Michael E. Vinyard

scDiffEq: drift-diffusion modeling of single-cell dynamics with neural stochastic differential equations

scDiffEq models single-cell dynamics using neural stochastic differential equations, improving trajectory reconstruction and fate prediction in hematopoiesis.

SIMBA: SIngle-cell eMBedding Along with features

SIMBA is a graph embedding method that jointly embeds single cells and their features into a common space, enabling diverse single-cell analysis tasks.

Integrative dissection of gene regulatory elements at base resolution

The paper identifies critical base-resolution regulatory elements in immune gene expression using base editing and deep learning.

singlecellVR: interactive visualization of single-cell data in virtual reality

singlecellVR provides an accessible VR tool for visualizing single-cell data, supporting various modalities and offering a companion package for data conversion and pre-analyzed datasets.

Assessment of computational methods for the analysis of single-cell ATAC-seq data

The paper benchmarks 10 scATAC-seq analysis methods on synthetic and real datasets, finding SnapATAC, Cusanovich2018, and cisTopic perform best in separating cell populations across varying coverage and noise levels.