Xiang 'Anthony' Chen

Reactivation of a TAL1 progenitor cell enhancer region by non-coding somatic variants in T-lineage acute lymphoblastic leukemia

The paper identifies non-coding somatic variants in TAL1 regulatory regions that reactivate enhancers normally active in hematopoietic stem cells in T-lineage acute lymphoblastic leukemia.

CanID: a robust and accurate RNAseq Expression-based diagnostic classification scheme for pediatric malignancies

CanID is a machine learning classifier for pediatric cancer subtypes using RNAseq data, achieving 99% accuracy for solid tumors and 92-93% for hematologic malignancies.

RBM39 degrader invigorates natural killer cells to eradicate neuroblastoma despite cancer cell plasticity

This study shows that targeting RBM39 with indisulam promotes natural killer cell activity and eradicates neuroblastoma regardless of cellular state plasticity.

Seq2Karyotype (S2K): A Method for in-silico Karyotyping Using Single-Sample Whole-Genome Sequencing Data

Seq2Karyotype (S2K) enables in-silico karyotyping from whole-genome sequencing data, revealing intratumoral heterogeneity and evolutionary trajectories in cancer samples.

Directional growth of developing myelin mediated by Wnt gradient and required for proper axon functions

This study shows that directional myelin growth in zebrafish is driven by a Wnt4b gradient and is essential for proper axon function and behavior.

Latent Epigenetic Programs in Muller Glia Contribute to Stress, Injury, and Disease Response in the Retina

The paper identifies 'pliancy genes' in Muller glia that enable rapid response to retinal stress, injury, and disease, showing species-specific differences in their activation between zebrafish and mammals.

Rod-genesis driven by mafba in an nrl knockout zebrafish model with altered photoreceptor compositions and progressive retinal degeneration

This study identifies mafba as a regulator of nrl-independent rod genesis in zebrafish and reveals a bipotent rod/green-cone precursor cell fate decision controlled by nrl.

Accurate Genomic Variant Detection in Single Cells with Primary Template-Directed Amplification

This paper introduces PTA, a new WGA method that improves variant calling accuracy in single cells, enabling studies of genetic diversity and CRISPR off-target effects.

MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors

MethylationToActivity infers promoter activity from DNA methylation data in tumors, showing high accuracy across multiple cancer types.

LCA robustly reveals subtle diversity in large-scale single-cell RNA-seq data

LCA identifies subtle cell population diversity in large-scale single-cell RNA-seq data using a dual-space model with spectral clustering and technical variation control.

The Nucleome of Developing Murine Rod Photoreceptors

The paper studies the chromatin structure of rod photoreceptors in mice using Hi-C and machine learning to identify regulatory elements involved in retinal development.

Contribution Of Genetic Variation And Developmental Stage To Methylome Dynamics In Myeloid Differentiation

The paper identifies differentially methylated regions in myeloid differentiation, showing genetic and developmental influences on methylome dynamics.

VCF2CNA: A tool for efficiently detecting copy-number alteration in VCF genotype data

VCF2CNA detects copy-number alterations from VCF data with high accuracy and platform independence, outperforming existing methods in neuroblastoma samples.