Conference Schedule
Day 01 — Monday
November 17 · LKSC
08:00
Break
Breakfast
09:00
Talk
Welcome Session
Emma Dann (scverse)
09:15
Talk
State of scverse
Mikaela Koutrouli (scverse)
09:45
Keynote
John Marioni
Chair: Emma Dann (scverse)
10:30
Break
Coffee
11:00
Talk
Clonally resolved Perturb-seq uncovers lineage-level responses to genetic perturbation
Dillon Lue (Princeton)
11:15
Talk
PerTurbo: A scalable Bayesian framework for whole-transcriptome differential expression analysis and optimal design of single-cell CRISPR screens
Logan Blaine (Harvard)
11:30
Talk
ChronoSeq: minute scale automated scRNA-seq for real time profiling of perturbations
Kanishk Asthana (UCSD)
11:45
Talk
Sponsor Talk: Towards a virtual cell signaling model rooted in human development
Samantha Dale Strasser (Somite Therapeutics)
12:00
Lunch
Lunch
13:30
Keynote
Panos Roussos
Chair: Mikaela Koutrouli (scverse)
14:15
Talk
Universal MPRA: Zero-shot regulatory element activity prediction across tissue and cell types
Laura Gunsalus (Genentech)
14:30
Talk
LIVI: An interpretable deep learning framework for mapping genetic effects at cellular resolution using population-scale single-cell RNA sequencing data
Danai Vagiaki (EMBL)
14:45
Talk
Attention-based multiple instance learning predicts CAR T cell therapy outcomes from infusion product single-cell RNA-seq data and identifies engineering targets in large B cell lymphoma
Kameron Rodrigues (Stanford)
15:00
Break
Coffee
15:30
Panel
Agentic Workflows for Bioinformatics
Jonah Cool (Anthropic), Vega Shah (NVIDIA), Loic Royer (CZ Biohub), Kexin Huang (Stanford). Chair: Giovanni Palla (scverse)
16:30
Poster
Poster Session 1
18:00
Social
Reception
Day 02 — Tuesday
November 18 · LKSC
08:00
Break
Breakfast
09:00
Talk
Opening Day 2 / Housekeeping
Danila Bredikhin (scverse)
09:15
Keynote
Erika Alden de Benedictis
Chair: Danila Bredikhin (scverse)
10:00
Talk
SPLISOSM: Unlocking hidden isoform landscapes in spatial transcriptomics data
Jiayu Su (Columbia)
10:15
Talk
Robust integration of sparse single-cell alternative splicing and gene expression data with SpliceVI
Smriti Vaidyanathan (Columbia)
10:30
Talk
Sponsor Talk: Powering the Virtual Cell: Frontier Datasets for AI-Driven Biology
Johnny Yu (Tahoe Therapeutics)
10:45
Poster
Poster Session 2
12:00
Lunch
Lunch
13:30
Keynote
Elham Azizi
Chair: Pau Badia (scverse)
14:15
Talk
X-Atlas/Orion: Genome-wide Perturb-seq datasets via a scalable fix-cryopreserve platform for training dose-dependent biological foundation models
Ann Huang (Xaira)
14:30
Talk
Decoding sequence determinants of gene expression across cellular and disease states
Avantika Lal (Genentech)
14:45
Talk
MACS3: A versatile peak caller for single-cell genomics
Tao Liu (Roswell Park)
15:00
Talk
Sponsor Talk: Solving complex challenges in human health at the intersection of AI and biology
Angela Oliveira Pisco (CZI)
15:15
Break
Coffee
15:45
Talk
grassp: An integrated framework for graph-based analysis of spatial/subcellular proteomics
Max Frank (CZ Biohub)
16:00
Talk
InterSCellar: surface-based cell interaction volume analysis in 3D spatial omics
Eunice Lee (Harvard)
16:15
Talk
EasyVitessce: Adding interactivity to scverse single-cell and spatial biology plots
Eric Mörth (Harvard)
16:30
Panel
Closing Remarks
scverse core team
Day 03 — Wednesday
November 19 · Arc Institute
08:30
Break
Arrival and registration
Session 1
Generating Perturb-seq data
09:00
Talk
Opening Remarks
Yusuf Roohani (Arc Institute)
09:10
Talk
Designing and running a Perturb-seq experiment: Common challenges and considerations for data generation
Tony Hua, Po-Yuan Tung (Arc)
Session 2
Processing data from Perturb-seq experiments
