Saisai Ding

Bio

I am a dedicated and innovative researcher with a significant background in computational biology, bioinformatics, and alternative proteins, particularly in the realm of cell-cultivated meat. My academic and professional pursuits have helped me contribute to both plant cell research and the cell-cultivated meat industry. At the Department of Food Science in University Park, PA, I engage deeply in the scRNA data analysis of plant cells, utilizing advanced molecular dynamic tools including Gromacs and Amber as well as GNN,GTN and CNN deep learning models to uncover novel proteins and predict protein/peptide properties.

I am currently a Ph.D. student at PSU, mentored by Yi Zhang. I got my B.Eng.from Jiangsu University of Science and Technology in Food Engineering. Throughout my studies, I spent several years doing internships and gaining experience in industry, including biotechs and cultured meat companies.

Research Interests

Bioinformatics

My experience encompasses a vast array of omics data analysis, including genomics, transcriptomics, proteomics, and single-cell RNA sequencing (scRNA-seq). Utilizing tools like Scanpy and seurat, I have adeptly extracted, analyzed, and interpreted complex biological data. Specifically, through scRNA-seq data analysis, I identified critical targets essential for the development of serum-free media in cell-cultivated meat production.

Computational Biology

My research is deeply entrenched in plant cell transcriptomics, with a primary focus on identifying alternative proteins, reminiscent of Rubisco. I possess a robust foundation in utilizing molecular dynamics tools, notably QM/MM like Gromacs and Amber, to explore the complexities of enzymatic products and gauge their consequential impacts. Additionally, I specialize in the application of deep learning, especially graph neural networks, for discerning protein-protein interactions and mechanisms.

Looking forward to any academic networking and feel free to contact me!

News

• [2023/10] This website was born!

Publications

Most recent publications on Google Scholar.
^‡ indicates equal contribution.

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• All

Vitæ

Full Resume in PDF.

• The Pennsylvania State University 2023 - now

  Research Scientist
  Zhang Lab, Laboratory for alternative proteins,computational biology and bioinformatics
• Joes Future Food 2021 - 2023

  R&D Manager
  Creator of China's First Cultured Meat, Work on serum-free media development
• GenScript Summer 2021

  Research Scientist, Intern
  gene synthesis
• Jiangsu University of Science and Technology 2017 - 2021

  B.Eng. Student
  Food Engineering
  First Class Honours