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 2020-04-01 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
Fewer Exposed Lysine Residues May Explain Relative Resistance of Chicken Serum Albumin to In Vitro Protein Glycation in Comparison to Bovine Serum Albumin	14
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
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
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
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
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
Domain Evolution of Vertebrate Blood Coagulation Cascade Proteins	4
Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution	4
Insights into Dietary Switch in Cetaceans: Evidence from Molecular Evolution of Proteinases and Lipases	4
A Thermodynamic Model for Water Activity and Redox Potential in Evolution and Development	4
Identifying Targets of Selection in Laboratory Evolution Experiments	4
Benchmarking Methods of Protein Structure Alignment	4

Spiralian Genomes Reveal Gene Family Expansions Associated with Adaptation to Freshwater	4
The Chemosensory Repertoire of the Eastern Diamondback Rattlesnake (Crotalus adamanteus) Reveals Complementary Genetics of Olfactory and Vomeronasal-Type Receptors	4
Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species	4
Structural Computational Analysis of the Natural History of Class I aminoacyl-tRNA Synthetases Suggests their Role in Establishing the Genetic Code	4
Non-random Codon Usage of Synonymous and Non-synonymous Mutations in the Human HLA-A Gene	4
Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited	4
Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation	4
Functional or Vestigial? The Genomics of the Pineal Gland in Xenarthra	4
Correlation Analysis Reveals an Important Role of GC Content in Accumulation of Deletion Mutations in the Coding Region of Angiosperm Plastomes	4
Exploring Evolutionary Constraints in the Proteomes of Zika, Dengue, and Other Flaviviruses to Find Fitness-Critical Sites	4
mPartition: A Model-Based Method for Partitioning Alignments	3
A New Perspective on the Maillard Reaction and the Origin of Life	3
The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms	3
Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers	3
A Re-Assessment of Positive Selection on Mitochondrial Genomes of High-Elevation Phrynocephalus Lizards	3
Prions: Roles in Development and Adaptive Evolution	3
Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth	3
A Phylogenetic Rate Parameter Indicates Different Sequence Divergence Patterns in Orthologs and Paralogs	3
Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models	3
Cell Communication-mediated Nonself-Recognition and -Intolerance in Representative Species of the Animal Kingdom	3
uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response	3
Functional Diversity of the Lepidopteran ATP-Binding Cassette Transporters	3
The Mystery of Cancer Resistance: A Revelation Within Nature	3
Analysis of the MCTP Amino Acid Sequence Reveals the Conservation of Putative Calcium- and Lipid-Binding Pockets Within the C2 Domains In Silico	3
How Many Factors Influence Genomic GC Content Among Prokaryotes?	3
Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups	3
Informatic Capabilities of Translation and Its Implications for the Origins of Life	3
Decoding ‘Unnecessary Complexity’: A Law of Complexity and a Concept of Hidden Variation Behind “Missing Heritability” in Precision Medicine	3
Ancestral Sequence Reconstruction of the Ribosomal Protein uS8 and Reduction of Amino Acid Usage to a Smaller Alphabet	3
Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics?	2
The Memory Problem for Neutral Mutational Models of Evolution	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
Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designs	2
Newly Discovered AqE Gene is Highly Conserved in Non-tetrapod Vertebrates	2
Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection	2
Amino Acid Specificity of Ancestral Aminoacyl-tRNA Synthetase Prior to the Last Universal Common Ancestor Commonote commonote	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
Hemocyanins of Muricidae: New ‘Insights’ Unravel an Additional Highly Hydrophilic 800 kDa Mass Within the Molecule	2
Detecting Selection on Segregating Gene Duplicates in a Population	2
Molecular Evolution of clock Genes in Vertebrates	2
Next Generation Sequencing Revolutionizes Organismal Biology Research in Bats	2
Complex Evolution of the Mismatch Repair System in Eukaryotes is Illuminated by Novel Archaeal Genomes	2
Evidence Supporting That C-to-U RNA Editing Is the Major Force That Drives SARS-CoV-2 Evolution	2
Consequences of Genetic Recombination on Protein Folding Stability	2
Diversification Rate is Associated with Rate of Molecular Evolution in Ray-Finned Fish (Actinopterygii)	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
Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure	2
A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet	2
Main Factors Shaping Amino Acid Usage Across Evolution	2
Decay of Skin-Specific Gene Modules in Pangolins	2
Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals	2
Origin of Sex-Biased Mental Disorders: Do Males and Females Experience Different Selective Regimes?	2