OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Molecular Evolution is 5. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-04-01 to 2024-04-01.)

Article	Citations
A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila	59
Cofactors are Remnants of Life’s Origin and Early Evolution	48
Codon Usage Bias: An Endless Tale	43
Constructive Neutral Evolution 20 Years Later	42
Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution	30
Evolutionary History of Alzheimer Disease-Causing Protein Family Presenilins with Pathological Implications	29
Water and Life: The Medium is the Message	29
The Origins and Functions of De Novo Genes: Against All Odds?	27
Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond	25
Evolution of the Standard Genetic Code	18
Evolutionary Aspects of the Structural Convergence and Functional Diversification of Kunitz-Domain Inhibitors	17
Spatial Patterns of Gene Expression in Bacterial Genomes	16
EasyDIVER: A Pipeline for Assembling and Counting High-Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Peptides	14
The Coevolution of Cellularity and Metabolism Following the Origin of Life	14
Fewer Exposed Lysine Residues May Explain Relative Resistance of Chicken Serum Albumin to In Vitro Protein Glycation in Comparison to Bovine Serum Albumin	14
G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases	13
Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes	13
Crick Wobble and Superwobble in Standard Genetic Code Evolution	13
Evolution of DNA Methylation Across Ecdysozoa	12
Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli	12
Revisiting the Relationships Between Genomic G + C Content, RNA Secondary Structures, and Optimal Growth Temperature	12
Adaptation and Exaptation: From Small Molecules to Feathers	12
Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes	11
The Marginal Stability of Proteins: How the Jiggling and Wiggling of Atoms is Connected to Neutral Evolution	11
The Multiple Paths to Multiple Life	11

Genome-Wide Investigation of Major Enzyme-Encoding Genes in the Flavonoid Metabolic Pathway in Tartary Buckwheat (Fagopyrum tataricum)	11
Optimal Evolution of the Standard Genetic Code	11
Plant Mitochondria are a Riddle Wrapped in a Mystery Inside an Enigma	10
Felsenstein Phylogenetic Likelihood	9
Molecular Evolution of Tooth-Related Genes Provides New Insights into Dietary Adaptations of Mammals	9
Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires	9
Loss of Heterozygosity and Its Importance in Evolution	9
Animal-to-Human Viral Transitions: Is SARS-CoV-2 an Evolutionarily Successful One?	9
Evolution of Superoxide Dismutases and Catalases in Cyanobacteria: Occurrence of the Antioxidant Enzyme Genes before the Rise of Atmospheric Oxygen	8
Protein Evolution in the Flaviviruses	8
The Evolution of Severe Acute Respiratory Syndrome Coronavirus-2 during Pandemic and Adaptation to the Host	8
Expansion and Diversification of the 14-3-3 Gene Family in Camellia sinensis	7
Structural Variation of the Turtle Mitochondrial Control Region	7
The Semi-Enzymatic Origin of Metabolic Pathways: Inferring a Very Early Stage of the Evolution of Life	7
FLAVI: An Amino Acid Substitution Model for Flaviviruses	7
Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes	7
An Evolutionary Remedy for an Abominable Physiological Mystery: Benign Hyperglycemia in Birds	7
Recombination Between High-Risk Human Papillomaviruses and Non-Human Primate Papillomaviruses: Evidence of Ancient Host Switching Among Alphapapillomaviruses	6
Moderate Amounts of Epistasis are Not Evolutionarily Stable in Small Populations	6
Directed Evolution. The Legacy of a Nobel Prize	6
The Possible Role of Prion-Like Viral Protein Domains on the Emergence of Novel Viruses as SARS-CoV-2	6
Molecular Evolution and Local Root Heterogeneous Expression of the Chenopodium quinoa ARF Genes Provide Insights into the Adaptive Domestication of Crops in Complex Environments	6
Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	6
Pheromone Gene Diversification and the Evolution of Courtship Glands in Plethodontid Salamanders	6
Origin of the 16S Ribosomal Molecule from Ancestor tRNAs	6
Stem Region of tRNA Genes Favors Transition Substitution Towards Keto Bases in Bacteria	6
Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea	6
Origin of Sex-Biased Mental Disorders: An Evolutionary Perspective	6
The Ancient Origins of Death Domains Support the ‘Original Sin’ Hypothesis for the Evolution of Programmed Cell Death	6
Selection Shapes Synonymous Stop Codon Use in Mammals	6
Bayesian Cross-Validation Comparison of Amino Acid Replacement Models: Contrasting Profile Mixtures, Pairwise Exchangeabilities, and Gamma-Distributed Rates-Across-Sites	5
Site-Specific Amino Acid Distributions Follow a Universal Shape	5
Evolution of the Cytokinin Dehydrogenase (CKX) Domain	5
Evolution of Biomineralization Genes in the Prismatic Layer of the Pen Shell Atrina pectinata	5
Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa	5
Transposable Element Diversity Remains High in Gigantic Genomes	5
Evolutionary Rates are Correlated Between Buchnera Endosymbionts and the Mitochondrial Genomes of Their Aphid Hosts	5
The Effects of Ecological Traits on the Rate of Molecular Evolution in Ray-Finned Fishes: A Multivariable Approach	5
Evolutionary Processes and Biophysical Mechanisms: Revisiting Why Evolved Proteins Are Marginally Stable	5
Richard Dickerson, Molecular Clocks, and Rates of Protein Evolution	5
Evolutionary History of TOPIIA Topoisomerases in Animals	5
A Case Study of Eukaryogenesis: The Evolution of Photoreception by Photolyase/Cryptochrome Proteins	5
Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch	5
Phylogenetic and Ancestral Sequence Reconstruction of SARS-CoV-2 Reveals Latent Capacity to Bind Human ACE2 Receptor	5