Stanford Advisors

Contact

  • Academic
    sgorji@stanford.edu
    University - Scholar Department: Genetics Position: Postdoctoral Scholar

All Publications

  • The yEvo Mutation Browser: Enhancing student understanding of experimental evolution and genomics through interactive data visualization. bioRxiv : the preprint server for biology Anderson, L., Schoch, J., Anastasia, E., Wang, V., Zeng, Z., Gorjifard, S., Dunham, M. J. 2025

    Abstract

    Experimental evolution is a powerful method for studying the relationship between genotype and phenotype by observing how populations genetically adapt to controlled selective pressures. In educational settings, this approach also offers a dynamic way for students to engage with molecular genetics. One such educational effort, known as "yEvo" (yeast evolution), introduces experimental evolution into high school classrooms, allowing students to evolve the baker's yeast Saccharomyces cerevisiae under various stressors and investigate the resulting de novo genetic changes. While the hands-on experiments have been successful in fostering student interest and understanding of evolution, the downstream data analysis-interpreting whole-genome sequencing results of evolved yeast compared to the ancestor-remains a challenge. Students often struggle to grasp the significance of their mutated genes and lack the broader context to determine which mutations are most phenotypically relevant. To address these issues, we developed the yEvo Mutation Browser, an intuitive web tool designed to assist students and researchers alike in visualizing and contextualizing genome sequencing data. Developed using R Shiny, this tool features an interactive chromosome map displaying mutated genes, graphs categorizing mutation types, and a gene viewer illustrating specific mutation sites within genes. The app also features an option for non-yEvo-affiliated users to upload their own experimental evolution or genetic screen datasets and compare them with all yEvo data collected since 2018. The yEvo Mutation Browser streamlines data interpretation, helping students understand how organisms employ diverse genetic strategies to adapt to environmental stress. In the future, this framework could be adapted for use with other model organisms, offering a valuable resource for both genetics research and education.

    View details for DOI 10.1101/2025.07.18.665463

    View details for PubMedID 40777289