All Stories

  1. A systematic assessment of phylogenomic approaches for microbial species tree reconstruction
  2. Leptospira interrogans encodes a canonical BamA and three novel noNterm Omp85 outer membrane protein paralogs
  3. Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes
  4. Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense
  5. Neighboring inteins interfere with one another’s homing capacity
  6. Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense
  7. The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination
  8. The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination
  9. Bacterial cooperation through horizontal gene transfer
  10. An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets
  11. Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support
  12. The Evolutionary Origins of Extreme Halophilic Archaeal Lineages
  13. Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes
  14. Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model Archaeon
  15. The Impact of Restriction-Modification Systems on Mating in Haloferax volcanii
  16. Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum
  17. Expanding the utility of sequence comparisons using data from whole genomes
  18. Reconstructing the evolutionary origins of extreme halophilic Archaeal lineages
  19. Identification and characterization of putative Aeromonas spp. T3SS effectors
  20. Complete Genome Sequence of Halorubrum ezzemoulense Strain Fb21
  21. The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria
  22. Identification and characterization of putative Aeromonas spp. T3SS effectors
  23. The Patchy Distribution of Restriction-Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria.
  24. Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d’Ivoire
  25. Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax
  26. Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing
  27. Short branches lead to systematic artifacts when BLAST searches are used as surrogate for phylogenetic reconstruction
  28. Does Sequence Conservation Provide Evidence for Biological Function?
  29. Is LUCA a thermophilic progenote?
  30. Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios
  31. Impact of a homing intein on recombination frequency and organismal fitness
  32. Horizontal gene transfer: building the web of life
  33. The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis
  34. Ancient horizontal gene transfer and the last common ancestors
  35. Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes
  36. Bioinformatic Genome Comparisons for Taxonomic and Phylogenetic Assignments Using Aeromonas as a Test Case
  37. Inteins as indicators of gene flow in the halobacteria
  38. AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees
  39. Population and genomic analysis of the genus Halorubrum
  40. Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations
  41. Reconstructed Ancestral Myo-Inositol-3-Phosphate Synthases Indicate That Ancestors of the Thermococcales and Thermotoga Species Were More Thermophilic than Their Descendants
  42. The effects of model choice and mitigating bias on the ribosomal tree of life
  43. Distribution and Evolution of the Mobile vma-1b Intein
  44. Thermotoga lettingae Can Salvage Cobinamide To Synthesize Vitamin B12
  45. Reconstruction of Ancestral 16S rRNA Reveals Mutation Bias in the Evolution of Optimal Growth Temperature in the Thermotogae Phylum
  46. Orthologues, Paralogues and Horizontal Gene Transfer in the Human Holobiont
  47. Systematic inference of highways of horizontal gene transfer in prokaryotes
  48. Biased Gene Transfer Contributes to Maintaining the Tree of Life
  49. Pre-Posting and OLEB
  50. The impact of HGT on phylogenomic reconstruction methods
  51. Erratum to: Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life
  52. Genes for the Major Structural Components of Thermotogales Species’ Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs
  53. How Bacterial Lineages Emerge
  54. Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales
  55. Quantifying Homologous Replacement of Loci between Haloarchaeal Species
  56. Quartet decomposition server: a platform for analyzing phylogenetic trees
  57. The Role of Reticulate Evolution in Creating Innovation and Complexity
  58. Vitamin B12 Synthesis and Salvage Pathways Were Acquired by Horizontal Gene Transfer to the Thermotogales
  59. Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life
  60. Genome Sequence of Thermotoga sp. Strain RQ2, a Hyperthermophilic Bacterium Isolated from a Geothermally Heated Region of the Seafloor near Ribeira Quente, the Azores
  61. Genome Sequence of Kosmotoga olearia Strain TBF 19.5.1, a Thermophilic Bacterium with a Wide Growth Temperature Range, Isolated from the Troll B Oil Platform in the North Sea
  62. Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer
  63. Detecting Highways of Horizontal Gene Transfer
  64. Reassessment of the Lineage Fusion Hypothesis for the Origin of Double Membrane Bacteria
  65. Biased gene transfer in microbial evolution
  66. Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data
  67. Home and away- the evolutionary dynamics of homing endonucleases
  68. Evolution of the archaea: emerging views on origins and phylogeny
  69. A Rooted Net of Life
  70. Biased gene transfer and its implications for the concept of lineage
  71. Biased gene transfer mimics patterns created through shared ancestry
  72. Natural taxonomy in light of horizontal gene transfer
  73. Using comparative genome analysis to identify problems in annotated microbial genomes
  74. Inferring the Ancient History of the Translation Machinery and Genetic Code via Recapitulation of Ribosomal Subunit Assembly Orders
  75. Rooting the Ribosomal Tree of Life
  76. Bioinformatics Research and Applications
  77. Detecting Highways of Horizontal Gene Transfer
  78. Filling the gaps in the genomic landscape
  79. Evolution of Genes and Organisms
  80. Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life
  81. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales
  82. Estimating the size of the bacterial pan-genome
  83. Horizontal Gene Transfer
  84. Gene Transfer: Who Benefits?
  85. Ancient Gene Transfer as a Tool in Phylogenetic Reconstruction
  86. Trees in the Web of Life
  87. Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia
  88. Prokaryotic evolution and the tree of life are two different things
  89. Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements
  90. Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus
  91. Computational Methods for Understanding Bacterial and Archaeal Genomes
  92. HORIZONTAL GENE TRANSFER: ITS DETECTION AND ROLE IN MICROBIAL EVOLUTION
  93. Orthologues, Paralogues and Xenologues in Human and Other Genomes
  94. Computational Methods for Understanding Bacterial and Archaeal Genomes
  95. Concerted gene recruitment in early plant evolution
  96. Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales
  97. Unsupervised Learning in Detection of Gene Transfer
  98. Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia
  99. Signature of a Primitive Genetic Code in Ancient Protein Lineages
  100. Gene Transfer and the Reconstruction of Life’s Early History from Genomic Data
  101. GPX: A Tool for the Exploration and Visualization of Genome Evolution
  102. A hyperconserved protein in Prochlorococcus and marine Synechococcus
  103. The Evolution of Eukaryotes
  104. BranchClust: a phylogenetic algorithm for selecting gene families
  105. Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?
