I am a PhD student at MIT co-advised by Bryan Bryson and Paul Blainey. Trained as a molecular biologist 🧬, microbiologist 🦠, immunologist 🧫, and artificial‑intelligence scientist 🤖, I focus on using AI and high-throughput experiments to study functional genomics at the host–microbe co‑evolutionary interface. My specific aims are:

1. At the molecular level, develop novel molecular tools and tricks to unlock the hidden dimensions of molecular biology.
2. At the systems level, leverage computer vision and high‑content screening to explore uncharted aspects of cell biology.
3. At the interorganismal level, use AI and biochemistry to model the molecular evolutionary dynamics of bacteria and viruses.

🔥 News

• 2024.09:  🎉🎉 I started at MIT as a PhD student!

📝 Publications

🦠 Host-Microbe Co-Evolution

Preprint available

Immunopeptidomics informs the design of mRNA immunogens for delivery of Mycobacterium tuberculosis MHC-II antigens

Owen Leddy, Paul Ogongo, Julia Huffaker, Mingyu Gan, Ryan Milligan, Sheikh Mahmud, Heyuan Michael Ni, Yuko Yuki, Kidist Bobosha, Liya Wassie, Mary Carrington, Qingyun Liu, Joel D. Ernst, Forest M. White, and Bryan D. Bryson

• Human cell immunopeptidomics revealing MHC-II epitopes presented by dendritic cells infected by Mycobacterium tuberculosis is enriched for surface and secreted proteins and virulence factors.

Preprint available

Mycobacterium tuberculosis suppresses protective Th17 responses during infection

Alex Zilinskas, Amir Balakhmet, Douglas M. Fox, Heyuan Michael Ni, Carolina Agudelo, Helia Samani, and Sarah A. Stanley

• in vivo immunological characterization in mice reveals that Mycobacterium tuberculosis ESX-1 and PDIM skew the T helper response toward a Th1 bias and suppresses the protective Th17 response.

🧬 Molecular Tool Development

Nature Biotechnology

Evolution-guided protein design of IscB for persistent, in vivo epigenome editing

Soumya Kannan, Han Altae-Tran, Shiyou Zhu, Peiyu Xu, Daniel Strebinger, Rachel Oshiro, Guilhem Faure, Lukas Moeller, Julie Pham, Kepler S. Mears, Heyuan Michael Ni, Rhiannon K. Macrae, and Feng Zhang

• Bioinformatics-guided engineering of the CRISPR-Cas9 progenitor IscB as a compact genomic and epigenomic editor in living cells and animals.

Communications Biology

Delivered complementation in planta (DCIP) enables measurement of peptide-mediated protein delivery efficiency in plants

Jeffrey W. Wang, Henry J. Squire, Natalie S. Goh, Heyuan Michael Ni, Edward Lien, Cerise Wong, Eduardo González-Grandío, and Markita P. Landry

• A split-GFP tool allowing quantitative confocal microscopy readout of protein cargo delivery efficiency in plant leaves.

🤖 Computer Vision in Biological Applications

• The state of the art in artificial intelligence and digital pathology in prostate cancer. Heyuan Michael Ni*, Ramez Kouzy*, Ali Sabbagh*, Michael K. Rooney, Jean Feng, Simon P. Castillo, Sherif M. Gadoue, Zakaria El Kouzi, Karen Hoffman, Yinyin Yuan, Anant Madabhushi, and Osama Mohamad. In revision for Nature Reviews Urology.

* equal contributions

💬 Invited Talks

• 2024.05  Unbiased exoproteomic screen reveals novel Staphylococcus aureus virulence factors, UC Berkeley Molecular and Cell Biology Department Honors Research Symposium.
• 2024.04  Discovery of novel virulence factors provides basis for effective treatment of Staphylococcus aureus infections, UC Berkeley Molecular and Cell Biology Undergraduate Student Association Research Symposium.

📖 Education

• 2024 - 2030 (expected)  Ph.D. Biological Engineering. School of Engineering, Massachusetts Institute of Technology.
• 2022 - 2024  B.S. Business Administration. Haas School of Business, University of California, Berkeley.
• 2020 - 2024  B.A. Data Science. College of Computing, Data Science, and Society, University of California, Berkeley.
• 2020 - 2024  B.A. Molecular and Cell Biology. College of Letters and Science, University of California, Berkeley.

