All Stories

  1. Do viruses age?
  2. AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Nucleocapsid Protein Variants
  3. AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Nucleocapsid Protein Variants
  4. Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment
  5. Are Viruses Taxonomic Units? – A Protein Domain and Loop-Centric Phylogenomic Assessment
  6. On Protein Loops, Prior Molecular States and Common Ancestors of Life
  7. AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Spike Protein Variants
  8. Advances in Molecular Exploration of Crop Plants under Environmental Stresses from Genetic and Genomic Perspectives
  9. Evolution of Intrinsic Disorder in Protein Loops
  10. Evolution of Intrinsic Disorder in Protein Loops
  11. Seasonal effects decouple SARS-CoV-2 haplotypes worldwide
  12. Dissecting “Evolution – The origins and mechanisms of diversity” by Jonathan Bard
  13. The origin and language-like evolutionary behavior of proteins and translation
  14. Menzerath–Altmann’s Law of Syntax in RNA Accretion History
  15. The tree of life describes a tripartite cellular world
  16. Temperature and Latitude Correlate with SARS-CoV-2 Epidemiological Variables but not with Genomic Change Worldwide
  17. Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea
  18. The origin and evolution of viruses inferred from fold family structure
  19. Editorial: Viruses, Genetic Exchange, and the Tree of Life
  20. New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release
  21. MANET 3.0: Hierarchy and modularity in evolving metabolic networks
  22. Genome-Wide Identification and Characterization of the Vacuolar H+-ATPase Subunit H Gene Family in Crop Plants
  23. Testing Empirical Support for Evolutionary Models that Root the Tree of Life
  24. Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis
  25. Correction to: Genome-wide analysis of the MYB-CC gene family of maize
  26. Evolution of Macromolecular Structure: A ‘Double Tale’ of Biological Accretion and Diversification
  27. Genome-wide analysis of the MYB-CC gene family of maize
  28. Archaea-First and the Co-Evolutionary Diversification of Domains of Life
  29. Order and polarity in character state transformation models that root the tree of life
  30. Commercial Applications of DNA Profiling by Amplification with Arbitrary Oligonucleotide Primers
  31. Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions
  32. RubisCO and the Search for Biomolecular Culprits of Planetary Change
  33. Long-term evolution of viruses: A Janus-faced balance
  34. Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification
  35. Commentary: History of the ribosome and the origin of translation
  36. The Compressed Vocabulary of the Proteins of Archaea
  37. RNA World ☆
  38. Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks
  39. The early history and emergence of molecular functions and modular scale-free network behavior
  40. The Phylogenomic Roots of Translation
  41. Arguments Reinforcing the Three-Domain View of Diversified Cellular Life
  42. A phylogenomic data-driven exploration of viral origins and evolution
  43. Ancestral Insertions and Expansions of rRNA do not Support an Origin of the Ribosome in Its Peptidyl Transferase Center
  44. Untangling the origin of viruses and their impact on cellular evolution
  45. Untangling Molecular Biodiversity
  46. Computing the origin and evolution of the ribosome from its structure — Uncovering processes of macromolecular accretion benefiting synthetic biology
  47. A Tree of Cellular Life Inferred from a Genomic Census of Molecular Functions
  48. The Natural History of Biocatalytic Mechanisms
  49. The importance of using realistic evolutionary models for retrodicting proteomes
  50. Global Patterns of Protein Domain Gain and Loss in Superkingdoms
  51. The Origin and Evolution of the Archaeal Domain
  52. Archaea: The First Domain of Diversified Life
  53. A Phylogenomic Census of Molecular Functions Identifies Modern Thermophilic Archaea as the Most Ancient Form of Cellular Life
  54. Structural Phylogenomics Retrodicts the Origin of the Genetic Code and Uncovers the Evolutionary Impact of Protein Flexibility
  55. CLUSTOM: A Novel Method for Clustering 16S rRNA Next Generation Sequences by Overlap Minimization
  56. Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes
  57. Structural Phylogenomics Reveals Gradual Evolutionary Replacement of Abiotic Chemistries by Protein Enzymes in Purine Metabolism
  58. Evolutionary Optimization of Protein Folding
  59. Molecular Clock
  60. RNA World
  61. Cellular structure predated diversified life
  62. 23 The phylogenomic roots of modern biochemistry, translation, and the genetic code
  63. The Coevolutionary Roots of Biochemistry and Cellular Organization Challenge the RNA World Paradigm
  64. Comparative Analysis of Proteomes and Functionomes Provides Insights into Origins of Cellular Diversification
  65. Comparative Analysis of Barophily-Related Amino Acid Content in Protein Domains ofPyrococcus abyssiandPyrococcus furiosus
  66. A General Framework of Persistence Strategies for Biological Systems Helps Explain Domains of Life
  67. Fast Folding as a Constraint in the Evolution of Protein Structures
  68. Stress induces biphasic-rewiring and modularization patterns in the metabolomic networks of Escherichia coli
  69. Viral evolution
  70. Structural phylogenomics uncovers the early and concurrent origins of cysteine biosynthesis and iron-sulfur proteins
  71. The Impact of Oxygen on Metabolic Evolution: A Chemoinformatic Investigation
  72. Ribosomal History Reveals Origins of Modern Protein Synthesis
  73. Erratum to: The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis
  74. Biphasic patterns of diversification and the emergence of modules
  75. The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis
  76. Benefits of using molecular structure and abundance in phylogenomic analysis
  77. Evolution of Protein Architecture for Mechanical Function
  78. Protein Domain Structure Uncovers the Origin of Aerobic Metabolism and the Rise of Planetary Oxygen
  79. The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms
  80. Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya
  81. Evolutionary Genomics and Systems Biology . Edited by Gustavo Caetano‐Anollés. Hoboken (New Jersey): Wiley‐Blackwell. $125.00. xix + 465 p. + 32 pl.; ill.; index. ISBN: 978‐0‐470‐19514‐7. 2010.
