Deng‐Ke Niu

This study examines how localized evolutionary changes affect ancestral state reconstruction and shows that tree partitioning can reduce errors in these reconstructions.

This paper develops a framework to quantify effective information in species-level analyses by accounting for phylogenetic dependence, showing that nominal species counts overestimate independent information.

This paper optimizes phylogenetic eigenvector regression by improving eigenvector selection, robustness to evolutionary shifts, and flexibility in model complexity.

This paper introduces O(D)GC, a method to improve phylogenetic correlation analysis by detecting and handling abrupt evolutionary shifts, showing lower error rates than existing methods.

This study analyzes CRISPR spacer number evolution in bacteria, finding correlations with repeat length, polymorphism, and immune demand, and identifying degenerative patterns in obsolete arrays.

This study examines how bacterial defenses and growth rates vary across ecological contexts, finding that defense systems are not universally present and depend on factors like habitat and nutrient availability.

The paper investigates the relationship between GC content and growth temperature in prokaryotes, finding a positive correlation in bacteria but not in archaea, and suggests sample size and environmental factors may explain discrepancies.

The paper shows bacterial CRISPR-Cas systems increase at ~45°C due to reduced grazing risk and increased viral lysis pressure.

The paper analyzes intron losses and gains across 104 nematode genomes, showing nematodes are not an outlier in intron evolution but follow typical eukaryotic patterns.

The paper identifies dosage-sensitive transcription factor genes by analyzing their enrichment in multiple datasets and finds that nuclear receptors are consistently dosage-sensitive, while some families like C2H2-ZF are not.