Proceedings of the 6th Asia-Pacific Bioinformatics Conference.
Title:
Proceedings of the 6th Asia-Pacific Bioinformatics Conference.
Author:
Brazma, Alvis.
ISBN:
9781848161092
Personal Author:
Physical Description:
1 online resource (413 pages)
Series:
Series on Advances in Bioinformatics and Computational Biology ; v.6
Series on Advances in Bioinformatics and Computational Biology
Contents:
CONTENTS -- Preface -- APBC 2008 Organization -- Program Committee -- Additional Reviewers -- Keynote Papers -- Recent Progress in Phylogenetic Combinatorics Andreas Dress -- 1. Background -- 2. Discussion -- References -- KEGG for Medical and Pharmaceutical Applications Minoru Kanehisa -- Protein Interactions Extracted from Genomes and Papers Alfonso Valencia -- Contributed Papers -- String Kernels with Feature Selection for SVM Protein Classification Wen-Yun Yang and Bao-Liang Lu -- 1. Introduction -- 2. A string kernel framework -- 2.1. Notations -- 2.2. Pramework definition -- 2.3. Relations with existing string kernels -- 3. Efficient computation -- 3.1. Tree data structure with leaf links -- 3.2. Leaf traversal algorithm -- 4. Selecting feature groups and weights -- 4.1. Reduction of spectrum string kernel -- 4.2. Statistically selecting feature groups -- 5. Experiment -- 6. Discussion and future work -- Acknowledgments -- References -- Predicting Nucleolar Proteins Using Support-Vector Machines Mikael Bod&. -- 1. Introduction -- 2. Background -- 3. Methods -- 3.1. Data set -- 3.2. Model -- 4. Results -- 5 . Conclusion -- Acknowledgments -- References -- Supervised Ensembles of Prediction Methods for Subcellular Localization Johannes Apfalg, Jing Gong, Hans-Peter Kriegel, Alexey Pryakhin, Tiandi Wei and Arthur Zimek -- 1. Introduction -- 2. Survey on Prominent Prediction Methods for Subcellular Localization -- 2.1. Amino Acid Composition -- 2.2. Sorting Signals -- 2.3. Homology -- 2.4. Hybrid Methods -- 3. Ensemble Methods -- 3.1. Theory -- 3.2. Selection of Base Methods for Ensembles -- 3.3. Ensemble Method Based on a Voting Schema -- 3.4. Ensemble Method Based on Decision Trees -- 4. Evaluation -- 5. Conclusions -- References.
Chemical Compound Classification with Automatically Mined Structure Patterns Aaron M. Smalter, J. Huan and Gerald H. Lushington -- 1. Introduction -- 2. Related Work -- 2.1. Marginalized and Optimal Assignment Graph Kernels -- 2.2. Frequent Subgraph Mining -- 3. Background -- 3.1. Chemical Structure -- 4. Algorithm Design -- 4.1. Structure Pattern Mining -- 4.2. Optimal Assignment Kernel -- 4.3. Reduced Graph Representation -- 4.4. Pattern-based Descriptors -- 5. Experimental Study -- 5.1. Data Sets -- 5.2. Methods -- 5.3. Results -- 6. Conclusions -- Acknowledgments -- References -- Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine Monomers Alireza Hadj Khodabakhshi, Jdn Mariuch, Arash Rafiey and Arvind Gupta -- 1. Introduction -- 2. Definitions -- 2.1. Hydropho bic-polar- c ysteine (HP C) model -- 2.2. Snake structures -- 2.3. The strong HPC model -- 3. Proof techniques -- 3.1. Saturated folds -- 3.2. 2DHPSolver: a semi-automatic prover -- 4. Stability of the snake structures -- 5. Conclusions -- References -- Discrimination of Native Folds Using Network Properties of Protein Structures Alper Kiiciikural, 0. Ug'ur Sezerman and Aytiil Ercal -- 1 Introduction -- 2 Methods -- 3 Background and Related Works -- 4 Dataset -- 5 Results -- 6 Conclusion and Discussion -- References -- Interacting Amino Acid Preferences of 3D Pattern Pairs at the Binding Sites of Transient and Obligate Protein Complexes Suryani Lukman, Kelvin Sim, Jinyan Li and Yi-Ping Phoebe Chen -- 1. Introduction -- 2. AAPAZRS: Our algorithm to discover 3D pattern pairs -- 2.1. Classifying pairs of interacting proteins into obligate or transient complexes -- 2.2. Mpair (step one): Discovering maximal quasi-bidique subgraphs from transient and obligate complexes -- 2.3. AApair (step two): Identifying significant 3 0 pattern pairs -- 3. Results.
