Publications
Note
Solanum pan-genetics reveals paralogues as contingencies in crop engineering
2025Nature
View Publication →Establishing Physalis as a new Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome
2023The Plant Cell
View Publication →The complete sequence of a human genome
2022Science
As a member of the Telomere-to-Telomere Consortium, I helped polish the initial CHM13 draft assembly to correct small and structural misassemblies. For example, I finished the telomere on the p-arm of chromosome 18.
View Publication →Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies (first author)
2022Nature Methods
A companion paper to the CHM13 assembly paper, my colleagues and I describe our methods for polishing the initial draft assembly.
View Publication →Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing (first author)
2022Genome Biology
I introduced RagTag, a general-purpose genome assembly scaffolding and improvement tool.
View Publication →The genetic and epigenetic landscape of the Arabidopsis centromeres (first author)
2021Science
I led the assembly of all five Columbia Arabidopsis thaliana centromeres—the first time this had ever been accomplished for a plant species, to our knowledge.
View Publication →Pan-genomics and the structural diversity of plant genomes (first author)
2021Ph.D. Dissertation, Johns Hopkins University
View Publication →Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato (first author)
2020Cell
I led an effort to catalog and characterize structural variation in 100 tomato varieties using Oxford Nanopore sequencing. I led an analysis that found that breeding introgressions from wild material substantially altered the genome structure of modern varieties.
View Publication →Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies (first author)
2020Genetics
View Publication →Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato
2019Nature Plants
View Publication →Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
2019Nature Biotechnology
I helped benchmark the accuracy of structural variant calls generated from PacBio HiFi sequencing.
View Publication →The bracteatus pineapple genome and domestication of clonally propagated crops
2019Nature Genetics
View Publication →RaGOO: fast and accurate reference-guided scaffolding of draft genomes (first author)
2019Genome Biology
View Publication →The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)
2018GigaScience
View Publication →Total publications: 16