Wataru Iwasaki

Genomic, spatial, and evolutionary insights into a dominant Mycoplasmatota symbiont colonizing the body wall of deep-sea holothurians

The paper identifies a novel dominant symbiont in deep-sea holothurians, characterizes its genome and spatial distribution, and explores its evolutionary adaptations at the host interface.

Genomic and evolutionary factors influencing the prediction accuracy of optimal growth temperature in prokaryotes

This study develops a model to predict optimal growth temperature in prokaryotes using genomic data, finding that incorporating gene presence/absence improves accuracy for psychrophiles.

Integrated reanalysis of global riverine fish eDNA datasets shows robustness and congruence of biodiversity conclusions

This study reanalyzes global riverine fish eDNA datasets to show that biodiversity conclusions are robust despite varying bioinformatic workflows and reference databases.

Cooperation shapes bacterial niche breadth evolution and patterns of diversification

The paper investigates how cooperation genes influence bacterial niche breadth evolution and diversification patterns across 25,785 species, finding positive correlations and effects on speciation/extinction rates.

MitoNGS: an online platform to analyze fish metabarcoding data in high-resolution

MitoNGS improves fish metabarcoding analysis by enhancing reference databases and introducing a species group strategy to resolve ambiguous taxa.

CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset

The paper introduces two phylogenetic methods, ASA and SEV, to identify functionally related gene pairs in prokaryotic genomes by considering evolutionary history, showing improved performance over existing methods.

Globally unified analysis of riverine eDNA reveals common associations of fish biodiversity with drainage characteristics

This study uses global eDNA data to show how riverine fish biodiversity relates to drainage characteristics, revealing climate and human activity effects vary by biodiversity facet and catchment size.

Repeatability of protein structural evolution following convergent gene fusions

The paper investigates structural convergence in fusion enzymes from different gene fusions, showing similar dimeric structures despite distinct overall architectures and amino acid sequences.

Bioinformatics classification of the MgtE Mg2+ channel and de novo protein design for the stabilization of its novel subclass

The paper identifies a novel subclass of MgtE Mg2+ channels and demonstrates that de novo protein design can stabilize and enable structural analysis of otherwise unstable homologs.

CoLaML: Inferring latent evolutionary modes from heterogeneous gene content

CoLaML infers latent evolutionary modes from gene content heterogeneity across clades and gene families, outperforming previous models in fitting empirical datasets.

Marine biofilms: cyanobacteria factories for the global oceans

This study reveals marine biofilms as a major habitat for cyanobacteria, showing distinct diversity and functional adaptations compared to seawater, with diversification linked to key geological events.

SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models

SonicParanoid2 improves orthology inference speed and accuracy using machine learning and language models, achieving 18X faster performance and higher recall on benchmark datasets.

Resolving the haplotypes of arbuscular mycorrhizal fungi highlights the role of two nuclear populations in host interactions

The paper resolves the haplotypes of arbuscular mycorrhizal fungi and identifies two nuclear populations involved in host interactions.

Inverse Potts model improves accuracy of phylogenetic profiling

The paper introduces IPM-based evaluation measures to reduce biases in phylogenetic profiling and shows they improve prediction accuracy.

Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis

The paper uses long reads and Hi-C sequencing to analyze genome structure and compartmentalization in Rhizophagus irregularis, revealing two distinct chromatin compartments with different gene and repeat content.

Mirage: A phylogenetic mixture model to reconstruct gene-content evolutionary history using a realistic evolutionary rate model

Mirage reconstructs gene-content evolutionary history using a realistic rate model, showing better fit to empirical data and frequent gains/losses in metabolic gene families.

Environmental DNA enables detection of terrestrial mammals from forest pond water

The paper detects terrestrial mammals using eDNA from forest pond water, identifying species like deer and raccoon through metabarcoding.