Evolutionary Bioinformatics

An In-depth Analysis of a Multilocus Phylogeny Identifies leuS As a Reliable Phylogenetic Marker for the Genus Pantoea (344 Views since 27 Jul 2014)

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Regulation of Human PAX6 Expression by miR-7 (1000 Views since 14 Jul 2014)

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Influence of Modularity and Regularity on Disparity of Atelostomata Sea Urchins (1118 Views since 29 Jun 2014)

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Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation (1556 Views since 12 Jun 2014)

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Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates (1994 Views since 07 May 2014)

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A Multistep Screening Method to Identify Genes Using Evolutionary Transcriptome of Plants (2050 Views since 21 Apr 2014)

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TreSpEx—Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information (2183 Views since 31 Mar 2014)

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Phylogenetic Relationships of Some Filamentous Cyanoprokaryotic Species (2166 Views since 23 Feb 2014)

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The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection (2041 Views since 16 Feb 2014)

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Netmes: Assessing Gene Network Inference Algorithms by Network-Based Measures (2411 Views since 06 Feb 2014)

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RapidMic: Rapid Computation of the Maximal Information Coefficient (2042 Views since 06 Feb 2014)

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Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model (3621 Views since 10 Dec 2013)

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A Comprehensive Phylogenetic Analysis of Deadenylases (2743 Views since 02 Dec 2013)

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EASER: Ensembl Easy Sequence Retriever (2648 Views since 24 Nov 2013)

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Computational Identification of MicroRNAs from the Expressed Sequence Tags of Toxic Dinofiagellate Alexandrium Tamarense (2880 Views since 20 Nov 2013)

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Grouped False-Discovery Rate for Removing the Gene-Set-Level Bias of RNA-seq (2542 Views since 13 Nov 2013)

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The Origin of Parasitism Gene in Nematodes: Evolutionary Analysis Through the Construction of Domain Trees (3224 Views since 06 Nov 2013)

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Identification of New Aquaporin Genes and Single Nucleotide Polymorphism in Bread Wheat (3561 Views since 03 Nov 2013)

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PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics (3347 Views since 29 Oct 2013)

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Analysis of New Functional Profiles of Protein Isoforms Yielded by Ds Exonization in Rice (4373 Views since 09 Oct 2013)

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Prediction of Protein Essentiality by the Support Vector Machine with Statistical Tests (3013 Views since 03 Oct 2013)

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Identification, Nomenclature, and Evolutionary Relationships of Mitogen-Activated Protein Kinase (MAPK) Genes in Soybean (9832 Views since 22 Sep 2013)

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POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments (4278 Views since 01 Sep 2013)

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SBEToolbox: A Matlab Toolbox for Biological Network Analysis (4971 Views since 01 Sep 2013)

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Analysis of Protein Thermostability Enhancing Factors in Industrially Important Thermus Bacteria Species (4543 Views since 18 Aug 2013)

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Conventional Simulation of Biological Sequences Leads to a Biased Assessment of Multi-Loci Phylogenetic Analysis (3130 Views since 13 Aug 2013)

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Evolutionary Modeling of Genotype-Phenotype Associations, and Application to Primate Coding and Non-coding mtDNA Rate Variation (3786 Views since 28 Jul 2013)

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Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data (3481 Views since 28 Jul 2013)

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Conserved Nonsense-Prone CpG Sites in Apoptosis-Regulatory Genes: Conditional Stop Signs on the Road to Cell Death (4033 Views since 14 Jul 2013)

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SARP: A Novel Algorithm to Assess Compositional Biases in Protein Sequences (3883 Views since 11 Jul 2013)

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Effective Encoding for DNA Sequence Visualization Based on Nucleotide’s Ring Structure (3702 Views since 07 Jul 2013)

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Molecular Evolution and Functional Divergence of Soluble Starch Synthase Genes in Cassava (Manihot Esculenta Crantz) (5134 Views since 03 Jul 2013)

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rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection (4346 Views since 12 Jun 2013)

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Comment on “The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway” (3509 Views since 10 Jun 2013)

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Analysis of Synonymous Codon Usage Patterns in Seven Different Citrus Species (5026 Views since 23 May 2013)

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Antiviral Stratagems Against HIV-1 Using RNA Interference (RNAi) Technology (5679 Views since 16 May 2013)

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Top-Down Clustering for Protein Subfamily Identification (4131 Views since 06 May 2013)

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A Tool Preference Choice Method for RNA Secondary Structure Prediction by SVM with Statistical Tests (3852 Views since 14 Apr 2013)

