Qian Zhang

scCircaSim: A Circadian Simulator for Single-Cell and Spatial Transcriptomics

scCircaSim generates circadian single-cell and spatial transcriptomic data with known ground truth to evaluate analysis methods.

Decoding Cell-level Circadian Phase and Rhythm-state Remodeling in Single-cell Transcriptomes With scRhythmBayes

scRhythmBayes infers cell-level circadian phase and rhythm-state remodeling in single-cell transcriptomes, revealing distinct temporal patterns in liver zonation and heart disease.

Information regimes in population-graph neuroimaging: cohort context and implementation-dependent evaluation sensitivity

The paper evaluates how population-graph models' performance varies with evaluation context, showing implementation-dependent differences in AUC across splits.

Reliable Evaluation of Transductive Population Graph Neural Networks for Multisite Autism fMRI

Site-aware population GNN on ABIDE-I: cohort AUC about 0.94 (kept with site-only edges) was not reproduced by a site-prior classifier (0.506); a directed-edge support gain (+0.252) vanished when symmetrised (−0.003).

The cellular and genetic basis of inflorescence divergence between maize and teosinte

This study identifies cellular and genetic changes in maize and teosinte ears, showing how cytokinin signaling and transcription factor expression differences drive cob thickening and increased kernel number during domestication.

A BRRF1-CCR4-NOT axis underlies conserved transcriptome-wide loss of splicing fidelity during gammaherpesvirus reactivation

The paper identifies BRRF1 as a key driver of transcriptome-wide splicing defects during gammaherpesvirus reactivation by hijacking the CCR4-NOT complex.

Base-resolution DNA methylome of human MDS hematopoietic stem cell reveals TET2-GFI1 epigenetic axis repressing MDS

The paper maps the base-resolution DNA methylome of human MDS HSCs and identifies a TET2-GFI1 epigenetic axis that regulates HSC homeostasis.

Synthetic ratio computation for programming population composition and multicellular morphology

This paper introduces genetic devices for precise control of cell-type ratios and multicellular morphology in synthetic biology systems.

CHPT1-LCAT rewires lipolysis towards ferroptosis

This study identifies DAG as a licensing lipid intermediate for ferroptosis, revealing a novel CHPT1-iLCAT axis that routes DAG to promote ferroptosis and suppress tumor growth.

Molecular mechanisms of dynamics-mediated effects of pathogenic missense mutations on Menin protein function

This study shows that pathogenic missense mutations affect Menin function through dynamic changes and allostery, not just structural destabilization.

MtDNA heteroplasmy controls tumor immune reprogramming through mitochondrial translation

The paper shows that mtDNA heteroplasmy regulates tumor progression by modulating mitochondrial translation and immune microenvironment remodeling through the LARS2-S100A8/A9 axis.

'Zipper' Grammar of CTD Governs the Spatial Programing of the Transcription Cycle of RNA Polymerase II

The paper defines the minimal sequence requirements of RNA polymerase II CTD across transcriptional stages using structural analysis and synthetic constructs, revealing a 'zipper' model for PIC assembly and transcription progression.

Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding

The paper develops genomic resources to improve American chestnut resistance to pathogens through breeding and gene editing.

Engineered Living Glues for Autonomous Detection and On-Demand Treatment of Inflammatory Bowel Disease

This paper introduces a living glue made of engineered bacteria that detects and treats inflammatory bowel disease in mice by monitoring bleeding and producing therapeutic proteins.

Whole-genome resequencing reveals the population structure, genomic diversity, and demographic history of American chestnut (Castanea dentata)

This study uses whole-genome resequencing to analyze population structure, genomic diversity, and demographic history of American chestnut, identifying regions under positive selection for blight resistance.

MUNIn (Multiple sample UNifying long-range chromatin Interaction detector): a statistical framework for identifying long-range chromatin interactions from multiple samples

MUNIn identifies long-range chromatin interactions across multiple samples by accounting for sequencing depth and heterogeneity, achieving lower false positives and higher power for shared peaks.

Genomic selection analyses reveal tradeoff between chestnut blight tolerance and genome inheritance from American chestnut (Castanea dentata) in (C. dentata x C. mollissima) x C. dentata backcross populations

The paper uses genomic selection analyses to show that blight tolerance in chestnut hybrids is polygenic, not controlled by major genes, and that higher American chestnut genome inheritance correlates with lower blight tolerance.

Regulation by HSP70/90 in the different tissues and testis development of male cattle (Cattle-yak and Yak)

This study examines HSP70/90 expression and localization in cattle-yak and yak, finding tissue-specific differences and suggesting HSP90 upregulation may contribute to cattle-yak infertility.

N6-Methyladenine DNA Modification in Human Genome

This study identifies widespread N6-methyladenine (6mA) modification in the human genome, links it to gene expression, and shows its role in cancer by demonstrating reduced 6mA levels in tumors.

Projected spread of Zika virus in the Americas

This paper projects the spread of Zika virus in the Americas using a data-driven stochastic model, estimating introduction timing and infection patterns.