Runxi Shen

Postdoctoral Associate in Broad Institute Imaging Platform, Ph.D. In Computational Biology

Cambridge, Massachusetts, United States

About

Computational Biologist | Image-Based Profiling | Deep Learning for Therapeutic Discovery I am a computational biologist focused on applying deep learning methods to image-based profiling to advance therapeutic discovery, particularly in rare diseases and complex biological systems. My work centers on extracting high-dimensional phenotypic signals from cellular images and integrating them with multi-omics data to identify disease-relevant biology, discover biomarkers, and predict drug response. I am especially interested in using representation learning to bridge cellular phenotypes with molecular mechanisms and translational outcomes. With a background spanning quantitative genetics, bioinformatics, and machine learning, I bring a cross-disciplinary approach to understanding disease biology and enabling data-driven drug development. I value open, collaborative science and building computational frameworks that scale across datasets and therapeutic areas.

Experience

  • Postdoctoral Associate at Broad Institute of MIT and Harvard
    Jan 2025 - Present · 1 yr 6 mos

  • Senior Scientist at BeiGene
    Jul 2022 - Jan 2025 · 2 yrs 7 mos

    Senior Scientist, Bioinformatics

  • Algorithm Engineer at XtalPi Inc.
    Dec 2021 - Jun 2022 · 7 mos

    Developed machine learning algorithms based on evolutionary histories of B-cell receptors to facilitate the de-novo antibody design and protein optimization.

  • Doctoral Student at Cornell University
    Aug 2017 - May 2022 · 4 yrs 10 mos

    A Ph.D. student in computational biology focused on population genetics and evolutionary biology.

  • Bioinformatics Engineer Intern at Singleron Biotechnologies
    Feb 2021 - Aug 2021 · 7 mos

    Implemented a new cell-calling procedure and optimized the SNP-calling process in the analysis pipeline for single-cell RNA sequencing data