Undergraduate mentees are italicized.

Rando HM, Wadlington WH, Johnson JL, Stutchman JT, Trut LN, Farré M, Kukekova AV. (2019). The red fox Y-chromosome in comparative context. Genes, 10, 409.
— Raw data available here
— Code available here
— Visualization here (note: this site works best in Internet Explorer)

Sacks BN, Lounsberry Z, Rando H, Kluepfel K, Fain S, Brown S, Kukekova A. (2019). Sequencing red fox Y chromosome fragments to develop phylogenetically informative SNP markers and glimpse male-specific trans-Pacific phylogeography. bioRxiv, 552323.

Bastounes ER, Rando HM, Johnson JL, Trut LN, Sacks BN, Driscoll CA, vonHoldt B, Kukekova AV. (2019). Four structural variants associated with human-directed sociability in dogs are not found in tame red foxes (Vulpes vulpes). Animal Genetics, 50, 116-18.

Kukekova AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, … Zhang G. (2018). The red fox genome assembly identifies genomic regions associated with tame and aggressive behaviors. Nature Ecology and Evolution, 2, 1479-91.
— Red fox reference genome available in NCBI.
NOTE: The version in NCBI is likely to be the best version for most biological analyses, but it is not the version used in some of my analyses where I want to consider messy data. Please contact the Kukekova Lab if you need access to the full draft genome.

Rando HM, Farré M, Robson MP, Won NB, Johnson JL, Buch R, Bastounes ER, Xiang X, Feng S, Liu S, Xiong Z, Kim J, Zhang G, Trut LN, Larkin DM, Kukekova AV. (2018). Construction of red fox chromosomal fragments from the short-read genome assembly. Genes, 9, 308.
— Assembly available here
— Visualization available here (note: this site works best in Internet Explorer)
— Scripts available here
Uneek was developed by Michael Robson and Ronak Buch from the Parallel Programming Lab to diff read names across SAM files efficiently

Donaldson ME, Rico Y, Hueffer K, Rando HM, Kukekova AV, Kyle CJ. (2018). Immuno-genetic profiling of red fox with and without endemic rabies exposure. Ecology and Evolution, 8, 572–83.

Rando HM, Stutchman JT, Bastounes ER, Johnson JL, Driscoll CA, Barr CS, Trut LN, Sacks BN, Kukekova AV. (2017). Y-chromosome markers for the red fox. Journal of Heredity, 108, 678-85.
— Raw data available here