From January 13-15, 2026, the Brain Cell Atlas: From Data to Knowledge Workshop brought together researchers and data scientists to address the challenges and opportunities in the analyses and integration of the brain cell atlas data by leveraging recent artificial intelligence and machine learning (AI/ML) advancements. By fostering collaboration and innovation, the workshop created a roadmap for building a scalable, community-driven brain cell atlas that serves as a foundational resource for studying brain function and disorders, accelerating discoveries in neuroscience and precision medicine. View workshop session recordings here.
The past decade has witnessed thriving cell atlas research activities in elucidating human cell types and their organization principles. The NIH BRAIN Initiative launched a pilot 3-year BRAIN Initiative Cell Census Consortium (BICCC) in 2014, followed by two successive large-scale 5-year consortia, BRAIN Initiative Cell Census Network (BICCN) in 2017 and BRAIN Initiative Cell Atlas Network (BICAN) in 2022, aiming to create comprehensive spatially resolved brain cell atlases in human and other mammalian species as a foundational framework for the study of brain function and disorders. Massive amounts of brain cell atlas data have been collected using approaches including single-cell RNA-seq and ATAC-seq, spatial transcriptomics, DNA and chromatin conformation and modifications, immunoimaging, calcium imaging, electrophysiology, histology, MRI, whole genome sequencing, and clinical metadata. However, these data remain to be fully integrated to reap the maximum value. From January 13-15, 2026, the Brain Cell Atlas: From Data to Knowledge Workshop brought together researchers and data scientists to address the challenges and opportunities in the analyses and integration of the brain cell atlas data by leveraging recent artificial intelligence and machine learning (AI/ML) advancements.
The 3-day interactive virtual event featured keynote presentations, panel discussions, and demonstrations of AI/ML-driven tools for data analysis and integration. By fostering collaboration and innovation, the workshop created a roadmap for building a scalable, community-driven brain cell atlas that serves as a foundational resource for studying brain function and disorders, accelerating discoveries in neuroscience and precision medicine.
View workshop session recordings here.
Agenda Day 1 of the Brain Cell Atlas: From Data to Knowledge Workshop
| Time (ET) | Agenda Item |
|---|---|
| 11:30 AM - 11:50 AM | Opening Remarks by John Ngai (Director, NIH BRAIN Initiative) Introduction of BRAIN Initiative Cell Atlas Program and the Workshop by Yong Yao (Program Officer, NIMH) |
| 11:50 AM - 12:30 PM | Session 1: Data Analysis, Annotation, and Integration Keynote Presentations
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| 12:50 PM - 2:20 PM | Panel 1-1: Brain Cell Atlas Data Annotation and Integration Moderators: Aparna Bhaduri and Rahul Satija Panelists: Anton Arkhipov, Trygve Bakken, Evan Biederstedt, Xiaoyin Chen, Joseph Ecker, Jesse Gillis, Mike Hawrylycz, David Kleinfeld, Arnold Kriegstein, Fenna Krienen, Ed Lein, Boudewijn Lelieveldt, Brian Long, Eran Mukamel, Tomasz Nowakowski, Bing Ren, Davide Risso, Jay Ashok Shendure, Kimberly Siletti, Kimberly Smith, Noah Snyder-Mackler, Zizhen Yao, Jimmie Ye, Guo-cheng Yuan, Hongkui Zeng, Jingchun Zhu, Xiaowei Zhuang |
| 2:20 PM - 2:40 PM | Keynote Presentation Training sequence-to-function models on single-cell brain atlases to decipher cis-regulatory logic and design cell type specific enhancers by Stein Aerts, University of Leuven |
| 2:40 PM - 4:20 PM | Keynote Presentation Training sequence-to-function models on single-cell brain atlases to decipher cis-regulatory logic and design cell type specific enhancers by Stein Aerts, University of Leuven |
