subject area of

• A 22-mer Segment in the Structurally Pliable Regulatory Domain of Metazoan CTP: Phosphocholine Cytidylyltransferase Facilitates Both Silencing and Activating Functions  Academic Article
• A Portrait of the Transcriptome of the Neglected Trematode, Fasciola gigantica—Biological and Biotechnological Implications  Academic Article
• A Robust Elicitation Algorithm for Discovering DNA Motifs Using Fuzzy Self-Organizing Maps  Academic Article
• A comparative map viewer integrating genetic maps for Brassica and Arabidopsis  Academic Article
• A complex gene cluster for indole-diterpene biosynthesis in the grass endophyte Neotyphodium lolii  Academic Article
• A computational model for emergent dynamics in the kidney  Academic Article
• A curated compendium of phosphorylation motifs  Academic Article
• A further study on mining DNA motifs using fuzzy self-organizing maps  Academic Article
• A knowledge-based scoring function based on residue triplets for protein structure prediction  Academic Article
• A method to incorporate prior information into score test for genetic association studies  Academic Article
• A motif and amino acid bias bioinformatics pipeline to identify hydroxyproline-rich glycoproteins  Academic Article
• A novel role for the pol I transcription factor ubtf in maintaining genome stability through the regulation of highly transcribed pol II genes  Academic Article
• A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts  Academic Article
• A scalable permutation approach reveals replication and preservation patterns of network modules in large datasets  Academic Article
• A secreted Plasmodium falciparum kinase reveals a signature motif for classification of tyrosine kinase-like kinases  Academic Article
• Abundance of intrinsically unstructured proteins in P. falciparum and other apicomplexan parasite proteomes  Academic Article
• Accumulating Variation at Conserved Sites in Potyvirus Genomes Is Driven by Species Discovery and Affects Degenerate Primer Design  Academic Article
• Accuracy of Predicting the Genetic Risk of Disease Using a Genome-Wide Approach  Academic Article
• Accurate and interpretable nanoSAR models from genetic programming-based decision tree construction approaches  Academic Article
• Advances in bioinformatics: Selected papers from APBC 2014 [Editorial]  Editorial Article
• AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments  Academic Article
• An Accessible Proteogenomics Informatics Resource for Cancer Researchers  Academic Article
• An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis  Academic Article
• Analysis on relationship between extreme pathways and correlated reaction sets  Academic Article
• Application of neural networks to large dataset QSAR, virtual screening, and library design.  Academic Article
• Approaches to defining dual-targeted proteins in Arabidopsis  Academic Article
• Arabinogalactan Proteins Are Required for Apical Cell Extension in the Moss Physcomitrella patens  Academic Article
• Assembly of the Type II Secretion System such as Found in Vibrio cholerae Depends on the Novel Pilotin AspS  Academic Article
• Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour  Academic Article
• BASC: an integrated bioinformatics system for Brassica research  Academic Article
• Bacterial genomic G+C composition-eliciting environmental adaptation  Academic Article
• Bioavailability Prediction Based on Molecular Structure for a Diverse Series of Drugs  Academic Article
• Bioinformatic approaches for predicting substrates of proteases  Academic Article
• Bioinformatics in protein kinases regulatory network and drug discovery  Academic Article
• Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment  Academic Article
• Bioinformatics tools and resources for analyzing protein structures  Chapter
• Bioinformatics tools for extracellular vesicles research  Chapter
• Breaking an impasse in pectin biosynthesis  Academic Article
• CHOMPER: A bioinformatic tool for rapid validation of tandem mass spectrometry search results associated with high-throughput proteomic strategies  Conference Paper
• CIDB: Chlamydia Interactive Database for cross-querying genomics, transcriptomics and proteomics data  Academic Article
• Caenorhabditis elegans NONO-1: Insights into DBHS protein structure, architecture, and function  Academic Article
