Ying Zhou

Calibrating developmental dynamics from single-cell atlases: lineage paths outrun least-action routes

The paper introduces LADD to measure lineage path deviations from inferred developmental dynamics in single-cell RNA-seq data and finds lineages move faster than optimal paths.

Defining nutrient dependencies of intestinal Klebsiella pneumoniae guides rational probiotic engineering

This study identifies nutrient dependencies of intestinal Klebsiella pneumoniae and develops a probiotic consortium to restrict its expansion.

Cell type-resolved proteomics reveals intra- and intercellular signalingin Alzheimers disease

The paper presents a cell type-resolved proteomic atlas of Alzheimer's disease mouse models, identifying thousands of cell-specific protein changes and highlighting astrocyte-microglia signaling.

Longitudinal multi-omics reveals pathogenic TSC2 variants disrupt developmental trajectories of human cortical organoids derived from Tuberous Sclerosis Complex

This study uses longitudinal multi-omics analysis of cortical organoids to show that TSC2 pathogenic variants disrupt neurodevelopmental trajectories, leading to synaptic and mitochondrial dysfunction.

Non-Invasive Quality Control of Organoid Cultures Using Mesofluidic CSTR Bioreactors and High-Content Imaging

This paper develops a mesofluidic bioreactor platform with high-content imaging for non-invasive quality control of brain organoids, improving their development and reducing cell death.

FMRP phosphorylation modulates neuronal translation through YTHDF1

This study shows that FMRP phosphorylation regulates neuronal translation via YTHDF1, revealing a mechanism for FXS pathology and suggesting YTHDF1 as a therapeutic target.

CaSee: A lightning transfer-learning model directly used to discriminate cancer/normal cells from scRNA-seq

CaSee is a transfer-learning model that accurately discriminates cancer/normal cells from scRNA-seq data with 96.69% average accuracy across multiple datasets.

Parvalbumin interneurons in the nucleus accumbens regulate impairment of risk avoidance in DISC1 transgenic mice

This study shows DISC1-NTM mice have impaired risk avoidance, linked to reduced activity in nucleus accumbens parvalbumin interneurons.

AdmixSim: A Forward-Time Simulator for Various and Complex Scenarios of Population Admixture

AdmixSim generates synthetic admixture data under complex scenarios, enabling accurate simulation of population admixture dynamics and facilitating comparative studies.

Modeling Continuous Admixture

The paper develops a method to infer admixture history using weighted LD, improving accuracy in complex admixture scenarios with isolation after continuous gene flow.

Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions

This paper introduces MALDmef, a method for inferring multiple-wave admixture by modeling LD decay with multiple exponential functions, showing improved accuracy over existing methods in simulated and real data.

Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference

This paper derives the length distribution of ancestral tracks under a general admixture model and applies it to infer population histories with high accuracy.