Melanie Pham

The control of prickle formation in Rubus

This study identifies WOX1 mutations as the genetic basis of the prickleless S locus in blackberry and red raspberry, enabling gene editing to create prickleless cultivars.

Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when adjacent sequences do not

The paper uses ultra-deep Hi-C and a new computational method to fine-map nuclear compartments, revealing that active promoters and enhancers localize in the A compartment even when adjacent sequences are inactive.

A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. Hillquist)

The paper presents a chromosome-length genome assembly and annotation of the blackberry species Rubus argutus, identifying candidate genes for primocane-fruiting.

Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum

The paper uses Hi-C data to improve the genome assembly of Trifolium subterraneum, resulting in chromosome-length scaffolds covering 95% of the genome.

The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000

Point-and-click correction of misassemblies on Hi-C heatmaps, paired with the automated 3D-DNA pipeline, gave chromosome-length wombat, opossum and raccoon scaffolds from just short-insert DNA-Seq and in situ Hi-C reads.