comparative / phylogenetic analysis

This paper introduces a compartmental model of the gut-brain axis to simulate gastric function regulation, showing inhibitory and excitatory effects of sympathetic and parasympathetic pathways on digestion.

This study examines the seasonal phenology of Empoasca fabae in Quebec using degree-day models and CLIMEX ecological niche modeling, finding earlier emergence and higher generational potential in warmer regions.

This study reconstructs the evolution of SMC complexes across eukaryotes, showing LECA had all four types and condensin II was repeatedly lost.

The paper examines whether body color polymorphism in birds correlates with ecological success, finding that polymorphic species have larger ranges, lower extinction risk, and more stable populations.

This study analyzes the structural and evolutionary origin of thyroglobulin in sea lamprey, revealing conserved domains and proposing an evolutionary model for its complex architecture.

The paper shows that clitellates experienced a burst of genomic rearrangements leading to loss of macrosynteny with marine annelids and new chromosomal interactions.

This study analyzes gene regulatory programs in primate gonads, finding shared and species-specific regulatory dynamics and candidate genes for sex development disorders.

The paper reports the genome analysis of a new Tequintavirus bacteriophage, Salmonella phage Tennessee Salten, and compares it to its closest relative, identifying unique and divergent genes.

The paper examines opsin gene evolution in Morpho butterflies, finding positive selection and co-evolving amino acids linked to light environment and wing coloration.

This study compares transcriptomes of two fungi during conidial germination, showing F. graminearum upregulates genes for CAZymes and effectors, while M. anisopliae upregulates indole-3-acetic acid synthesis genes, reflecting their pathogenic and endophytic lifestyles.

The paper identifies Avr6 as the effector gene in Fulvia fulva that overcomes Cf-6-mediated immunity in tomato, showing its loss or mutation leads to resistance breakdown.

The paper selects and evaluates ASFV antigens for subunit mRNA vaccines, showing divergent immune responses and developing a computational method to design antigen cocktails.

Hybrid type-II inhibitors RN277 and RN341 target inactive LRRK2 with far fewer kinase off-targets than Rebastinib, preserve S935 phosphorylation, and rescue kinesin motility in vitro.

The paper identifies 39 gene families consistently expressed in neurons across eight animal species and finds one unique family linked to nervous systems.

This study investigates the evolutionary history of cultivated rice and identifies genomic signatures of heterosis in super-hybrid rice varieties.

The paper investigates the evolutionary origin and functional diversification of plant GBF1-type ARF-GEFs, showing how AtGNOM and AtGNL1 orthologs evolved distinct roles in membrane trafficking.

The paper examines the EDVID motif in plant NLR coiled-coil domains, showing its role in structural diversity and function, including the presence of a preEDVID motif and loss of EDVID in some NLRs.

This study examines the evolution of drug-metabolizing genes across vertebrates, showing gene loss, duplication, and positive selection contribute to interspecies variability in drug metabolism.

The paper investigates the evolutionary factors influencing telomere length across vertebrates and finds no direct link between body mass, lifespan, or metabolism but identifies an interactive effect between metabolism and body mass, along with a positive correlation between telomerase activity and telomere length.

The paper analyzes subterminal heterochromatin in great apes, identifying its evolutionary origins and epigenetic features across chimpanzees, gorillas, and bonobos.

Hypoxic induction of glycolysis and fermentation genes spans the land plant divisions tested, while oxygen-regulated group VII Ethylene Response Factors (ERFVIIs) carrying Cys2 occur only in vascular plants.

The paper analyzes the evolutionary and functional roles of RIPK3 and its RHIM domain across vertebrates, finding that RHIM diversity tunes NF-κB activation while preserving cell death function.

This study identifies molecular determinants of USP18's specificity for ISG15 through comparative analysis with its paralog USP41, revealing structural features essential for enzymatic activity.

The paper computationally designs monomeric Fc variants with distinct pH-responsive FcRn-binding profiles, showing enhanced binding at acidic pH and weak binding at neutral pH.

The paper shows that pollinator species have minimal overlap in molecular responses to insecticides, with species-level differences outweighing chemical differences.

The paper characterizes a new Escherichia cryptic clade IV strain from an urban stream, revealing genomic features linked to environmental adaptation and ecological origin.

The paper identifies 584 recent intron gain events in human genes by comparing human and vertebrate genomes and analyzing intronization mechanisms.

The paper compares cold-responsive proteomes across five PACMAD grasses to assess conservation of protein-level responses and identifies LEA3 as a key cold-tolerant protein.

The paper investigates the evolutionary origin of self-sustained Kai protein circadian oscillators in cyanobacteria by analyzing ancestral Kai proteins and their functional and structural development.

The paper examines macroevolutionary dynamics in African cichlid radiations, finding inverse correlation between vertebral count evolution rates and radiation age, but no early burst pattern within individual systems.