Samantha Jones

Ms. Samantha Jones


Research Focus & Metrics

Academic Career Length

10Years (2017-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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11 December 2017 in Genes
Verified
Journal Article
Open access
PDF file
SJSteven Jones
Steven Jones
GTGregory Taylor
Gregory Taylor
SCSimon Chan
Simon Chan
RWRené L. Warren
René L. Warren
SHS. Austin Hammond
S. Austin Hammond
MHMartin Haulena
Martin Haulena
The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A.

11 December 2017 in Genes
Verified
Journal Article
Open access
PDF file
SJSamantha Jones
Samantha Jones
MHMartin Haulena
Martin Haulena
GTGregory Taylor
Gregory Taylor
SCSimon Chan
Simon Chan
SBSteven Bilobram
Steven Bilobram
SJSteven Jones
Steven Jones
The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly provided 2.426 Gbp of highly contiguous assembled genomic sequences with a scaffold N50 length of over 38 Mbp. We generated transcriptome data derived from a lymphoma to aid in the determination of functional elements. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA388419.

14 December 2017 in bioRxiv
Verified
Preprint
Open access
PDF file
CNChristina Nieuwoudt
Christina Nieuwoudt
SJSamantha Jones
Samantha Jones
ABAngela Brooks-Wilson
Angela Brooks-Wilson
JGJinko Graham
Jinko Graham
Background: Studies that ascertain families containing multiple relatives affected by disease can be useful for identification of causal, rare variants from next-generation sequencing data. Results: We present the R package SimRVPedigree , which allows researchers to simulate pedigrees ascertained on the basis of multiple, affected relatives. By incorporating the ascertainment process in the simulation, SimRVPedigree allows researchers to better understand the within-family patterns of relationship amongst affected individuals and ages of disease onset. Conclusions: Through simulation, we show that affected members of a family segregating a rare disease variant tend to be more numerous and cluster in relationships more closely than those for sporadic disease. We also show that the family ascertainment process can lead to apparent anticipation in the age of onset. Finally, we use simulation to gain insight into the limit on the proportion of ascertained families segregating a causal variant. SimRVPedigree should be useful to investigators seeking insight into the family-based study design through simulation.