OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Molecular Evolution is 2. 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 2020-11-01 to 2024-11-01.)

Article	Citations
Cofactors are Remnants of Life’s Origin and Early Evolution	64
Codon Usage Bias: An Endless Tale	58
Constructive Neutral Evolution 20 Years Later	47
The Origins and Functions of De Novo Genes: Against All Odds?	35
Water and Life: The Medium is the Message	33
Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond	31
Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli	21
Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes	19
Revisiting the Relationships Between Genomic G + C Content, RNA Secondary Structures, and Optimal Growth Temperature	18
Evolution of the Standard Genetic Code	18
Genome-Wide Investigation of Major Enzyme-Encoding Genes in the Flavonoid Metabolic Pathway in Tartary Buckwheat (Fagopyrum tataricum)	16
Evolution of DNA Methylation Across Ecdysozoa	16
Adaptation and Exaptation: From Small Molecules to Feathers	15
Crick Wobble and Superwobble in Standard Genetic Code Evolution	15
Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch	13
Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes	13
The Multiple Paths to Multiple Life	13
Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires	12
Optimal Evolution of the Standard Genetic Code	12
Loss of Heterozygosity and Its Importance in Evolution	12
Pheromone Gene Diversification and the Evolution of Courtship Glands in Plethodontid Salamanders	12
Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	12
Felsenstein Phylogenetic Likelihood	12
Plant Mitochondria are a Riddle Wrapped in a Mystery Inside an Enigma	11
Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes	11

Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea	10
Evolution of Superoxide Dismutases and Catalases in Cyanobacteria: Occurrence of the Antioxidant Enzyme Genes before the Rise of Atmospheric Oxygen	10
An Evolutionary Remedy for an Abominable Physiological Mystery: Benign Hyperglycemia in Birds	9
Identifying Targets of Selection in Laboratory Evolution Experiments	9
Molecular Evolution of Tooth-Related Genes Provides New Insights into Dietary Adaptations of Mammals	9
Evolution of the Cytokinin Dehydrogenase (CKX) Domain	9
Expansion and Diversification of the 14-3-3 Gene Family in Camellia sinensis	8
Stem Region of tRNA Genes Favors Transition Substitution Towards Keto Bases in Bacteria	8
The Semi-Enzymatic Origin of Metabolic Pathways: Inferring a Very Early Stage of the Evolution of Life	8
The Evolution of Severe Acute Respiratory Syndrome Coronavirus-2 during Pandemic and Adaptation to the Host	8
Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution	8
Bayesian Cross-Validation Comparison of Amino Acid Replacement Models: Contrasting Profile Mixtures, Pairwise Exchangeabilities, and Gamma-Distributed Rates-Across-Sites	7
Functional or Vestigial? The Genomics of the Pineal Gland in Xenarthra	7
Origin of the 16S Ribosomal Molecule from Ancestor tRNAs	7
Evolution of Biomineralization Genes in the Prismatic Layer of the Pen Shell Atrina pectinata	7
Correlation Analysis Reveals an Important Role of GC Content in Accumulation of Deletion Mutations in the Coding Region of Angiosperm Plastomes	7
The Possible Role of Prion-Like Viral Protein Domains on the Emergence of Novel Viruses as SARS-CoV-2	7
Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa	6
The Mystery of Cancer Resistance: A Revelation Within Nature	6
Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited	6
The Ancient Origins of Death Domains Support the ‘Original Sin’ Hypothesis for the Evolution of Programmed Cell Death	6
Richard Dickerson, Molecular Clocks, and Rates of Protein Evolution	6
Evolutionary Rates are Correlated Between Buchnera Endosymbionts and the Mitochondrial Genomes of Their Aphid Hosts	6
The Chemosensory Repertoire of the Eastern Diamondback Rattlesnake (Crotalus adamanteus) Reveals Complementary Genetics of Olfactory and Vomeronasal-Type Receptors	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
Structural Computational Analysis of the Natural History of Class I aminoacyl-tRNA Synthetases Suggests their Role in Establishing the Genetic Code	6
Evolutionary History of TOPIIA Topoisomerases in Animals	6
Origin of Sex-Biased Mental Disorders: An Evolutionary Perspective	6
Directed Evolution. The Legacy of a Nobel Prize	6
Non-random Codon Usage of Synonymous and Non-synonymous Mutations in the Human HLA-A Gene	5
Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation	5
Domain Evolution of Vertebrate Blood Coagulation Cascade Proteins	5
Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production	5
Phylogenetic and Ancestral Sequence Reconstruction of SARS-CoV-2 Reveals Latent Capacity to Bind Human ACE2 Receptor	5
Functional Diversity of the Lepidopteran ATP-Binding Cassette Transporters	5
Transposable Element Diversity Remains High in Gigantic Genomes	5
Site-Specific Amino Acid Distributions Follow a Universal Shape	5
Decoding ‘Unnecessary Complexity’: A Law of Complexity and a Concept of Hidden Variation Behind “Missing Heritability” in Precision Medicine	5
Alternative Reading Frames are an Underappreciated Source of Protein Sequence Novelty	4
Complex Evolution of the Mismatch Repair System in Eukaryotes is Illuminated by Novel Archaeal Genomes	4
Evolutionary Consequences of Functional and Regulatory Divergence of HD-Zip I Transcription Factors as a Source of Diversity in Protein Interaction Networks in Plants	4
Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models	4
Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers	4
uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response	4
Analysis of the MCTP Amino Acid Sequence Reveals the Conservation of Putative Calcium- and Lipid-Binding Pockets Within the C2 Domains In Silico	4
Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species	4
Informatic Capabilities of Translation and Its Implications for the Origins of Life	4
A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet	4
Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth	4
The MultiFurcating Neighbor-Joining Algorithm for Reconstructing Polytomic Phylogenetic Trees	4

