I am a PhD student at MIT co-advised by Bryan Bryson and Paul Blainey. Trained as a molecular biologist 🧬, microbiologist 🦠, immunologist 🧫, and machine learning scientist 🤖, I focus on using AI and high-throughput screening to study functional genomics at the host–microbe co‑evolutionary interface. My specific aims are:
- At the molecular level, develop de novo molecules and novel tricks to make measurements in conventionally intractable systems.
- At the systems level, leverage high‑content screening and computer vision to explore uncharted aspects of cell biology.
- At the evolutionary level, use machine learning and bioinformatics to model the evolutionary dynamics between host and pathogen.
🔥 News
- 2024.09: 🎉🎉 I started at MIT as a PhD student!
📝 Publications
🦠 Host-Microbe Co-Evolution
Jonathan Padilla-Gomez, Rachel McGinn, Yisha Liang, Kendra Libby, Heyuan Michael Ni, Alison E. Ringel, Charles Evavold, and Bryan D. Bryson
- Mycobacterium tuberculosis RNA-seq and high-content imaging in human and mice macrophage infection models reveal bacterial lipid metabolism differences in different host species.
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.
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 Technology Development
SwitchCraft: Programmatic Design of State-Switching Proteins
Bowen Jing, Mihir Bafna, Anisha Parsan, Heyuan Michael Ni, David Kwabi-Addo, Bryan D. Bryson, Adam Klivans, and Bonnie Berger
- Optimization-based programmable design protocol for conditionally conformational switching proteins.
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 genome and epigenome editor in living cells and animals.
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 coupled with high-content imaging, enabling quantitative confocal microscopy readout of protein cargo delivery efficiency in plant leaves.
🤖 Computer Vision in Biological/Medical 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
- A review on state of the art AI/ML models in digital pathology for prostate cancer, and good practices in model development.
* 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 - Present 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 Strategy & Operations Lead | Nucleate Boston. Facilitate Nucleate’s flagship Activator program with the Boston Chapter.
- 2024 - Present Content Creator | Regenesis. Create Chinese content on biomolecular engineering, synthetic biology, and systems biology.
- 2024 - 2025 Associate | MIT-China Innovation and Entrepreneurship Forum. Organize entrepreneurship forums highlighting Chinese key opinion leaders in the Boston area.
- 2022 - 2025 North American Ambassador | iGEM Community. Advocate for open science, biosafety, and biosecurity in the synthetic biology ecosystem.
- 2022 - 2024 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.