3.1. Amino acid dishibutions on each side of 3Dpattern pairs -- 3.2. Amino acid pairing preferences of 3 0 pattern pairs -- 4. Discussion -- References -- Structural Descriptors of Protein-Protein Binding Sites Oliver Sander, Francisco S. Domingues, Hongbo Zhu, Thomas Lengauer and Ingolf Sommer -- 1. Introduction -- 2. Comparison of protein binding sites and surface patches -- 2.1. Structural descriptors of protein-protein binding sites -- 2.2. Comparison and retrieval of structural descriptors -- 2.3. Structural descriptors of protein surface patches -- 3. Experiments & Evaluation -- 3.1. Retrieving SimilQr Binding Sites - Kinases -- 3.2. Scanning fur similar surface patches -- 4. Conclusion and Outlook -- Acknowledgement -- References -- A Memory Efficient Algorithm for Structural Alignment of RNAs with Embedded Simple Pseudoknots Thomas Wong, Y. S. Chiu, Tak- Wah Lam and S. M. Yiu -- 1. Introduction -- 2. Definitions -- 3. Algorithm -- 3.1. Structural alignment -- 3.2. Structural alignment for simple pseudoknot -- 3.3. Our memory-efficient algorithm -- 3.4 Structural alignment for embedded simple pseudoknot -- 4. Experimental Results -- 5. Discussion and Conclusions -- Acknowledgments -- References -- A Novel Method for Reducing Computational Complexity of Whole Genome Sequence Alignment Ryuichiro Nakato and Osamu Gotoh -- 1. Introduction -- 2. Method -- 2.1. Outline -- 2.2. Block-level alignment -- 2.3. Nucleotide-level alignment -- 2.4. Computational complexity -- 2.5. Preparation of data -- 3. Results -- 3.1. Comparison of accuracy by dotplots -- 3.2. Comparison of computational time and memory -- 4. Discussion -- Acknowledgments -- References -- f RMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information for Pairs with Low Sequence Identity Huzefa Rangwala and George Karypis -- 1. Introduction.
2. Definitions and Notations -- 3. Materials -- 3.1. Datasets -- 3.2. Evaluation Methodology -- 3.3. Projile Generation -- 3.4. Secondary Structure Prediction -- 3.5. f RMSD Estimation -- 3.6. Gap Modeling and Shvt Parameters -- 4. Methods -- 4.1. Scoring Schemes -- 4.1.1. Projile-Projile Scoring Scheme -- 4.1.2. Predicted Secondary Structure-based Scoring Scheme -- 4.1.3. f RMSD-based Scoring Scheme -- 4.2. Combination Schemes -- 4.3. Speedup Optimization -- 4.3.1. Seeded Alignment -- 4.3.2. Iterative Sampling Alignment -- 5. Results -- 5.1. Comparison to Other Alignment Schemes -- 5.2. Optimization Performance -- 6. Conclusion -- Acknowledgment -- References -- Run Probability of High-Order Seed Patterns and Its Applications to Finding Good Transition Seeds Jialiang Yang and Louxin Zhang -- 1. Introduction -- 2. Seeds, Sensitivity and Specificity -- 2.1. Spaced seeds -- 2.2. Seed sensitivity and specificity -- 3. High-order Seed Patterns and Their Run Probabilities -- 3.1. A recurrence formula f o r hit probability -- 3.2. An Inequality on Hit Probability -- 3.3. Asymptotic Analysis of Hit Probability -- 4. The Average Distance Between Successive Non-overlapping Hits -- 4.1. Bounding p -- 4.1.1. Bounding XQ in terms of Q -- 5. Identifying Good Transition Seeds -- 6 . Conclusion -- Acknowledgments -- References -- Seed Optimization Is No Easier than Optimal Golomb Ruler Design Bin Ma and Hongyi Yao -- 1. Introduction and Notations -- 1.1. Seed optimization -- 1.2. Golomb ruler -- 2. I.I.D. Seed Optimization -- 2.1. Reduction from optimal Golomb ruler design to i.i.d. seed optimization -- 2.2. Counterexample -- 3. Uniform Seed Optimization -- 4. Discussion and Open Problems -- Acknowledgment -- References.
