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2008

Alignment of Minisatellite Maps: A Minimum Spanning Tree-based ApproachMohamed Ibrahim Abouelhoda, Robert Giegerich, Behshad Behzadi, Jean-Marc Steyaert. apbc 2008: 261-272 [doi]

GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative TranscriptsTyler S. Alioto, Roderic Guigó, Ernesto Picardi, Graziano Pesole. apbc 2008: 363-372 [doi]

Supervised Ensembles of Prediction Methods for Subcellular LocalizationJohannes Aßfalg, Jing Gong, Hans-Peter Kriegel, Alexey Pryakhin, Tiandi Wei, Arthur Zimek. apbc 2008: 29-38 [doi]

Predicting Nucleolar Proteins Using Support-Vector MachinesMikael Bodén. apbc 2008: 19-28 [doi]

PrefaceAlvis Brazma, Satoru Miyano, Tatsuya Akutsu. apbc 2008: [doi]

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, JapanAlvis Brazma, Satoru Miyano, Tatsuya Akutsu, editors, Volume 6 of Advances in Bioinformatics and Computational Biology, Imperial College Press, 2008.

A Fixed-Parameter Approach for Weighted Cluster EditingSebastian Böcker, Sebastian Briesemeister, Quang Bao Anh Bui, Anke Truß. apbc 2008: 211-220 [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. apbc 2008: 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. apbc 2008: 343-352 [doi]

Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMPBhaskar DasGupta, Jin Jun, Ion I. Mandoiu. apbc 2008: 353-362 [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. apbc 2008: 145-154 [doi]

Recent Progress in Phylogenetic CombinatoricsAndreas W. M. Dress. apbc 2008: 1-4 [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. apbc 2008: 373-382 [doi]

Image Compression-based Approach to Measuring the Similarity of Protein StructuresMorihiro Hayashida, Tatsuya Akutsu. apbc 2008: 221-230 [doi]

KEGG for Medical and Pharmaceutical ApplicationsMinoru Kanehisa. apbc 2008: 5 [doi]

Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine MonomersAlireza Hadj Khodabakhshi, Ján Manuch, Arash Rafiey, Arvind Gupta. apbc 2008: 49-58 [doi]

From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical LiteratureJin-Dong Kim, Tomoko Ohta, Kanae Oda, Jun-ichi Tsujii. apbc 2008: 165-176 [doi]

Estimation of Population Allele Frequencies from Small Samples Containing Multiple GenerationsDmitry A. Konovalov, Dik Heg. apbc 2008: 321-332 [doi]

Discrimination of Native Folds Using Network Properties of Protein StructuresAlper Küçükural, Osman Ugur Sezerman, Aytul Ercil. apbc 2008: 59-68 [doi]

Symbolic Approaches for Finding Control Strategies in Boolean NetworksChristopher James Langmead, Sumit Kumar Jha. apbc 2008: 307-320 [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. apbc 2008: 383-392 [doi]

Semantic Similarity Definition over Gene Ontology by Further Mining of the Information ContentYuan-Peng Li, Bao-Liang Lu. apbc 2008: 155-164 [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. apbc 2008: 273-286 [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. apbc 2008: 69-78 [doi]

Seed Optimization Is No Easier than Optimal Golomb Ruler DesignBin Ma, Hongyi Yao. apbc 2008: 133-144 [doi]

A Novel Method for Reducing Computational Complexity of Whole Genome Sequence AlignmentRyuichiro Nakato, Osamu Gotoh. apbc 2008: 101-110 [doi]

fRMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information for Pairs with Low Sequence IdentityHuzefa Rangwala, George Karypis. apbc 2008: 111-122 [doi]

Structural Descriptors of Protein-Protein Binding SitesOliver Sander, Francisco S. Domingues, Hongbo Zhu, Thomas Lengauer, Ingolf Sommer. apbc 2008: 79-88 [doi]

Chemical Compound Classification with Automatically Mined Structure PatternsAaron M. Smalter, Jun Huan, Gerald H. Lushington. apbc 2008: 39-48 [doi]

Phylogenetic Reconstruction from Complete Gene Orders of Whole GenomesKrister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret. apbc 2008: 241-250 [doi]

