Alexandra Lee

Career Profile

  • Computational research scientist with 10+ years of experience in data analysis and 4+ years of experience developing and applying machine learning tools.


  • Ph.D. in Genomics and Computational Biology

    May 2022
    University of Pennsylvania
  • M.S. in Applied Mathematics

    June 2012
    University of Washington
  • B.A. in Mathematics and Minor in Computer Science

    May 2011
    Bryn Mawr College

Skills & Proficiency

  • Github
  • Python
  • R
  • Matlab
  • Latex
  • sci-kit learn
  • keras
  • tensorflow
  • Machine Learning
  • Applied mathematics
  • Deep Learning, generative neural networks
  • Topology
  • Dynamical systems


  • Sr. Community engagement/Biomedical data scientist

    October 2022 - Present
    • Prototype cloud-based computational workflows to analyze genomic, proteomic large-scale datasets
    • Train users how to apply the workflows for their own research via online webinars
  • Scientific consultant

    July 2022 - Present
    Soma Logic
    • Advise technical aspects of projects that applied machine learning methods to proteomics data
  • Graduate Researcher

    August 2017 - May 2022
    University of Pennsylvania
    • Performed gene-gene correlation analyses that revealed transcriptional patterns within and between core and accessory genes across P. aeruginosa strain types
    • Designed an approach to distinguish between common and context-specific transcriptional signals using a generative neural network to simulate a set of background transcriptome experiments:
    • Developed and published a python package to simulate a compendium of genome-wide gene expression data using a generative neural network:
    • Built an analysis pipeline in python to measure the effect of varying amounts of technical noise in simulated compendia
  • Bioinformatics analyst

    September 2012 - June 2017
    J. Craig Venter Institute
    • Designed and implemented a computational analysis workflow to identify candidate Zika-specific epitopes to improve diagnostic tests
    • Assisted in the development of a user-constrained computational pipeline to semi-automatically gate flow cytometry data (python)
    • Used data mining to identify antigenic regions of Influenza A virus HA protein that could be candidate targets of protective immunity
    • Facilitated enhancements to Influenza Research Databases ( and Virus Pathogen Resource Database ( Bioinformatics Research Center
    • Performed research on: Influenza virus, Flaviviruses, Chikungunya virus, MERS-CoV, Arenavirus, RSV, Ebolavirus

Teaching Experience

Co-organizer for Deep Learning for Biologists Workshop

November 2020
  • Designed structure of the workshop
  • Presented about recurrent neural networks and dimensionality reduction methods (PCA, autoencoders)
  • Materials: Blog advertisement; workshop recording

Co-organizer and lecturer for Python BootCamp

Summer 2018 - 2020
  • Designed structure of the course
  • Wrote weekly HW assignments with built in test cases
  • Gave lecture about python pandas
  • Assisted students with HW and gave them feedback on assignments
  • Course material

Graduate student mentor

Fall 2020, Spring 2021
  • Mentored one undergraduate student through GCB’s Summer in Computational Biology pilot program
  • Guided students through their research projects; helped them to decide next steps; Provided technical support

Differential equations teaching assistant

Fall 2011
  • Tutored and assisted students in lecture content and homework at bi-weekly office hour sessions

Introduction to computer science teaching assistant

Fall 2009
  • Tutored and assisted students in studying/programming scribbler robots to perform simple tasks

Leadership Experience

Founding member of GCB EDI committee

July 2020 - March 2022
  • Lead initiatives to help 1st/2nd year graduate students adjust to Penn, Philadelphia, and graduate-school life
  • Attended bi-monthly committee meetings to discuss the progress of initiatives and provide feedback on new proposals

Chair of GCB committee of social affairs

September 2018 - September 2021
  • Organized venue, activities, food, and refreshment for social events
  • Coordinated with external vendors