Naoki Konno

The global β-lactam resistome revealed by comprehensive sequence analysis

The paper maps the global distribution of β-lactamases across environments and microbes, revealing their abundance and potential origins in plant and wastewater ecosystems.

Growth rate structures the dynamics of bacterial trait evolution

This study shows growth rate is a major organizing axis shaping bacterial trait evolution across timescales, with distinct slow- and fast-growing regimes and varying coupling with other traits.

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.

PantheonOS: An Evolvable Multi-Agent Framework for Automatic Genomics Discovery

PantheonOS introduces a multi-agent framework for automated genomics analysis, achieving super-human performance in batch correction and gene panel selection across diverse biological tasks.

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.

Host range and ARG dissemination are shaped by distinct survival strategies of conjugative plasmids

This study identifies two survival strategies in conjugative plasmids that correlate with their host range and antibiotic resistance gene dissemination.

Widespread promiscuous alkaline phosphatases underscore early microbial phosphite utilization

The paper identifies alkaline phosphatase (AP) as a widespread promiscuous enzyme capable of oxidizing phosphite, contributing to microbial phosphorus cycling.