Simultaneously Segmenting Multiple Gene Expression Time Courses by Analyzing Cluster DynamicsSatish Tadepalli, Naren Ramakrishnan, Layne T. Watson, Bhubaneshwar Mishra, Richard F. Helm. apbc 2008: 297-306 [doi]

SPR-based Tree Reconciliation: Non-binary Trees and Multiple SolutionsCuong Than, Luay Nakhleh. apbc 2008: 251-260 [doi]

Finding Non-coding RNAs Through Genome-Scale ClusteringHuei-Hun Tseng, Zasha Weinberg, Jeremy Gore, Ronald R. Breaker, Walter L. Ruzzo. apbc 2008: 199-210 [doi]

Protein Interactions Extracted from Genomes and PapersAlfonso Valencia. apbc 2008: 7 [doi]

Genome Halving with Double Cut and JoinRobert Warren, David Sankoff. apbc 2008: 231-240 [doi]

Analysis of Structural Strand Asymmetry in Non-coding RNAsJiayu Wen, Brian J. Parker, Georg F. Weiller. apbc 2008: 187-198 [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. apbc 2008: 89-100 [doi]

String Kernels with Feature Selection for SVM Protein ClassificationWen-Yun Yang, Bao-Liang Lu. apbc 2008: 9-18 [doi]

Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition SeedsJialiang Yang, Louxin Zhang. apbc 2008: 123-132 [doi]

Classification of Protein Sequences Based on Word Segmentation MethodsYang Yang, Bao-Liang Lu, Wen-Yun Yang. apbc 2008: 177-186 [doi]

Automatic Modeling of Signal Pathways from Protein-Protein Interaction NetworksXing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara. apbc 2008: 287-296 [doi]

2007

Inferring a Chemical Structure from a Feature Vector Based on Frequency of Labeled Paths and Small FragmentsTatsuya Akutsu, Daiji Fukagawa. apbc 2007: 165-174 [doi]

Exploring Genome Rearrangements using Virtual HybridizationM. Belcaid, Anne Bergeron, Annie Chateau, Cedric Chauve, Yannick Gingras, Guylaine Poisson, M. Vendette. apbc 2007: 205-214 [doi]

Selecting Genes with Dissimilar Discrimination Strength for Sample Class PredictionZhipeng Cai, Randy Goebel, Mohammad R. Salavatipour, Yi Shi, Lizhe Xu, Guohui Lin. apbc 2007: 81-90 [doi]

Combining N-grams and Alignment in G-protein Coupling Specificity PredictionBetty Yee Man Cheng, Jaime G. Carbonell. apbc 2007: 363-372 [doi]

Using Formal Concept Analysis for Microarray Data ComparisonV. Choi, Y. Huang, Vy Lam, D. Potter, Reinhard C. Laubenbacher, Karen Duca. apbc 2007: 57-66 [doi]

Subtle Motif Discovery for Detection of DNA Regulatory SitesMatteo Comin, Laxmi Parida. apbc 2007: 27-36 [doi]

Semi-supervised Pattern Learning for Extracting Relations from Bioscience TextsShilin Ding, Minlie Huang, Xiaoyan Zhu. apbc 2007: 307-316 [doi]

A Probabilistic Method to Identify Compensatory Substitutions for Pathogenic MutationsB. C. Easton, A. V. Isaev, Gavin A. Huttley, Peter Maxwell. apbc 2007: 195-204 [doi]

Algorithmic Approaches to Selecting Control Clones in DNA Array Hybridization ExperimentsQi Fu, Elizabeth Bent, James Borneman, Marek Chrobak, Neal E. Young. apbc 2007: 17-26 [doi]

Computing the Breakpoint Distance between Partially Ordered GenomesZheng Fu, Tao Jiang. apbc 2007: 237-246 [doi]

Exploring Genomes of Distantly Related MammalsJennifer A. Marshall Graves. apbc 2007: 1 [doi]

A Novel Clustering Method for Analysis of Biological Networks using Maximal Components of GraphsMorihiro Hayashida, Tatsuya Akutsu, Hiroshi Nagamochi. apbc 2007: 257-266 [doi]

Exact and Heuristic Approaches for Identifying Disease-Associated SNP MotifsGaofeng Huang, Peter Jeavons, Dominic Kwiatkowski. apbc 2007: 175-184 [doi]

etagenome Analysis using MeganDaniel H. Huson, Alexander F. Auch, Qi Ji, Stephan C. Schuster. apbc 2007: 7-16 [doi]

