Advances of AI methods in single cell spatial omics
Workshop at PSB2026
Workshop at PSB2026
January 3–7, 2026 | Big Island, Hawaii
This workshop will bring together researchers developing and applying artificial intelligence to analyze spatially resolved single-cell data, including spatial transcriptomics, proteomics, and metabolomics. This rapidly evolving field presents unique computational challenges and opportunities for discovering spatially organized cellular interactions and disease mechanisms. The workshop will feature invited talks, contributed presentations, and discussions focused on cutting-edge methods and their biological applications.
Invited Speakers
Ben Raphael, Professor of Computer Science, Princeton University, is a leading researcher in computational genomics and cancer genomics, with a strong focus on spatial transcriptomics and tumor heterogeneity. His work has pioneered algorithmic methods for analyzing single-cell and spatial omics data, particularly in understanding cellular organization in cancer. His research has led to widely used computational tools for inferring spatial domains, tumor evolution, and network/pathway analysis of genetic variants.
Theodore Alexandrov, Assistant Professor at the Department of Pharmacology, UCSD, is a global expert in spatial metabolomics and computational mass spectrometry. He has developed machine learning methods to analyze spatial omics data, particularly for metabolite localization and tissue microenvironment profiling, with applications in drug discovery & therapy development.
Xuegong Zhang, Professor at Tsinghua University, is a pioneering researcher in computational biology and bioinformatics. His work focuses on developing AI-driven algorithms including foundation models to improve the analysis and interpretation of single cell multiomics data and spatially resolved gene expression data. His contributions have significantly advanced cell type identification, spatial domain detection, and embedding learning of cells. Xuegong currently serves as the vice-president of the International Society for Computational Biology (ISCB).
Workshop Schedule (Jan 3, 1:00-4:45)
1:00-1:05 Opening remarks - 5min
1:05-1:35 Invited talk - Ben Raphael
Modeling tissue organization across space and time
1:35-1:45 Inferring cell migration, differentiation, and signaling from spatial transcriptomics
Joshua Welch*, Yichen Gu, Jialin Liu and Justin Lee
1:45-1:55 Mapping lineage-resolved scRNA-seq data with spatial transcriptomics using TemSOMap
Xinhai Pan, Yiru Chen, Alejandro Danies-Lopez, and Xiuwei Zhang*
1:55-2:05 Learning mechanistic models of gene regulatory dynamics from spatial multi-omic datasets
Suryanarayana Maddu*, Victor Chardes and Michael Shelley
2:05-2:20 Break
2:20-2:50 Invited talk - Xuegong Zhang
AI Models for Building Virtual Cells in Spatial Contexts
2:50-3:00 DeepCell at 10 years – AI for spatial biology
David Van Valen*
3:00-3:10 A scalable human brain cell atlas foundation model dissects the cellular immune codes and cognitive resilience
Feixiong Chen*
3:10-3:20 STDrug: a computational method to use spatial transcriptomics to aid personalized drug-reposition recommendation
Yiwen Yang, Thatchayut Unjitwattana, Shu Zhou, Abdullah Karaaslanli, Xiaotong Yang, Yi Liu, Tianao Chen, Yuheng Du, Suguru Kadomoto, Yijun Guo, Haodong Liang, Evan Keller and Lana Garmire*
3:20-3:30 Break
3:30-4:00 Invited talk 3 - Theodore Alexandrov
Title TBA
4:00-4:10 CELLestial: an end-to-end spatial proteomics framework for rapid cell type annotation and interactive visualization at scale for foundation model fine-tuning and large-scale clinical trial analyses
Audrey Lacy*, Muhammad Shaban, Andressa Dias Costa, Faisal Mahmood, Brian Wolpin, Jonathan Nowak and Simona Cristea*
4:10-4:20 STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition
Chuhanwen Sun and Yi Zhang*
4:20-4:45 Panel discussion - 25min
Call for Abstracts (expired)
We will select short talks from submitted abstracts. Each abstract is limited to 400 words. Abstracts need to be submitted to EasyChair using this link by August 20th 18th, 2025 (any time zone) for consideration of talks. If you have problem submitting your abstracts through EasyChair, you can email your submission to xiuwei.zhang@gatech.edu before the deadline. Notifications on acceptance of abstracts will be sent to authors by September 11th 5th, 2025. We do not have a poster session at this workshop.
Organizers
Lana Garmire (lgarmire@med.umich.edu), Associate Professor at University of Michigan
Xiuwei Zhang (xiuwei.zhang@gatech.edu), Associate Professor at Georgia Tech
Joshua Levy (Joshua.Levy@cshs.org), Assistant Professor at Cedars-Sinai Medical Center