Stanford University
Showing 1-10 of 55 Results
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Sijie Chen
Postdoctoral Scholar, Radiation Physics
BioI am a postdoctoral fellow working with Dr. Lei Xing at Stanford University, where I develop trustworthy autonomous AI agents and foundational informatics systems for single-cell biology. My long-term vision is to build auditable computational infrastructure and virtual cell models that transform massive single-cell atlases into reliable, steerable systems for mechanistic discovery across tissues, diseases, and species. My doctoral work with Prof. Xuegong Zhang established my foundation in single-cell bioinformatics and atlas-scale integration, which I have since extended into large-scale representation modeling, AI agent workflows, and LLM-driven scientific discovery. My current work focuses on developing governed, agentic lifecycles for continuous single-cell data curation and foundation model evaluation, while applying these autonomous systems to power cross-organ virtual cell retrieval and simulate immune-tolerance breakdown.
My ongoing efforts build directly upon my prior work in atlas integration and algorithmic development. As the first author of hECA (Chen et al., 2022), I built a unified human cell atlas integrating one million high-quality cells across 38 organs with a logic-expression query interface. This experience exposed the central bottlenecks—such as heterogeneous formats and ontology grounding—that I now address using LLM-powered agents to enable autonomous metadata harmonization and iterative quality control. I am converting manual curation into an autonomous, agent-driven paradigm where new datasets are continuously ingested and versioned in a traceable manner. Furthermore, my co-development of TorchGW for cell state alignment, TFcomb for perturbation prediction, and TransMap for cross-species alignment provides the algorithmic foundation for next-generation cell foundation models and virtual cell simulation.
By integrating these components into trustworthy, benchmarked, and human-in-the-loop AI infrastructure, my research bridges scalable scientific computing with complex biomedical questions. Through close collaboration with Prof. Edgar Engleman, I am utilizing immune-tolerance breakdown—specifically focusing on a tolerogenic dendritic cell program—as a mechanistic testbed to validate our virtual cell simulations. A core focus of my work is ensuring that every agent-generated hypothesis and retrieved state remains bound to the exact data and model checkpoints that produced it, making findings fully re-derivable as the biological knowledge base evolves. Ultimately, I aim to advance the frontier of trustworthy autonomous single-cell informatics, bridging AI agents, virtual cell engineering, and biological discovery. -
Wenting Chen
Postdoctoral Scholar, Radiation Physics
BioI am currently a Postdoc Fellow in the Department of Radiation Oncology of Stanford University, advised by Prof. Lei Xing. Before joining Stanford, I obtained my Ph.D degree in the Department of Electrical Engineering, City University of Hong Kong, supervised by Prof. Yixuan YUAN, Prof. W.S Tommy Chow, and Prof. L.H. Leanne Chan. I visited Massachusetts General Hospital and Harvard Medical School, supervised by Prof. Xiang Li and Prof. Quanzheng Li. Before that, I received the B. Eng and M. Eng degree from College of Computer Science and Software Engineering in Shenzhen University of China in 2017 and 2020, supervised by Prof. Linlin Shen. From Dec. 2019 to Nov. 2020, I had interned in Tencent Jarvis Lab, supervised by Dr. Shuang Yu and Prof. Yefeng Zheng.
My research interests lie in vision-language model, multi-modal large language model, generative AI, computer vision and their applications on medical AI, with a focus on report generation, medical image synthesis, endoscopy super-resolution, retinal image segmentation, multi-modality diagnosis, etc. -
Cynthia Chuang
Clinical Professor, Radiation Oncology - Radiation Physics
BioEducation:
1990-B.S., Bioelectrical Engineering (6-1B), Massachusetts Institute of Technology, Cambridge, MA
1992-M.S., Bioengineering, University of Pennsylvania, Philadelphia, PA
1994-M.S., Nuclear Engineering (NMR Spectroscopy), Massachusetts Institute of Technology, Cambridge, MA
1999-Ph.D., Nuclear Engineering (Boron Neutron Capture Therapy), Massachusetts Institute of Technology, Cambridge, MA
2001-Postdoctoral Fellowship (Peregrine Project), Lawrence Livermore National Laboratory
2003-Medical Physics Residency, University of California, San Francisco (joint 3.5-year postdoctoral and residency program)
Academic Appointments:
2003 - 2005-Clinical Instructor, Radiation Oncology, University of California, San Francisco, San Francisco, California
2005 - 2009-Assistant Adjunct Professor, Radiation Oncology, University of California, San Francisco, San Francisco, California
2009 - 2013-Assistant Professor In Residence, Radiation Oncology, University of California, San Francisco, San Francisco, California
2013 - 2017-Associate Professor In Residence, Radiation Oncology, University of California, San Francisco, San Francisco, California
2017 - 2018-Associate Professor of Clinical Radiation Oncology, University of California, San Francisco, San Francisco, California
2019 - 2023-Clinical Associate Professor, Department of Radiation Oncology, Clinical Educator Line, Stanford University, Stanford, CA
2023- Present-Clinical Professor, Department of Radiation Oncology, Clinical Educator Line, Stanford University, Stanford, CA -
Xianjin Dai, PhD, DABR
Assistant Professor of Radiation Oncology (Radiation Physics)
Current Research and Scholarly InterestsIntelligent Image-guided intervention
AI in Medicine
Medical Image Analysis
Biomedical Physics
Multimodal Imaging
Ultrasound Imaging
Medical Device
Biomedical Optics (Optical, Photoacoustic, OCT) -
Piotr Dubrowski
Clinical Instructor, Radiation Oncology - Radiation Physics
BioPiotr Dubrowski is a Canadian trained and board-certified Therapy Medical Physicist. Throughout his career Piotr has had the opportunity to bring several new Cancer Clinics operational from the ground up, where he was able to hone a broad, systems-approach to Radiation Oncology. He was recently promoted to Associate Quality Director of Physics responsible for improving patient safety and workflow/technology improvements across a wide cancer care network. Piotr’s research interests focus mainly on improving the treatment planning process and increasing clinic safety through software development and hardware 3D-print prototyping. Additionally, Piotr has sought out opportunities to give back to the Global community with participation in the Stanford Global Radiation Oncology Outreach efforts expanding education and access to care in Tanzania and Kenya and throughout the developing world via online Radiation Therapy courses.