| 2:40 PM - 4:20 PM | Panel 1-2: Challenges and Opportunities in Leveraging AI/ML Advancements Moderators: Peter Koo and Hongkui Zeng Panelists: Reza Abbasi-Asi, Stein Aertz, Anton Arkhipov, Ziga Avsec, Mark Gerstein, Bingxing Huo, Trey Ideker, Viren Jain, David R Kelley, Jure Leskovec, Jingyi Jessica Li, Jie Liu, Yuan Luo, Partha Mitra, Elizabeth Purdom, Davide Risso, Yusuf Roohani, Rahul Satija, Sudipta Sengupta, Jay Ashok Shendure, Fabian Theis, Daifeng Wang, Wenjin Jim Zheng, Jian Zhou, James Zou |
| 4:20 PM - 4:30 PM | Day 1 Wrap Up and Conclusions |
Day 2 of the Brain Cell Atlas: From Data to Knowledge Workshop
| Time (ET) | Agenda Item |
|---|---|
| 11:30 AM-12:00 PM | Plenary Session Summary and Highlights of Day |
| 12:00 PM - 12:20 PM | Session 2: Brain Cell Atlas Data Ecosystem and Knowledge Pipelines Keynote Presentations AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model by Žiga Avsec, Google DeepMind |
| 12:40 PM - 2:10 PM | Panel 2-1: Brain Cell Atlas Data to Knowledge Pipelines Moderators: Michael Hawrylycz and Tim Tickle Panelists: Paola Arlotta, Anita Bandrowski, Evan Biederstedt, Dawen Cai, Jean Fan, David Feng, Satrajit Ghosh, Jesse Gillis, Maximilian Haeussler, Brian Herb, Bingxing Huo, David Kleinfeld, Maryann Martone, Partha Mitra, Kimberly Siletti, Sarah Teichmann, Carol Thompson, Ting Wang, Alan Watson, Brock Wester, Owen White, Guo-Qiang Zhang |
| 2:10 PM - 2:30 PM | Keynote Presentation Foundation Models and Agentic AI: Building the Intelligent Infrastructure for the Brain Cell Atlas by Jure Leskovec, Stanford University |
| 2:30 PM - 4:20 PM | Panel 2-2: AI-Enabled Brain Cell Atlas Knowledge Base Training sequence-to-function models on single-cell brain atlases to decipher cis-regulatory logic and design cell type specific enhancers by Stein Aerts, University of Leuven |
| 2:40 PM - 4:20 PM | Panel 1-2: Challenges and Opportunities in Leveraging AI/ML Advancements Moderators: Shoaib Mufti and Richard Scheuermann Panelists: Giorgio Ascoli, Laura Brattain, Jean Fan, David Feng, Satrajit Ghosh, David Haussler, Trey Ideker, Viren Jain, Jure Leskovec, Daofeng Li, Mingyao Li, Jie Liu, Yuan Luo, Jeremy Miller, Tyler Mollenkopf, Qing Nie, Burke Rosen, Panos Roussos, Sudipta Sengupta, Valentine Svensson, Fabian Theis, Wenjin Jim Zheng, Jingtian Zhou, James Zou |
| 4:20 PM - 4:30 PM | Day 2 Wrap Up and Conclusions Summary and Highlights of Day 2 -Toward an Integrated Data Ecosystem and Knowledgebase |
Day 3 of the Brain Cell Atlas: From Data to Knowledge Workshop
| Time (ET) | Agenda Item |
|---|---|
| 11:30 AM - 12:10 PM | Session 3: Brain Cell Atlases in Health and Disorders Keynote Presentations
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| 12:30 PM - 2:00 PM | Panel 3-1: Brain Cell Atlases for Brain Disorder Research Moderators: Evan Macosko and Nenad Sestan Panelists: Aparna Bhaduri, Long Cai, Joseph Ecker, Rongxin Fang, Mark Gerstein, Dirk Keene, Yongsoo Kim, Genevieve Konopka, Arnold Kriegstein, Ed Lein, Chongyuan Luo, Steven McCarroll, Tomasz Nowakowski, Mercedes Paredes, Bing Ren, Panos Roussos, Kimberly Siletti, Jason Stein, Sarah Teichmann, Gustavo Turecki, Hyejung Won, Xiangmin Xu |
| 2:00 PM - 2:20 PM | Keynote Presentation Cell type specific analysis of neural circuits and their dynamics at the Allen Institute for Neural Dynamics by Karel Svoboda, Allen Institute for Neural Dynamics |
| 2:20 PM - 3:50 PM | Panel 3-2: Brain Cell Atlases for Neuroscience Research Moderators: Jeremiah Cohen and Xiaowei Zhuang Panelists: Margarita Behrens, Dawen Cai, Jayaram Chandrashekar, Xiaoyin Chen, Carlo Colantuoni, Song-Lin Ding, Hongwei Dong, Winrich Freiwald, Hao Huang, Yongsoo Kim, David Kleinfeld, Genevieve Konopka, Helen Lai, Burke Rosen, Karel Svoboda, Bosiljka Tasic, Cindy van Velthoven, Zhuhao Wu, Xiangmin Xu, Peng Yin |
| 4:00 PM - 4:30 PM | Plenary Session Workshop Summary, Next Steps and Roadmap |