Bingqing Zhao

BiomniBench: Process-level Evaluation of LLM Agents for Real-world Biomedical Research

BiomniBench evaluates LLM agents' research processes in biomedical tasks using expert rubrics, revealing performance gaps in method selection and reasoning.

Multi-omic identification of key transcriptional regulatory programs during endurance exercise training in rats

The paper identifies tissue-specific transcriptional regulatory programs in rats undergoing endurance exercise training by integrating chromatin accessibility, DNA methylation, and gene expression data.

TDP-43 toxic gain of function links ALS, FTD and Alzheimers Disease through splicing dysregulation

This study identifies TDP-43-driven splicing dysregulation as a common mechanism in ALS, FTD, and Alzheimer's disease, linking them through mis-spliced mRNAs like APP.

Contextualising transcription factor binding during embryogenesis using natural sequence variation

The paper identifies genetic variants affecting TF binding during Drosophila embryogenesis and uses a CNN to predict functional variants.

The mitochondrial multi-omic response to exercise training across tissues

This study maps multi-omic mitochondrial changes across 19 tissues in rats after endurance exercise training, identifying tissue-specific adaptations and disease-related hubs.

Temporal dynamics of the multi-omic response to endurance exercise training across tissues

This study profiles multi-omic changes in multiple tissues of rats during endurance exercise training, identifying molecular adaptations and sex-specific responses across time.

scDALI: Modelling allelic heterogeneity of DNA accessibility in single-cells reveals context-specific genetic regulation

scDALI models allelic heterogeneity in single-cell chromatin accessibility to identify context-specific genetic regulation.

Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programs

The paper quantifies how cis-acting genetic variation affects chromatin accessibility, histone modifications, and gene expression in Drosophila embryos, finding that much of this variation does not propagate to gene expression.

Tyrosine kinase inhibitors induce mitochondrial dysfunction during cardiomyocyte differentiation through alteration of GATA4-mediated networks

This study shows that tyrosine kinase inhibitors cause mitochondrial dysfunction in cardiomyocytes by altering GATA4-mediated networks, and GATA4 overexpression can rescue these effects.