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 2022-06-01 to 2026-06-01.)

Article	Citations
Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins	45
Prebiotic N-(2-Aminoethyl)-Glycine (AEG)-Assisted Synthesis of Proto-RNA?	44
Correction: Analysis of Cancer-Resisting Evolutionary Adaptations in Wild Animals and Applications for Human Oncology	41
Correction: Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates	33
Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans)	29
Avoiding Catastrophic Mutations Accurately Predicts Amino Acid to Codon Pairing	28
Molecular Evolution of the Green-Sensitive Opsins (RH2) in Sulawesi Oryzias Species with a Single Origin	25
Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation	22
The evolutionary path of widespread IR heteroplasmy of chloroplast genomes in the context of Rhodophyta phylogeny	21
How Binding Affinity and Binding Specificity Map to Sequence Space	20
An Ultimate Question for Functional A-to-I mRNA Editing: Why Not a Genomic G?	17
Screening for Viruses in Pallas’s Long-Tongued Bats (Glossophaga soricina) in Brazil	17
Evaluating Pretrained Protein Language Model Embeddings as Proxies for Functional Similarity	16
Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin	15
Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing	15
Unusual Evolution of Cephalopod Tryptophan Indole-Lyases	15
Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation	15
Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth	14
Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair	14
Post-Subfunctionalization Functions of HIF-1αA and HIF-1αB in Cyprinid Fish: Fine-Tuning Mitophagy and Apoptosis Regulation Under Hypoxic Stress	14
Odorant-Binding and Chemosensory Proteins in Fig Wasps: Evolutionary Insights From Comparative Studies	13
Understanding Functional Evolution in Orthologs and Paralogs	13
Phylogenetic and Evolutionary Analysis of Plant Small RNA 2′-O-Methyltransferase (HEN1) Protein Family	12
MEGA 12.1: Cross-Platform Release for macOS and Linux Operating Systems	12
On the Nature of the Last Common Ancestor: A Story from its Translation Machinery	12

Systematic Detection of Alternative Open Reading Frames (altORFs) in Cancer Driver Genes	12
Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions	12
Mapping Patterns of G-Quadruplex-Forming Sequence Conservation in Primates	11
Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians	11
dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution	11
Possible Acquisition and Molecular Evolution of vpu Genes Inferred from Comprehensive Sequence Analysis of Human and Simian Immunodeficiency Viruses	11
On Protein Loops, Prior Molecular States and Common Ancestors of Life	11
Conservation of Protein Kinase A Substrates in the Cnidarian Coral Spermatozoa Among Animals and Their Molecular Evolution	10
Evolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model	10
A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet	10
Cystathionine Gamma-Lyase: A Potential Longevity Gene Under Selection?	10
Biochemical Property Based Positional Matrix: A New Approach Towards Genome Sequence Comparison	10
Type II LDH/MDH Oxidoreductases in Pacific Oyster Magallana gigas (Thunberg, 1793): Gene Organization and Expression Patterns During Development and Across Tissues	9
Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea	9
RNA or DNA? Revisiting the Chemical Nature of the Cenancestral Genome	9
2025 Zuckerkandl Prize	9
Advances in Contact Tracing: A Bayesian Framework to Improve Network and Transmission Models	8
Reduction of Tooth Replacement Disproportionately Affects the Evolution of Enamel Matrix Proteins	8
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	8
Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups	8
A New View of the Last Universal Common Ancestor	8
Informatic Capabilities of Translation and Its Implications for the Origins of Life	8
The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA	8
The De Novo Emergence of Two Brain Genes in the Human Lineage Appears to be Unsupported	8
GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences	8
Evolutionary Study of Transposable Elements: Structural Characterization and Phylogenomic Profiling in Plant Genomes	7
Correction: Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups	7
Codon Usage Evolution in Viruses: Implications for Survival and Pathogenicity	7
Evolution and Functional Diversification of Serine Racemase Homologs in Bacteria	7
Correction: Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation–Drift Equilibrium	7
Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes	7
PAReTT: A Python Package for the Automated Retrieval and Management of Divergence Time Data from the TimeTree Resource for Downstream Analyses	6
A Law of Redundancy Compounds the Problem of Cancer and Precision Medicine	6
Origins and Functional Significance of Eukaryotic Protein Folds	6
Correlated Evolution Drives Structural Convergence of Interacting Proteins	6
EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids	6
Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1	6
Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	6
Caspase Domain Duplication During the Evolution of Caspase-16	6
FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus	6
Decoding the Evolution and Co-Phospho-Regulatory Networks of SHROOM Proteins	6
OrthoGrafter: Rapid Identification of Orthologs from Precomputed Placement in Phylogenetic Trees	6
Main Factors Shaping Amino Acid Usage Across Evolution	6
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
Transposable Element Diversity Remains High in Gigantic Genomes	5
Putative MutS2 Homologs in Algae: More Goods in Shopping Bag?	5
Genetic Exchanges Shape the Evolutionary Diversification Among Shigella phages	5
Evolutionary Nonindependence Between Human piRNAs and Their Potential Target Sites in Protein-Coding Genes	5
The Mystery of Cancer Resistance: A Revelation Within Nature	5

