Daniel P. Miller

Machine learning-predicted chromatin organization landscape across pediatric tumors

The paper uses a convolutional neural network to predict chromatin organization disruptions caused by somatic structural variants in pediatric tumors, identifying high-impact SVs and regions associated with cancer.

Alternative splicing in pediatric central nervous system tumors highlights oncofetal candidate CLK1 exon 4

The paper analyzes splicing in 729 pediatric brain tumors, identifies splicing-defined subgroups, and highlights CLK1 exon 4 as an oncofetal event linked to tumor prognosis.

The Open Pediatric Cancer Project

The paper introduces OpenPedCan, a harmonized multi-omic dataset of pediatric cancer patients, providing integrated genomic, transcriptomic, and proteomic data for research and clinical applications.

AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification

AutoGVP classifies germline variants using ClinVar and modified InterVar criteria, enabling large-scale variant pathogenicity assessment in research.

OpenPBTA: An Open Pediatric Brain Tumor Atlas

OpenPBTA provides a collaborative platform to genomically characterize 1,074 pediatric brain tumors and 22 cell lines, offering analysis modules and somatic datasets for research and clinical applications.

Uniform Genomic Data Analysis in the NCI Genomic Data Commons

The paper describes the pipelines and workflows used to process and harmonize genomic data in the NCI Genomic Data Commons, including data types like somatic mutations and gene expression.