  82. Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms
  83. Evolution of protein architectures inferred from phylogenomic analysis of CATH
  84. Integration of statistical models and visualization tools to characterize microRNA networks influencing cancer
  85. The functional make up of proteomes is remarkably conserved
  86. Additive and multiplicative genome-wide association models identify genes associated with growth
  87. Reductive evolution of proteomes and protein structures
  88. The proteomic complexity and rise of the primordial ancestor of diversified life
  89. Genetic structure and diversity of Phakopsora pachyrhizi isolates from soyabean
  90. Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome
  91. Proteome Evolution and the Metabolic Origins of Translation and Cellular Life
  92. A Universal Molecular Clock of Protein Folds and Its Power in Tracing the Early History of Aerobic Metabolism and Planet Oxygenation
  93. Reply to Mulkidjanian and Galperin: Zn may have constrained evolution during the Proterozoic but not the Archean
  94. BioEssays 8/2010
  95. Exploring the interplay of stability and function in protein evolution
  96. Frontmatter
  97. Index
  98. Color Plates
  99. Modularity and Dissipation in Evolution of Macromolecular Structures, Functions, and Networks
  100. Phylogenetic Utility of RNA Structure: Evolution's Arrow and Emergence of Early Biochemistry and Diversified Life
  101. The Origin of Modern 5S rRNA: A Case of Relating Models of Structural History to Phylogenetic Data
  102. History of biological metal utilization inferred through phylogenomic analysis of protein structures
  103. Emergence and Evolution of Modern Molecular Functions Inferred from Phylogenomic Analysis of Ontological Data
  104. The ancient history of the structure of ribonuclease P and the early origins of Archaea
  105. Evolutionary Genomics and Systems Biology
  106. Comparative Genomic and Phylogenetic Analyses Reveal the Evolution of the Core Two-Component Signal Transduction Systems in Enterobacteria
  107. The Evolutionary History of the Structure of 5S Ribosomal RNA
  108. The evolutionary significance of the long variable arm in transfer RNA
  109. The origin, evolution and structure of the protein world
  110. The origin and evolution of modern metabolism
  111. The Evolutionary Mechanics of Domain Organization in Proteomes and the Rise of Modularity in the Protein World
  112. Transfer RNA and the Origins of Diversified Life
  113. An approach of orthology detection from homologous sequences under minimum evolution
  114. Evolutionary Patterns in the Sequence and Structure of Transfer RNA: A Window into Early Translation and the Genetic Code
  115. NOBAI: a web server for character coding of geometrical and statistical features in RNA structure
  116. Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses
  117. Origins and evolution of modern biochemistry: insights from genomes and molecular structure
  118. Evolutionary Genomics: Linking Macromolecular Structure, Genomes and Biological Networks
  119. Introductory Editorial
  120. The Origin and Evolution of tRNA Inferred from Phylogenetic Analysis of Structure
  121. Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
  122. The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture
  123. Common evolutionary trends for SINE RNA structures
  124. Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event?