• Candidate effector gene identification in the ascomycete fungal phytopathogen Venturia inaequalis by expressed sequence tag analysis  Academic Article
• Characterisation and expression of an Hsp70 gene from Parastrongyloides trichosuri  Academic Article
• Chimeric antigen receptor T cells form nonclassical and potent immune synapses driving rapid cytotoxicity  Academic Article
• Comparative study of computational methods to detect the correlated reaction sets in biochemical networks  Academic Article
• Computational Characterization of 3′ Splice Variants in the GFAP Isoform Family  Academic Article
• Computational developments in microRNA-regulated protein-protein interactions  Academic Article
• Computational methods for protein interaction and structural prediction: Preface  Editorial Article
• Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer  Academic Article
• Conformational Features of Topologically Classified RNA Secondary Structures  Academic Article
• Construct optimization for studying protein complexes: obtaining diffraction-quality crystals of the pseudosymmetric PSPC1–NONO heterodimer  Academic Article
• Correlating gene and protein expression data using Correlated Factor Analysis  Academic Article
• DIA1R Is an X-Linked Gene Related to Deleted In Autism-1  Academic Article
• DSB proteins and bacterial pathogenicity  Academic Article
• De Novo Characterisation of the Greenlip Abalone Transcriptome (Haliotis laevigata) with a Focus on the Heat Shock Protein 70 (HSP70) Family  Academic Article
• Deep Sequencing of RNA from Three Different Extracellular Vesicle (EV) Subtypes Released from the Human LIM1863 Colon Cancer Cell Line Uncovers Distinct Mirna-Enrichment Signatures  Academic Article
• Detection and validation of structural variations in bovine whole-genome sequence data  Academic Article
• Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts  Academic Article
• Dietary fat quality impacts genome-wide DNA methylation patterns in a cross-sectional study of Greek preadolescents  Academic Article
• Dihydrodipicolinate synthase is absent in fungi  Academic Article
• Discovery of Cyclotide-Like Protein Sequences in Graminaceous Crop Plants: Ancestral Precursors of Circular Proteins?  Academic Article
• Discovery of Genes Activated by the Mitochondrial Unfolded Protein Response (mtUPR) and Cognate Promoter Elements  Academic Article
• Dissemination of scientific software with Galaxy ToolShed  Academic Article
• Diversity of S-Alleles and Mate Availability in 3 Populations of Self-Incompatible Wild Pear (Pyrus pyraster)  Academic Article
• EVpedia: a community web portal for extracellular vesicles research  Academic Article
• Effective mosquito and arbovirus surveillance using metabarcoding  Academic Article
• Effects of Heterogeneous and Clustered Contact Patterns on Infectious Disease Dynamics  Academic Article
• Evaluation of Different Oligonucleotide Base Substitutions at CpG Binding sites in Multiplex Bisulfite-PCR sequencing  Academic Article
• Evidence of Evolutionary Constraints That Influences the Sequence Composition and Diversity of Mitochondrial Matrix Targeting Signals  Academic Article
• Evolution of Vertebrate Genes Related to Prion and Shadoo Proteins—Clues from Comparative Genomic Analysis  Academic Article
• Exceptionally high conservation of the MHC class I-related gene, MR1, among mammals  Academic Article
• Experimental Analysis of the Arabidopsis Mitochondrial Proteome Highlights Signaling and Regulatory Components, Provides Assessment of Targeting Prediction Programs, and Indicates Plant-Specific Mitochondrial Proteins  Academic Article
• Exploring Cross-Species-Related miRNAs Based on Sequence and Secondary Structure  Academic Article
• Exploring consensus RNA substructural patterns using subgraph mining  Academic Article
• Exploring the ncRNA–ncRNA patterns based on bridging rules  Academic Article
• Extraction of high quality k-words for alignment-free sequence comparison  Academic Article
• Finding rule groups to classify high dimensional gene expression datasets  Academic Article
• FunRich: An open access standalone functional enrichment and interaction network analysis tool  Academic Article
• GWIS - model-free, fast and exhaustive search for epistatic interactions in case-control GWAS  Academic Article
• Gene expression in diplosporous and sexual Eragrostis curvula genotypes with differing ploidy levels  Academic Article
