The paper develops Paraphase, a HiFi-based method to resolve highly similar paralogous genes, revealing genetic diversity and de novo events in segmental duplications.

Nature Communications · Mar 8, 2025Peer-reviewedGenomics

CNA Explorer and anaLyzer (CNAEL): an interactive web application and standard operating procedure enabling efficient clinical review and reporting of complex NGS-derived tumor copy number profiles

Ellen Chen, Jinlian Wang, Robert Kueffner, Hussam Al‐Kateb, Antonina Silkov, Andrew V. Uzilov, Lucas Lochovsky, Hui Li, Scott Newman

CNAEL is a web application and protocol that streamlines clinical analysis and reporting of NGS-derived tumor copy number profiles, reducing curation time significantly.

medRxiv · Oct 24, 2022 · PreprintGenetic & Genomic Medicine

RNAIndel: a machine-learning framework for discovery of somatic coding indels using tumor RNA-Seq data

Kohei Hagiwara, Liang Ding, Michael N. Edmonson, Stephen V. Rice, Scott Newman, John B. Easton, Juncheng Dai, Soheil Meshinchi, Rhonda E. Ries, Michael Rusch, Jinghui Zhang

RNAIndel identifies somatic coding indels in tumor RNA-Seq data with high sensitivity and low false positives, outperforming existing methods.

Bioinformatics · Oct 1, 2019Peer-reviewedBioinformatics

Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): A Cloud-based Platform for Curating and Classifying Germline Variants

Michael N. Edmonson, Aman Patel, Dale J. Hedges, Zhaoming Wang, Evadnie Rampersaud, Chimene A. Kesserwan, Xin Zhou, Yanling Liu, Scott Newman, Michael Rusch, Clay McLeod, Mark R. Wilkinson, Stephen V. Rice, Thierry Soussi, J. Paul Taylor, , Jinghui Zhang

PeCanPIE is a cloud-based platform for annotating and classifying germline variants in pediatric cancer, using ACMG guidelines to rank and classify variants from VCF files.

Genome Research · Sep 1, 2019Peer-reviewedBioinformatics