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Molecular Biology and Evolution | 26:953–956
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Phylogenetic Construction of 17 Bacterial Phyla by New Method and Carefully Selected Orthologs
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Positional Conservation and Amino Acids Shape the Correct Diagnosis and Population Frequencies of Benign and Damaging Personal Amino Acid Mutations
Genome Research | 19:1562–1569
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The Origin of Metazoa: A Transition from Temporal to Spatial Cell Differentiation
BioEssays | 31:758–768
Methods for Incorporating the Hypermutability of CpG Dinucleotides in Detecting Natural Selection Operating at the Amino Acid Sequence Level
Molecular Biology and Evolution | 26:2275–2284
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Automated Annotation of Drosophila Gene Expression Patterns Using a Controlled Vocabulary
Bioinformatics | 24:1881–1888
MEGA: A Biologist-centric Software for Evolutionary Analysis of DNA and Protein Sequences
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Detecting Molecular Signatures of Adaptive Evolution
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Nullomers: Really a Matter of Natural Selection?
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Evolution of Genes and Genomes on the Drosophila Phylogeny
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Lower Bounds on Multiple Sequence Alignment Using Exact 3-way Alignment
BMC Bioinformatics | 8:140 (8 pp)
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Multiple Sequence Alignment: In Pursuit of Homologous DNA Positions
Genome Research | 17:127–135
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
Molecular Biology and Evolution | 24:1596–1599
Constraint and Turnover in Sex-biased Gene Expression in the Genus Drosophila
Nature | 450:233–237
Classification of Drosophila Embryonic Developmental State Range Based on Gene Expression Pattern Images
Computational Systems Bioinformatics Conference | 2006:293–298
Codon-based Detection of Positive Selection Can be Biased by Heterogeneous Distribution of Polar Amino Acids along Protein Sequences
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Signatures of Ecological Resource Availability in the Animal and Plant Proteomes
Molecular Biology and Evolution | 23:1946–1951
TimeTree: A Public Knowledge-base of Divergence Times among Organisms
Bioinformatics | 22:2971–2972
Constraining Fossil Calibrations for Molecular Clocks
BioEssays | 28:770–771
Evolutionary Anatomies of Positions and Types of Disease-associated and Neutral Amino Acid Mutations in the Human Genome
BMC Genomics | 7:306 (9 pp)
Higher Intensity of Purifying Selection on >90% of the Human Genes Revealed by the Intrinsic Replacement Mutation Rates
Molecular Biology and Evolution | 23:2283–2287
The Evolution of the Genome: Comparative Genomics in Eukaryotes
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Maximum Likelihood Outperforms Maximum Parsimony Even When Evolutionary Rates are Heterotachous
Molecular Biology and Evolution | 22:2139–2141
Inferring Species Phylogenies from Multiple Genes: Concatenated Sequence Tree versus Consensus Gene Tree
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution | 304:64–74
Automatic Annotation Techniques for Gene Expression Images of the Fruit Fly Embryo
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Molecular Clocks: Four Decades of Evolution
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Placing Confidence Limits on the Molecular Age of the Human-Chimpanzee Divergence
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Pushing Back the Expansion of Introns in Animal Genomes
Cell | 123:1182–1184
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Trends in Genetics | 20:242–247
Gene Expression Intensity Shapes Evolutionary Rates of the Proteins Encoded by the Vertebrate Genome
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Prospects for Inferring Very Large Phylogenies by Using the Neighbor-joining Method
Proceedings of the National Academy of Sciences (USA) | 101:11030–11035
Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks
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MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment
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Genomic Clocks and Evolutionary Timescales
Trends in Genetics | 19:200–206
Genomic Sequence of a Ranavirus (family Iridoviridae) Associated with Salamander Mortalities in North America
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Quantifying the Intragenic Distribution of Human Disease Mutations
Annals of Human Genetics | 67:567–579
Heterogeneity of Nucleotide Frequencies among Evolutionary Lineages and Phylogenetic Inference
Molecular Biology and Evolution | 20:610–621
Taxon Sampling, Bioinformatics, and Phylogenomics
Systematic Biology | 52:119–124
Patterns of Transitional Mutation Biases within and among Mammalian Genomes
Molecular Biology and Evolution | 20:988–993
Neutral Substitutions Occur at a Faster Rate in Exons than in Noncoding DNA in Primate Genomes
Genome Research | 13:838–844
Vertebrate Genomes Compared
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Measuring Conservation of Contiguous Sets of Autosomal Markers on Bovine and Porcine Genomes in relation to the Map of the Human Genome
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BEST: A Novel Computational Approach for Comparing Gene Expression Patterns from Early Stages of Drosophila melanogaster Development
Genetics | 162:2037–2047
Mutation Rates in Mammalian Genomes
Proceedings of the National Academy of Sciences (USA) | 99:803–808
Evolutionary Distance Estimation under Heterogeneous Substitution Pattern among Lineages
Molecular Biology and Evolution | 19:1727–1736
Elucidating Gene Interaction Networks Based on Gene Expression Pattern Image Analysis
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Does Nonneutral Evolution Shape Observed Patterns of DNA Variation in Animal Mitochondrial Genomes?
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A Genomic Timescale for the Origin of Eukaryotes
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Mutation and Linkage Disequilibrium in Human mtDNA
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Classification and Indexing of Gene Expression Images
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Disparity Index: A Simple Statistic to Measure and Test the Homogeneity of Substitution Patterns between Molecular Sequences
Genetics | 158:1321–1327
Determination of the Number of Conserved Chromosomal Segments between Species
Genetics | 157:1387–1395
MEGA2: Molecular Evolutionary Genetics Analysis Software
Bioinformatics | 17:1244–1245
Understanding Human Disease Mutations through the Use of Interspecific Genetic Variation
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Incomplete Taxon Sampling is Not a Problem for Phylogenetic Inference
Proceedings of the National Academy of Sciences (USA) | 98:10751–10756
Traditional Phylogenetic Reconstruction Methods Reconstruct Shallow and Deep Evolutionary Relationships Equally Well
Molecular Biology and Evolution | 18:1823–1827
Efficiency of the Neighbor-joining Method in Reconstructing Deep and Shallow Evolutionary Relationships in Large Phylogenies
Journal of Molecular Evolution | 51:544–553
Questioning Evidence for Recombination in Human Mitochondrial DNA
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Expansion and Molecular Evolution of the Interferon-induced 2 '-5 ' Oligoadenylate Synthetase Gene Family
Molecular Biology and Evolution | 17:738–750
Single Column Discrepancy and Dynamic Max-Mini Optimizations for Quickly Finding the Most Parsimonious Evolutionary Trees
Bioinformatics | 16:140–151