• Genome-wide SNP identification in multiple morphotypes of allohexaploid tall fescue (Festuca arundinacea Schreb)  Academic Article
• Grouping miRNAs of similar functions via weighted information content of gene ontology  Academic Article
• Guest Editorial for the 12th Asia Pacific Bioinformatics Conference  Editorial Article
• Guest Editorial for the 13th Asia Pacific Bioinformatics Conference  Academic Article
• Guest Editorial for the 14th Asia Pacific Bioinformatics Conference (APBC2016)  Editorial Article
• Guest Editorial: Advanced Algorithms of Bioinformatics  Editorial Article
• Guest Editorial: Application and Development of Bioinformatics  Editorial Article
• High-Throughput Data of Circular RNA Profiles in Human Temporal Cortex Tissue Reveals Novel Insights into Temporal Lobe Epilepsy  Academic Article
• Human kallikrein 4 signal peptide induces cytotoxic T cell responses in healthy donors and prostate cancer patients  Academic Article
• IDENTIFYING CO-REGULATING MICRORNA GROUPS  Academic Article
• Identification of protein complexes by integrating multiple alignment of protein interaction networks  Academic Article
• Identifying Interactions Between Long Noncoding RNAs and Diseases Based on Computational Methods  Chapter
• Identifying targets for drug discovery using bioinformatics  Academic Article
• Inferring microRNA-environmental factor interactions based on multiple biological information fusion  Academic Article
• Information Integration in Molecular Bioscience  Academic Article
• Insight into the self-association of key enzymes from pathogenic species  Academic Article
• Insights into the Immunological Properties of Intrinsically Disordered Malaria Proteins Using Proteome Scale Predictions  Academic Article
• Insulin mediated activation of PI3K/Akt signalling pathway modifies the proteomic cargo of extracellular vesicles  Academic Article
• International Journal of Bioinformatics Research and Applications: Editorial  Academic Article
• Interval-based distance function for identifying RNA structure candidates  Academic Article
• Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data  Academic Article
• K-Partite cliques of protein interactions: a novel subgraph topology for functional coherence analysis on PPI networks  Academic Article
• KSIMC: Predicting kinase–Substrate interactions based on matrix completion  Academic Article
• Knockdown of stem cell regulator Oct4A in ovarian cancer reveals cellular reprogramming associated with key regulators of cytoskeleton-extracellular matrix remodelling  Academic Article
• Label-based and label-free strategies for protein quantitation  Chapter
• Linear ubiquitin chain assembly complex coordinates late thymic T-cell differentiation and regulatory T-cell homeostasis  Academic Article
• MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences  Academic Article
• Marsupial and monotreme genomes.  Academic Article
• MedDietScore: A computer program that evaluates the adherence to the Mediterranean dietary pattern and its relation to cardiovascular disease risk  Academic Article
• Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems  Academic Article
• Metagenomic arbovirus detection using MinION nanopore sequencing  Academic Article
• MidA is a putative methyltransferase that is required for mitochondrial complex I function  Academic Article
• Mining Characteristic Relations Bind to RNA Secondary Structures  Conference Paper
• Mining a Tandem Mass Spectrometry Database To Determine the Trends and Global Factors Influencing Peptide Fragmentation  Academic Article
• Mining featured patterns of MiRNA interaction based on sequence and structure similarity  Academic Article
• Modelling the structure of the fusion protein from human respiratory syncytial virus  Academic Article
• Molecular characterisation and genetic mapping of candidate genes for qualitative disease resistance in perennial ryegrass (Lolium perenne L.)  Academic Article
• Multi-omic data analysis using Galaxy  Academic Article
• NetPath: a public resource of curated signal transduction pathways  Academic Article
• Network tools for the analysis of proteomic data  Chapter
• Nonlinear predictive modeling of MHC class II-peptide binding using Bayesian neural networks.  Academic Article
