Zhenjia Wang

BART-spatial identifies transcriptional regulators from spatial omics data by integrating spatial and pseudotemporal information with TR binding profiles, outperforming existing methods.

This study identifies CEBPD as a tumor suppressor gene in acute myeloid leukemia through functional experiments and genomic analyses.

BARTsc identifies key transcriptional regulators from single-cell omics data by integrating ChIP-seq profiles and outperforms existing methods in multiple biological systems.

This study investigates the role of ORC2 in epigenetic regulation and chromosome structure through a multi-omics analysis of a human cell line with ORC mutations.

DARDN uses deep learning to classify cancer-specific CTCF binding sites and identify oncogenic transcription factors in multiple cancer types.

The paper analyzes DNA replication origins and ORC/MCM binding sites in human cells, finding minimal overlap and suggesting origins are specified by stochastic events rather than specific binding sites.

The paper identifies spatially clustered transcription factor binding patterns at super-enhancers and links them to phase-separated transcriptional condensates.

The paper identifies Fob1-dependent condensin recruitment and loop extrusion at the RDT1 locus on yeast chromosome III, linking it to MATa-specific organization during mating-type switching.

BART3D identifies transcriptional regulators linked to differential chromatin interactions using Hi-C data and ChIP-seq, showing effectiveness in detecting TRs during cellular differentiation or perturbation.

The paper identifies cancer-specific CTCF binding patterns across six cancer types and shows they are linked to oncogenic transcriptional changes without always involving DNA methylation or mutations.

BARTweb identifies transcription factors associated with genomic features using public ChIP-seq data, outperforming existing tools and reducing computation time.

This study identifies persistent transcriptional and epigenetic changes in human lung epithelial cells after nickel exposure, revealing mechanisms behind long-term health effects.

The paper shows that polyadenylation of H3.1 mRNA displaces H3.3 from gene regulatory elements, leading to cell transformation and genomic instability.

BART predicts functional transcription factors regulating a gene set or associated with a genomic profile using existing ChIP-seq data.