Pattern Recognition in Bioinformatics: Third IAPR International Conference, PRIB 2008, Melbourne, Australia, October 15-17, 2008. Proceedings (Lecture Notes in Computer Science, 5265)

This book constitutes the refereed proceedings of the International Workshop on Pattern Recognition in Bioinformatics, PRIB 2008, held in Melbourne, Australia, in October 2008. The 39 revised full papers presented were carefully reviewed and selected from 121 submissions. The papers discuss the applications of pattern recognition methods in the field of bioinformatics to solve problems in life sciences. The papers are organized in 6 topical parts on protein: structure, function and interaction; learning, classification and clustering; bio-molecular networks and pathways analysis; microarray and gene expression analysis; data mining and knowledge discovery; applications of high performance computing. Front Matter....Pages - Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins....Pages 1-12 A Method to Find Sequentially Separated Motifs in Biological Sequences (SSMBS)....Pages 13-27 Predicting SUMOylation Sites....Pages 28-40 DFS Based Partial Pathways in GA for Protein Structure Prediction....Pages 41-53 Evaluation of the Stability of Folding Nucleus upon Mutation....Pages 54-65 Prediction of Protein Beta-Sheets: Dynamic Programming versus Grammatical Approach....Pages 66-77 Using Multi-scale Glide Zoom Window Feature Extraction Approach to Predict Protein Homo-oligomer Types....Pages 78-86 Extraction of Binding Sites in Proteins by Searching for Similar Local Molecular Surfaces....Pages 87-97 A Clustering Based Hybrid System for Mass Spectrometry Data Analysis....Pages 98-109 A Modified Markov Clustering Approach for Protein Sequence Clustering....Pages 110-120 Feature Selection and Classification for Small Gene Sets....Pages 121-131 Pseudoknot Identification through Learning TAG RNA ....Pages 132-143 Support Vector Based T-Score for Gene Ranking....Pages 144-153 Prediction of Transcription Factor Families Using DNA Sequence Features....Pages 154-164 g-MARS: Protein Classification Using Gapped Markov Chains and Support Vector Machines....Pages 165-177 Domain-Domain Interaction Identification with a Feature Selection Approach....Pages 178-186 Dividing Protein Interaction Networks by Growing Orthologous Articulations....Pages 187-200 Constraint Minimization for Efficient Modeling of Gene Regulatory Network....Pages 201-213 Fusion of Gene Regulatory and Protein Interaction Networks Using Skip-Chain Models....Pages 214-224 TopEVM: Using Co-occurrence and Topology Patterns of Enzymes in Metabolic Networks to Construct Phylogenetic Trees....Pages 225-236 Generating Synthetic Gene Regulatory Networks....Pages 237-249 Gene Selection for Microarray Data by a LDA-Based Genetic Algorithm....Pages 250-261 Sequential Forward Selection Approach to the Non-unique Oligonucleotide Probe Selection Problem....Pages 262-275 On Finding and Interpreting Patterns in Gene Expression Data from Time Course Experiments....Pages 276-287 Microarray Design Using the Hilbert–Schmidt Independence Criterion....Pages 288-298 Identifying Non-random Patterns from Gene Expression Profiles....Pages 299-310 A Study on the Importance of Differential Prioritization in Feature Selection Using Toy Datasets....Pages 311-322 Weighted Top Score Pair Method for Gene Selection and Classification....Pages 323-333 Identifying Conserved Discriminative Motifs....Pages 334-348 Exploratory Data Analysis for Investigating GC-MS Biomarkers....Pages 349-358 Multi-relational Data Mining for Tetratricopeptide Repeats (TPR)-Like Superfamily Members in Leishmania spp .: Acting-by-Connecting Proteins....Pages 359-372 Heuristic Non Parametric Collateral Missing Value Imputation: A Step Towards Robust Post-genomic Knowledge Discovery....Pages 373-387 Protein Expression Molecular Pattern Discovery by Nonnegative Principal Component Analysis....Pages 388-399 Gene Ontology Assisted Exploratory Microarray Clustering and Its Application to Cancer....Pages 400-411 Discovery of Biomarkers for Hexachlorobenzene Toxicity Using Population Based Methods on Gene Expression Data....Pages 412-423 Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study....Pages 424-435 Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA....Pages 436-447 GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences....Pages 448-459 Accelerating BLASTP on the Cell Broadband Engine....Pages 460-470 Back Matter....Pages - In The Post-genomic Era, A Holistic Understanding Of Biological Systems And P- Cesses,inalltheircomplexity,is Criticalincomprehendingnature’schoreography Of Life. As A Result, Bioinformatics Involving Its Two Main Disciplines, Namely, The Life Sciences And The Computational Sciences, Is Fast Becoming A Very Promising Multidisciplinary Research ?eld. With The Ever-increasing Application Of Lar- Scalehigh-throughputtechnologies,suchasgeneorproteinmicroarraysandmass Spectrometry Methods, The Enormous Body Of Information Is Growing Rapidly. Bioinformaticians Are Posed With A Large Number Of Di?cult Problems To Solve, Arising Not Only Due To The Complexities In Acquiring The Molecular Infor- Tion But Also Due To The Size And Nature Of The Generated Data Sets And/or The Limitations Of The Algorithms Required For Analyzing These Data. Although The ?eld Of Bioinformatics Is Still In Its Embryonic Stage, The Recent Advancements In Computational And Information-theoretic Techniques Are Enabling Us To C- Ductvariousinsilicotestingandscreeningofmanylab-basedexperimentsbefore These Are Actually Performed In Vitro Or In Vivo. These In Silico Investigations Are Providing New Insights For Interpretation And Establishing A New Direction For A Deeper Understanding. Among The Various Advanced Computational Methods Currently Being Applied To Such Studies, The Pattern Recognition Techniques Are Mostly Found To Be At The Core Of The Whole Discovery Process For Apprehending The Underlying Biological Knowledge. Thus, We Can Safely Surmise That The - Going Bioinformatics Revolution May, In Future, Inevitably Play A Major Role In Many Aspects Of Medical Practice And/or The Discipline Of Life Sciences. This book constitutes the refereed proceedings of the 8th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2013, held in Nice, France, in June 2013. The 25 revised full papers presented were carefully reviewed and selected from 43 submissions. The papers are organized in topical sections on bio-molecular networks and pathway analysis; learning, classification, and clustering; data mining and knowledge discovery; protein: structure, function, and interaction; motifs, sites, and sequence analysis. Constitutes the refereed proceedings of the International Workshop on Pattern Recognition in Bioinformatics, PRIB 2008, held in Melbourne, Australia, in October 2008. This book discusses the applications of pattern recognition methods in the field of bioinformatics to solve problems in life sciences.