10:00
Talk
Cyto, Cell-eval: High throughput processing of sequencing records, quality control, evaluating perturbation effect prediction
Noam Teyssier (Arc Institute)
10:30
Talk
Assessing perturbation effects and differential expression analysis
Basak Eraslan (Arc Institute)
11:00
Talk
Studying perturbation effects one cell at a time with scvi-tools
Can Ergen (scverse)
11:30
Talk
PerTurbo: A scalable notebook framework for whole-transcriptome differential expression analysis and optimal design of single-cell CRISPR screens
Logan Blaine (Harvard)
12:00
Lunch
Lunch
Session 3
Building machine learning models using single-cell transcriptomics data
13:00
Talk
scBaseCount: AI-agent curated, uniformly processed single-cell data for over 500 million cells
Nick Youngblut, Chris Carpenter (Arc)
13:30
Talk
Working with big AnnData stores
Ilan Gold (scverse)
14:00
Talk
Heimdall: A modular framework for tokenization in single-cell foundation models
Ellie Haber, Shahul Alam (Carnegie Mellon University)
14:30
Talk
State: Predicting perturbation effects across diverse cellular contexts
Abhinav Adduri (Arc Institute)
Session 4
Evaluating progress towards a virtual cell. Planning ahead for VCC2
15:15
Panel
Evaluating progress towards a virtual cell. Planning ahead for VCC2
Dave Burke, Alexander Dobin, Noam Teyssier, Hani Goodarzi (Arc Institute), Stefan Peidli (scverse/Genentech), VCC Participating Team. Moderator: Yusuf Roohani (Arc Institute)
16:00
Social
Networking Happy Hour Mixer (with posters)
Day 03 — Wednesday
November 19 · CZI
08:00
Break
Check in at CZI - Light breakfast available
09:00
Talk
Session One: Foundation (CxG) & Community Landscape
Max Lombardo (Biohub)
09:30
Talk
Session Two: GPU-Accelerated Single-Cell Analysis in collaboration with NVIDIA
TJ Chen (NVIDIA), Gary Burnett (NVIDIA)
10:30
Break
Break
11:00
Talk
Session Three: Community Showcase I
Luca Marconato (3D Spatial Data)
12:00
Lunch
Lunch
13:15
Talk
Session Four: VCP Model Development Ecosystem, Benchmarking, and AI Workspaces
Elizabeth Fahsbender (Biohub), Katrina Kalantar (Biohub), Alec Tarashansky (Biohub), Max Lombardo (Biohub)
14:15
Talk
Session Five: Community Showcase II - LazySlide: Accessible and interoperable whole slide image analysis in the scverse
Yimin Zheng
15:15
Break
Break
15:45
Talk
Session Six: Community Showcase III - SIMBA+, ProteoImager, and Celldega
Junxi Feng (SIMBA+), Zhenru Zhou (ProteoImager), Huan Wang (Celldega)
16:45
Talk
Closing
Max Lombardo (Biohub)
Day 03 — Wednesday
November 19 · Tahoe
08:00
Break
Breakfast
09:00
Talk
Welcome / opening remarks
09:15
Talk
GPU-accelerated single-cell data analysis at scale with rapids-singlecell
Severin Dicks (scverse)
10:15
Talk
scDataset: Scalable data loading for deep learning on large-scale single-cell omics
Davide d'Ascenzo (University of Milan)
10:45
Break
Coffee break
11:00
Talk
Build your own MCP servers and AI agents with BioContextAI
Darius Schaub (University Medical Center Hamburg-Eppendorf)
12:00
Talk
SigSpace: An LLM-based agent for drug response signature interpretation
Siddhant Sanghi (UC Davis)
12:30
Talk
Kepler AI: Agents for large-scale biomedical dataset mining
Kepler team
13:00
Lunch
Lunch
14:00
Talk
Tahoe-x1: Scaling perturbation-trained single-cell foundation models to 3 billion parameters
Shreshth Gandhi (Tahoe Therapeutics)
14:45
Break
Coffee break
15:00
Talk
Enrichment analysis with decoupler
Pau Badia i Mompel (scverse)
16:00
Panel
Panel Discussion
Tahoe Therapeutics
16:45
Social
Networking / mingle

This schedule is preliminary and provided for convenience. All sessions, times, and locations are subject to change.