slzarate.github.io

Hello! My name is Samantha Zarate (she/her) and I am currently a PhD student at Johns Hopkins University in Baltimore, MD, working in Mike Schatz’s lab. Before this, I worked at DNAnexus in Mountain View, CA as a bioinformatics scientist. I graduated from Stanford University in 2016 with a BS in biomedical computation.

I work in computational genomics and my primary interest is large-scale variant calling. Please feel free to get in touch if you are interested in collaborating!

Contact Information & Social Media

• Email: slzarate AT jhu DOT edu
• Twitter: @sz_genomics
• GitHub: https://github.com/slzarate
• LinkedIn: https://www.linkedin.com/in/slzarate/
• Google Scholar: https://scholar.google.com/citations?user=dIVMoGYAAAAJ&hl=en

CV

• CV

Projects

• A complete reference genome improves analysis of human genetic variation (as part of the T2T consortium)
  • BioRxiv (2021): https://doi.org/10.1101/2021.07.12.452063
  • GitHub: https://github.com/schatzlab/t2t-variants
  • Terra blog post: https://terra.bio/calling-variants-from-telomere-to-telomere-with-the-new-t2t-chm13-genome-reference/
• Parliament2: An ensemble short-read structural variant caller (initially developed at DNAnexus)
  • GitHub: https://github.com/slzarate/parliament2 (includes WDL version as well as corresponding Docker images)
  • DockerHub: https://hub.docker.com/r/dnanexus/parliament2
  • GigaScience article (2020): https://doi.org/10.1093/gigascience/giaa145
  • DNAnexus blog post: https://blog.dnanexus.com/2018-09-24-parliament2-fast-structural-variant-calling/

Miscellaneous

• Fall 2020: Co-developed a meme generator as a final project for Machine Learning: Deep Learning
• November 2018: Featured on Women of Silicon Valley
• Summer 2018: Mentored a summer intern at DNAnexus, co-authoring a DNAnexus blog post with her

Last updated 12/20/21