Jinghui Zhang

The landscape of structural variation in pediatric cancer

This study analyzes structural variants in 1,616 pediatric cancer genomes, revealing unique SV hotspots and patterns distinct from adult cancers.

Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples

The paper shows that mutant allele enrichment in bulk tumor RNA can be confounded by tumor purity and NMD, and demonstrates RNA-Seq can improve driver indel detection.

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.

PepSeek: Universal Functional Peptide Discovery with Cooperation Between Specialized Deep Learning Models and Large Language Model

PepSeek identifies functional peptides using a combination of large language models and specialized models, achieving high accuracy in antimicrobial peptide discovery.

Somatic mitochondrial DNA mutations are a source of heterogeneity among primary leukemic cells

The paper identifies differences in mtDNA mutation accumulation and selective pressures in pediatric leukemias using bulk and single-cell sequencing, linking these to functional heterogeneity among leukemic cells.

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

SigProfilerExtractor is a tool for de novo mutational signature extraction that outperforms existing methods and identifies four novel signatures, including one linked to tobacco smoking.

Evolution of the open-access CIViC knowledgebase is driven by the needsof the cancer variant interpretation community

The paper describes the evolution of the CIViC knowledgebase to meet the needs of the cancer variant interpretation community by expanding its functionality and data types.

Persistent Variations of Blood DNA Methylation Associated with Treatment Exposures and Risk for Cardiometabolic Outcomes among Long-term Survivors of Childhood Cancer: A Report from the St. Jude Lifetime Cohort

This study identifies DNA methylation sites associated with cancer treatments and mediates cardiometabolic risks in childhood cancer survivors.

Generalizability of "GWAS hits" in clinical populations: Lessons from childhood cancer survivors

The paper evaluates the generalizability of GWAS findings in childhood cancer survivors and finds limited replication of meta-GWAS hits in these populations.

XenoCP: Cloud-based BAM cleansing tool for RNA and DNA from Xenograft

XenoCP is a cloud-based tool that removes mouse reads from xenograft BAM files to improve RNA-seq and WGS analysis accuracy.

RNAIndel: a machine-learning framework for discovery of somatic coding indels using tumor RNA-Seq data

RNAIndel identifies somatic coding indels in tumor RNA-Seq data with high sensitivity and low false positives, outperforming existing methods.

Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): A Cloud-based Platform for Curating and Classifying Germline Variants

PeCanPIE is a cloud-based platform for annotating and classifying germline variants in pediatric cancer, using ACMG guidelines to rank and classify variants from VCF files.

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.