AI Models of Gene Regulation: Codes, Circuits, Context, and Control (S2)
January 1-5, 2028
| Location to be Determined
Anshul B. Kundaje
Saturday, January 1, 2028
| 4:00–8:00 PM |
Registration |
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| 6:00–8:00 PM |
Welcome Mixer |
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| 8:00–8:10 AM |
Welcome Remarks |
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| 8:10–9:00 AM |
Keynote Address |
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Jay Ashok Shendure †, University of Washington
From Functional Genomics to Predictive Models of Gene Regulation |
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| 9:00–11:15 AM |
Cell State, Perturbation, and Trans Regulation |
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| 9:00–11:15 AM |
Panel Discussion 1: Aligning Experimental Design with AI Model Development |
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Sarah Teichmann †, Cambridge University
Mapping Cell States and Regulatory Programs with Single-Cell Genomics |
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Trey Ideker †, University of California, San Diego and University of Oxford
Building Cell Maps for Predictive Models of Disease |
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Shana Kelley †, Chan Zuckerberg Biohub Chicago and Northwestern University
AI-Guided CRISPR Screens for Functional Genomics and Target Discovery |
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Short Talk(s) Chosen from Abstracts
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|
| 9:30–9:50 AM |
Coffee Break |
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| 11:15–1:00 PM |
Poster Setup |
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| 11:15–5:00 PM |
On Own for Lunch |
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| 1:00–10:00 PM |
Poster Viewing |
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| 2:30–4:30 PM |
Symposia Spotlight 1: Connecting Cis and Trans Regulation Across Cellular Contexts |
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Short Talks Chosen from Abstracts
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| 4:30–5:00 PM |
Coffee Available |
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| 5:00–7:00 PM |
Predictive Models of Cellular Response, Disease, and Intervention |
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Berton Earnshaw †, University of Utah
Virtual Cell Models for Predicting Cellular Responses |
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Samantha A. Morris †, Brigham and Women’s Hospital
Dissecting Cell Identity through Network Inference and In Silico Perturbation |
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Christina V. Theodoris †, University of California, San Francisco
AI Models for Programming Cell State Trajectories |
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Short Talk(s) Chosen from Abstracts
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| 7:00–8:00 PM |
Social Hour with Dinner |
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| 8:00–11:00 AM |
Cis Regulation, Epigenetics, and Genome Function |
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Žiga Avsec †, Google DeepMind
Predicting Regulatory Function from DNA Sequence at Genome Scale |
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Joanna Wysocka †, Stanford University
Decoding Gene Regulatory Logic in Development and Evolution |
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Johannes Linder †, Helmholtz Munich
Predicting Gene Expression and RNA Processing from DNA Sequence |
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Christina S. Leslie †, Memorial Sloan-Kettering Cancer Center
Modeling Gene Regulation Across Differentiation and Disease |
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Short Talk(s) Chosen from Abstracts
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|
| 9:00–9:20 AM |
Coffee Break |
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| 11:00–1:00 PM |
Poster Setup |
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| 11:00–5:00 PM |
On Own for Lunch |
|
| 1:00–10:00 PM |
Poster Viewing |
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| 3:00–4:30 PM |
Career Roundtable |
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| 4:30–5:00 PM |
Coffee Available |
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| 5:00–7:00 PM |
Interpretable, Causal, and Generalizable Models of Gene Regulation |
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Anshul B. Kundaje, Stanford University
Interpretable Deep Learning Models of Regulatory Sequence and Chromatin |
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Sara-Jane Dunn †, Relation Therapeutics
Learning Causal Models of Gene Regulation from Perturbation Data |
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Peter Koo, Cold Spring Harbor Laboratory
Interpretable and Generalizable AI for Regulatory Genomics |
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Short Talk(s) Chosen from Abstracts
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| 7:00–8:00 PM |
Social Hour with Dinner |
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| 8:00–11:00 AM |
Spatial and Multimodal Models of Cell State and Regulation |
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| 8:00–11:00 AM |
Panel Discussion 2: Connecting Models Across Regulatory Scales |
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Bianca Dumitrascu †, Columbia University
Statistical and Machine Learning Models for Spatial and Multimodal Cell-State Data |
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Xiaowei Zhuang †, Harvard University
Spatially Resolved Molecular Imaging for Understanding Cellular Organization and Gene Regulation |
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Maria Brbic, EPFL
Multimodal Models for Decoding Cellular Organization and Function |
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Arjun Raj †, University of Pennsylvania and Cellular Intelligence
Predictive Models of Cell Signaling and Response |
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Short Talk(s) Chosen from Abstracts
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|
| 9:00–9:20 AM |
Coffee Break |
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| 11:00–5:00 PM |
On Own for Lunch |
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| 2:30–4:30 PM |
Symposia Spotlight 2: Decoding Cis-Regulatory Function with AI and Functional Genomics |
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Short Talks Chosen from Abstracts
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|
| 4:30–5:00 PM |
Coffee Available |
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| 5:00–6:45 PM |
Connecting Cis and Trans Regulation Across Cellular Contexts |
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Kyle Kai-How Farh †, Illumina
Atlas-Scale Perturb-seq for Predictive Models of Regulatory Programs and Cell State |
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Luca Pinello †, Massachusetts General Hospital / Harvard Medical School
Integrating Regulatory Sequence and Cellular Context to Predict Gene Expression |
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Jingtian Zhou †, Arc Institute
Integrating 3D Genome Organization, DNA Methylation, and Gene Expression Across Cell Types |
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Short Talk(s) Chosen from Abstracts
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| 6:45–7:00 PM |
Meeting Wrap-Up: Outcomes and Future Directions |
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| 7:00–8:00 PM |
Social Hour with Dinner |
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| 8:00–11:00 PM |
Entertainment |
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Wednesday, January 5, 2028
