slzarate.github.io

Hello! My name is Samantha Zarate (she/her) and I am a PhD candidate at Johns Hopkins University in Baltimore, MD in Mike Schatz’s lab. I am currently looking for senior-level science or engineering positions in genomics or bioinformatics with a start date of Q3 2023.

For the spring and fall of 2022, I worked remotely with the genomics team at Google Health on DeepVariant. For the summer of 2022, I interned at the Regeneron Genetics Center with the Genome Informatics & Data Engineering team in Tarrytown, NY. Before starting grad school, 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: sl ${LASTNAME} AT jhu DOT edu
• GitHub: https://github.com/slzarate
• LinkedIn: https://www.linkedin.com/in/slzarate/
• Google Scholar: https://scholar.google.com/citations?user=dIVMoGYAAAAJ&hl=en
• Twitter: I deleted my Twitter account for various reasons, so if you see one under my name, it’s not me.

CV

• CV

Projects

• A complete reference genome improves analysis of human genetic variation (as part of the T2T consortium)
  • Science (2022): https://doi.org/10.1126/science.abl3533
  • 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 (2020): https://doi.org/10.1093/gigascience/giaa145
  • DNAnexus blog post: https://blog.dnanexus.com/2018-09-24-parliament2-fast-structural-variant-calling/

Miscellaneous

• October 2022: Received 2022 Mark O. Robbins Prize in High-Performance Computing
• May 2022: T2T Consortium featured in TIME Magazine’s 100 Most Influential People of 2022
• Fall 2020: Co-developed a meme generator as a final project for Machine Learning: Deep Learning
• Fall 2020: Wrote questions for Trivia Mafia, a Minneapolis-based bar trivia company, part-time
• 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 2023-04-05