Yichen Si

This study identifies mosaic chromosomal alterations in healthy human tissues, revealing tissue-specific patterns of mitotic errors and purifying selection across aging.

The paper introduces FICTURE2, a statistical model that infers transcriptional programs from individual RNA molecules in spatial transcriptomics data, revealing spatial organization and cellular identity without segmentation.

The paper introduces SCRIBBLE, a lineage tracing tool that enables high-resolution, multigenerational lineage tracking in embryonic mouse retina.

This study identifies genetic factors influencing mosaic aneuploidies in blood genomes using whole-genome sequencing data from 840,853 individuals.

Seq-Scope-X improves spatial transcriptomics resolution by expanding tissues, revealing detailed nuclear and cytoplasmic transcriptome differences in liver cells and enabling proteomic analysis in other tissues.

The paper integrates in situ hybridization and scRNA-seq data to create 2D topographic maps of the developing retina across species, revealing conserved and divergent patterning programs.

This paper describes a protocol to repurpose Illumina sequencing flow cells for high-resolution spatial transcriptomics, enabling detailed spatial gene expression analysis with improved resolution and cost efficiency.

FICTURE provides a scalable segmentation-free method for analyzing high-resolution spatial transcriptomics data, revealing detailed tissue architecture in complex regions.

The paper introduces clue, a reference-free framework for multiplexed single-cell sequencing to identify genetic modifiers of immune responses using SNP-based clustering and eQTL mapping.

The paper infers germline CpG methylation signatures in the human population using polymorphism data and a new method, achieving high concordance with WGBS data while capturing previously missed CpG sites.

The paper develops a coalescent model to analyze theoretical limits of rare variant imputation, showing that model misspecification leads to significant imputation errors.