Katharine M. Jenike

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.

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

This study uses CRISPR to reposition centromeres in Arabidopsis, showing how neo-chromosomes with altered centromere positions lead to meiotic segregation distortion and aneuploidy.

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

Uncalled4 improves nanopore signal alignment for DNA and RNA modification detection, identifying more modifications than existing tools in human cell lines.

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.

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 introduces MEMO, a pangenome indexing method that efficiently handles k-mer queries and conservation analysis across pangenomes.

The paper presents the genome of the Wollemi pine, revealing ancient transposon activity and insights into its conservation and evolutionary history.

The paper optimizes an expression microdissection method to improve miRNA yield and in vivo cell-type specificity for qPCR analysis.