Hongyu Zheng

MOSAICField aligns spatial slices across modalities to reconstruct 3D tissue models and map morphology, outperforming existing methods on simulated and prostate cancer data.

This paper introduces SIID, an algorithm that integrates spatial transcriptomics data from different platforms to impute missing gene expression and deconvolve mixed cell-type signals.

The paper presents a spatially resolved transcriptomic and gene regulatory atlas of primate subcortical regions, revealing spatially tuned transcriptional and regulatory programs across cell types.

The paper introduces a differentiable framework for optimizing sequence-specific minimizer schemes, showing improved performance on genomic sequences.

The paper introduces polar sets for sequence-specific minimizer construction, showing their effectiveness on the human reference genome.

The paper introduces a randomized algorithm called Miniception to design minimizers with optimal density guarantees for practical bioinformatics applications.

The paper addresses non-identifiability in RNA-seq expression quantification by calculating confidence ranges for transcript abundances, showing up to 50% of transcripts may have inaccurate estimates.

This study models ZIKV transmission through sexual contact networks with double asymmetric percolation, revealing a quadruple epidemic transition.