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 2021-05-01 to 2025-05-01.)

Article	Citations
Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins	71
Correction: Analysis of Cancer-Resisting Evolutionary Adaptations in Wild Animals and Applications for Human Oncology	43
Prebiotic N-(2-Aminoethyl)-Glycine (AEG)-Assisted Synthesis of Proto-RNA?	27
Correction: Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates	27
Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans)	21
Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation	20
Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing	19
An Ultimate Question for Functional A-to-I mRNA Editing: Why Not a Genomic G?	18
The Ancient Origins of Death Domains Support the ‘Original Sin’ Hypothesis for the Evolution of Programmed Cell Death	16
Unusual Evolution of Cephalopod Tryptophan Indole-Lyases	15
Post-Subfunctionalization Functions of HIF-1αA and HIF-1αB in Cyprinid Fish: Fine-Tuning Mitophagy and Apoptosis Regulation Under Hypoxic Stress	14
Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin	14
Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation	14
dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution	13
Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair	13
Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth	13
Odorant-Binding and Chemosensory Proteins in Fig Wasps: Evolutionary Insights From Comparative Studies	13
Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions	11
On the Nature of the Last Common Ancestor: A Story from its Translation Machinery	11
On Protein Loops, Prior Molecular States and Common Ancestors of Life	10
Pheromone Gene Diversification and the Evolution of Courtship Glands in Plethodontid Salamanders	9
Phylogenetic and Evolutionary Analysis of Plant Small RNA 2′-O-Methyltransferase (HEN1) Protein Family	9
Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians	8
Biochemical Property Based Positional Matrix: A New Approach Towards Genome Sequence Comparison	8
Detecting Selection on Segregating Gene Duplicates in a Population	8

RNA or DNA? Revisiting the Chemical Nature of the Cenancestral Genome	8
A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet	8
Functional Diversity of the Lepidopteran ATP-Binding Cassette Transporters	8
Informatic Capabilities of Translation and Its Implications for the Origins of Life	7
Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea	7
Conservation of Protein Kinase A Substrates in the Cnidarian Coral Spermatozoa Among Animals and Their Molecular Evolution	7
Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes	7
The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA	7
GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences	7
The De Novo Emergence of Two Brain Genes in the Human Lineage Appears to be Unsupported	7
Adaptation and Exaptation: From Small Molecules to Feathers	7
Evolution and Functional Diversification of Serine Racemase Homologs in Bacteria	6
The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms	6
Promiscuous Domains in Eukaryotes and HAT Proteins in FUNGI Have Followed Different Evolutionary Paths	6
Biothermodynamics of Hemoglobin and Red Blood Cells: Analysis of Structure and Evolution of Hemoglobin and Red Blood Cells, Based on Molecular and Empirical Formulas, Biosynthesis Reactions, and Therm	6
A Law of Redundancy Compounds the Problem of Cancer and Precision Medicine	6
EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids	6
A New View of the Last Universal Common Ancestor	6
PAReTT: A Python Package for the Automated Retrieval and Management of Divergence Time Data from the TimeTree Resource for Downstream Analyses	6
Correction: Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation–Drift Equilibrium	6
Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes	5
Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	5
Costly circRNAs, Effective Population Size, and the Origins of Molecular Complexity	5
Correction: Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	5
Selection Pressure Regulates the Evolution-Structure–Function Paradigm of Monocyte Chemoattractant Protein Family	5
Molecular Evolution of clock Genes in Vertebrates	5
Origins and Functional Significance of Eukaryotic Protein Folds	5
Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1	5
Main Factors Shaping Amino Acid Usage Across Evolution	5
Putative MutS2 Homologs in Algae: More Goods in Shopping Bag?	5
Evolutionary Nonindependence Between Human piRNAs and Their Potential Target Sites in Protein-Coding Genes	5
Jump-Chain Simulation of Markov Substitution Processes Over Phylogenies	5
Analysis of the MCTP Amino Acid Sequence Reveals the Conservation of Putative Calcium- and Lipid-Binding Pockets Within the C2 Domains In Silico	5
FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus	5
Reenacting the Birth of a Function: Functional Divergence of HIUases and Transthyretins as Inferred by Evolutionary and Biophysical Studies	5
The Mystery of Cancer Resistance: A Revelation Within Nature	5
Transposable Element Diversity Remains High in Gigantic Genomes	5
Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species	5
A Simple Evolutionary Model of Genetic Robustness After Gene Duplication	4
Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups	4
Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes	4
A Genomic Conceptualization of Species	4
2024 Zuckerkandl Prize	4
How Many Factors Influence Genomic GC Content Among Prokaryotes?	4
Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics?	4
2022 Zuckerkandl Prize	4
Phylogenetic and Ancestral Sequence Reconstruction of SARS-CoV-2 Reveals Latent Capacity to Bind Human ACE2 Receptor	4
Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	4
The Role of Selection and Migration in the Evolution of (Auto)Immunity Genes	4
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	4