• Nonsense Mediated Decay Resistant Mutations Are a Source of Expressed Mutant Proteins in Colon Cancer Cell Lines with Microsatellite Instability  Academic Article
• Optimisation of Milk Protein Top-Down Sequencing Using In-Source Collision-Induced Dissociation in the Maxis Quadrupole Time-of-Flight Mass Spectrometer  Academic Article
• Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database  Academic Article
• PROSPER: An Integrated Feature-Based Tool for Predicting Protease Substrate Cleavage Sites  Academic Article
• PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy  Academic Article
• Plant mitochondrial transcriptomics by quantitative RT-PCR.  Academic Article
• Platelet-Derived Growth Factor Receptor Beta: A Novel Urinary Biomarker for Recurrence of Non-Muscle-Invasive Bladder Cancer  Academic Article
• Post-genomic nematode parasitology  Academic Article
• Potent Agonists of a Hematopoietic Stem Cell Cytokine Receptor, c-Mpl  Academic Article
• Potent agonists of a hematopoietic stem cell cytokine receptor, c-Mpl.  Academic Article
• Potential epigenetic regulatory proteins localise to distinct nuclear sub-compartments in Plasmodium falciparum  Academic Article
• Predicting miRNA-mediated gene silencing mode based on miRNA-target duplex features  Academic Article
• Predicting serpin/protease interactions  Academic Article
• Prediction of pre-miRNA with multiple stem-loops using pruning algorithm  Academic Article
• Proteotypic peptides and their applications  Chapter
• Quantitative analysis of exosomal miRNA via qPCR and digital PCR  Chapter
• Riding the Spermatogenic Wave: Profiling Gene Expression Within Neonatal Germ and Sertoli Cells During a Synchronized Initial Wave of Spermatogenesis in Mice  Academic Article
• Role of Plasmepsin V in Export of Diverse Protein Families from the Plasmodium falciparum Exportome  Academic Article
• Seasonality in risk of pandemic influenza emergence  Academic Article
• Semantically predicting protein functions based on protein functional connectivity  Academic Article
• SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction  Academic Article
• StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations  Academic Article
• Statistical evaluation of labeled comparative profiling proteomics experiments using permutation test  Chapter
• Stem cell decision making and critical-like exploratory networks  Academic Article
• Structural and Dynamic Requirements for Optimal Activity of the Essential Bacterial Enzyme Dihydrodipicolinate Synthase  Academic Article
• Structural, kinetic and computational investigation of Vitis vinifera DHDPS reveals new insight into the mechanism of lysine-mediated allosteric inhibition  Academic Article
• Structure of the tetrameric form of human L-Xylulose reductase: Probing the inhibitor-binding site with molecular modeling and site-directed mutagenesis  Academic Article
• Structure-based drug design to augment hit discovery  Academic Article
• Supercomputing enabling exhaustive statistical analysis of genome wide association study data: Preliminary results.  Academic Article
• Systematic identification of immunodominant CD8+ T-cell responses to influenza A virus in HLA-A2 individuals  Academic Article
• Systems analysis identifies miR-29b regulation of invasiveness in melanoma  Academic Article
• Targeted mining of drought stress-responsive genes from EST resources in Cleistogenes songorica  Academic Article
• The CELLULOSE-SYNTHASE LIKE C (CSLC) Family of Barley Includes Members that Are Integral Membrane Proteins Targeted to the Plasma Membrane  Academic Article
• The Genome 10K Project : A Way Forward.  Academic Article
• The Status of Dosage Compensation in the Multiple X Chromosomes of the Platypus  Academic Article
• The Tenth Asia Pacific Bioinformatics Conference (APBC 2012)  Conference Paper
• Toward a systematic exploration of nano-bio interactions  Academic Article
• Transcriptome analysis of Neotyphodium and Epichloë grass endophytes  Academic Article
• Transcriptomic Coordination in the Human Metabolic Network Reveals Links between n-3 Fat Intake, Adipose Tissue Gene Expression and Metabolic Health  Academic Article
• Unassigned MS/MS spectra: Who Am I?  Chapter
• Using Bioinformatics Techniques for Gene Identification in Drug Discovery and Development  Academic Article
• miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set  Academic Article