Yang Zhang

SpiderNet identifies cell-cell communication programs from spatial transcriptomics data, revealing key interactions and their associations with phenotypes and therapeutic responses.

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

The paper introduces DNALO_SCPLOWONGC_SCPLOWBO_SCPLOWENCHC_SCPLOW, a benchmark suite for long-range DNA prediction tasks, and evaluates five methods on five genomics tasks.

The paper examines genome organization in human cells relative to nuclear locales, finding that gene expression and replication timing correlate with different nuclear structures and that LADs and iLADs compete for lamina attachment.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

The paper uses TSA-seq to map genomic regions near nucleoli and pericentric heterochromatin in human cell lines, revealing variable heterochromatin localization and complex nuclear organization.

Nucleome Browser integrates heterogeneous 4D Nucleome data into an interactive platform for visualization and exploration across biological contexts.

The paper introduces a machine learning method to predict DNA replication timing from sequence features and identifies genome-wide sequence elements that modulate replication timing.

The paper introduces SPIN, a method to identify genome-wide nuclear spatial localization patterns by integrating nuclear compartment mapping and chromatin interaction data.

MOCHI identifies heterogeneous interactome modules in the nucleus by clustering gene loci with frequent spatial contacts and shared transcription factor regulation across five cell types.

This paper introduces Phylo-HMRF, a probabilistic model to analyze 3D genome organization across species using Hi-C data, revealing evolutionary patterns in chromatin structure.

The paper introduces TSA-Seq, a method to measure chromosomal distances to nuclear structures and reveals a spatial gradient in genome activity correlated with nuclear compartments.

This paper introduces a probabilistic model to compare multi-species functional genomic data, showing it can identify genomic regions with distinct evolutionary patterns of DNA replication timing across primates.

This study identifies sequence-based features that predict CTCF-mediated chromatin loops using a machine learning model called CTCF-MP.