Algorithm Engineering for Color-Coding to Facilitate Signaling Pathway DetectionFalk Hüffner, Sebastian Wernicke, Thomas Zichner. apbc 2007: 277-286 [doi]

Protein Structure-Structure Alignment with Discrete Fr echet DistanceMinghui Jiang, Ying Xu, Binhai Zhu. apbc 2007: 131-141 [doi]

Deriving Protein Structure Topology from the Helix Skeletion in Low Resolution Density Map using RosettaYonggang Lu, Jing He, Charlie E. M. Strauss. apbc 2007: 143-151 [doi]

An Efficient Biclustering Algorithm for Finding Genes with Similar Patterns in Time-series Expression DataSara C. Madeira, Arlindo L. Oliveira. apbc 2007: 67-80 [doi]

All Hits All The Time: Parameter Free Calculation of Seed SensitivityDenise Y. F. Mak, Gary Benson. apbc 2007: 327-340 [doi]

Fitting Protein Chains to Cubic Lattice is NP-CompleteJán Manuch, Daya Ram Gaur. apbc 2007: 153-164 [doi]

Bugs, Guts and Fat - A Systems Approach to the Metabolic Axis of Evil Joseph H. Nadeau. apbc 2007: 3 [doi]

De Novo Peptide Sequencing for Mass Spectra Based on Multi-Charge Strong TagsKang Ning, Ket Fah Chong, Hon Wai Leong. apbc 2007: 287-296 [doi]

Flow Model of the Protein-protein Interaction Network for Finding Credible InteractionsKinya Okada, Kiyoshi Asai, Masanori Arita. apbc 2007: 317-326 [doi]

Fast Structural Similarity Search Based on Topology String MatchingSung-Hee Park, David Gilbert, Keun Ho Ryu. apbc 2007: 341-351 [doi]

Protein Identification via Spectral Networks AnalysisPavel A. Pevzner. apbc 2007: 5 [doi]

Two Plus Two Does not Equal Three: Statistical Tests for Multiple Genome ComparisonNarayanan Raghupathy, Rose Hoberman, Dannie Durand. apbc 2007: 215-225 [doi]

PrefaceDavid Sankoff, Lusheng Wang, Francis Chin. apbc 2007: [doi]

Proceedings of 5th Asia-Pacific Bioinformatics Conference, APBC 2007, 15-17 January 2007, Hong Kong, ChinaDavid Sankoff, Lusheng Wang, Francis Chin, editors, Volume 5 of Advances in Bioinformatics and Computational Biology, Imperial College Press, 2007.

Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass SpectrometryBaozhen Shan, Bin Ma, Kaizhong Zhang, Gilles Lajoie. apbc 2007: 297-306 [doi]

Computing the Quartet Distance Between Evolutionary Trees of Bounded DegreeM. Stissing, Christian N. S. Pedersen, Thomas Mailund, Gerth Stølting Brodal, Rolf Fagerberg. apbc 2007: 101-110 [doi]

Computing the All-Pairs Quartet Distance on a Set of Evolutionary TreesM. Stissing, Thomas Mailund, Christian N. S. Pedersen, Gerth Stølting Brodal, Rolf Fagerberg. apbc 2007: 91-100 [doi]

Genotype-Based Case-Control Analysis, Violation of Hardy-Weinberg Equilibrium, and Phase DiagramsYoung Ju Suh, Wentian Li. apbc 2007: 185-194 [doi]

A Randomized Algorithm for Comparing Sets of Phylogenetic TreesSeung-Jin Sul, Tiffani L. Williams. apbc 2007: 121-130 [doi]

Inferring Gene Regulatory Networks by Machine Learning MethodsJochen Supper, Holger Fröhlich, Christian Spieth, Andreas Dräger, Andreas Zell. apbc 2007: 247-256 [doi]

Gene Regulatory Network Inference via Regression Based Topological RefinementJochen Supper, Holger Fröhlich, Andreas Zell. apbc 2007: 267-276 [doi]

A Global Maximum Likelihood Super-Quartet Phylogeny MethodPinghao Wang, Bing Bing Zhou, Monther Tarawneh, Daniel Chu, Chen Wang, Albert Y. Zomaya, Richard P. Brent. apbc 2007: 111-120 [doi]

