Yuntao Zhang

Welcome! I am a research scientist based in the San Francisco Bay Area, specializing in the application of AI to accelerate drug discovery. My work combines deep expertise in bioanalytical chemistry, mass spectrometry, and molecular modeling with a passion for AI-driven innovation. My goal is to bridge these fields to improve our understanding of human health and aging and to drive impactful discoveries in health and medicine.

About Me

• Current Role: Senior Scientist at Bristol Myers Squibb (BMS)
• Expertise:
  • Biologics Mass Spectrometry: Characterizing biologics with peptide mapping, carbene footprinting (epitope/paratope mapping), and bottom-up proteomics.
  • Computational & AI: Applying molecular modeling, deep learning, and AI agents to solve complex scientific problems.
  • Workflow Automation: Developing automated systems to enhance research efficiency and reproducibility.
• Education:
  • Ph.D. in Bioanalytical and Physical Chemistry, University of the Pacific
  • M.S. in Environmental Engineering, University of the Pacific
  • B.S. in Ecology, University of Science and Technology Beijing

Unique Skillset

With a strong foundation in analytical chemistry and a deep interest in computer science and AI, I have developed a unique interdisciplinary profile. My work combines hands-on expertise in mass spectrometry and biologics with advanced computational approaches. I specialize in fine-tuning and applying state-of-the-art foundation models—such as ST-Tahoe for single-cell perturbation prediction and Boltz-2 for structural biology—to solve complex scientific challenges. My skills span the full MLOps lifecycle, from setting up and managing GPU-powered training environments on GCP and Domino Data Lab to employing modern development tools like Docker and UV for reproducibility. This enables me to bridge the gap between cutting-edge AI and practical scientific discovery, from high-throughput data processing to generating deep biological insights.

Impact & Achievements

• Advanced Model Fine-Tuning: Systematically fine-tuned the ST-Tahoe foundation model for gene perturbation analysis, diagnosing and resolving complex issues like representation mismatch and optimizer state conflicts to significantly improve performance. This work involves deep analysis of model architecture, loss functions, and training dynamics on enterprise-level platforms.
• Biologics Characterization at BMS: Led the implementation of carbene footprinting for high-resolution epitope/paratope mapping, and developed novel LC-MS methods to support bispecific, ADC, and CAR-T programs.
• Workflow Automation: Created automated toolkits for LC-MS sequence generation and AI-powered data communication, reducing manual setup time from minutes to seconds and minimizing errors.
• AI for Analytical Chemistry: Built tools that leverage large language models (LLMs) for expert comment generation and interactive data visualization, improving clarity and decision-making.
• Mentorship & Collaboration: Trained and mentored scientists in advanced MS and computational techniques, fostering a collaborative and innovative environment.

Publications & Research

I have authored multiple peer-reviewed publications in leading journals, advancing the field of mass spectrometry, peptide/peptoid analysis, and molecular modeling. My research is rooted in fundamental physical chemistry, exploring the interplay between molecular structure, chirality, and analytical measurement. Through both experimental and computational approaches, I have developed a deep understanding of mass spectrometry and am an expert in molecular modeling.
See my publications for details.

Professional Development & Certificates

I am committed to continuous learning in scientific programming, AI, and leadership. I enjoy building innovative tools, exploring new technologies, and deepening my understanding of strategy and entrepreneurship. I hold certificates in:

• Machine Learning (Stanford/Coursera)
• Deep Learning Specialization (DeepLearning.AI)
• AI Agents (Hugging Face)
• Associate Python Developer (DataCamp)

Explore all certificates and projects.

Vision

I believe the future of biopharma and health research lies at the intersection of rigorous biological insights and cutting-edge technology and AI. By integrating domain expertise with advanced computational tools, we can accelerate discoveries, improve therapies, and deepen our understanding of aging and disease. I am excited to help advance our understanding of human biology and contribute to the development of new therapies for serious diseases and aging.

Feel free to explore my CV, publications, projects, and certificates to learn more about my work. I am always open to new collaborations and opportunities to make a positive impact in the scientific community.