Ben Busby

The paper describes a project from the 4D Nucleome Hackathon aimed at developing a workflow for comparing and validating chromatin models, identifying challenges in model comparison and software development.

The paper introduces genomic stratifications for human reference genomes GRCh37, GRCh38, and T2T-CHM13v2.0 to benchmark variant caller performance in difficult regions.

This paper reassesses Hardy-Weinberg equilibrium (HWE) filtering in large genomic studies, showing that current p-value thresholds are too strict for large samples and proposing alternative post-hoc filtering strategies.

This study determines individualized tryptase reference ranges by modeling BST levels based on TPSAB1 copy number, showing that elevated levels can indicate clonal myeloid neoplasms or be normal in HT carriers.

The paper describes the evolution of iCn3D from a web-based 3D viewer to a batch-mode structural analysis tool with Node.js scripts for large-scale structural dataset analysis.

OpenCRAVAT provides an open-source platform for variant and gene prioritization by integrating diverse data resources and computational methods.

Magic-BLAST is an RNA-seq aligner that excels in intron discovery and mapping long reads across multiple platforms.

GeneHummus is an R-based pipeline for automated gene family identification and expression analysis in plants, reducing manual effort while maintaining accuracy.

The paper uses a consensus machine learning approach to identify gene targets associated with pediatric AML risk, finding recurrently selected genes like HOXA9 and MEIS1 across multiple algorithms.

PhenotypeXpression identifies disease subtypes by clustering gene expression data and analyzing literature to create phenotypic profiles.

The paper describes a hackathon where bioinformatician teams developed open-source genomic analysis pipelines for DNA-seq, epigenomics, metagenomics, and RNA-seq using publicly available or soon-to-be-submitted data.