Bioinformatics Research and Applications

Predicting Disease Risks Using Feature Selection Based on Random Forest and Support Vector Machine.- Phylogenetic Bias in the Likelihood Method Caused by Missing Data Coupled with Among-Site Rate Variation: An Analytical Approach.- An Eigen decomposition Method for Protein Structure Alignment.- Functional Interplay between Hemagglutinin and Neuraminidase of Pandemic 2009 H1N1 from the Perspective of Virus Evolution.- Predicting Protein Submitochondrial Locations Using a K-Nearest Neighbors Method Based on the Bit-Score Weighted Euclidean Distance.- Algorithms Implemented for Cancer Gene Searching and Classifications.- Dysregulated microRNA Profile in HeLa Cell Lines Induced by Lupeol.- A Simulation for Proportional Biological Operational Mu-Circuit.- Computational Prediction of Human Saliva-Secreted Proteins.- A Parallel Scheme for Three-Dimensional Reconstruction in Large-Field Electron Tomography.- An Improved Correlation Method Based on Rotation Invariant Feature for Automatic Particle Selection.- An Effective Algorithm for Peptide de novo Sequencing from Mixture MS/MS Spectra.- Identifying Spurious Interactions in the Protein-Protein Interaction Networks Using Local Similarity Preserving Embedding.- Multiple RNA Interaction with Sub-optimal Solutions.- Application of Consensus String Matching in the Diagnosis of Allelic Heterogeneity (Extended Abstract).- Continuous Time Bayesian Networks for Gene Network Reconstruction: A Comparative Study on Time Course Data.- Drug Target Identification Based on Structural Output Controllability of Complex Networks.- NovoGMET: De Novo Peptide Sequencing Using Graphs with Multiple Edge Types (GMET) for ETD/ECD Spectra.- Duplication Cost Diameters.- Computational Identification of De-Centric Genetic Regulatory Relationships from Functional Genomic Data.- Classification of Mutations by Functional Impact Type: Gain of Function, Loss of Function and Switch of Function.- Network Analysis of Human Disease Comorbidity Patterns Based on Large-Scale Data Mining.- Identification of Essential Proteins by Using Complexes and Interaction Network.- GenoScan: Genomic Scanner for Putative miRNA Precursors.- Searching SNP Combinations Related to Evolutionary Information of Human Populations on HapMap Data.- 2D Pharmacophore Query Generation.- Structure-Based Analysis of Protein Binding Pockets Using Von Neumann Entropy.- A New Mathematical Model for Inbreeding Depression in Large Populations.- dSpliceType: A Multivariate Model for Detecting Various Types of Differential Splicing Events Using RNA-Seq.- Conformational Transitions and Principal Geodesic Analysis on the Positive Semidefinite Matrix Manifold.- Joint Analysis of Functional and Phylogenetic Composition for Human Microbiome Data.- schematikon: Detailed Sequence-Structure Relationships from Mining a Non-redundant Protein Structure Database (Extended Abstract).- PNImodeler: Web Server for Inferring Protein Binding Nucleotides from Sequence Data.- A MCI Decision Support System Based on Ontology.- Context Similarity Based Feature Selection Methods for Protein Interaction Article Classification.- Network Propagation Reveals Novel Genetic Features Predicting Drug Response of Cancer Cell Lines.- Splice Site Prediction Using Support Vector Machine with Markov Model and Codon Information.- Exploiting Topic Modeling to Boost Metagenomic Sequences Binning.- Network-Based Method for Identifying Overlapping Mutated Driver Pathways in Cancer.- Completing a Bacterial Genome with in silico and Wet Lab Approaches.- Protein Function Prediction: A Global Prediction Method with Multiple Data Sources.- A microRNA-Gene Network in Ovarian Cancer from Genome-Wide QTL Analysis.- K-Profiles Nonlinear Clustering.- Estrogen Induced RNA Polymerase II Stalling in Breast Cancer Cell Line MCF7.- A Knowledge-Driven Approach in Constructing a Large-Scale Drug-Side Effect Relationship Knowledge Base for Computational Drug Discovery.- Systems Biology Approach to Understand Seed Composition.- Prediction of the Cooperative cis-regulatory Elements for Broadly Expressed Neuronal Genes in Caenorhabditis Elegans.- Improving the Mapping of the Smith-Waterman Sequence Database Search Algorithm onto CUDA GPUs.- VFP: A Visual Tool for Predicting Gene-Fusion Base on Analyzing Single-end RNA-Sequence.- A Novel Method for Identifying Essential Proteins from Active PPI Networks.- RAUR: Re-alignment of Unmapped Reads with Base Quality Score.- PIGS: Improved Estimates of Identity-by-Descent Probabilities by Probabilistic IBD Graph Sampling.- Clustering PPI Data through Improved Synchronization-Based Hierarchical Clustering Method.- Order Decay in Transcription Regulation in Type 1 Diabetes.- Simulated Regression Algorithm for Transcriptome Quantification.