Yue Zhang

KGBN: Augmenting and optimizing logical gene regulatory networks using knowledge graphs

KGBN enhances logical gene regulatory networks by integrating knowledge graphs and experimental data to create context-aware models for drug response prediction in AML.

Massively parallel assay of human splice variants reveals cis-regulatory drivers of disease-associated and cell type-specific splicing regulation

The paper develops COMPASS, a method to assess splicing variant effects across cell types, identifying disease-associated variants and cell type-specific splicing programs.

Generating Biomedical Knowledge Graphs from Knowledge Bases, Registries, and Multiomic Data

The paper describes the transformation of multiomics and EHR data into privacy-preserving biomedical knowledge graphs within the Biomedical Data Translator ecosystem.

CellMeSH: Probabilistic Cell-Type Identification Using Indexed Literature

CellMeSH automatically annotates cell types from scRNA-seq data using a probabilistic method and a literature-based database of gene-cell type associations.

UNCURL-App: Interactive Database-Driven Analysis of Single Cell RNA Sequencing Data

UNCURL-App provides an interactive tool for scRNA-seq analysis, integrating cell type databases and allowing user-driven re-analysis of clusters and pathways.

Scalable preprocessing for sparse scRNA-seq dataexploiting prior knowledge

UNCURL improves scRNA-seq preprocessing by incorporating prior knowledge and scaling to large datasets, enhancing clustering and lineage estimation performance.