Howard Y. Chang

This study identifies mitosis as a critical window for ecDNA hub organization in cancer cells and shows WEE1 regulates hub integrity and oncogene expression.

The paper shows ecDNA localizes to the nuclear periphery in cancer, resisting silencing and enhancing transcriptional output through interactions with the nuclear lamina.

This study shows that inflammation-induced changes in 3D genome conformation regulate immune signal integration and transcriptional memory in macrophages.

This study uses spatial transcriptomics and lineage tracing to show how tumor subclones drive microenvironmental changes that promote metastasis in a mouse model.

This study identifies the epigenetic signature and key transcription factors regulating human antigen-specific Tr1 cells, revealing their unique biology and potential for therapeutic applications.

This study uses somatic mutations to track marrow-derived cell infiltration into the human brain, finding widespread microglia replenishment and a protective link between clonal hematopoiesis and Alzheimer's disease.

Cycle-Extractor accurately reconstructs ecDNA structures from both short- and long-read sequencing data, outperforming existing methods in speed and completeness.

This study develops lipid nanoparticles (LNPs) for spleen-targeted RNA delivery without altering charge, showing improved splenic accumulation and distinct transcriptomic effects compared to conventional LNPs.

This study shows ecDNA copy number plasticity drives tumour evolution by generating functional heterogeneity and promoting drug resistance.

scAmp detects and analyzes ecDNA at single-cell resolution, showing its impact on chromatin accessibility in cancer cells.

This study designs cell type-specific AAV promoters using deep learning, outperforming rational approaches in mouse retinal cells and showing promise for human applications.

The paper introduces ec3D, a method to reconstruct 3D structures of ecDNA from Hi-C data, revealing spherical configurations and unique long-range interactions in cancer.

A genome-wide plasmid screen, Retain-seq, identifies thousands of CpG-rich promoter-like human elements that tether episomes to mitotic chromosomes, shape ecDNA structure, and lose function when methylated.

The paper identifies cis-regulatory elements and transcription factors controlling FOXP3 expression in human Tregs and Tconvs, revealing mechanisms that restrict FOXP3 to Tregs in mice.

The paper identifies enhancer-like elements on ecDNA in colorectal cancer that are derived from transposable elements and are functionally active in cancer cell fitness.

PLI-Analyzer evaluates AI-predicted biomolecular interfaces by analyzing atomic contacts and domain annotations, revealing discrepancies in predicted protein-protein complexes.

The paper identifies local translation of circular RNAs in the prefrontal cortex of mice, revealing a micropeptide involved in synaptic activity and memory.

This study investigates the spatial-temporal evolution of extrachromosomal DNA (ecDNA) in glioblastoma, showing that EGFR ecDNA drives tumor evolution and identifies a potential therapeutic window for early intervention.

The paper introduces interSeg, a deep learning tool that accurately predicts oncogene amplification status from interphase FISH images, achieving high accuracy in detecting ecDNA and chromosomal amplifications.

This study identifies induced B-cell receptor diversity as a predictor of PD-1 blockade immunotherapy response across multiple cancer types.

This study shows that ecDNA mis-segregation leads to micronuclei formation, reduced oncogene transcription, and improved patient survival in neuroblastoma.

The paper shows that ecDNA-borne PVT1 fusions stabilize oncogenic mRNAs by interacting with SRSF1, enhancing RNA stability and supporting MYC dependency in cancer.

The paper creates a single-cell multiome atlas of RPE and choroid tissues to identify pathogenic variants and mechanisms in AMD using HiChIP, Activity-by-Contact, and STARR-seq.

The paper introduces OM2BFB, an algorithm detecting BFB amplifications using OGMs, showing high precision and recall, and finds BFB events are common in certain cancers but not linked to intratumoral heterogeneity or rapid genome change.

The paper identifies autoantibody hotspots on the XIST RNP complex in female-biased autoimmune diseases and links them to clinical outcomes.

This paper identifies transcription-replication conflict as a vulnerability in ecDNA-containing cancers and demonstrates that CHK1 inhibition selectively kills these tumors.

This study identifies a STAG2-PAXIP1/PAGR1 tumor-suppressive axis in lung cancer by showing their combined role in suppressing oncogenic KRAS-driven tumorigenesis.

The paper investigates how 3D genome organization, specifically through Cohesin, influences gene co-expression in single cells and reveals its role in maintaining long-range chromatin interactions.

This study introduces CRISPRai, a bidirectional epigenetic editing system, to investigate gene regulation hierarchies and interactions in T cells and hematopoietic lineage transcription factors.

ProteinCLIP refines pre-trained protein language model embeddings using contrastive learning between amino acid sequences and functional text, achieving state-of-the-art results in protein tasks.