Matthew D. Clark

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SUMMARY Illumina's recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assemblies and other downstream bioinformatics analyses such as the characterization of structural variants. However, LMP libraries are intrinsically noisy and to(More)
We present here the results of forward and reverse genetic screens for chemically-induced mutations in Xenopus tropicalis. In our forward genetic screen, we have uncovered 77 candidate phenotypes in diverse organogenesis and differentiation processes. Using a gynogenetic screen design, which minimizes time and husbandry space expenditures, we find that if a(More)
MOTIVATION The Oxford Nanopore MinION sequencer, currently in pre-release testing through the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA/Q from the MinION base calling output and to provide basic yield statistics. However, no single tool yet exists to(More)
The apple cultivar Honeycrisp is emerging in North American markets due to its outstanding eating quality. A set of three ‘Honeycrisp’ progeny populations from the University of Minnesota apple breeding program were utilized to construct parental and consensus ‘Honeycrisp’ linkage maps to enable marker-assisted breeding. Two populations were segregated for(More)
  • Jonathan Fresnedo-Ramírez, Qi Sun, Chin-Feng Hwang, Craig A. Ledbetter, David W. Ramming, Anne Y. Fennell +7 others
  • 2016
Plants have an intriguing tripartite genetic system: Nuclear genome × Mitochondria × Plastids and their interactions may impact germplasm breeding. In grapevine, the study of cytoplasmic genomes has been limited, and their role with respect to grapevine germplasm diversity has yet to be elucidated. In the present study, the results of an analysis of the(More)
The RAB5 gene family is the best characterised of all human RAB families and is essential for in vitro homotypic fusion of early endosomes. In recent years, the disruption or activation of Rab5 family proteins has been used as a tool to understand growth factor signal transduction in whole animal systems such as Drosophila melanogaster and zebrafish. In(More)
The apple cultivar Honeycrisp exhibits genetic resistance to apple scab. The characterization of the macroscopic and microscopic responses on leaves infected by the pathogen Venturia inaequalis is described. The macroscopic resistance reactions observed in ‘Honeycrisp’, its parent ‘Keepsake’, and grandparents ‘Frostbite’ and ‘Northern Spy’ ranged from 0 (no(More)
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