Pattern Recognition in Bioinformatics

Protein: Structure, Function, and Interaction.- Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins.- A Method to Find Sequentially Separated Motifs in Biological Sequences (SSMBS).- Predicting SUMOylation Sites.- DFS Based Partial Pathways in GA for Protein Structure Prediction.- Evaluation of the Stability of Folding Nucleus upon Mutation.- Prediction of Protein Beta-Sheets: Dynamic Programming versus Grammatical Approach.- Using Multi-scale Glide Zoom Window Feature Extraction Approach to Predict Protein Homo-oligomer Types.- Extraction of Binding Sites in Proteins by Searching for Similar Local Molecular Surfaces.- Learning, Classification, and Clustering.- A Clustering Based Hybrid System for Mass Spectrometry Data Analysis.- A Modified Markov Clustering Approach for Protein Sequence Clustering.- Feature Selection and Classification for Small Gene Sets.- Pseudoknot Identification through Learning TAGRNA.- Support Vector Based T-Score for Gene Ranking.- Prediction of Transcription Factor Families Using DNA Sequence Features.- g-MARS: Protein Classification Using Gapped Markov Chains and Support Vector Machines.- Bio-Molecular Networks and Pathways Analysis.- Domain-Domain Interaction Identification with a Feature Selection Approach.- Dividing Protein Interaction Networks by Growing Orthologous Articulations.- Constraint Minimization for Efficient Modeling of Gene Regulatory Network.- Fusion of Gene Regulatory and Protein Interaction Networks Using Skip-Chain Models.- TopEVM: Using Co-occurrence and Topology Patterns of Enzymes in Metabolic Networks to Construct Phylogenetic Trees.- Generating Synthetic Gene Regulatory Networks.- Microarray and Gene Expression Analysis.- Gene Selection for Microarray Data by a LDA-Based Genetic Algorithm.- Sequential Forward Selection Approach to the Non-unique Oligonucleotide Probe Selection Problem.- On Finding and Interpreting Patterns in Gene Expression Data from Time Course Experiments.- Microarray Design Using the Hilbert-Schmidt Independence Criterion.- Identifying Non-random Patterns from Gene Expression Profiles.- A Study on the Importance of Differential Prioritization in Feature Selection Using Toy Datasets.- Weighted Top Score Pair Method for Gene Selection and Classification.- Data Mining and Knowledge Discovery.- Identifying Conserved Discriminative Motifs.- Exploratory Data Analysis for Investigating GC-MS Biomarkers.- Multi-relational Data Mining for Tetratricopeptide Repeats (TPR)-Like Superfamily Members in Leishmania spp.: Acting-by-Connecting Proteins.- Heuristic Non Parametric Collateral Missing Value Imputation: A Step Towards Robust Post-genomic Knowledge Discovery.- Protein Expression Molecular Pattern Discovery by Nonnegative Principal Component Analysis.- Gene Ontology Assisted Exploratory Microarray Clustering and Its Application to Cancer.- Discovery of Biomarkers for Hexachlorobenzene Toxicity Using Population Based Methods on Gene Expression Data.- Applications of High Performance Computing.- Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study.- Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA.- GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences.- Accelerating BLASTP on the Cell Broadband Engine.