Noah Spies

The paper introduces Caris-ComBat-seq, a method to harmonize RNA-seq data by directionally adjusting batches, separating training and adjustment steps, and handling outliers, validated on large tumor datasets.

The paper introduces SVCurator, a crowdsourcing app for evaluating structural variants in the human genome, finding high concordance among curators and with existing benchmarks.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

The paper provides a comprehensive whole-genome analysis of K562, identifying genomic structural features and their impact on functional genomics data.

This paper provides a haplotype-resolved genome analysis of the HepG2 cell line, identifying genomic features and allele-specific regulation to support functional genomics studies.

The paper introduces genomeview, a Python-based genomics visualization engine designed for extensibility and integration into analysis pipelines.

This paper introduces GROC-SVs, a method for detecting and assembling structural variants using read cloud data, showing improved specificity and enabling complex breakpoint reconstruction in cancer samples.

svclassify classifies structural variants as true or false positives using multi-technology annotations, achieving high concordance with PCR validation and MetaSV.

The paper presents extensive sequencing data from seven human genomes to serve as benchmark reference materials for improving sequencing technologies and variant calling.

svviz validates structural variants by visualizing relevant reads aligned to candidate SV alleles, enabling evidence assessment and breakpoint refinement.