Co-evolution of alpha-helical transmembrane protein residues: large-scale variant profiling and complete mutational landscape of 2277 known PDB entries representing 504 unique human protein sequences	5
Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics?	4
2022 Zuckerkandl Prize	4
Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway	4
A Simple Evolutionary Model of Genetic Robustness After Gene Duplication	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
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
Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration	4
Origin of Sex-Biased Mental Disorders: Do Males and Females Experience Different Selective Regimes?	4
Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species	4
Jump-Chain Simulation of Markov Substitution Processes Over Phylogenies	4
Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage	4
Replication Rate-Information Storage Trade-Off Shapes Genome Architecture Across Domains	4
2024 Zuckerkandl Prize	4
The GFI1 Gene Family: Evolution, Structure, and Its Role in Immune Responses	4
Introduction to the Special Issue on Early Evolution and the Last Common Ancestor	3
User Guided Selection and Alignment of Sequence Data by GeneMatrix	3
How Many Factors Influence Genomic GC Content Among Prokaryotes?	3
Recurrent Independent Pseudogenization Events of the Sperm Fertilization Gene ZP3r in Apes and Monkeys	3
A Multi-level Perspective on the Evolution of Orthologs and Their Functions	3
On the Unknown Proteins of Eukaryotic Proteomes	3
Epistasis-Driven Evolution of the SARS-CoV-2 Secondary Structure	3
Efficiency of Ancestral Inference and Characterization of Genetic Structure of Chinese Kazakh Group with a Novel InDel Panel	3
The Unfinished Reconstructed Nature of the Last Universal Common Ancestor	3
The Role of Selection and Migration in the Evolution of (Auto)Immunity Genes	3
First Report on Presence of Mitochondrial Introns in Freshwater Sponges, and Pseudogenic Evidence of Their Loss	3
Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection	3
OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data	3
A Comparative Genomics Approach to Understanding the Evolution of Olfaction in Cetaceans	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
Decay of Skin-Specific Gene Modules in Pangolins	3
When Complex Models Fit the Wrong Mechanistic Complexity in Phylogenomic Analysis	3
Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	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
A Bayesian Framework for the Network Analysis of Transmission Dynamics in Infectious Disease	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
Positive Selection Shapes Breast Cancer Tumor Suppressor Genes: Unveiling Insights into BRCA1, BRCA2, and MDC1 Stability	2
Correction to: Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	2
Clay Minerals, Panacea or Parameter in RNA Oligomerization?	2
Functional Diversification and the Plant Secondary Cell Wall	2
Functionality versus Adaptation: Insights from Transcriptional Adaptation	2
Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	2
Correction: G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases	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
Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere	2
In Silico Investigation of the Interactions Between Cotton Leaf Curl Multan Virus Proteins and the Transcriptional Gene Silencing Factors of Gossypium hirsutum L.	2
Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production	2
Mutations Inactivating Biosynthesis of Dispensable Carbohydrate-Antigens Prevented Extinctions in Primate/Human Lineage Evolution	2
Conservation of a Chromosome 8 Inversion and Exon Mutations Confirm Common Gulonolactone Oxidase Gene Evolution Among Primates, Including H. Neanderthalensis	2
Structural and Evolutionary Analysis of Proteins Endowed with a Nucleotidyltransferase, or Non-canonical Palm, Catalytic Domain	2
Expansion and Functional Diversification of Long-Wavelength-Sensitive Opsin in Anabantoid Fishes	2
Nucleobases in Meteorites to Nucleobases in RNA and DNA?	2
The Amphibian Major Histocompatibility Complex—A Review and Future Outlook	2
Best Practices in Microbial Experimental Evolution	2
In Memoriam of Giorgio Bernardi and Noboru Sueoka: A Personal View	2
A Concept of Complementarity Between Complexity and Redundancy can Account for Kant’s Biological Teleology and Unify Mechanistic and Finalistic Biology	2
The Abundance of Viroid-Like RNA Obelisk-S.s in Streptococcus sanguinis SK36 May Suffice for Evolutionary Persistence	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
Correction: Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	2
Breathing Air and Living Underwater: Molecular Evolution of Genes Related to Antioxidant Response in Cetaceans and Pinnipeds	2
Left–Right Reversal Recurrently Evolved Regardless of Diaphanous-Related Formin Gene Duplication or Loss in Snails	2
Fascination with RNA Editing: In the Lights of Evolution and Biology	2
Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations	2
Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors	2
Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host	2
Human Riboviruses: A Comprehensive Study	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
NCBI Orthologs: Public Resource and Scalable Method for Computing High-Precision Orthologs Across Eukaryotic Genomes	2
Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis	2
Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch	2
Stem Life: A Framework for Understanding the Prebiotic-Biotic Transition	2
Diversification of von Willebrand Factor A and Chitin-Binding Domains in Pif/BMSPs Among Mollusks	2
nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models	2
Lectin Gene Families in Three Phaseolus Species: Genome-Wide Identification, Evolutionary Analysis, Pleiotropic Effect, and Regulation Under Multiple Stress Conditions	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