Origin of Sex-Biased Mental Disorders: Do Males and Females Experience Different Selective Regimes?	4
Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway	4
uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response	3
Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	3
Recurrent Independent Pseudogenization Events of the Sperm Fertilization Gene ZP3r in Apes and Monkeys	3
A Concept of Complementarity Between Complexity and Redundancy can Account for Kant’s Biological Teleology and Unify Mechanistic and Finalistic Biology	3
Genome Scan for Variable Genes Involved in Environmental Adaptations of Nubian Ibex	3
Structural Computational Analysis of the Natural History of Class I aminoacyl-tRNA Synthetases Suggests their Role in Establishing the Genetic Code	3
Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals	3
Epistasis-Driven Evolution of the SARS-CoV-2 Secondary Structure	3
Ancestral Information Analysis of Chinese Korean Ethnic Group via a Novel Multiplex DIP System	3
Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited	3
In Memoriam of Giorgio Bernardi and Noboru Sueoka: A Personal View	3
The Unfinished Reconstructed Nature of the Last Universal Common Ancestor	3
Correction: G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases	3
Evolution of the Cytokinin Dehydrogenase (CKX) Domain	3
The Evolution of Hemocyanin Genes in Caenogastropoda: Gene Duplications and Intron Accumulation in Highly Diverse Gastropods	3
Selection Across the Three-Dimensional Structure of Venom Proteins from North American Scolopendromorph Centipedes	3
A Comparative Genomics Approach to Understanding the Evolution of Olfaction in Cetaceans	3
Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus)	3
Evolution of the Major Components of Innate Immunity in Animals	3
The Hypervariable Tpr Multigene Family of Theileria Parasites, Defined by a Conserved, Membrane-Associated, C-Terminal Domain, Includes Several Copies with Defined Orthology Between Species	3
Decay of Skin-Specific Gene Modules in Pangolins	3
On the Unknown Proteins of Eukaryotic Proteomes	3
Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes	3
Introduction to the Special Issue on Early Evolution and the Last Common Ancestor	3
Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli	2
Structural and Evolutionary Analysis of Proteins Endowed with a Nucleotidyltransferase, or Non-canonical Palm, Catalytic Domain	2
Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere	2
Positive Selection Shapes Breast Cancer Tumor Suppressor Genes: Unveiling Insights into BRCA1, BRCA2, and MDC1 Stability	2
Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production	2
Left–Right Reversal Recurrently Evolved Regardless of Diaphanous-Related Formin Gene Duplication or Loss in Snails	2
Analysis of Programmed Cell Death-1 (PD-1) Gene Variations (re11568821 and rs41386349) in HTLV-1 Infection Using One Primer Pair and Proviral Load	2
Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch	2
Nucleobases in Meteorites to Nucleobases in RNA and DNA?	2
Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host	2
Conservation of a Chromosome 8 Inversion and Exon Mutations Confirm Common Gulonolactone Oxidase Gene Evolution Among Primates, Including H. Neanderthalensis	2
Codon Usage Bias: An Endless Tale	2
Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models	2
Diversification of von Willebrand Factor A and Chitin-Binding Domains in Pif/BMSPs Among Mollusks	2
Correction to: Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	2
Best Practices in Microbial Experimental Evolution	2
Variables Influencing Differences in Sequence Conservation in the Fission Yeast Schizosaccharomyces pombe	2
Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors	2
A New Perspective on the Maillard Reaction and the Origin of Life	2
Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations	2
Expansion and Functional Diversification of Long-Wavelength-Sensitive Opsin in Anabantoid Fishes	2
nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models	2
Functional Diversification and the Plant Secondary Cell Wall	2
Human Riboviruses: A Comprehensive Study	2