Yanxiao Zhang

The paper introduces DeepTrack, a lineage tracing model that combines cellular barcoding with single-cell multi-omics to study cell fate transitions and molecular changes during mammalian development.

The paper shows PAX6 expression occurs post-replicatively during neuroectoderm differentiation, coupling NPC fate to cell cycle progression after DNA replication.

The paper maps chromatin interactions in mouse fetal tissues and links them to gene expression and disease risk variants in humans.

The paper shows that E75/NR1D2 integrates Hippo and Notch pathways to drive tumor malignancy in response to hormone inhibition.

SnapHiC-D identifies differential chromatin contacts between two scHi-C datasets with high sensitivity and accuracy, showing correlation with cell-type-specific gene expression and epigenomic features.

This study shows that budding yeast adapts to long-term high temperature by reducing temperature-sensitive proteins, relocalizing the proteome, and altering protein conformations, which may confer new functions.

The paper defines cardiac cell type-specific cis-regulatory elements and links disease risk variants to these elements in human hearts.

This study shows that deleting TAD boundaries in mice often causes molecular or developmental phenotypes, highlighting their importance for genome function.

SnapATAC is a software package for analyzing scATAC-seq data, revealing regulatory elements and transcriptional regulators in mouse brain cells.

SnapHiC identifies high-resolution chromatin loops from scHi-C data and demonstrates cell-type-specific chromatin architecture in mouse and human cells.

The paper systematically maps chromatin state landscapes during mouse development by profiling histone modifications across 72 tissue-stages, identifying dynamic enhancers and transcriptional regulators.

This study investigates how CTCF binding sites mediate transcriptional insulation in mouse embryonic stem cells, showing that insulation depends on CTCF site number, sequence context, and TAD boundary location.

This study identifies one known and two novel genetic variants associated with heart failure through GWAS and multi-omic analyses, revealing potential causal mechanisms and shared heritability with musculoskeletal traits.

The paper investigates chromatin architecture changes during human cardiomyocyte differentiation and identifies HERV-H retrotransposons as key regulators of TAD boundaries and gene regulation.

MAPS processes PLAC-seq and HiChIP data to identify long-range chromatin interactions by removing biases and analyzing contact frequencies.

The paper introduces Methyl-HiC, a method that simultaneously profiles DNA methylation and chromatin architecture, revealing coordinated methylation and dynamic chromatin contacts in mouse embryonic stem cells.

The paper uses single nucleus ATAC-seq to analyze chromatin accessibility in mouse forebrain development, identifying cell-type-specific regulatory sequences and transcriptional regulators.