🧪 Research Experience

• 2022 - 2024  Undergraduate Researcher | Sarah Stanley Lab. Microbiology and structural bioinformatics for unbiased virulence factor discovery in Staphylococcus aureus. Helper T cell dynamics in Mycobacterium tuberculosis pathogenesis.
• 2022 - 2024  Clinical Researcher | Osama Mohamad Lab. Use of artificial intelligence in digital pathology for prostate cancer.
• 2021 - 2022  Undergraduate Researcher | Markita Landry Lab. Biochemistry and synthetic biology for CRISPR and TF delivery in plants.

📃 Industry Experience

• 2023 - 2024  Contract Consultant | Gilead Sciences. Dynamic financial forecasting, temporal and inter-organizational comparative analysis.
• 2021  ESG Consulting Intern | PricewaterhouseCoopers. Climate change physical and transition risks, carbon assets, and green investment.
• 2020  Research and Development Intern | Bluepha. Recombinant protein biomanufacturing in Pichia pastori.

🤝 Services

• 2024 - Present  Content Creator | Regenesis. Create Chinese content on biomolecular engineering, synthetic biology, and systems biology.
• 2024 - Present  Alumni Relations Lead | Nucleate Boston. Manage relationships with Nucleate Activator alumni.
• 2024 - Present  Associate | MIT-China Innovation and Entrepreneurship Forum. Organize entrepreneurship forums highlighting Chinese key opinion leaders in the Boston area.
• 2022 - Present  North American Ambassador | iGEM Community. Advocate for open science, biosafety, and biosecurity in the synthetic biology ecosystem.
• 2022 - Present  Co-Founder & Executive Board | US-China Life Science Venture Club. Facilitating collaboration between the US and China’s entrepreneurial and venture capital ecosystems.
• 2023 - 2024  Founder | Bay Area Synthetic Biology Alliance. Organized the inaugural Bay Area Bioengineering Symposium.
• 2022 - 2024  Co-President | Translational Medicine and Stem Cell Association. Form strategic partnerships and host Bay Area-wide conferences on translational medicine.
• 2020 - 2024  Experimental Director | iGEM at Berkeley. Create student-led research opportunities for undergraduates. Host campus-wide and Bay Area-wide research symposia.

🎖 Awards and Fellowships

• 2024.05  Outstanding Scholar in Biophysics, Biochemistry, and Structural Biology | UC Berkeley. 1/3 awards to graduating seniors in biophysics, biochemistry, and structural biology.
• 2024.05  Society Member | Beta Gamma Sigma International Business Honors Society.
• 2024.02  Society Member | Phi Beta Kappa Honors Society.
• 2023.10  Rhodes Scholarship 2024 Finalist | Rhodes Trust. 14/750 applicants in the China constituency.
• 2023.08  The Leadership Award (TLA) 2023-2024 | Cal Alumni Association. Awarded to 2.4% of UC Berkeley student leader applicants.
• 2023.05  Paul Westberg Research Scholar Fund | UC Berkeley. Awarded to the most outstanding student researcher in the Robinson Life Science, Business, and Entrepreneurship Program who envisions serving unmet needs in their research career.
• 2023.04  Jeremy Thorner Research Prize | UC Berkeley. 1/3 awards to undergraduate researchers in biophysics, biochemistry, and structural biology who are in their penultimate year.
• 2022.08  The Leadership Award (TLA) 2022-2023 | Cal Alumni Association. Awarded to 2.4% of UC Berkeley student leader applicants.
• 2020.11  Gold Medal | iGEM 2020. Awarded gold medal for project “Acneutralizer” with team Beijing_4ELEVEN.
• 2019.11  Gold Medal | iGEM 2019. Awarded gold medal for project “Digitized bistable module for conditional suicide in engineered bacteria” with team BHSF_ND.
• 2019.06  Gold Medal | British Biology Olympiad China Mainland Division. Top 5% (51th place) out of 733 contestants nationwide.
• 2019.06  Gold Medal & National 1st Place| United States of America Biology Olympiad China Mainland Division. Ranked 1st place out of 526 contestants nationwide.