Siyuan S. Wang

Differential analysis of image-based chromatin tracing data with Dory

Dory identifies differential spatial patterns in chromatin tracing data by analyzing structural differences between groups, linking changes to gene regulation.

Excessive immune responses in preterm placental villi compromise trophoblast health

The paper examines immune cell composition and function in placental villi, finding that excessive T cells and cytokines in preterm cases impair trophoblast health.

Non-disruptive 3D profiling of combinations of epigenetic marks in single cells

This paper introduces Epi-PHR, a non-disruptive method for single-cell spatial epigenetic profiling, revealing region-specific epigenetic profiles and allele-specific chromatin states.

Perturb-tracing enables high-content screening of multiscale 3D genome regulators

The paper introduces Perturb-tracing, a high-content screening platform to identify regulators of 3D chromatin organization, discovering new factors that influence chromatin folding and nuclear architecture.

Sequencing-free whole genome spatial transcriptomics at molecular resolution in intact tissue

This paper introduces RAEFISH, a spatial transcriptomics technology that achieves whole-genome coverage and single-molecule resolution in intact tissues, enabling comprehensive analysis of RNA localization and cell interactions.

Long-range genomic loci stochastically assemble into hierarchical chromosome structures

The paper identifies long-range chromosomal loops spanning over 100 Mb and shows they form via multivalent binding, independent of known nuclear structures, suggesting a distributed mechanism for chromosome organization.

Epigenetic priming promotes acquisition of tyrosine kinase inhibitor resistance and oncogene amplification in human lung cancer

The paper identifies METTL7A as a factor that promotes TKI resistance and oncogene amplification in lung cancer by remodeling chromatin structure before copy number gains.

Longitudinal single-cell transcriptional dynamics throughout neurodegeneration in SCA1

This study uses longitudinal single-nucleus RNA sequencing to analyze transcriptional dynamics in SCA1 cerebellum, identifying early cellular changes and applying deep learning to predict disease state.

Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo

The paper uses live imaging to study chromatin compaction and transcriptional dynamics during stem cell differentiation in live mouse epidermis, showing that chromatin changes follow transcriptional activity.

TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

This study uses chromatin tracing to show that single-cell domains exist on both active and inactive X chromosomes and remain stable under epigenetic perturbations.