Hello, I'm Gideon.

I’m a student at the University of Michigan studying computer science and biology (CV). My focus lies in the intersection of these fields — bioinformatics and computational biology.

In my free time, I like to do photography, run, read, and scuba dive, and I’m currently working towards more advanced certifications in technical / cave diving.

I care deeply about making a positive impact in what I do. I want to build things that make a difference.

Here’s some stuff that I’m working on:

  • I’m working with Jason Ernst and Jingyuan Fu @ UCLA on functionally annotating the epigenome of iPS cells. Symposium poster.

  • I’m working with Matthew Patrick, Lam Tsoi, and Haihan Zhang @ the University of Michigan on Loopsim, a tool that analyzes chromosome conformation capture data (the 3D structure of DNA) and finds statistically significant genomic interactions. Preprint.

  • I worked with Hagai Levi and Ron Shamir @ Tel Aviv University on integrating DOMINO, an active module identification tool, with Drugst.One, a biological network enrichment analysis program. Journal article (Nucleic Acids Research).

  • I am developing a model to impute spatial transcriptomics data, with the idea being to integrate spatial transcriptomics data with single-cell RNA sequencing data, with the overarching goal of merging the accuracy inherent in single-cell sequencing with the spatial context provided by spatial transcriptomics.

  • I designed a robotic arm to perform laser spectroscopy with the aim of increasing data quality, efficiency, and safety. Conference poster.

  • I developed Nextinspace, a tool for keeping track of rocket launches. Press.

You can email me at gideonshaked [at] gmail [dot] com or gshaked [at] umich [dot] edu. I’m always interested in meeting new people.

Coral Restoration

Conducting a coral reef biodiversity survey with the Coral Restoration Foundation