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Circulation of Human Respiratory Syncytial Virus Strains Among Hospitalized Children with Acute Lower Respiratory Infection in Malaysia (4854 Views since 10 Apr 2013)

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Design of Synthetic Genetic Oscillators Using Evolutionary Optimization (4333 Views since 10 Mar 2013)

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EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes (6635 Views since 10 Mar 2013)

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CMCpy: Genetic Code-Message Coevolution Models in Python (4965 Views since 27 Feb 2013)

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A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-off on Phenotype Robustness in Biological Networks Part I: Gene Regulatory Networks in Systems and Evolutionary Biology (4694 Views since 26 Feb 2013)

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A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Tradeoff on Phenotype Robustness in Biological Networks Part II: Ecological Networks (4219 Views since 26 Feb 2013)

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A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-offs on Phenotype Robustness in Biological Networks. Part III: Synthetic Gene Networks in Synthetic Biology (4499 Views since 26 Feb 2013)

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A Proximity-Based Method to Identify Genomic Regions Correlated with a Continuously Varying Environmental Variable (4128 Views since 29 Jan 2013)

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TIRfinder: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats (4030 Views since 22 Jan 2013)

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The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway (6175 Views since 10 Jan 2013)

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Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus (4773 Views since 19 Nov 2012)

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A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence (7369 Views since 14 Nov 2012)

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Phylogenetic Analysis and Comparative Genomics of Purine Riboswitch Distribution in Prokaryotes (6038 Views since 06 Nov 2012)

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Genome-Wide Survey of Ds Exonization to Enrich Transcriptomes and Proteomes in Plants (9640 Views since 08 Oct 2012)

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Translation Efficiency in Upstream Region of microRNA Targets in Arabidopsis thaliana (5177 Views since 25 Sep 2012)

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Phylogenomic Study of Lipid Genes Involved in Microalgal Biofuel Production—Candidate Gene Mining and Metabolic Pathway Analyses (10639 Views since 20 Sep 2012)

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Evolution of Type II Antifreeze Protein Genes in Teleost Fish: A Complex Scenario Involving Lateral Gene Transfers and Episodic Directional Selection (5461 Views since 17 Sep 2012)

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Cloud Computing for Comparative Genomics with Windows Azure Platform (7568 Views since 30 Aug 2012)

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Meta-Analysis of General Bacterial Subclades in Whole-Genome Phylogenies Using Tree Topology Profiling (5853 Views since 07 Aug 2012)

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Inference of Self-Regulated Transcriptional Networks by Comparative Genomics (5040 Views since 06 Aug 2012)

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TreeCmp: Comparison of Trees in Polynomial Time (5824 Views since 06 Aug 2012)

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Efficiency of Nuclear and Mitochondrial Markers Recovering and Supporting Known Amniote Groups (4482 Views since 06 Aug 2012)

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The Chordate Proteome History Database (5241 Views since 01 Aug 2012)

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PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny (5701 Views since 23 Jul 2012)

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Reliable Phylogenetic Trees Building: A New Web Interface for FIGENIX (5905 Views since 05 Jul 2012)

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Determinants of Exon-Level Evolutionary Rates in Arabidopsis Species (4657 Views since 04 Jul 2012)

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Phylogenomic and Domain Analysis of Iterative Polyketide Synthases in Aspergillus Species (6370 Views since 04 Jul 2012)

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RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity (5765 Views since 25 Jun 2012)

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AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots (8483 Views since 21 Jun 2012)

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Cross-Genome Clustering of Human and C. elegans G-Protein Coupled Receptors (5777 Views since 19 Jun 2012)

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Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion (5972 Views since 19 Jun 2012)

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MiIP: The Monomer Identification and Isolation Program (8212 Views since 14 Jun 2012)

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PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences (4817 Views since 11 Jun 2012)

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Evolution of the RALF Gene Family in Plants: Gene Duplication and Selection Patterns (6058 Views since 11 Jun 2012)

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Mitochondrial Genetic Differentiation of Spirlin (Actinopterigii: Cyprinidae) in the South Caspian Sea basin of Iran (4978 Views since 21 May 2012)

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Impact of the Partitioning Scheme on Divergence Times Inferred from Mammalian Genomic Data Sets (4584 Views since 14 May 2012)

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Efficient Feature Selection and Multiclass Classification with Integrated Instance and Model Based Learning (5585 Views since 30 Apr 2012)

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Promoter Sequences Prediction Using Relational Association Rule Mining (6375 Views since 23 Apr 2012)

