Cassandra Rodriguez TWS-WS 2026

Poster references:

  1. Piertney, S. B. and M. K. Oliver, 2006. The evolutionary ecology of the major histocompatibility complex. Heredity, 96:7-21.
  2. Radwan, Jacek; Babik, Wiesław; Kaufman, J.; Lenz, Tobias L.; and Martin E. P. Smee, 2020. MHC diversity, disease and parasite coevolution. Philosophical Transactions of the Royal Society B, 375(1796): 20190248. https://doi.org/10.1098/rstb.2019.0248
  3. Eichler, E. E., Genetic Variation, Comparative Genomics, and the Diagnosis of Disease. PMC, 381(1):64-74.
  4. Veckemans, X., Castric, V., Hipperson, H. Mller, N.A., Westerdahl, H. and Q. Cronk, 2021. Whole-genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plan sefl-incompatibility. Molecular Ecology, 30(23):6072-6086.
  5.  Supple, M. A., et al. (In Prep/2025). Statewide genomic connectivity and inbreeding in California mountain lions. Part of the California Conservation Genomics Project.
  6. Supple, M., Escalona, M. Alexandre, N., Buchalski, M. R., Riley, Seth P. D., Dellinger, J. A., Vickers, T. W., Sahasrabudhe, R., Nguyen, O., Fairbairn, C. W., Seligmann, W, Wilmers, C and B. Shapiro, 2024. Journal of Heredity, 116(4):479-487.
  7. Gustafson, K. D., Gagne, R. B., Vickers, T. W., Riley, S. P. D., Wilmers, C. C., Bleich, V. C., Pierce, B. M., Kenyon, M., Drazenovich, T. L., Sikich, J. A., Walter, M. B., and H. B. Ernest, 2019. Genetic source–sink dynamics among naturally structured and anthropogenically fragmented puma populations. Conservation Genetics, 20(2), 215–227. https://doi.org/10.1007/s10592-018-1125-2.
  8. Trim Galore: Krueger, F. (2015). Trim Galore was developed at The Babraham Institute by @FelixKrueger, now part of Altos Labs.
  9. Cock, P. J., Fields, C. J., Goto, N., Heuer, M. L. and P. M. Rice, 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res., 38(6):1767-71.
  10. Li, Heng, 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997.
  11. Li, Heng; and Richard Durbin, 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14): 1754–1760.
  12. Picard Toolkit: Broad Institute. (2019)
  13. Pedersen, Brent S.; and Aaron R. Quinlan, 2018. Mosdepth: Quick coverage calculation for genomes and exomes. Bioinformatics, 34(5): 867–868.
  14. Heng Li, 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18):3094–3100, https://doi.org/10.1093/bioinformatics/bty191.
  15. Yuhki, N., Mullikin, J. C., Beck, T., Stephens, R. and S. J. O’Brien, 2008. Sequences, annotation and single nucleotide polymorphism of the major histocompatibility complex in the domestic cat. PLoS One, 3(7):e2674. doi: 10.1371/journal.pone.0002674. PMID: 18629345; PMCID: PMC2453318.
  16. Okano, M., Miyamae, J., Suzuki, S., Nishiya, K., Katakura, F., Kulski, J. K., Moritomo, T. and T. Shiina, 2020. Identification of Novel Alleles and Structural Haplotypes of Major Histocompatibility Complex Class I and DRB Genes in Domestic Cat (Felis catus) by a Newly Developed NGS-Based Genotyping Method. Front Genet, 15;11:750. doi: 10.3389/fgene.2020.00750. PMID: 32760428; PMCID: PMC7375346.
  17. Plasil, M., Futas, J., Jelinek, A., Burger, P. A. and P. Horin, 2022. Comparative Genomics of the Major Histocompatibility Complex (MHC) of Felids. Frontiers in Genetics, doi: 10.3389/fgene.2022.829891.

Additional:

Plots

Bernat Gel & Eduard Serra. (2017). karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics, 31–33. doi:10.1093/bioinformatics/btx346.

Thank you!

 

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