Integrating Hierarchical Controlled Vocabularies with OWL Ontology: A Case Study from the Domain of Molecular Interactions Melissa J. Davis, Andrew Newman, Imran Khan, Jane Hunter and Mark A. Ragan -- 1 Introduction -- 2 Results -- 3 Discussion -- Acknowledgments -- References -- Semantic Similarity Definition over Gene Ontology by Further Mining of the Information Content Yuan- Peng Li and Bao- Liang Lu -- 1. Introduction -- 1.1. Gene Ontology -- 1.2. GO and Similarity between Gene Products -- 1.3. Related Work -- 2. Method -- 2.1. Notations -- 2.2. Traditional Definition -- 2.3. Proposed Similarity Definitions -- 3. Results -- 3.1. Dataset -- 3.2. Classifier -- 3.3. Tables and Graphs -- 4. Discussion -- 4.1. The Use of Edges and Negative Information -- 4.2. The Difference among Classes -- 4.3. More Comparison Results -- 5. Conclusions -- Acknowledgments -- References -- From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature Jan-Dong Kim, Tomoko Ohta, Kanae Oda and Jun'ichi Tsujii -- 1. Introduction -- 2. GENIA corpus -- 3. Event annotation -- 3.1. Annotation scheme -- 3.2. Annotation results -- 4. Pathway corpus -- 4.1. NF-6.B pathway and corpus, the full-text version -- 4.2. NF-KB pathway and corpus, the GENIA version -- 5 . Discussion: Pathway construction from Event annotation -- 5.1. Finding instances from continuants -- 5.2. Integration of fragmentary evidences -- 6. Conclusion -- Acknowledgments -- References -- Classification of Protein Sequences Based on Word Segmentation Methods Yang Yang, Bao-Liang Lu and Wen-Yun Yang -- 1. Introduction -- 2. Method -- 2.1. Dictionary Building -- 2.2. Segmentation -- 3. Results -- 3.1. SCOP family Classfication -- 3.2. GPCR protein subfamily Classication -- 4. Conclusion -- References.
Analysis of Structural Strand Asymmetry in Non-coding RNAs Jaayu Wen, Brian J. Parker and Georg F. Weiller.
Abstract:
High-throughput sequencing and functional genomics technologies have given us the human genome sequence as well as those of other experimentally, medically, and agriculturally important species, thus enabling large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, structures, metabolic pathways, and gene expression profiles of normal and diseased tissues are rapidly being generated for human and model organisms. Bioinformatics is therefore gaining importance in the annotation of genomic sequences; the understanding of the interplay among and between genes and proteins; the analysis of the genetic variability of species; the identification of pharmacological targets; and the inference of evolutionary origins, mechanisms, and relationships. This proceedings volume contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics by researchers, professionals, and industry practitioners at the 6th Asia-Pacific Bioinformatics Conference held in Kyoto, Japan, in January 2008. Sample Chapter(s). Chapter 1: Recent Progress in Phylogenetic Combinatorics (185 KB). Contents: Recent Progress in Phylogenetic Combinatorics (A Dress); Predicting Nucleolar Proteins Using Support-Vector Machines (M Bodén); Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine Monomers (A H Khodabakhshi et al.); Seed Optimization Is No Easier than Optimal Golomb Ruler Design (B Ma & H Yao); Analysis of Structural Strand Asymmetry in Non-coding RNAs (J Wen et al.); Genome Halving with Double Cut and Join (R Warren & D Sankoff); Symbolic Approaches for Finding Control Strategies in Boolean Networks (C J Langmead & S K Jha); Optimal Algorithm for Finding DNA Motifs with Nucleotide Adjacent Dependency (F Y L Chin et
al.); and other papers. Readership: Academics, researchers, and graduate students in bioinformatics and computer science.
Local Note:
Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2017. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.
Genre:
Electronic Access:
Click to View