Jia‐Xing Yue

Multidimensional telomere diversity and inheritance at individual and population scales

This paper introduces TeloXplorer, a framework for analyzing telomere features in long-read data, showing how telomere diversity is inherited across species and populations.

Genetic background diversifies mutational paths but converges on membrane depolarization for bleomycin resistance in yeast

This study shows that while genetic background shapes mutational paths to bleomycin resistance in yeast, all backgrounds converge on membrane depolarization via PMA1 and PTK2 mutations.

The genome of the early diverged amphioxus, Asymmetron lucayanum, illuminates the evolution of genome architecture and gene repertoires in cephalochordates

This study presents a chromosome-anchored genome assembly of Asymmetron lucayanum, revealing genome architecture and gene evolution in cephalochordates.

Regulation of cell proliferation by a novel feedback system on Cdk function

This study identifies a novel feedback system regulating Cdk function through Spo12, a small disordered protein that inhibits PP2A, and shows its role in enhancing cell proliferation in fission yeast.

Super-pangenome analysis of 3562 human and animal papillomavirus isolates illuminates their genome and pathogenicity evolution

The paper analyzes 3562 human and animal papillomavirus genomes to uncover genomic diversity, evolutionary patterns, and pathogenicity drivers, identifying key mutations and variants associated with cancer risk and prognosis.

VRPG: an interactive visualization framework for reference-projected pangenome graph

VRPG provides an interactive visualization framework for pangenome graphs, enabling exploration, annotation, and comparison of genomic variation across species.

Availability of an inflammatory macrophage niche drives phenotypic and functional alterations in Kupffer cells

The paper shows that blocking monocytes alone is insufficient to reduce LMAMs, as KCs can replenish them through proliferation or infiltration, and their reprogramming contributes to immunosuppression.

NanoTrans: an integrated computational framework for comprehensive transcriptome analysis with Nanopore direct-RNA sequencing

NanoTrans provides a comprehensive computational framework for analyzing Nanopore direct-RNA sequencing data, covering isoform clustering, poly(A) tail length estimation, RNA modification profiling, and fusion gene detection across multiple organisms.

GetPrimers: a generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems

GetPrimers is a computational tool for designing PCR-based genetic targeting primers, validated across multiple organisms and experimental setups.

Genome instability footprint under rapamycin and hydroxyurea treatments

This study quantifies mutation rates and spectra in yeast under rapamycin and hydroxyurea treatments, revealing distinct mutagenic effects and their impact on cell fitness.

142 telomere-to-telomere assemblies reveal the genome structural landscape in Saccharomyces cerevisiae

This paper presents 142 high-quality yeast genomes to improve pangenome understanding, identifying structural variants and complex genomic regions.

Telomeres are shorter in wild Saccharomyces cerevisiae isolates than in domesticated ones

The paper finds that wild Saccharomyces cerevisiae isolates have shorter telomeres than domesticated ones, linked to genetic and metabolic differences.

RecombineX: a generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis

RecombineX automates tetrad analysis workflows for meiotic recombination, supporting diverse organisms and genetic backgrounds with simulation and batch processing capabilities.

Diverse natural variants suppress mutations in hundreds of essential genes

The paper measures how natural genetic variation can suppress mutations in essential yeast genes, finding that 35% of tested genes can be suppressed by modifier genes in different backgrounds.

Aborting meiosis overcomes hybrid sterility

Aborting meiosis followed by return-to-growth promotes genome-wide recombination in sterile yeast hybrids, enabling adaptation and genetic mapping.

Intragenic repeat expansions control yeast chronological aging

The paper identifies intragenic repeat expansions in yeast that influence chronological aging by altering cellular metabolism and environmental interaction.

simuG: a general-purpose genome simulator

simuG generates simulated genomes with predefined and random variants for benchmarking genomic analyses.

LRSDAY: Long-read sequencing data analysis for yeasts

LRSDAY streamlines long-read sequencing analysis for yeasts, producing high-quality genome assemblies and annotations for S. cerevisiae and other eukaryotes.

Patterns of selection reveal shared molecular targets over short and long evolutionary timescales

The paper investigates how standing and de novo genetic variants contribute to drug adaptation in yeast, finding they act on shared molecular targets but via different mechanisms.