  125. Global Phylogeny Determined by the Combination of Protein Domains in Proteomes
  126. A phylogenomic reconstruction of the protein world based on a genomic census of protein fold architecture
  127. Grass Evolution Inferred from Chromosomal Rearrangements and Geometrical and Statistical Features in RNA Structure
  128. Universal Sharing Patterns in Proteomes and Evolution of Protein Fold Architecture and Life
  129. Evolution of Genome Size in the Grasses
  130. Population Genetics and Spatial Structure of the Fairy Ring Fungus Marasmius oreades in a Norwegian Sand Dune Ecosystem
  131. An Evolutionarily Structured Universe of Protein Architecture
  132. Extensive and specific responses of a eukaryote to bacterial quorum-sensing signals
  133. Tracing the evolution of RNA structure in ribosomes
  134. Evolved RNA Secondary Structure and the Rooting of the Universal Tree of Life
  135. DNA Markers: Protocols, Applications, and Overview. Edited by Gustavo Caetano-Anollés and Peter M. Gresshoff
  136. High genome-wide mutation rates in vegetatively propagated bermudagrass
  137. DNA Analysis of Turfgrass Genetic Diversity
  138. Arbitrary oligonucleotides: primers for amplification and direct identification of nucleic acids, genes and organisms
  139. Molecular dissection and improvement of the nodule symbiosis in legumes
  140. DNA Amplification Fingerprinting
  141. Fingerprint Tailoring
  142. Recovering Amplified DNA from Silver Stained Gels
  143. The Origin of Bermudagrass (Cynodon) Off-Types Inferred by DNA Amplification Fingerprinting
  144. Resolving DNA Amplification Products Using Polyacrylamide Gel Electrophoresis and Silver Staining
  145. Molecular and Genetic Insights into Shoot Control of Nodulation in Soybean
  146. Scanning of nucleic acids by in vitro amplification: New developments and applications
  147. Nucleic Acid Scanning-by-Hybridization of Enterohemorrhagic Escherichia Coli Isolates Using Oligodeoxynucleotide Arrays
  148. Molecular phylogeny and DNA amplification fingerprinting of Petunia taxa
  149. Advances in the positional cloning of nodulation genes in soybean
  150. DNA Amplification Fingerprinting Provides Evidence That Discula destructiva, the Cause of Dogwood Anthracnose in North America, Is an Introduced Pathogen
  151. DNA Amplification Fingerprinting and Hybridization Analysis of Centipedegrass
  152. Positional Cloning of Nodulation Genes in Soybean: Coupling Dna Amplification and Bulked Segregant Analysis
  153. Nodulation of white clover (Trifolium repens) in the absence ofRhizobium
  154. Buffer components tailor DNA amplification with arbitrary primers.
  155. DNA Amplification Fingerprinting Using Arbitrary Mini-hairpin Oligonucleotide Primers
  156. DNA amplification fingerprinting: A general tool with applications in breeding, identification and phylogenetic analysis of plants
  157. Amplifying DNA with arbitrary oligonucleotide primers.
  158. DNA amplification fingerprinting using arbitrary oligonucleotide primers
  159. Silver staining of DNA in polyacrylamide gels
  160. Nodule Morphogenesis in the Absence of Rhizobium
  161. DNA Fingerprinting: MAAPing out a RAPD Redefinition?
  162. Growth and Movement of Spot Inoculated Rhizobium meliloti on the Root Surface of Alfalfa
  163. Anatomical analysis of nodule development in soybean reveals an additional autoregulatory control point
  164. DNA amplification fingerprinting: A strategy for genome analysis
  165. Plant Genetic Control of Nodulation
  166. Excision of Nodules Induced by Rhizobium meliloti Exopolysaccharide Mutants Releases Autoregulation in Alfalfa
  167. Fast and sensitive silver staining of DNA in polyacrylamide gels
  168. DNA Amplification Fingerprinting Using Very Short Arbitrary Oligonucleotide Primers
  169. Alfalfa Controls Nodulation during the Onset of Rhizobium-induced Cortical Cell Division
  170. Mature Nodules and Root Tips Control Nodulation in Soybean
  171. Plant Genetic Control Of Nodulation
  172. Plant Genetic Control of Nodulation in Legumes
  173. Chemotaxis, induced gene expression and competitiveness in the rhizosphere
  174. Rhizobium meliloti exopolysaccharide Mutants Elicit Feedback Regulation of Nodule Formation in Alfalfa
  175. Optimization of Surface Sterilization for Legume Seed
  176. Early induction of feedback regulatory responses governing nodulation in soybean
  177. Adsorption ofRhizobium meliloti to alfalfa roots: Dependence on divalent cations and pH
  178. Role of Motility and Chemotaxis in Efficiency of Nodulation by Rhizobium meliloti
  179. Plant genotyping using arbitrarily amplified DNA.