Scholar
Xiaojie Qiu
Google Scholar ID: XlMd8TAAAAAJ
Assistant Professor, BASE, Department of Genetics & Computer Science, Stanford
Citations & Impact
Citations
15,033
H-index
23
i10-index
25
Publications
20
Co-authors
27
list available
Publications
Resume (English only)
Academic Achievements
- Pioneered several powerful computational software including Monocle 2/3, Dynamo, and Spateo. Actively working on building foundational models of single cells using attention-based transformers and diffusion models, aiming to develop an end-to-end predictive foundational software ecosystem, Aristotle, for quantitative spatiotemporal modeling of spatial and single-cell multiomics.
Research Experience
- Developed Monocle 2/3 software for inferring developmental trajectories from single-cell genomics data. Collaborated with Sreeram Kannan and Arman Rahimzamani on Scribe, a tool for learning causal regulatory networks. Co-created Dynamo with Yan Zhang, capable of making non-trivial predictions about the optimal set of reprogramming factors. Worked with Joseph Min to develop Dynast, an efficient quantification toolkit for metabolically labeled enabled scRNA-seq datasets. Currently leading a team developing the Spateo framework for multi-scale modeling of emerging spatial genomics datasets.
Education
- Ph.D. from the University of Washington under the guidance of Dr. Cole Trapnell; Postdoctoral fellow with Dr. Jonathan Weissman at the Whitehead Institute and MIT.
Background
- Research interests include single cell/spatial genomics, machine learning, and heart evolution/development/disease. Committed to unraveling and predicting the intricacies of gene regulatory networks and cell-cell interactions critical in mammalian cell fate transitions over time and space.
