Bioinformatics and Biology Insights

Cross-Disciplinary Detection and Analysis of Network Motifs (Published on 19 Apr 2015)

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An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences (Published on 15 Apr 2015)

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A Systems Biology Approach Reveals the Dose- and Time-Dependent Effect of Primary Human Airway Epithelium Tissue Culture After Exposure to Cigarette Smoke In Vitro (Published on 09 Mar 2015)

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Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum (Published on 09 Feb 2015)

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POEAS: Automated Plant Phenomic Analysis Using Plant Ontology (Published on 21 Dec 2014)

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Computational Methods for CLIP-seq Data Processing (Published on 01 Oct 2014)

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Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes (Published on 10 Sep 2014)

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Integrated Analysis of Dysregulated miRNA-gene Expression in HMGA2-silenced Retinoblastoma Cells (Published on 04 Sep 2014)

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Computational Identification of Dengue Virus MicroRNA-Like Structures and their Cellular Targets (Published on 14 Aug 2014)

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In Silico Studies of Medicinal Compounds Against Hepatitis C Capsid Protein from North India (Published on 23 Jun 2014)

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Identification of Chicken Pulmonary miRNAs Targeting PB1, PB1-F2, and N40 Genes of Highly Pathogenic Avian Influenza Virus H5N1 In Silico (Published on 12 Jun 2014)

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DOR – a Database of Olfactory Receptors – Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes (Published on 12 Jun 2014)

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A Protocol for mtGenome Analysis on Large Sample Numbers (Published on 11 Jun 2014)

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High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism (Published on 08 Jun 2014)

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The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins (Published on 20 May 2014)

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Promise and Reality in the Expanding Field of Network Interaction Analysis: Metabolic Networks (Published on 16 Apr 2014)

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Computational Insights of the Interaction among Sea Anemones Neurotoxins and Kv1.3 Channel (Published on 15 Apr 2014)

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An In Silico Approach for Characterization of an Aminoglycoside Antibiotic-Resistant Methyltransferase Protein from Pyrococcus furiosus (DSM 3638) (Published on 20 Mar 2014)

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Postpartal Subclinical Endometritis Alters Transcriptome Profiles in Liver and Adipose Tissue of Dairy Cows (Published on 19 Feb 2014)

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Probing the Unknowns in Cytokinin-Mediated Immune Defense in Arabidopsis with Systems Biology Approaches (Published on 13 Feb 2014)

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Longitudinal Analysis of Whole Blood Transcriptomes to Explore Molecular Signatures Associated With Acute Renal Allograft Rejection (Published on 22 Jan 2014)

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GeneSV – an Approach to Help Characterize Possible Variations in Genomic and Protein Sequences (Published on 08 Jan 2014)

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Three Dimensional Structure Prediction of Fatty Acid Binding Site on Human Transmembrane Receptor CD36 (Published on 02 Dec 2013)

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ChIP-Seq Data Mining: Remarkable Differences in NRSF/REST Target Genes between Human ESC and ESC-Derived Neurons (Published on 01 Dec 2013)

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A Computational Assay to Design an Epitope-Based Peptide Vaccine Against Saint Louis Encephalitis Virus (Published on 24 Nov 2013)

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On Crowd-verification of Biological Networks (Published on 10 Oct 2013)

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Automatic Identification of Algal Community from Microscopic Images (Published on 10 Oct 2013)

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Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights (Published on 10 Oct 2013)

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Molecular Insights on Post-chemotherapy Retinoblastoma by Microarray Gene Expression Analysis (Published on 18 Sep 2013)

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Molecular Modeling of Differentially Phosphorylated Serine 10 and Acetylated lysine 9/14 of Histone H3 Regulates their Interactions with 14-3-3ζ, MSK1, and MKP1 (Published on 26 Aug 2013)

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Bioinformatics Analysis of Transcriptome Dynamics During Growth in Angus Cattle Longissimus Muscle (Published on 04 Aug 2013)

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Systematic Verification of Upstream Regulators of a Computable Cellular Proliferation Network Model on Non-Diseased Lung Cells Using a Dedicated Dataset (Published on 23 Jul 2013)