Simple and Fast Alignment of Metabolic Pathways by Exploiting Local DiversitySebastian Wernicke, Florian Rasche. apbc 2007: 353-362 [doi]

An Effective Promoter Detection Method using the Adaboost AlgorithmXudong Xie, Shuanhu Wu, Kin-Man Lam, Hong Yan. apbc 2007: 37-46 [doi]

The Distance Between Randomly Constructed GenomesWei Xu. apbc 2007: 227-236 [doi]

A New Strategy of Geometrical Biclustering for Microarray Data AnalysisHongya Zhao, Alan Wee-Chung Liew, Hong Yan. apbc 2007: 47-56 [doi]

2006

Disentangling the Role of Tetranucleotide in the Sequence-Dependence of DNA Conformation: A Molecular Dynamics ApproachMarcos J. Araúzo-Bravo, Satoshi Fujii, Hidetoshi Kono, Akinori Sarai. apbc 2006: 227-236 [doi]

Structure-Based Chemical Shift Prediction Using Random Forests Non-Linear RegressionK. Arun, Christopher James Langmead. apbc 2006: 317-326 [doi]

An Efficient Algorithm for String Motif DiscoveryFrancis Y. L. Chin, Henry C. M. Leung. apbc 2006: 79-88 [doi]

Trends in Codon and Amino Acid Usage in Human Pathogen Tropheryma Whipplei, the only Known Actinobacteria with Reduced GenomeSabyasachi Das, Sandip Paul, Chitra Dutta. apbc 2006: 139-148 [doi]

Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed GenesShao-Shan Huang, Debra L. Fulton, David J. Arenillas, Paul Perco, Shannan J. Ho Sui, James R. Mortimer, Wyeth W. Wasserman. apbc 2006: 247-256 [doi]

Accuracy of Four Heuristics for the Full Sibship Reconstruction Problem in the Presence of Genotype ErrorsDmitry A. Konovalov. apbc 2006: 7-16 [doi]

A Randomized Algorithm for Learning Mahalanobis Metrics: Application to Classification and Regression of Biological DataChristopher James Langmead. apbc 2006: 217-226 [doi]

On the Inference of Regulatory Elements, Circuits, and ModulesWen-Hsiung Li. apbc 2006: 1 [doi]

System Identification and Robustness Analysis of the Circadian Regulatory Network via Microarray Data in Arabidopsis ThalianaC. W. Li, W. C. Chang, B. S. Chen. apbc 2006: 27-37 [doi]

Inference of Gene Regulatory Networks from Microarray Data: A Fuzzy Logic ApproachPatrick C. H. Ma, Keith C. C. Chan. apbc 2006: 17-26 [doi]

A Recursive Method for Solving Haplotype Frequencies in Multiple Loci Linkage AnalysisMichael K. Ng. apbc 2006: 129-138 [doi]

Consequences of Mutation, Selection, and Physico-Chemical Properties of Encoded Proteins on Synonymous Codon Usage in AdenovirusesSandip Paul, Sabyasachi Das, Chitra Dutta. apbc 2006: 149-158 [doi]

Automating the Search for Lateral Gene TransferMark A. Ragan. apbc 2006: 3 [doi]

Techniques for Assessing Phylogenetic Branch Support: A Performance StudyDerek A. Ruths, Luay Nakhleh. apbc 2006: 187-196 [doi]

RECOMP: A Parsimony-Based Method for Detecting RecombinationDerek A. Ruths, Luay Nakhleh. apbc 2006: 59-68 [doi]

Genome Wide Computational Analysis of Small Nuclear RNA Genes for Oryza Sativa (Indica and Japonica)M. Shashikanth, A. Snethalatharani, S. K. Mubarak, K. Ulaganathan. apbc 2006: 277-286 [doi]

Property-Dependent Analysis of Aligned Proteins from Two Or More PopulationsSteinar Thorvaldsen, Elinor Ytterstad, Tor Flå. apbc 2006: 169-178 [doi]

Whole Genome Optical MappingMichael S. Waterman. apbc 2006: 5 [doi]

A New Neural Network for B-Turn Prediction: the Effect of Site-Specific Amino Acid PreferenceZhong-Ru Xie, Ming-Jing Hwang. apbc 2006: 237-246 [doi]

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