Foodie • STEM Student • Truth Seeker

Hi, I'm Runyu Qi.

I am a PhD student in Biomedical Engineering with a passion for various sciences and trans-/inter-disciplinary research.

My research combines computational and experimental methods across multi-omics, molecular simulation, biomaterials, and nanoparticle-based delivery.

Research experience Curriculum vitae PDF · 2 pages
Heatmap comparing genomic signal patterns across experimental conditions
Genomic signal heatmap Comparison across experimental conditions.

Selected research

Research experience

Projects in bioinformatics, molecular dynamics, biomaterials, and chemical sensing.

Heatmap used to compare retrotransposon-associated genomic signals

Multi-omics · Experimental biology

Computational and experimental analysis of retrotransposons

Advisor: Dr. Yejing Ge · MD Anderson Cancer Center · Jul–Dec 2024

Built and optimized RNA-seq, ChIP-seq, and ATAC-seq workflows to investigate retrotransposon function, comparing computational findings with laboratory data.

  • RNA-seq
  • ChIP-seq
  • ATAC-seq
  • HPC workflows
  • qPCR

Deep learning · Molecular dynamics

Deep learning and molecular dynamics for GPCR pathway analysis

Advisor: Dr. Diwakar Shukla · UIUC · Jan 2024–present

Adapted Neural Relational Inference for larger molecular systems and trained the model on GPU clusters alongside Smoothened GPCR simulations.

  • NRI-MD
  • GPU computing
  • MD simulation

Biomaterials · Drug delivery

Metabolic glycan engineering and mRNA delivery

Advisor: Dr. Hua Wang · UIUC · Sep 2023–present

Engineered metabolic labeling in human mesenchymal stem cells and synthesized ionizable polypeptide nanoparticles for mRNA delivery.

  • Nanoparticles
  • ¹H NMR
  • Hydrogels
Schematic of a gold-silver composite SERS sensing surface

Nanomaterials · Chemical sensing

Trace detection with SERS and electrochemistry

Advisor: Dr. Yunhan Ling · Tsinghua University · Jan–Jun 2023

Developed gold and gold-silver SERS substrates with surface modification and molecular imprinting, achieving TNT detection at 10−6 M and quantitative detection of methylene blue and perchlorate.

  • SERS
  • SEM
  • Electrochemistry

Selected methods

Methods and techniques

Computational

RNA-seq · ChIP-seq · ATAC-seq · HPC workflows · deep learning · molecular dynamics

Experimental

Cell culture · RNA extraction · qPCR · nanoparticle synthesis · hydrogel fabrication

Characterization

¹H NMR · scanning electron microscopy · electrochemistry · Raman spectroscopy

Project archive

Additional projects

Selected projects spanning additive manufacturing, simulation, soft electronics, and optical materials.

3D-printed dental resin model held in a hand
Biomaterials · 3D printing

Nano-ZrO2 reinforced dental resin

Developed a nano-ZrO2-reinforced PMMA resin for stereolithography additive manufacturing.

Finite-element simulation outputs for autoclave processing
Simulation · Automation

Autoclave modeling and scripting

Modeled autoclave processing with CFD and developed automated modeling scripts.

Academic poster about PDMS-based electronic skin
Review · Soft electronics

PDMS-based electronic skin

Reviewed self-healing mechanisms in PDMS-based electronic skins.

View poster
Optical spectra and metallic-glass light-filter samples
Optics · Materials

Metallic-glass visible-light filters

Developed full-spectrum visible-light filters using metallic glass.

Background

Education

Biomedical engineering builds on my training in materials science and computational science and engineering.

Education

  1. Aug 2025 – Present

    PhD, Biomedical Engineering

    UT Southwestern Medical Center

    Dallas, Texas
  2. Aug 2023 – Dec 2024

    MS, Materials Science & Engineering

    University of Illinois Urbana-Champaign

    Urbana, Illinois · Computational Science & Engineering concentration
  3. Sep 2019 – Jun 2023

    BE, Materials Science & Engineering

    Tsinghua University

    Beijing, China

Activities

Service & leadership

Selected leadership and service beyond the laboratory.

Sep 2022 – Jun 2023

Future Sci-tech Interests Club

President · Tsinghua University

Feb – Mar 2022

Beijing Olympic and Paralympic Winter Games

Event Services Volunteer

Apr 2024

Tau Beta Pi · Illinois Alpha

Member

Contact

Contact

For research-related inquiries or potential collaborations:

[email protected] GitHub Curriculum vitae