Jue Ruan

PanSVmerger reduces redundant multiallelic structural variants in pangenome graphs with minimal loss of sensitivity, improving precision and F1-score.

The paper assesses autoluminescence potential in Phalaenopsis orchids by analyzing floral traits and finds that color lightness, organ textures, and epidermal cell types are key predictors.

The paper introduces TSTA, a parallel sequence alignment method that improves efficiency using thread and SIMD parallelism for pairwise and multiple sequence alignments.

The paper introduces MIPDB, a maize image-phenotype database with multi-angle and multi-time images, providing a high-quality dataset for deep learning-based phenomics research.

BSAlign improves nucleotide sequence alignment speed by integrating three optimization strategies, achieving faster performance than existing SIMD-based methods.

This study generates haplotype-resolved assemblies and a variant benchmark for a Chinese monozygotic twin quartet using advanced sequencing and computational methods.

NextDenovo corrects noisy Nanopore reads faster and more accurately than Canu and Necat; its maize and 35 human-genome assemblies are more contiguous, with fewer misassemblies, than Flye's.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The paper presents the first high-quality chromosome-level genome of sika deer and identifies UGT and CYP gene family expansions linked to tannin tolerance.

The paper presents a high-quality reference genome for Fasciola gigantica, identifying transposon-mediated evolutionary events and parasitic adaptations contributing to its genomic features and tropical prevalence.

This study presents a chromosome-level genome assembly of wild castor, identifying genes under positive selection linked to adaptation to extreme environments.

This study uses population sequencing to analyze tea plant evolution, revealing stronger selection for disease resistance and flavor in C. sinensis var. sinensis compared to C. sinensis var. assamica.

The paper introduces a computational method for efficiently sorting long reads from sex-limited chromosomes to improve genome assembly.

The paper introduces wtdbg2, a long-read assembler that is significantly faster than existing tools while maintaining comparable accuracy and contiguity for human genomes.

LRScaf improves draft genome assemblies using long reads, achieving higher contiguity and efficiency compared to existing methods.

This paper develops a long-read sequencing protocol to improve variant detection and genome assembly in a human genome, achieving high accuracy and contiguity.