Wuming Gong

scEPS integrates genetic and single-cell disease atlas data to provide granular mechanistic insights into complex human diseases

scEPS integrates GWAS and single-cell data to identify disease-associated cell neighborhoods by testing gene expression variance explained in disease contexts.

Evaluation and optimization of sequence-based gene regulatory deep learning models

The paper evaluates and optimizes sequence-based gene regulatory deep learning models using a DREAM Challenge dataset, showing improvements through architectural and training strategy refinements.

Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences

Proformer predicts gene expression from promoter sequences using a hybrid transformer model with improved performance over conventional designs.

SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors

SeATAC is a tool that uses a conditional variational autoencoder to detect differential chromatin accessibility in ATAC-seq data, outperforming existing methods in multiple tasks.

A novel algorithm for the collective integration of single cell RNA-seq during embryogenesis

This paper introduces a novel algorithm to integrate heterogeneous temporal scRNA-seq datasets and reconstruct lineage trajectories, identifying Ebf1 as a key transcription factor for mouse endothelial development.

DrImpute: Imputing dropout events in single cell RNA sequencing data

DrImpute imputes dropout events in scRNA-seq data, improving statistical tools that do not account for these events.