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Articles by Carson Holt
The Utah NeoSeq Project: a collaborative multidisciplinary program to facilitate genomic diagnostics in the neonatal intensive care unit - npj Genomic Medicine
Abstract Rapid genomic diagnostics in the Neonatal Intensive Care Unit represents a paradigm shift in medicine with increasing evidence of the utility of early diagnosis, impacting management. The goal of the Utah NeoSeq Project was to implement and evaluate a multidisciplinary and longitudinal rapid sequencing program while transitioning to CLIA-certified sequencing. Enrollment of 65 infants resulted in 26 (40%) with a diagnostic variant(s) and 7 (11%) harboring a strong candidate.
Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F1 hybrid
Abstract Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for colubids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for two columbid species, Columba livia and C. guinea. We simultaneously assembled C. livia and C.
A ROR2 coding variant is associated with craniofacial variation in domestic pigeons
Highlights • Beak size and shape are highly variable among breeds of domestic pigeon • A Z chromosome locus is associated with beak length in a pigeon F2 intercross • Diverse short-beaked breeds have the same derived haplotype at this locus • A coding variant in ROR2 is a putative regulator of beak length in domestic pigeons Summary Vertebrate craniofacial morphogenesis is a highly orchestrated process that is directed by evolutionarily conserved developmental pathways., Within species,...
Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution
When published, this article did not initially appear open access. This error has been corrected, and the open access status of the paper is noted in all versions of the paper. Additionally, affiliation 16 denoting equal contribution was missing from author Robb Krumlauf in the PDF originally published. This error has also been corrected.
Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution
In the version of this article initially published, the present addresses for authors Dorit Hockman and Chris Amemiya were switched. The error has been corrected in the HTML and PDF versions of the article.
The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution
Sower, S. A. et al. Emergence of an ancestral glycoprotein hormone in the pituitary of the sea lamprey, a basal vertebrate. Endocrinology 156, 3026–3037 (2015). Ye, C., Hill, C. M., Wu, S., Ruan, J. & Ma, Z. S. DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies. Sci. Rep. 6, 31900 (2016). Mehta, T. K. et al. Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). Proc. Natl. Acad. Sci. USA 110, 16044–16049 (2013).
Improved genome assembly and annotation for the rock pigeon (Columba livia)
Improved genome assembly and annotation for the rock pigeon (Columba livia) Carson Holt, Michael Campbell, David Keays, Nathaniel Edelman, Aurelie Kapusta, Emily Maclary, Eric Domyan, Alexander Suh, Wesley Warrenb, Mark Yandell, Thomas Gilbert, Michael D. Shapiro bioRxiv 220947; doi: https://doi.org/10.1101/220947
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