Table of Contents

• PrefaceAlvis Brazma, Satoru Miyano, Tatsuya Akutsu. [doi]
• Recent Progress in Phylogenetic CombinatoricsAndreas W. M. Dress. 1-4 [doi]
• KEGG for Medical and Pharmaceutical ApplicationsMinoru Kanehisa. 5 [doi]
• Protein Interactions Extracted from Genomes and PapersAlfonso Valencia. 7 [doi]
• String Kernels with Feature Selection for SVM Protein ClassificationWen-Yun Yang, Bao-Liang Lu. 9-18 [doi]
• Predicting Nucleolar Proteins Using Support-Vector MachinesMikael Bodén. 19-28 [doi]
• Supervised Ensembles of Prediction Methods for Subcellular LocalizationJohannes Aßfalg, Jing Gong, Hans-Peter Kriegel, Alexey Pryakhin, Tiandi Wei, Arthur Zimek. 29-38 [doi]
• Chemical Compound Classification with Automatically Mined Structure PatternsAaron M. Smalter, Jun Huan, Gerald H. Lushington. 39-48 [doi]
• Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine MonomersAlireza Hadj Khodabakhshi, Ján Manuch, Arash Rafiey, Arvind Gupta. 49-58 [doi]
• Discrimination of Native Folds Using Network Properties of Protein StructuresAlper Küçükural, Osman Ugur Sezerman, Aytul Ercil. 59-68 [doi]
• Interacting Amino Acid Preferences of 3D Pattern Pairs at the Binding Sites of Transient and Obligate Protein ComplexesSuryani Lukman, Kelvin Sim, Jinyan Li, Yi-Ping Phoebe Chen. 69-78 [doi]
• Structural Descriptors of Protein-Protein Binding SitesOliver Sander, Francisco S. Domingues, Hongbo Zhu, Thomas Lengauer, Ingolf Sommer. 79-88 [doi]
• A Memory Efficient Algorithm for Structural Alignment of RNAs with Embedded Simple PseudoknotsThomas K. F. Wong, Y. S. Chiu, Tak Wah Lam, Siu-Ming Yiu. 89-100 [doi]
• A Novel Method for Reducing Computational Complexity of Whole Genome Sequence AlignmentRyuichiro Nakato, Osamu Gotoh. 101-110 [doi]
• fRMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information for Pairs with Low Sequence IdentityHuzefa Rangwala, George Karypis. 111-122 [doi]
• Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition SeedsJialiang Yang, Louxin Zhang. 123-132 [doi]
• Seed Optimization Is No Easier than Optimal Golomb Ruler DesignBin Ma, Hongyi Yao. 133-144 [doi]
• Integrating Hierarchical Controlled Vocabularies With OWL Ontology: A Case Study from the Domain of Molecular InteractionsMelissa J. Davis, Andrew Newman, Imran Khan, Jane Hunter, Mark A. Ragan. 145-154 [doi]
• Semantic Similarity Definition over Gene Ontology by Further Mining of the Information ContentYuan-Peng Li, Bao-Liang Lu. 155-164 [doi]
• From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical LiteratureJin-Dong Kim, Tomoko Ohta, Kanae Oda, Jun-ichi Tsujii. 165-176 [doi]
• Classification of Protein Sequences Based on Word Segmentation MethodsYang Yang, Bao-Liang Lu, Wen-Yun Yang. 177-186 [doi]
• Analysis of Structural Strand Asymmetry in Non-coding RNAsJiayu Wen, Brian J. Parker, Georg F. Weiller. 187-198 [doi]
• Finding Non-coding RNAs Through Genome-Scale ClusteringHuei-Hun Tseng, Zasha Weinberg, Jeremy Gore, Ronald R. Breaker, Walter L. Ruzzo. 199-210 [doi]
• A Fixed-Parameter Approach for Weighted Cluster EditingSebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui, Anke Truß. 211-220 [doi]
• Image Compression-based Approach to Measuring the Similarity of Protein StructuresMorihiro Hayashida, Tatsuya Akutsu. 221-230 [doi]
• Genome Halving with Double Cut and JoinRobert Warren, David Sankoff. 231-240 [doi]
• Phylogenetic Reconstruction from Complete Gene Orders of Whole GenomesKrister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret. 241-250 [doi]
• SPR-based Tree Reconciliation: Non-binary Trees and Multiple SolutionsCuong Than, Luay Nakhleh. 251-260 [doi]
• Alignment of Minisatellite Maps: A Minimum Spanning Tree-based ApproachMohamed Ibrahim Abouelhoda, Robert Giegerich, Behshad Behzadi, Jean-Marc Steyaert. 261-272 [doi]
• Metabolic Pathway Alignment (M-Pal) Reveals Diversity and Alternatives in Conserved NetworksYunlei Li, Dick de Ridder, Marco J. L. de Groot, Marcel J. T. Reinders. 273-286 [doi]
• Automatic Modeling of Signal Pathways from Protein-Protein Interaction NetworksXing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara. 287-296 [doi]
• Simultaneously Segmenting Multiple Gene Expression Time Courses by Analyzing Cluster DynamicsSatish Tadepalli, Naren Ramakrishnan, Layne T. Watson, Bhubaneshwar Mishra, Richard F. Helm. 297-306 [doi]
• Symbolic Approaches for Finding Control Strategies in Boolean NetworksChristopher James Langmead, Sumit Kumar Jha. 307-320 [doi]
• Estimation of Population Allele Frequencies from Small Samples Containing Multiple GenerationsDmitry A. Konovalov, Dik Heg. 321-332 [doi]
• Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from SNP FragmentsZhixiang Chen, Bin Fu, Robert T. Schweller, Boting Yang, Zhiyu Zhao, Binhai Zhu. 333-342 [doi]
• Optimal Algorithm for Finding DNA Motifs with Nucleotide Adjacent DependencyFrancis Y. L. Chin, Henry C. M. Leung, Man-Hung Siu, Siu-Ming Yiu. 343-352 [doi]
• Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMPBhaskar DasGupta, Jin Jun, Ion I. Mandoiu. 353-362 [doi]
• GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative TranscriptsTyler S. Alioto, Roderic Guigó, Ernesto Picardi, Graziano Pesole. 363-372 [doi]
• Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpressYannick Haudry, Chuang Kee Ong, Laurence Ettwiller, Hugo Berube, Ivica Letunic, Misha Kapushesky, Paul-Daniel Weeber, Xi Wang, Julien Gagneur, Charles Girardot, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, Thorsten Henrich. 373-382 [doi]
• Near-sigmoid Modeling to Simultaneously Profile Genome-wide DNA Replication Timing and Efficiency in Single DNA Replication Microarray StudiesJuntao Li, Majid Eshaghi, Jianhua Liu, Karuturi R. Krishna Murthy. 383-392 [doi]