Jianquan Liu

A multi-tissue atlas of genetic regulatory effects in sheep

The paper presents a multi-tissue sheep atlas identifying regulatory variants and their effects on molecular phenotypes, revealing allelic heterogeneity and evolutionary patterns.

Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors

This study shows that minor molecular clock deviations in shallow phylogenies can lead to high false-positive rates in introgression detection using site-pattern methods.

Development and application of a genotyping by target sequencing SNP array panel in Salix suchowensis

The paper develops a SNP array panel for Salix suchowensis to improve genotyping and identifies SNPs associated with growth traits.

EasyOmics-A graphical interface for population-scale omics data association, integration and visualization

EasyOmics provides a user-friendly R Shiny interface for population-scale omics data association, integration, and visualization without requiring advanced programming skills.

The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research

The paper curates and presents a collection of long-read genome assemblies for Arabidopsis thaliana accessions to enhance plant genome research.

A reference genome and its epigenetic landscape of potential Orychophragmus violaceus, an industrial crop species

This paper presents a high-quality genome and epigenetic data for Orychophragmus violaceus, revealing insights into its WGD copies and providing resources for breeding.

Evolutionary genomics predicts adaptive genetic and plastic gene expression responses to climate change in a key alpine forest tree species

This study predicts adaptive genetic and plastic gene expression responses to climate change in Populus lasiocarpa using genomic and transcriptomic data.

Chromosomal-level genome assembly of Populus adenopoda

The paper presents a chromosome-level genome assembly for Populus adenopoda using Illumina and PacBio sequencing with Hi-C, resulting in a high-quality reference genome.

Chromosomal-level genome assembly of Populus davidiana

This paper presents a high-quality chromosome-level genome assembly of Populus davidiana using long-read and Hi-C data, providing a resource for future association studies.

The pan-genome and local adaptation of Arabidopsis thaliana

This study de novo assembles high-quality genomes of 38 Arabidopsis thaliana ecotypes using long-read sequencing, identifies new genes and structural variations linked to local adaptation, and highlights the role of SVs in environmental adaptation.

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

WGDI is a Python toolkit for analyzing whole-genome duplications and ancestral karyotypes, offering improved collinearity detection and workflow flexibility.

Sex determination through X-Y heterogamety in Salix nigra

This study identifies a novel sex-linked region in Salix nigra, demonstrating XY heterogamety and recombination suppression, with implications for understanding sex chromosome evolution in plants.

A general model to explain repeated turnovers of sex determination in the Salicaceae

This study identifies an XY and ZW sex determination system in two Populus species and proposes a model linking transposon activity to sex chromosome turnover.

A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

The paper identifies large palindromic structures in the sex chromosome of Salix purpurea, showing convergent evolution with mammalian sex chromosomes.