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
Panos Roussos
Chair: Mikaela Koutrouli
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
12:00
Lunch
Lunch
13:30
Keynote
John Marioni
Chair: Emma Dann (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
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
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
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
Pertpy: scverse ecosystem framework for analyzing large-scale single-cell perturbation experiment
Stefan Peidli (scverse/Genentech)
11:30
Talk
PerTurbo: A scalable notebook framework for whole-transcriptome differential expression analysis and optimal design of single-cell CRISPR screens
Blaine Logan (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 (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
All Day
Workshop
CZI Workshop
Schedule TBA
Day 03 — Wednesday
November 19 · Tahoe
All Day
Workshop
Tahoe Workshop
Schedule TBA
This schedule is preliminary and provided for convenience. All sessions, times, and locations are subject to change.