G. G. Wu

BiNVaST: niche boundary-preserving and synthetic data-guided variational autoencoders for concordant inference across high-resolution spatial transcriptomic platforms

BiNVaST improves cell typing across spatial transcriptomic platforms by generating synthetic data that preserves niche boundaries and integrates molecular and spatial information.

Alternative organelle targeting of OPA1 mediates fatty acid release from lipid droplets

This study identifies OPA1's role in fatty acid release from lipid droplets and links its function to human metabolism.

Chemokine-Dependent Natural Killer Cells Prevent Pulmonary Metastasis in a Newly Established Mouse Osteosarcoma Model

This study identifies CCL2 as a chemokine that limits osteosarcoma metastasis via NK cell signaling in a mouse model.

Bridging Genomics and Clinical Medicine: RSVrecon Enhances RSV Surveillance with Automated Genotyping and Clinically-important Mutation Reporting

RSVrecon is a bioinformatics pipeline that enhances RSV surveillance by automating genotyping and reporting clinically important mutations, providing user-friendly results for clinical researchers.

TIRTL-seq: Deep, quantitative, and affordable paired TCR repertoire sequencing

TIRTL-seq provides a scalable, cost-effective method for paired TCR repertoire sequencing, enabling accurate identification of TCR chain pairings and clonotype dynamics in large cohorts.

Germline variation in DNA damage repair genes in children with cancer: Unveiling SMARCAL1 as novel osteosarcoma predisposition gene

The paper identifies SMARCAL1 as a novel predisposition gene for osteosarcoma by analyzing germline variants in DNA damage repair genes across childhood cancer cases.

MitoEdit: a pipeline for optimizing mtDNA base editing and predicting bystander effects

MitoEdit predicts optimal mtDNA base editing targets and bystander effects to reduce empirical testing.

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.

Preclinical Pediatric Molecular Analysis for Therapy Choice (MATCH)

This paper establishes a diverse collection of preclinical models for pediatric solid tumors and demonstrates their utility in precision medicine trials and drug testing.

scDeepC3: scRNA-seq Deep Clustering by A Skip AutoEncoder Network with Clustering Consistency

scDeepC3 improves scRNA-seq clustering by using a skip AutoEncoder with clustering consistency loss and adaptive shortcut connections, achieving better performance than existing methods.

CoCoRV: a rare variant analysis framework using publicly available genotype summary counts to prioritize germline disease-predisposition genes

CoCoRV prioritizes germline disease-predisposition genes by using public genotype summary counts as controls, effectively identifying cancer-predisposition genes in pediatric cancer cohorts.

CovidExpress: an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes

CovidExpress provides an open-access database and tool for exploring SARS-CoV-2 related gene expression data across tissues and conditions, identifying common regulated genes and a potential FURIN feedback loop.

Enrichment of rare protein truncating variants in amyotrophic lateral sclerosis patients

The paper identifies an enrichment of rare protein-truncating variants in ALS patients, highlighting novel genes like DNAJC7 and known ALS genes such as SOD1, NEK1, and FUS.