Kyle Ellrott

The GA4GH Workflow Execution Service: A Standard API for Workflow Execution and Management in Genomics

The paper introduces the GA4GH Workflow Execution Service API, which standardizes workflow execution across different compute environments and demonstrates its cross-site functionality.

FHIR as a Unifying Format for Genomic Research Data Tracking, Aggregation, and Integration

The paper explores using FHIR to integrate genomic research data from multiple repositories and evaluates its effectiveness for structured data representation and aggregation.

Robust software development practices improve citations of RNA-seq tools

This study shows that better software development practices for RNA-seq tools lead to more citations, as evidenced by a strong statistical association between development quality and citation counts.

Aggregating multimodal cancer data across unaligned embedding spaces maintains tumor of origin signal

This study aggregates multimodal cancer data across unaligned embedding spaces and finds that tumor of origin signal is preserved for learning tasks.

recountmethylation enables flexible analysis ofpublic blood DNA methylation array data

recountmethylation provides processed blood DNA methylation data and analysis tools, showing genetic ancestry and cell fractions explain most DNAm variation and validating DMPs between sexes.

Crowd-sourced benchmarking of single-sample tumour subclonal reconstruction

The paper benchmarks 31 subclonal reconstruction algorithms on simulated tumours, finding that algorithm choice significantly impacts performance and no single algorithm excels across all tasks.

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

The paper describes AnVIL, a cloud-based platform that enables genomic data analysis without data transfer, improving security, scalability, and collaboration.

A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants

The paper harmonizes clinical interpretations of cancer genomic variants across six knowledgebases, improving overlap and matching with patient cohorts.

Creating Standards for Evaluating Tumour Subclonal Reconstruction

This study develops quantitative metrics and simulated datasets to evaluate subclonal reconstruction methods in tumours.

neoepiscope Improves Neoepitope Prediction with Multi-variant Phasing

neoepiscope improves neoepitope prediction by incorporating germline context and somatic variant phasing, addressing limitations in existing tools.

Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic structural variant detection

The paper benchmarks somatic structural variant detection methods using synthetic tumors and crowd-sourced submissions, finding that ensembles do not always outperform individual methods.

Valection: Design Optimization for Validation and Verification Studies

Valection optimizes the selection of verification candidates to estimate error profiles in genomics studies by evaluating different strategies on synthetic data.

Germline Contamination and Leakage in Whole Genome Somatic Single Nucleotide Variant Detection

The paper quantifies germline leakage in somatic SNV detection across 259 datasets and introduces a tool to correct it, finding low leakage rates that can be further reduced with pre-filtering.

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.