IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 8, Issue 4

Special Section on Bioinformatics Research and Applications

865 Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications
Mark Borodovsky, Teresa M. Przytycka, Sanguthevar Rajasekaran, Alexander Zelikovsky

867 A Spectral Approach to Protein Structure Alignment
Yosi Shibberu, Allen Holder

876 Asymmetric Comparison and Querying of Biological Networks
Nicola Ferraro, Luigi Palopoli, Simona Panni, Simona E. Rombo

890 The Plexus Model for the Inference of Ancestral Multidomain Proteins
John Wiedenhoeft, Roland Krause, Oliver Eulenstein

902 Uncovering Hidden Phylogenetic Consensus in Large Data Sets
Nicholas D. Pattengale, Andre J. Aberer, Krister M. Swenson, Alexandros Stamatakis, Bernard M.E. Moret

912 Extensions and Improvements to the Chordal Graph Approach to the Multistate Perfect Phylogeny Problem
Rob Gysel, Dan Gusfield

918 A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure
Ming-Chi Tsai, Guy Blelloch, R. Ravi, Russell Schwartz
Regular Papers

929 A Biologically Inspired Measure for Coexpression Analysis
Sanghamitra Bandyopadhyay, Malay Bhattacharyya

943 A Survey on Methods for Modeling and Analyzing Integrated Biological Networks
Nuno Tenazinha, Susana Vinga

959 An Improved Heuristic Algorithm for Finding Motif Signals in DNA Sequences
Chao-Wen Huang, Wun-Shiun Lee, Sun-Yuan Hsieh

976 Determination of Glycan Structure from Tandem Mass Spectra
Sebastian Bocker, Birte Kehr, Florian Rasche

987 EvoMD: An Algorithm for Evolutionary Molecular Design
Samuel S.Y. Wong, Weimin Luo, Keith C.C. Chan

1004 Image-Based Surface Matching Algorithm Oriented to Structural Biology
Ivan Merelli, Paolo Cozzi, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi

1017 Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?
Pietro Di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio

1029 Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds
Katharina T. Huber, Andreas Spillner, Rados?aw Suchecki, Vincent Moulton

1041 Multiclass Kernel-Imbedded Gaussian Processes for Microarray Data Analysis
Xin Zhao, Leo Wang-Kit Cheung

1054 Peak Tree: A New Tool for Multiscale Hierarchical Representation and Peak Detection of Mass Spectrometry Data
Peng Zhang, Houqiang Li, Honghui Wang, Stephen T.C. Wong, Xiaobo Zhou

1067 Predicting MHC-II Binding Affinity Using Multiple Instance Regression
Yasser EL-Manzalawy, Drena Dobbs, Vasant Honavar

1080 Robust Feature Selection for Microarray Data Based on Multicriterion Fusion
Feng Yang, K.Z. Mao

1093 Searching for Coexpressed Genes in Three-Color cDNA Microarray Data Using a Probabilistic Model-Based Hough Transform
Peter Tino, Hongya Zhao, Hong Yan

1108 The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation
Li-San Wang, Jim Leebens-Mack, P. Kerr Wall, Kevin Beckmann, Claude W. dePamphilis, Tandy Warnow

1120 Toward a Robust Search Method for the Protein-Drug Docking Problem
Bashir S. Sadjad, Zsolt Zsoldos

Short Papers

1134 Accurate Reconstruction for DNA Sequencing by Hybridization Based on a Constructive Heuristic
Yang Chen, Jinglu Hu

1141 Computing a Smallest Multilabeled Phylogenetic Tree from Rooted Triplets
Sylvain Guillemot, Jesper Jansson, Wing-Kin Sung

1148 Two-Step Cross-Entropy Feature Selection for Microarrays-Power Through Complementarity
Tim Peters, David W. Bulger, To-Ha Loi, Jean Yee Hwa Yang, David Ma