Shujun Ou

This paper presents the first fully phased, diploid, telomere-to-telomere genome of the zebra finch, revealing new genes and structural features.

TIR-Learner v4 improves the speed and memory efficiency of TIR transposon annotation across large genomes.

EDTA v2 improves transposable element annotation in animal genomes by adding LINE/SINE detection and enhancing scalability and speed.

The paper identifies LTR retrotransposons in maize as having promoter-like features and regulatory roles through long-read transcriptomics and coexpression analysis.

TEgenomeSimulator generates synthetic genomes with configurable transposable element landscapes, offering greater flexibility and realism compared to existing simulators.

TEtrimmer automates TE curation by integrating alignment and classification methods, improving intact TE identification across six organisms.

PrinTE simulates genome evolution driven by transposable elements, revealing that genome size is strongly correlated with LTR retrotransposon dynamics and suggesting genome expansion followed by contraction in A. psidii.

This study introduces a method using LTR-RTs and SSM to assign subgenomes in polyploid genomes, applied to octoploid strawberry to identify three allopolyploidization events.

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.

The paper uses pan-genomics and genome editing in Solanum to show that paralog diversification hinders genotype-phenotype predictability in crop domestication.

The paper develops a pan-TE annotation tool to analyze TE variation in maize, finding that tropical maize has more TE sequences due to active and less methylated LTR retrotransposons.

AnnoSINE_v2 improves SINE annotation in animal genomes with higher accuracy and computational efficiency compared to previous tools.

The paper reports the genome assembly and annotation of Malus angustifolia, identifies SNPs and structural variants, and explores phylogenetic relationships with Eurasian Malus species.

The paper presents the genome of the Wollemi pine, revealing ancient transposon activity and insights into its conservation and evolutionary history.

This paper presents a high-quality, haplotype-resolved genome assembly of Malus fusca and identifies structural variants and a fire blight resistance locus.

The paper presents a contiguous de novo genome assembly of sugar beet EL10 using long-read sequencing and scaffolding, showing high congruence with the reference genome and reduced gene copy number variation.

The paper introduces modbamtools, a tool for analyzing single-molecule epigenetic data, enabling visualization, manipulation, and downstream analysis of base modifications in long-read sequencing data.

TEsorter classifies transposable elements at the lineage level using conserved protein domains, offering speed, sensitivity, and precision for LTR retrotransposons.

Trio-binned PacBio HiFi reads plus a 3.6 M-variant recombination map give phase-resolved assemblies of octoploid strawberry 'Royal Royce' and FaRR1, a 786.5 Mb haploid reference with 28 pseudomolecules.

The paper assembles and resolves two haplotypes of a cassava line using multiple sequencing technologies, revealing over 5,000 large structural variants.

A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

The paper presents a gapless maize genome assembly using long read technologies and optical maps, achieving telomere-to-telomere assemblies for chromosomes 3 and 9.

This study evaluates the impact of sequence depth and read length on long-read assembly quality for the maize genome, finding that lower depths and shorter reads result in fragmented assemblies.

The paper benchmarks TE annotation methods and develops a pipeline called EDTA to create a comprehensive, condensed TE library for both intact and fragmented elements in rice genomes.

LTR_FINDER_parallel accelerates LTR retrotransposon identification in plant genomes by parallelizing LTR_FINDER, reducing processing time from 1.16 years to 72 minutes for a 14.5 Gb wheat genome.

LTR_retriever identifies LTR retrotransposons with high sensitivity and specificity, including non-canonical variants, across plant genomes.