The paper identifies and characterizes human protein-coding duplicated genes using long-read genomic and transcriptomic data, revealing new gene models and constraint patterns.

bioRxiv · Aug 6, 2026 · PreprintGenomics

Genetic diversity and regulatory features of human-specific NOTCH2NL duplications

Taylor D. Real, Prajna Hebbar, DongAhn Yoo, Francesca Antonacci, Ivana Pačar, Danilo Dubocanin, Mark Diekhans, Gregory J Mikol, Oyeronke G. Popoola, Benjamin J. Mallory, Mitchell Robert Vollger, Philip C. Dishuck, Xavi Guitart, Allison N. Rozanski, Katherine M. Munson, , Evan E. Eichler

The paper characterizes the genetic diversity and regulatory features of human-specific NOTCH2NL duplications using long-read sequencing and organoid models.

Cell Genomics · Mar 30, 2026Peer-reviewedGenomics

NPEPPS segmental duplication drives position effect expression of TBC1D3 in the human brain

Xavi Guitart, Jessie Brunner, Luyao Ren, Hyeonsoo Jeong, DongAhn Yoo, David Porubskỳ, Kendra Hoekzema, Katherine M. Munson, Kaitlyn A. Sun, Marcelo Ayllon, Kaylynn Hoglin, Reed McMullen, Bryan J. Pavlovic, Mitchell Robert Vollger, Alex A. Pollen, Evan E. Eichler

The paper identifies a segmental duplication that drives position effect expression of TBC1D3 in the human brain, explaining its high structural heterozygosity.

bioRxiv · Jan 15, 2026 · PreprintGenomics

SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies

David Porubskỳ, Xavi Guitart, DongAhn Yoo, Philip C. Dishuck, William T. Harvey, Evan E. Eichler

SVbyEye is an open-source R package that visualizes and annotates structural variation between genome assemblies using PAF alignments.

Bioinformatics · Jun 1, 2025Peer-reviewedBioinformatics

Independent expansion, selection and hypervariability of the TBC1D3 gene family in humans

Xavi Guitart, David Porubskỳ, DongAhn Yoo, Max L. Dougherty, Philip C. Dishuck, Katherine M. Munson, Alexandra P. Lewis, Kendra Hoekzema, Jordan Knuth, Stephen Chang, Tomi Pastinen, Evan E. Eichler

The paper investigates the expansion, selection, and hypervariability of the TBC1D3 gene family in humans using long-read sequencing data, revealing multiple duplications, copy number variation, and expression patterns.

Genome Research · Nov 1, 2024Peer-reviewedGenetics

Increased mutation rate and interlocus gene conversion within human segmental duplications.

Mitchell Robert Vollger, William S. DeWitt, Philip C. Dishuck, William T. Harvey, Xavi Guitart, Michael E. Goldberg, Allison N. Rozanski, Julian Lucas, Mobin Asri, Katherine M. Munson, Alexandra P. Lewis, Kendra Hoekzema, Glennis A. Logsdon, David Porubskỳ, Benedict Paten, , Evan E. Eichler

The paper assesses SNVs within human segmental duplications, finding increased mutation rates and interlocus gene conversion, along with distinct mutational spectra.

bioRxiv · Jul 6, 2022 · PreprintGenomics

Epigenetic Patterns in a Complete Human Genome

Ariel Gershman, Michael E.G. Sauria, Xavi Guitart, Mitchell Robert Vollger, Paul W. Hook, Savannah J. Hoyt, Miten Jain, Alaina Shumate, Roham Razaghi, Sergey Koren, Nicolas Altemose, Gina Viviana Caldas, Glennis A. Logsdon, Arang Rhie, Evan E. Eichler, , Winston Timp

The paper uses a complete human genome assembly to analyze epigenetic patterns in previously uncharacterized genomic regions, revealing methylation and chromatin accessibility features in satellite DNA and centromeres.

Science · Mar 31, 2022Peer-reviewedGenomics

Segmental duplications and their variation in a complete human genome

Mitchell Robert Vollger, Xavi Guitart, Philip C. Dishuck, Ludovica Mercuri, William T. Harvey, Ariel Gershman, Mark Diekhans, Arvis Sulovari, Katherine M. Munson, Alexandra P. Lewis, Kendra Hoekzema, David Porubskỳ, Ruiyang Li, Sergey Nurk, Sergey Koren, , Evan E. Eichler

The paper presents a comprehensive analysis of segmental duplications in a complete human genome, revealing their distribution, variation, and evolutionary significance.

Science · Mar 31, 2022Peer-reviewedGenomics