  106. The power of phylogenetic approaches to detect horizontally transferred genes
  107. Unsupervised Learning in Spectral Genome Analysis
  108. Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein
  109. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography
  110. Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
  111. Orthologs, Paralogs and Xenologs in Human and Other Genomes
  112. Ancient horizontal gene transfer can benefit phylogenetic reconstruction
  113. Distribution of F- and A/V-type ATPases in Thermus scotoductus and other closely related species
  114. Ancient gene duplications and the root(s) of the tree of life
  115. Evolutionary and Diagnostic Implications of Intragenomic Heterogeneity in the 16S rRNA Gene in Aeromonas Strains
  116. Horizontal gene transfer, genome innovation and evolution
  117. The Presence of a Haloarchaeal Type Tyrosyl-tRNA Synthetase Marks the Opisthokonts as Monophyletic
  118. Cladistics: A Practical Primer on CD-ROM. By Peter Skelton and Andrew Smith, with accompanying booklet by NealeMonks. Cambridge University Press, 40 West 20th Street, New York, NY 10011-4211, ISBN: 0-521-52341-9, Price $55.00
  119. Were arachnids the first to use combinatorial peptide libraries?
  120. Erratum: Cladogenesis, coalescence and the evolution of the three domains of life
  121. Genome mosaicism and organismal lineages
  122. Cladogenesis, coalescence and the evolution of the three domains of life
  123. Spliceosomal Introns: New Insights into their Evolution
  124. Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach
  125. Gene Transfer: Gene Swapping Craze Reaches Eukaryotes
  126. Prokaryotic Evolution in Light of Gene Transfer
  127. Whole-Genome Analysis of Photosynthetic Prokaryotes
  128. Inteins: Structure, Function, and Evolution
  129. Progenote
  130. Horizontal Gene Transfer
  131. Comparing trees in a phylogenetic relationship repository
  132. Horizontal Transfer of Archaeal Genes into the Deinococcaceae: Detection by Molecular and Computer-Based Approaches
  133. Orthologs, paralogs and genome comparisons
  134. Horizontal Gene Transfer: Pitfalls and Promises
  135. Gene Transfer in Early Evolution
  136. The Prokaryote-to-Eukaryote Transition Reflected in the Evolution of the V/F/A-ATPase Catalytic and Proteolipid Subunits
  137. cDNA cloning of a mandibular organ inhibiting hormone from the spider crabLibinia emarginata
  138. Dating the Cenancester of Organisms
  139. Dating the Cenancester of Organisms
  140. Gene duplications and horizontal gene transfer during early evolution
  141. The V-ATPase A subunit gene (vma-1 from Giardia lamblia
  142. The effects of heavy meteorite bombardment on the early evolution — The emergence of the three Domains of life
  143. The early evolution of cellular life
  144. A Second Cell Wall Acid Invertase Gene in Arabidopsis thaliana
  145. Which is the most conserved group of proteins? Homology-orthology, paralogy, xenology, and the fusion of independent lineages
  146. Letter to the editor
  147. A conserved intron in the V-ATPase A subunit genes of plants and algae
  148. Horizontal transfer of ATPase genes — the tree of life becomes a net of life
  149. Evolution of proton pumping ATPases: Rooting the tree of life
  150. Evolution of structure and function of V-ATPases
  151. The Use of Antisense mRNA to Inhibit the Tonoplast H+ ATPase in Carrot
  152. Tracing origins with molecular sequences: rooting the universal tree of life
  153. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes.
  154. The H+ ATPase regulatory subunit of Methanococcus thermolithotrophicus : Amplification of an 800 bp fragment by polymerase chain reaction
  155. Substrate specifity of the hexose carrier in the plasmalemma of Chenopodium suspension cells probed by transmembrane exchange diffusion
  156. The electrogenic proton/hexose carrier in the plasmalemma of Chenopodium rubrum suspension cells: effects of Δc, ΔpH and Δψ on hexose exchange diffusion
  157. Sugar nucleotides dissipate ATP-generated transmembrane pH gradient in Golgi vesicles from suspension-cell protoplasts ofChenopodium rubrum L.
  158. Physical properties of the cell wall of photoautotrophic suspension cells fromChenopodium rubrum L.
  159. ATP-dependent acidification and tonoplast hyperpolarization in isolated vacuoles from green suspension cells of Chenopodium rubrum L
  160. Lateral electrophoresis versus 2D-diffusion
  161. A Patch Clamp Study of Tonoplast Electrical Properties in Vacuoles Isolated from Chenopodium rubrum Suspension Cells
  162. Kinetics and Specificity of ATP-dependent Proton Translocation Measured with Acridine Orange in Microsomal Fractions from Green Suspension Cells of Chenopodium rubrum L.
  163. Phlorizin inhibits hexose transport across the plasmalemma of Riccia fluitans
  164. Fluxes and compartmentation of 3-O-methyl-D-glucose in Riccia fluitans
  165. What’s in a Tree?
  166. Horizontal gene transfer, gene histories, and the root of the tree of life
  167. Gene Transfer and the Reconstruction of Life’s Early History from Genomic Data
  168. II.11. Evolution in the Prokaryotic Grade