Barbara Di Camillo, Marco Falda, Gianna Toffolo, Claudio Cobelli
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.116

Structural SCOP Superfamily Level Classification Using Unsupervised Machine Learning
Ulavappa B. Angadi, M. Venkatesulu
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.114

Subcellular Localization Prediction through Boosting Association Rules
Yongwook Yoon, Gary Geunbae Lee
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.131

The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes
Chien-Hao Su, Tse-Yi Wang, Ming-Tsung Hsu, Francis Cheng-Hsuan Weng, Cheng-Yan Kao, Daryi Wang, Huai-Kuang Tsai
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.111

The LASSO and Sparse Least Squares Regression Methods for SNP Selection in Predicting Quantitative Traits
Zeny Z. Feng, Xiaojian Yang, Sanjeena Subedi, Paul D. McNicholas
http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.139