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Association of Putative Members to Family of Mosquito Odorant Binding Proteins: Scoring Scheme Using Fuzzy Functional Templates and Cys Residue Positions (Published on 22 Jul 2013)

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Bioinformatics and Gene Network Analyses of the Swine Mammary Gland Transcriptome during Late Gestation (Published on 14 Jul 2013)

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A Modular Cell-Type Focused Inflammatory Process Network Model for Non-Diseased Pulmonary Tissue (Published on 20 Jun 2013)

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The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum (Published on 26 May 2013)

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Association Between a Multi-Locus Genetic Risk Score and Inflammatory Bowel Disease (Published on 19 May 2013)

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miR-Explore: Predicting MicroRNA Precursors by Class Grouping and Secondary Structure Positional Alignment (Published on 02 Apr 2013)

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Knowledge Discovery in Variant Databases Using Inductive Logic Programming (Published on 18 Mar 2013)

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Construction of a Computable Network Model for DNA Damage, Autophagy, Cell Death, and Senescence (Published on 07 Mar 2013)

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Computational Small RNA Prediction in Bacteria (Published on 07 Mar 2013)

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Integrative Approach for Computationally Inferring Interactions between the Alpha and Beta Subunits of the Calcium-Activated Potassium Channel (BK): a Docking Study (Published on 27 Feb 2013)

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A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences (Published on 24 Feb 2013)

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A Statistical Method without Training Step for the Classification of Coding Frame in Transcriptome Sequences (Published on 23 Jan 2013)

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PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation (Published on 10 Jan 2013)

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Identification and Insilico Analysis of Retinoblastoma Serum microRNA Profile and Gene Targets Towards Prediction of Novel Serum Biomarkers (Published on 09 Jan 2013)

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Methods of Combinatorial Optimization to Reveal Factors Affecting Gene Length (Published on 10 Dec 2012)

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Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR- Supported in silico Modeling (Published on 03 Dec 2012)

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Functional Annotation Analytics of Bacillus Genomes Reveals Stress Responsive Acetate Utilization and Sulfate Uptake in the Biotechnologically Relevant Bacillus megaterium (Published on 21 Nov 2012)

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A Fast Quad-Tree Based Two Dimensional Hierarchical Clustering (Published on 19 Nov 2012)

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Homology Modeling and Molecular Dynamics Simulation Studies of a Marine Alkaline Protease (Published on 19 Nov 2012)

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Myosinome: A Database of Myosins from Select Eukaryotic Genomes to Facilitate Analysis of Sequence-Structure-Function Relationships (Published on 12 Nov 2012)

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BioNetwork Bench: Database and Software for Storage, Query, and Analysis of Gene and Protein Networks (Published on 08 Nov 2012)

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The Role of Electrostatic Interactions on Klentaq1 Insight for Domain Separation (Published on 30 Oct 2012)

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Integrative Structural Modelling of the Cardiac Thin Filament: Energetics at the Interface and Conservation Patterns Reveal a Spotlight on Period 2 of Tropomyosin (Published on 03 Oct 2012)

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The Core Mouse Response to Infection by Neospora Caninum Defined by Gene Set Enrichment Analyses (Published on 03 Sep 2012)

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Simultaneous Analysis of Common and Rare Variants in Complex Traits: Application to SNPs (SCARVAsnp) (Published on 31 Jul 2012)

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Simple F Test Reveals Gene-Gene Interactions in Case-Control Studies (Published on 02 Jul 2012)

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DNA Structural Properties in the Classification of Genomic Transcription Regulation Elements (Published on 02 Jul 2012)

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An Integrated Statistical Approach to Compare Transcriptomics Data Across Experiments: A Case Study on the Identification of Candidate Target Genes of the Transcription Factor PPARα (Published on 19 Jun 2012)

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The Influence of Taxon Sampling and Tree Shape on Molecular Dating: An Empirical Example from Mammalian Mitochondrial Genomes (Published on 31 May 2012)

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Different Evolutionary Modifications as a Guide to Rewire Two-Component Systems (Published on 03 May 2012)

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Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations (Published on 23 Apr 2012)

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Mining Gene Ontology Data with AGENDA (Published on 18 Apr 2012)

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White Blood Cell Differentials Enrich Whole Blood Expression Data in the Context of Acute Cardiac Allograft Rejection (Published on 10 Apr 2012)