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A Lossy Compression Technique Enabling Duplication-Aware Sequence Alignment (3979 Views since 02 Apr 2012)

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Selection of Marker Genes Using Whole-Genome DNA Polymorphism Analysis (7883 Views since 19 Mar 2012)

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easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences (7357 Views since 14 Mar 2012)

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Inferring the Phylogeny of Bovidae Using Mitochondrial DNA Sequences: Resolving Power of Individual Genes Relative to Complete Genomes (6816 Views since 20 Feb 2012)

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Construction of a Pig Physical Interactome Using Sequence Homology and a Comprehensive Reference Human Interactome (5674 Views since 24 Jan 2012)

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Testing Synchrony in Historical Biogeography: The Case of New World Primates and Hystricognathi Rodents (8835 Views since 24 Jan 2012)

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Interkingdom Gene Transfer May Contribute to the Evolution of Phytopathogenicity in Botrytis Cinerea (6017 Views since 11 Jan 2012)

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Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group (6646 Views since 09 Jan 2012)

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BS-KNN: An Effective Algorithm for Predicting Protein Subchloroplast Localization (4959 Views since 05 Jan 2012)

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EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data (5927 Views since 21 Dec 2011)

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SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis (6429 Views since 18 Dec 2011)

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LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes (11792 Views since 13 Dec 2011)

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Species Delimitation and Global Biosecurity (11660 Views since 08 Dec 2011)

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Evolution of Antifreeze Protein Genes in the Diatom Genus Fragilariopsis: Evidence for Horizontal Gene Transfer, Gene Duplication and Episodic Diversifying Selection (6212 Views since 15 Nov 2011)

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Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of Oncidium Gower Ramsey (5658 Views since 14 Nov 2011)

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ColorPhylo: A Color Code to Accurately Display Taxonomic Classifications (5406 Views since 13 Nov 2011)

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In Silico Prediction of Evolutionarily Conserved GC-Rich Elements Associated with Antigenic Proteins of Plasmodium falciparum (5233 Views since 10 Nov 2011)

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On the Interplay between the Evolvability and Network Robustness in an Evolutionary Biological Network: A Systems Biology Approach (4842 Views since 01 Nov 2011)

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Characterization and Inference of Gene Gain/Loss Along Burkholderia Evolutionary History (6128 Views since 18 Oct 2011)

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Profiles and Majority Voting-Based Ensemble Method for Protein Secondary Structure Prediction (6639 Views since 10 Oct 2011)

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A Novel Model for DNA Sequence Similarity Analysis Based on Graph Theory (6746 Views since 04 Oct 2011)

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A New Support Measure to Quantify the Impact of Local Optima in Phylogenetic Analyses (4274 Views since 29 Sep 2011)

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Single-Domain Parvulins Constitute a Specific Marker for Recently Proposed Deep-Branching Archaeal Subgroups (5308 Views since 19 Sep 2011)

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IONS: Identification of Orthologs by Neighborhood and Similarity—an Automated Method to Identify Orthologs in Chromosomal Regions of Common Evolutionary Ancestry and its Application to Hemiascomycetous Yeasts (6895 Views since 30 Aug 2011)

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Phylogenomics-Based Reconstruction of Protozoan Species Tree (7366 Views since 31 Jul 2011)

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Three-Dimensional Structure of Arabidopsis thaliana Lipase Predicted by Homology Modeling Method (8109 Views since 28 Jun 2011)

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Functional Evolution of BRCT Domains from Binding DNA to Protein (6639 Views since 12 Jun 2011)

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How Fitch-Margoliash Algorithm can Benefit from Multi Dimensional Scaling (5568 Views since 07 Jun 2011)

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Structurama: Bayesian Inference of Population Structure (7314 Views since 02 Jun 2011)

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Evolutionary Implications and Physicochemical Analyses of Selected Proteins of Type III Polyketide Synthase Family (7078 Views since 29 May 2011)

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A Monte Carlo Method for Assessing the Quality of Duplication-Aware Alignment Algorithms (4858 Views since 10 May 2011)

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Phylogenetic Analysis of Kindlins Suggests Subfunctionalization of an Ancestral Unduplicated Kindlin into Three Paralogs in Vertebrates (7072 Views since 22 Mar 2011)

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FORS-D Analysis in P. falciparum can Differentiate Classes of Genes Under Selection (7744 Views since 20 Mar 2011)

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SOLiDzipper: A High Speed Encoding Method for the Next-Generation Sequencing Data (7015 Views since 10 Mar 2011)

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Cost-Effective Cloud Computing: A Case Study Using the Comparative Genomics Tool, Roundup (11985 Views since 22 Dec 2010)

