Zachary B. Lippman

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

Conservatory, an orthogroup-centric conserved noncoding sequence finder, catalogs 2.3 million unique CNSs across 314 plant genomes and reveals regulatory elements older than angiosperms and seed plants.

The paper shows a neofunctionalized gene in Solanaceae plants became a flowering antagonist, influencing adaptation across species and environments.

This paper uses CRISPR/Cas9 to engineer compact Physalis peruviana plants to improve yield and scalability for agricultural production.

The paper analyzes the CLE signaling peptide family across 2,000 angiosperm genomes to uncover evolutionary patterns and predict paralog diversification, revealing functional redundancies and regulatory mechanisms.

The paper identifies cryptic genetic variants in tomato that drive phenotypic change through hierarchical epistasis in a gene regulatory network.

The paper investigates how plant tissue culture parameters affect polyploidy in three Solanaceae species, finding that explant type and species influence polyploidy rates, but zeatin concentration has species-specific effects.

The paper identifies conserved cis-regulatory elements of the UFO gene in tomato and Arabidopsis, showing their role in maintaining developmental robustness through precise temporal control of gene expression.

The paper uses pan-genomics and genome editing in Solanum to show that paralog diversification hinders genotype-phenotype predictability in crop domestication.

The paper investigates convergent evolution of plant prickles, finding that mutations in a cytokinin gene repeatedly cause prickle loss across species.

The paper investigates cis-regulatory divergence in the CLV3 gene across Arabidopsis and tomato, revealing distinct regulatory strategies and lineage-specific functional redundancy.

SVCollector selects an optimal subset of individuals for long-read sequencing to maximize genetic diversity representation across subpopulations.

RaGOO rapidly and accurately scaffolds draft genomes using a reference genome, achieving chromosome-scale assemblies and identifying structural variants in tomato and Arabidopsis thaliana.

SVCollector selects optimal samples for validating and long-read resequencing of structural variants to maximize discovery and validation accuracy.