PRIME models physicochemical selection in protein evolution by incorporating biophysical properties, improving model fit and revealing adaptive tuning mechanisms in protein structures.

bioRxiv · Mar 11, 2026 · PreprintEvolutionary Biology

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

Jennifer McDaniel, Vaidehi Patel, Nathan D. Olson, Hua‐Jun He, Zhiyong He, Kenneth D. Cole, Alexander A Gooden, Anthony D. Schmitt, Kristin L Sikkink, Fritz Joachim Sedlazeck, HarshaVardhan Doddapaneni, Shalini N. Jhangiani, Donna Marie Muzny, Marie‐Claude Gingras, Heer Hemant Mehta, , Justin M. Zook

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

Scientific Data · Jul 16, 2025Peer-reviewedGenomics

Somatic small-variant calling methods in Illumina DRAGEN™ Secondary Analysis

Konrad Scheffler, Severine Catreux, Taylor O’Connell, Heejoon Jo, Varun Jain, Theo Heyns, Jeffrey Yuan, Lisa Murray, James Han, Rami Mehio

The paper introduces DRAGEN's somatic variant calling pipeline, demonstrating its speed and accuracy in whole-genome sequencing tumor-normal analysis compared to existing tools.

bioRxiv · Mar 23, 2023 · PreprintBioinformatics

REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats

Egor Dolzhenko, Ben Weisburd, Kristina Ibáñez, Indhu‐Shree Rajan‐Babu, Christine Anyansi, Mark F. Bennett, Kimberley J. Billingsley, Ashley Carroll, Samuel E. Clamons, Matt Christopher Danzi, Viraj Deshpande, Jinhui Ding, Sarah Fazal, Andreas Halman, Bharati Jadhav, , Michael A. Eberle

REViewer visualizes sequencing data around long repeat expansions by reconstructing haplotypes and aligning reads, improving the assessment of repeat genotype calls and detecting interruptions.

Genome Medicine · Aug 10, 2022Peer-reviewedBioinformatics

ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions

Egor Dolzhenko, Viraj Deshpande, Felix J. Schlesinger, Peter Krusche, Roman Petrovski, Sai Chen, Dorothea Emig-Agius, Andrew M. Gross, Giuseppe Narzisi, Brett N. Bowman, Konrad Scheffler, Joke J.F.A. van Vugt, Courtney E. French, Alba Sanchis‐Juan, Kristina Ibáñez, , Michael A. Eberle

ExpansionHunter is a tool for accurately genotyping short tandem repeats, particularly in complex regions with adjacent variants or imperfect repeats.

Bioinformatics · May 23, 2019Peer-reviewedBioinformatics

Strelka2: Fast and accurate variant calling for clinical sequencing applications

Sangtae Kim, Konrad Scheffler, Aaron L. Halpern, Mitchell A. Bekritsky, Eunho Noh, Morten Källberg, Xiaoyu Chen, Yeonbin Kim, Doruk Beyter, Peter Krusche, Christopher T. Saunders

Strelka2 is a variant calling tool that improves accuracy and reduces compute cost for germline and somatic variant detection in clinical sequencing.

Nature Methods · Jul 11, 2018Peer-reviewedBioinformatics