Xiaoyu Zhang

WheatPanRef: a unified linear pan-reference genome for wheat genomics

WheatPanRef provides a unified linear pan-reference genome for wheat, improving read alignment and enabling integration of genomic resources across diverse accessions.

Chaos and repetition in algal evolution: A Chrysophyceae eco-genomic framework

This study explores the eco-genomic diversity of Chrysophyceae algae, revealing their evolutionary adaptations and gene markers linked to trophic strategies and environmental responses.

An implantable sensor network for large-scale cellular force mapping in living embryos

The paper introduces FORCENET, an implantable sensor network that maps intercellular forces in living embryos, revealing coordinated mechanical patterns regulated by developmental signaling.

PASTRI: Resolving Stage-Specific Cell-State Dynamics from Annotated Cell Lineage Trees

PASTRI infers stage-specific cell-state transition rates from annotated cell lineages, revealing rate-limiting steps and attractor states in development and disease.

Skill-Augmented Frontier Agents Nearly Saturate BixBench-Verified-50

The paper evaluates three large language model configurations on a curated bioinformatics benchmark, finding they achieve high accuracy with proper scientific skill integration and external resource access.

MCT1 governs a metabolic checkpoint at pachytene during spermatogenesis

This study identifies MCT1 as a metabolic checkpoint regulator in spermatogenesis, showing its role in meiotic progression through epigenetic mechanisms.

Benchmarking Agentic Large Language Models for ComplexProtein-Set Functional Annotation

This study benchmarks agentic large language models for protein-set functional annotation, finding moderate reproducibility and common error modes, but improved evidence handling and reproducibility.

The actin motor protein MYO10 facilitates post-entry spread of respiratory syncytial virus

This study identifies MYO10 as a host factor critical for RSV post-entry spread, showing that its disruption reduces viral dissemination without affecting early infection stages.

Loss of Adaptive DNA Breaks in Alzheimer's Disease Brains

The paper investigates DNA breaks in Alzheimer's disease brains, finding a loss of adaptive DNA breaks at nervous system genes despite an overall increase in DNA breaks.

Genome of a novel Sediminibacterium discovered in association with two species of freshwater stream Cyanobacteria in Southern California

Nutrient restriction, inducer of yeast meiosis, induces mammalian meiosis

Nutrient restriction synergizes with retinoic acid to induce mammalian meiotic initiation.

Measurement of myofilament calcium in living cardiomyocytes using a targeted genetically encoded indicator

The paper develops a genetically encoded calcium indicator for cardiomyocytes that preserves contractile function, improving on chemical dyes and untargeted indicators.

On the Origin and Evolutionary Consequences of Gene Body DNA Methylation

The paper investigates the origin and evolutionary consequences of gene body DNA methylation by studying the loss of this feature in two angiosperms, finding that CMT3 is essential for its establishment.

Histone H1 limits DNA methylation in Neurospora crassa

This study shows that Histone H1 in Neurospora crassa limits DNA methylation by affecting the accessibility of the DNA methylation machinery.

FASTmC: a suite of predictive models for non-reference-based estimations of DNA methylation

FASTmC provides predictive models to estimate DNA methylation without a reference genome, using whole genome bisulfite sequencing data from as few as several thousand short-reads.