Daniel S. Rokhsar

The paper examines cellular changes during metamorphosis in hemichordates using single-cell RNA sequencing, revealing distinct transcriptional programs between larval and adult stages.

This study examines antero-posterior patterning in brittle stars to understand axial homologies in echinoderms and their evolution.

This study analyzes the hagfish genome to understand vertebrate evolution, identifying ancient genome duplications and their functional roles in vertebrate innovations.

The paper presents high-quality genomes and chromatin structure analyses of frogs, revealing conserved ancestral chromosomes and stable genome evolution.

The paper develops HiDENSEC to analyze Hi-C data in heterogeneous cancer samples, identifying chromosomal rearrangements and their impact on melanoma progression.

The paper investigates molecular patterning in sea stars to determine if their body plan retains similarities with deuterostomes, finding no ectodermal territory expressing bilaterian trunk genetic programs.

This paper presents a chromosome-scale genome assembly and genetic map for greater yam, identifies quantitative trait loci for disease and quality traits, and reveals domestication-related genetic patterns.

BELLA improves long-read sequencing overlap detection and assembly by balancing precision and recall, achieving high F1 scores on real and synthetic data.

This paper resolves the controversy over the ancestry of cultivated octoploid strawberry by analyzing the chromosomal distribution of transposable elements in its genome.

The paper analyzes chromosome evolution and architecture in muntjac deer by comparing genome assemblies and identifying fusion events across species.

The paper shows adaptation to copper-contaminated environments in Mimulus guttatus occurs through selection on pre-existing genetic variation rather than new mutations.