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Molecular Modelling of Oligomeric States of DmOR83b, an Olfactory Receptor in D. melanogaster (Published on 26 Mar 2012)

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Computational Design of Targeted Inhibitors of Polo-Like Kinase 1 (Plk1) (Published on 20 Feb 2012)

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Structural and Functional Insights on the Myosin Superfamily (Published on 01 Feb 2012)

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A Novel Approach for the Simultaneous Analysis of Common and Rare Variants in Complex Traits (Published on 22 Jan 2012)

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Functional Annotation Analytics of Rhodopseudomonas palustris Genomes (Published on 21 Sep 2011)

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Mouse Retinal Development: a Dark Horse Model for Systems Biology Research (Published on 22 May 2011)

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Gene Networks Driving Bovine Mammary Protein Synthesis During the Lactation Cycle (Published on 04 May 2011)

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Amino Acid Features of P1B-ATPase Heavy Metal Transporters Enabling Small Numbers of Organisms to Cope with Heavy Metal Pollution (Published on 17 Apr 2011)

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Identification of Drought-Responsive Universal Stress Proteins in Viridiplantae (Published on 07 Feb 2011)

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Conceptual Aspects of Large Meta-Analyses with Publicly Available Microarray Data: A Case Study in Oncology (Published on 23 Jan 2011)

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Different Functional Gene Clusters in Yeast have Different Spatial Distributions of the Transcription Factor Binding Sites (Published on 12 Jan 2011)

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Computational Analysis of Molecular Interaction Networks Underlying Change of HIV-1 Resistance to Selected Reverse Transcriptase Inhibitors (Published on 12 Dec 2010)

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Periodicity Detection Method for Small-Sample Time Series Datasets (Published on 22 Nov 2010)

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Candidate Single Nucleotide Polymorphism Markers for Arsenic Responsiveness of Protein Targets (Published on 11 Oct 2010)

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An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces (Published on 11 Oct 2010)

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Expression of Metabolic, Tissue Remodeling, Oxidative Stress, and Inflammatory Pathways in Mammary Tissue During Involution in Lactating Dairy Cows (Published on 20 Sep 2010)

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Comparative in Silico Analyses of Cpeb1–4 with Functional Predictions (Published on 30 Aug 2010)

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A Plausible Role for the Presence of Internal Shine-Dalgarno Sites (Published on 28 Jun 2010)

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Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data (Published on 21 Jun 2010)

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Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach (Published on 17 Jun 2010)

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Effect of Diet Supplementation on the Expression of Bovine Genes Associated with Fatty Acid Synthesis and Metabolism (Published on 31 Mar 2010)

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Evolutionary Pattern of N-Glycosylation Sequon Numbers  in Eukaryotic ABC Protein Superfamilies (Published on 17 Feb 2010)

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An Improved Approach for Mapping Quantitative Trait Loci in a Pseudo-Testcross: Revisiting a Poplar Mapping Study (Published on 04 Feb 2010)

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Domain Organization of Long Autotransporter Signal Sequences (Published on 14 Dec 2009)

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An Efficient Method to Identify Conditionally Activated Transcription Factors and their Corresponding Signal Transduction Pathway Segments (Published on 17 Nov 2009)

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Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences (Published on 11 Nov 2009)

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Classifying Coding DNA with Nucleotide Statistics (Published on 28 Oct 2009)

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Inferring Transcriptional Interactions by the Optimal Integration of ChIP-chip and Knock-out Data (Published on 21 Oct 2009)

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A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome (Published on 05 Oct 2009)

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Graphical User Interfaces for Molecular Dynamics—Quo Vadis? (Published on 23 Sep 2009)

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Gromita: A Fully Integrated Graphical User Interface to Gromacs 4 (Published on 07 Sep 2009)

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Gene Expression Based Leukemia Sub‑Classification Using Committee Neural Networks (Published on 03 Sep 2009)

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affyPara - a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data (Published on 22 Jul 2009)

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Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences (Published on 01 Jul 2009)

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Sequence Analysis of the Full-length cDNA and Protein Structure Homology Modeling of FABP2 from Paralichthys Olivaceus (Published on 04 Jun 2009)

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