A Thermodynamic Model for Water Activity and Redox Potential in Evolution and Development	4
Main Factors Shaping Amino Acid Usage Across Evolution	3
Evidence Supporting That C-to-U RNA Editing Is the Major Force That Drives SARS-CoV-2 Evolution	3
A New Perspective on the Maillard Reaction and the Origin of Life	3
Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics?	3
GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences	3
Ancestral Sequence Reconstruction of the Ribosomal Protein uS8 and Reduction of Amino Acid Usage to a Smaller Alphabet	3
Structural Characterization of the Chlorophyllide a Oxygenase (CAO) Enzyme Through an In Silico Approach	3
Newly Discovered AqE Gene is Highly Conserved in Non-tetrapod Vertebrates	3
Decay of Skin-Specific Gene Modules in Pangolins	3
How Many Factors Influence Genomic GC Content Among Prokaryotes?	3
The Memory Problem for Neutral Mutational Models of Evolution	3
Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups	3
Barcoding Populations of Pseudomonas fluorescens SBW25	3
Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designs	3
Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection	3
Evolutionary Aspects of Selenium Binding Protein (SBP)	3
Diversification Rate is Associated with Rate of Molecular Evolution in Ray-Finned Fish (Actinopterygii)	3
The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms	3
A Re-Assessment of Positive Selection on Mitochondrial Genomes of High-Elevation Phrynocephalus Lizards	3
Nucleobases in Meteorites to Nucleobases in RNA and DNA?	3
Evolutionary Aspects of the Oxido-Reductive Network of Methylglyoxal	3
On Protein Loops, Prior Molecular States and Common Ancestors of Life	3
Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1	2
Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals	2
Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway	2
Consequences of Genetic Recombination on Protein Folding Stability	2
Genomic Gigantism is not Associated with Reduced Selection Efficiency in Neotropical Salamanders	2
Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure	2
Detecting Selection on Segregating Gene Duplicates in a Population	2
Next Generation Sequencing Revolutionizes Organismal Biology Research in Bats	2
Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation–Drift Equilibrium	2
Reenacting the Birth of a Function: Functional Divergence of HIUases and Transthyretins as Inferred by Evolutionary and Biophysical Studies	2
Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes	2
Evolution of the N-Terminal Regulation of Cardiac Troponin I for Heart Function of Tetrapods: Lungfish Presents an Example of the Emergence of Novel Submolecular Structure to Lead the Capacity of Adap	2
Origin of Sex-Biased Mental Disorders: Do Males and Females Experience Different Selective Regimes?	2
APGW/AKH Precursor from Rotifer Brachionus plicatilis and the DNA Loss Model Explain Evolutionary Trends of the Neuropeptide LWamide, APGWamide, RPCH, AKH, ACP, CRZ, and GnRH Families	2
Evolutionary Adjustment of tRNA Identity Rules in Bacillariophyta for Recognition by an Aminoacyl-tRNA Synthetase Adds a Facet to the Origin of Diatoms	2
Discovery of Teleost Plasma Kallikrein/Coagulation Factor XI-Like Gene from Channel Catfish (Ictalurus punctatus) and the Evidence that the Protein Encoded by it Acts as a Lectin	2
On the Unknown Proteins of Eukaryotic Proteomes	2
Origins and Functional Significance of Eukaryotic Protein Folds	2
Evolution of the Major Components of Innate Immunity in Animals	2
The Fate of Duplicated Enzymes in Prokaryotes: The Case of Isomerases	2
Amino Acid Specificity of Ancestral Aminoacyl-tRNA Synthetase Prior to the Last Universal Common Ancestor Commonote commonote	2
Translation Comes First: Ancient and Convergent Selection of Codon Usage Bias Across Prokaryotic Genomes	2
Volatile Organic Compound Metabolism on Early Earth	2
Hemocyanins of Muricidae: New ‘Insights’ Unravel an Additional Highly Hydrophilic 800 kDa Mass Within the Molecule	2
Molecular Evolution of clock Genes in Vertebrates	2
dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution	2
Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus)	2