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 2021-09-01 to 2025-09-01.)

Article	Citations
Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins	47
Correction: Analysis of Cancer-Resisting Evolutionary Adaptations in Wild Animals and Applications for Human Oncology	32
Correction: Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates	31
Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans)	30
Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation	24
Prebiotic N-(2-Aminoethyl)-Glycine (AEG)-Assisted Synthesis of Proto-RNA?	20
Unusual Evolution of Cephalopod Tryptophan Indole-Lyases	20
Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation	19
Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin	19
The Ancient Origins of Death Domains Support the ‘Original Sin’ Hypothesis for the Evolution of Programmed Cell Death	15
Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing	14
An Ultimate Question for Functional A-to-I mRNA Editing: Why Not a Genomic G?	13
Odorant-Binding and Chemosensory Proteins in Fig Wasps: Evolutionary Insights From Comparative Studies	12
Screening for Viruses in Pallas’s Long-Tongued Bats (Glossophaga soricina) in Brazil	12
Post-Subfunctionalization Functions of HIF-1αA and HIF-1αB in Cyprinid Fish: Fine-Tuning Mitophagy and Apoptosis Regulation Under Hypoxic Stress	11
Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions	11
Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth	11
Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair	11
On the Nature of the Last Common Ancestor: A Story from its Translation Machinery	10
dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution	10
Phylogenetic and Evolutionary Analysis of Plant Small RNA 2′-O-Methyltransferase (HEN1) Protein Family	10
Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians	9
On Protein Loops, Prior Molecular States and Common Ancestors of Life	9
Possible Acquisition and Molecular Evolution of vpu Genes Inferred from Comprehensive Sequence Analysis of Human and Simian Immunodeficiency Viruses	9
A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet	8

Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea	8
The De Novo Emergence of Two Brain Genes in the Human Lineage Appears to be Unsupported	8
Conservation of Protein Kinase A Substrates in the Cnidarian Coral Spermatozoa Among Animals and Their Molecular Evolution	8
RNA or DNA? Revisiting the Chemical Nature of the Cenancestral Genome	8
Adaptation and Exaptation: From Small Molecules to Feathers	8
Functional Diversity of the Lepidopteran ATP-Binding Cassette Transporters	8
Biochemical Property Based Positional Matrix: A New Approach Towards Genome Sequence Comparison	8
The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA	8
Informatic Capabilities of Translation and Its Implications for the Origins of Life	7
GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences	7
PAReTT: A Python Package for the Automated Retrieval and Management of Divergence Time Data from the TimeTree Resource for Downstream Analyses	7
Evolution and Functional Diversification of Serine Racemase Homologs in Bacteria	7
A Law of Redundancy Compounds the Problem of Cancer and Precision Medicine	7
Reduction of Tooth Replacement Disproportionately Affects the Evolution of Enamel Matrix Proteins	7
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	7
A New View of the Last Universal Common Ancestor	7
Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes	7
EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids	6
FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus	6
Origins and Functional Significance of Eukaryotic Protein Folds	6
Main Factors Shaping Amino Acid Usage Across Evolution	6
Promiscuous Domains in Eukaryotes and HAT Proteins in FUNGI Have Followed Different Evolutionary Paths	6
Analysis of the MCTP Amino Acid Sequence Reveals the Conservation of Putative Calcium- and Lipid-Binding Pockets Within the C2 Domains In Silico	6
Caspase Domain Duplication During the Evolution of Caspase-16	6
Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1	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	6
Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	6
Costly circRNAs, Effective Population Size, and the Origins of Molecular Complexity	5
Putative MutS2 Homologs in Algae: More Goods in Shopping Bag?	5
Selection Pressure Regulates the Evolution-Structure–Function Paradigm of Monocyte Chemoattractant Protein Family	5
Correction: Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	5
The Mystery of Cancer Resistance: A Revelation Within Nature	5
Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species	5
Evolutionary Nonindependence Between Human piRNAs and Their Potential Target Sites in Protein-Coding Genes	5
Transposable Element Diversity Remains High in Gigantic Genomes	5
Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics?	5
Jump-Chain Simulation of Markov Substitution Processes Over Phylogenies	4
2022 Zuckerkandl Prize	4
Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage	4
Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	4
Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes	4
Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups	4
Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway	4
Phylogenetic and Ancestral Sequence Reconstruction of SARS-CoV-2 Reveals Latent Capacity to Bind Human ACE2 Receptor	4
A Genomic Conceptualization of Species	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
2024 Zuckerkandl Prize	4
Evolution of the Major Components of Innate Immunity in Animals	3