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PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences (9053 Views since 16 Dec 2010)

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Where Does the Alignment Score Distribution Shape Come from? (7581 Views since 12 Dec 2010)

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DNA Barcodes of Arabian Partridge and Philby's Rock Partridge: Implications for Phylogeny and Species Identification (9984 Views since 05 Dec 2010)

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Computational Identification of Anthocyanin-Specific Transcription Factors using a Rice Microarray and Maximum Boundary Range Algorithm (7430 Views since 20 Oct 2010)

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EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics (10962 Views since 20 Oct 2010)

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Identifying the Combinatorial Effects of Histone Modifications by Association Rule Mining in Yeast (6635 Views since 20 Sep 2010)

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A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA (7391 Views since 09 Sep 2010)

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Molecular Phylogeny of Edge Hill Virus Supports its Position in the Yellow Fever Virus Group and Identifies a New Genetic Variant (7172 Views since 15 Jun 2010)

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Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference Versus Group-Specific Taxon Sampling (7622 Views since 24 May 2010)

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An Application of Supertree Methods to Mammalian Mitogenomic Sequences (6859 Views since 12 May 2010)

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Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias (8686 Views since 05 May 2010)

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A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction (7486 Views since 09 Apr 2010)

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Comparative Molecular Evolution of Trichoderma Chitinases in Response to Mycoparasitic Interactions (8967 Views since 15 Mar 2010)

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Clustering Protein Sequences Using Affinity Propagation Based on an Improved Similarity Measure (7377 Views since 22 Jan 2010)

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Snapshots of Tree Space (7143 Views since 18 Jan 2010)

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Genome-Wide Identification and Evolutionary Analysis of the Animal Specific ETS Transcription Factor Family (7615 Views since 02 Oct 2009)

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A Model for Protein Sequence Evolution Based on Selective Pressure for Protein Stability: Application to Hemoglobins (7196 Views since 27 Aug 2009)

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On the Use of Bootstrapped Topologies in Coalescent-Based Bayesian MCMC Inference: A Comparison of Estimation and Computational Efficiencies (8607 Views since 31 Jul 2009)

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PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics (10196 Views since 30 Jul 2009)

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A Comprehensive Analysis of Gene Expression Evolution Between Humans and Mice (9460 Views since 06 Jul 2009)

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Initial Implementation of a Comparative Data Analysis Ontology (8401 Views since 03 Jul 2009)

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A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies (7649 Views since 25 Jun 2009)

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Phylogenetic Applications of the Minimum Contradiction Approach on Continuous Characters (6808 Views since 11 Jun 2009)

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Phylogenetic Analyses Reveal Monophyletic Origin of the Ergot Alkaloid Gene dmaW in Fungi (7560 Views since 04 Jun 2009)

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Evolution and Functional Diversification of the GLI Family of Transcription Factors in Vertebrates (7104 Views since 18 May 2009)

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REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era (8566 Views since 06 May 2009)

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The Austronesian Basic Vocabulary Database: From Bioinformatics to Lexomics (11127 Views since 03 Nov 2008)

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Evidence for a Complex Mosaic Genome Pattern in a Full-length Hepatitis C Virus Sequence (5980 Views since 30 Oct 2008)

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Inconsistent Distances in Substitution Matrices can be Avoided by Properly Handling Hydrophobic Residues (5772 Views since 09 Oct 2008)

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Bayesian, Maximum Parsimony and UPGMA Models for Inferring the Phylogenies of Antelopes Using Mitochondrial Markers (9634 Views since 06 Oct 2008)

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Minimum Contradiction Matrices in Whole Genome Phylogenies (5160 Views since 21 Jul 2008)

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Estimation of Genetic Effects and Genotype-Phenotype Maps (7429 Views since 28 Jun 2008)

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Testing the Accuracy of Eukaryotic Phylogenetic Profiles for Prediction of Biological Function (6568 Views since 18 Jun 2008)

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Electrostatic and Functional Analysis of the Seven-Bladed WD β-Propellers (6044 Views since 13 Jun 2008)

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Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification (17873 Views since 26 May 2008)

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Exploring the Evolutionary History of the Differentially Expressed Genes between Human Populations: Action of Recent Positive Selection (9324 Views since 15 May 2008)

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Maximum Gene-Support Tree (5875 Views since 15 May 2008)

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Examining Ancient Inter-domain Horizontal Gene Transfer (8014 Views since 09 May 2008)

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Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology (5905 Views since 08 May 2008)

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