comparative / phylogenetic analysis

This study compares bariatric surgery and intermittent fasting in rats, showing they affect hepatic metabolism differently through distinct metabolic pathways.

This study identifies a biphasic developmental program in hemichordates, revealing conserved gene regulatory networks and cis-regulatory elements across deuterostomes.

This study investigates SNBP gene evolution in Drosophila, finding that genetic conflicts between sex chromosomes drive their expansion and loss.

This study assembled the chromosome-level genome of Rorippa aquatica to investigate its allotetraploid origin and the molecular mechanisms of heterophylly under submergence.

The paper examines phylogeographic patterns in Baja California bird species, finding concordant patterns in some and divergence in others, highlighting conservation implications of the Vizcaino Desert boundary.

This study investigates the molecular mechanism of inhibitors at the Qi site of T. cruzi cytochrome bc1 using computational methods to guide drug discovery.

The paper identifies conserved plasmodesmal proteins through comparative proteomics across Arabidopsis and moss, revealing core components like β-1,3-glucanases and tetraspanins.

This study investigates the genomic properties of Bacteroides fragilis, revealing its role as a reservoir of antibiotic resistance genes through comparative genomics.

The paper identifies a proton pump enhancing photosynthesis in marine phytoplankton and links it to phagocytosis in symbiogenesis.

The paper examines structural changes and mutation profiles in SARS-CoV-2 spike protein variants and subvariants to identify potential drug targets and neutralizing antibodies.

This study identifies novel resistance genes against basil downy mildew using comparative transcriptomics in resistant and susceptible plants.

The paper compares pangenomes of different Escherichia coli sequence types to show that pangenome evolution is influenced by sequence type-specific factors rather than phylogroup relationships.

The paper examines the evolution of GATA-type transcription factors in the Caenorhabditis genus, finding that despite gene duplications and sequence divergence, most GATA factors maintain similar DNA binding preferences.

The paper shows how gene duplication rewired the endoderm specification network in Caenorhabditis elegans through the evolution of GATA factors during a radiation event.

The paper analyzes Borg genomes to show tandem repeats evolve rapidly and create intrinsically disordered regions in proteins, contributing to functional diversity and host associations.

The paper investigates the dynamic evolution of the PON gene family across metazoa, identifying multiple expansion and loss events in different lineages and suggesting environmental factors like pathogen infection and oxidative stress as drivers.

The paper investigates why some fruit fly species show strong sexual dimorphism, finding that shared host plants and female mate-searching behavior may favor the evolution of dimorphic wing patterns.

This study analyzes mitochondrial tropism in three additional Midichloria species and sequences nine novel genomes, revealing non-monophyletic patterns and genomic signatures associated with mitochondrial colonization.

This study uses multiple phylogenomic and molecular approaches to identify the likely living relatives of the ancestral bacteria from which mitochondria originated.

The paper shows mycorrhizal strategies and drought adaptation co-evolve, with ecto- and ericoid mycorrhizas accelerating drought tolerance evolution compared to arbuscular mycorrhizas.

The paper identifies recent HML-2 provirus activity in rhesus macaques and shows interspecies transmission to gibbons, with a novel RNA transport element replacing the ancestral Rec-RcRE system.

The paper investigates freeze tolerance in the Amur sleeper using genomic, transcriptomic, and metabolomic analyses to identify genetic and molecular mechanisms underlying this adaptation.

The paper introduces phylogenetic completeness as a method to maximize protection of evolutionary innovations in conservation scenarios.

This study compares genome rearrangement features across ciliates to understand the evolutionary origin of massively scrambled genomes.

This study investigates the evolution of TopoVI and TopoVI-like subunits, focusing on the divergence of TOPOVIBL and its role in meiotic DNA break generation.

The paper identifies a conserved extracellular electron uptake pathway in the uncultivated order Tenderiales using comparative genomics.

This paper develops a gene expression atlas of the bat star using snRNA-seq and compares it to sea urchin embryos to reinterpret the evolution of cell types.

The paper identifies cross-talk between horizontally acquired and endogenous two-component systems in VanA-type vancomycin-resistant Enterococcus faecalis that contributes to antibiotic synergy.

The paper compares 16 bottom-up proteomics sample preparation methods to identify optimal strategies for protein extraction and MS analysis.