The Abundance of Viroid-Like RNA Obelisk-S.s in Streptococcus sanguinis SK36 May Suffice for Evolutionary Persistence	3
A Concept of Complementarity Between Complexity and Redundancy can Account for Kant’s Biological Teleology and Unify Mechanistic and Finalistic Biology	3
The Evolution of Hemocyanin Genes in Caenogastropoda: Gene Duplications and Intron Accumulation in Highly Diverse Gastropods	3
The Unfinished Reconstructed Nature of the Last Universal Common Ancestor	3
Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals	3
Introduction to the Special Issue on Early Evolution and the Last Common Ancestor	3
Convergent Evolution of Two Dopamine Receptor Genes: Repeated Evolution of Exon 6 Skipping in Drd2, and Repeated Deletion of Exon 6 in Drd3	3
Evolution of the Cytokinin Dehydrogenase (CKX) Domain	3
Correction: G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases	3
On the Unknown Proteins of Eukaryotic Proteomes	3
Epistasis-Driven Evolution of the SARS-CoV-2 Secondary Structure	3
How Many Factors Influence Genomic GC Content Among Prokaryotes?	3
A Simple Evolutionary Model of Genetic Robustness After Gene Duplication	3
Decay of Skin-Specific Gene Modules in Pangolins	3
Recurrent Independent Pseudogenization Events of the Sperm Fertilization Gene ZP3r in Apes and Monkeys	3
Structural Computational Analysis of the Natural History of Class I aminoacyl-tRNA Synthetases Suggests their Role in Establishing the Genetic Code	3
Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus)	3
A Comparative Genomics Approach to Understanding the Evolution of Olfaction in Cetaceans	3
The Role of Selection and Migration in the Evolution of (Auto)Immunity Genes	3
Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes	3
Selection Across the Three-Dimensional Structure of Venom Proteins from North American Scolopendromorph Centipedes	3
Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited	3
Positive Selection Shapes Breast Cancer Tumor Suppressor Genes: Unveiling Insights into BRCA1, BRCA2, and MDC1 Stability	2
nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models	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
A New Perspective on the Maillard Reaction and the Origin of Life	2
Correction to: Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	2
Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli	2
Ancestral Information Analysis of Chinese Korean Ethnic Group via a Novel Multiplex DIP System	2
Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	2
Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host	2
Expansion and Functional Diversification of Long-Wavelength-Sensitive Opsin in Anabantoid Fishes	2
Left–Right Reversal Recurrently Evolved Regardless of Diaphanous-Related Formin Gene Duplication or Loss in Snails	2
Structural and Evolutionary Analysis of Proteins Endowed with a Nucleotidyltransferase, or Non-canonical Palm, Catalytic Domain	2
Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors	2
Functional Diversification and the Plant Secondary Cell Wall	2
Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch	2
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	2
Nucleobases in Meteorites to Nucleobases in RNA and DNA?	2
The Amphibian Major Histocompatibility Complex—A Review and Future Outlook	2
Conservation of a Chromosome 8 Inversion and Exon Mutations Confirm Common Gulonolactone Oxidase Gene Evolution Among Primates, Including H. Neanderthalensis	2
Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere	2
Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations	2
Human Riboviruses: A Comprehensive Study	2
Best Practices in Microbial Experimental Evolution	2
uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response	2
In Memoriam of Giorgio Bernardi and Noboru Sueoka: A Personal View	2