Runsheng Li

The paper investigates genomic inbreeding effects on growth depression in captive Chinese bahaba, identifying genetic factors linked to skeletal and immune pathways.

The paper investigates the genomic basis of metamorphosis in orbicular batfish, identifying gene family expansions and differentially expressed genes involved in developmental reprogramming during life-history transition.

This study analyzes the pan-genome and methylome of Vibrio alginolyticus from wild fish, identifying a low-virulence, low-resistance clade with distinct epigenetic features.

This study shows that M.FcoHsdM-dependent DNA methylation affects secretion systems, interbacterial competition, and virulence in Flavobacterium columnare.

The paper identifies a shared A-to-G and G-to-A substitution bias in nanopore sequencing, amplified by bacterial DNA methylation, and shows this bias is concentrated around methylation motifs.

This study identifies epigenetic changes in Flavobacterium columnare under prolonged starvation using DNA methylation profiling, revealing motif-specific demethylation patterns linked to adaptation.

The paper develops ANASFV, a pipeline for ASFV whole genome sequencing, assembly, and evaluation, addressing challenges like contamination, error rates, and recombination analysis.

The paper evaluates RNA modification detection in E. coli using nanopore RNA004 technology, introduces nanoSundial for improved detection, and identifies 190 modified CDS regions.

This study uses direct RNA sequencing to compare TGEV with and without gene 7, revealing changes in RNA modifications and polyA tails, and their impact on viral replication and host immunity.

This study maps pseudouridine modifications across bacterial species, revealing dynamic patterns and evolutionary conservation, and develops a deep learning framework for predicting modified sites.

Giraffe is a tool for comparative analysis and visualization of long-read sequencing data across multiple samples and platforms, showing Oxford Nanopore duplex reads outperform PacBio HiFi in homopolymer identification and GC evenness.

This paper improves transgenesis efficiency in C. briggsae by modifying a transposon-based method with a heat shock step, enabling single-copy insertions and applications in hybrid male sterility studies.

The paper characterizes the genomic structure and variation of the 5S rDNA cluster in C. elegans and C. briggsae strains, revealing differences in stability and transcriptional compatibility.

The paper benchmarks Oxford Nanopore assemblers for molluscan genomes, finding optimal coverage and tools for different genome complexities.

The paper reports dual symbiosis in the deep-sea snail Gigantopelta aegis, revealing its genome and two endosymbionts with complementary metabolic functions and immune adaptations.

The paper identifies multiple interacting genomic loci responsible for asymmetric hybrid male sterility and inviability between Caenorhabditis briggsae and C. nigoni.