Timestamps

----------- Day 1 ------------

[P1] Day 1 Morning Plenary Sessions

00:00:00 - 00:11:26 - Welcoming Remarks (Gary Bader)

00:11:26 - 00:46:34 - State of the Human Cell Atlas (Aviv Regev & Sarah Teichmann)

00:46:34 - 01:03:58 - Session 1: Uncovering the causal chain of cellular events leading to Alzheimer’s disease (Philip De Jager)

01:03:58 - 01:19:30 - Session 1: Multimodal decoding of human liver regeneration (Neil Henderson)

01:19:30 - 01:36:54 - Session 1: Functional variation in the human genome: Lessons from the transcriptome (Tuuli Lappalainen)

01:37:15 - 01:38:14 - Session 2: Evaluating and Enhancing our Approach to Building Atlases - introduction (John Marioni)

01:38:14 - 01:58:22 - Session 2: Update on Atlas integration pilots (Malte Luecken)

01:58:22 - 02:18:13 - Session 2: From draft to comprehensive human and comparative brain cell atlases (Ed Lein)

02:18:13 - 02:35:04 - Session 2: Insights from integration efforts (Alexandra-Chloé Villani and Shyam Prabhakar)

02:35:04 - 03:06:40 - Session 2: Panel discussion: How do we define Atlas 1.0?

03:06:40 - 03:16:07 - Updates from the HCA Data Ecosystem (John Randell)

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[P2] Day 1 Keynote #1

00:00:00 - 00:01:25 - Keynote introduction (Sagi Abelson)

00:01:27 - 00:36:32 - Keynote: What makes a stem cell a stem cell and how does it go bad? (John Dick)

00:36:32 - 00:45:40 - Audience Q&A

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[P3] Breakout session 1.1

00:00:00 - 00:03:48 - Breakout Session: Increasing accessibility/building great scientific communities introduction (Nir Yosef)

00:03:48 - 00:07:58 - Mariana Boroni, audience poll

00:07:58 - 01:11:43 - Group discussion

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[P4] Breakout session 1.2

00:00:24 - 00:09:37 - Breakout Session: Strengthening integration pipelines - Introduction (Emma Dann, Katy Borner)

00:09:37 - 00:15:35 - Integration pipelines within Genentech (Graham Heimberg)

00:15:44 - 00:20:34 - CELLxGENE integration pipelines (Ambrose Carr)

00:20:37 - 00:27:08 - HCA Integration QC Pipeline (Michaela F. Mueller)

00:27:40 - 01:11:03 - Panel discussion

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[P5] Breakout session 1.3

00:00:00 - 00:02:58 - Breakout Session: Ancestral diversity session introduction (Partha Majumder)

00:02:58 - 00:10:24 - Shyam Prabhakar slide presentation

00:10:29 - 00:11:55 - Sophia George slide presentation

00:11:55 - 01:10:23 - Group discussion

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[P6] Day 1 PM

00:00:00 - 00:00:22 - Lightning Talks: Introduction (Arathi Mani)

00:00:22 - 00:10:50 - The Asian Immune Diversity Atlas (AIDA): Determinants of diversity in circulating immune cell states across Asia (Kian Hong Kock)

00:10:50 - 00:23:24 - scRNA-Seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with clinical malaria (Collins Morang'a)

00:23:24 - 00:32:17 - Stem cell determination from scRNA-seq data using a protein network-based approach (Daniela Senra)

00:32:17 - 00:33:27 - Day 1 Closing (John Randell)

----------- Day 2 ------------

[P7] Day 2 AM

00:00:00 - 00:02:16 - Opening Remarks (Gary Bader)

00:02:16 - 00:21:26 - Spatial methods: A scalable platform for single-nucleus spatial genomics (Fei Chen)

00:21:26 - 00:36:40 - Spatial methods: A spatial thymus human cell atlas projected to a unidimensional tissue axis (Nadav Yayon)

00:36:40 - 00:51:57 - Spatial methods: Integrative single-cell spatial modeling of cell identity (Jian Ma)

00:51:57 - 00:52:13 - New dimensions to enable new questions introduction (Kerstin Meyer)

00:52:13 - 01:10:56 - Machine learning for single-cell regulatory genomics (Christina Leslie)

01:10:56 - 01:27:37 - Colonic Tissue Remodeling In A Mouse Model Of Inflammatory Bowel Disorder (Paolo Cadinu)

01:27:37 - 01:43:29 - Elucidating clonal mosaicism in human lymphocytes (Caleb Lareau)

01:43:29 - 01:44:08 - Session closing (John Randell)

[P8] Breakout session 2.1

00:00:00 - 00:14:30 - Breakout Session: Foundation models introduction and presentation (Fabian Theis, Bo Wang)

00:14:30 - 01:16:06 - Group discussion

[P9] Breakout session 2.2?

00:00:00 - 00:08:23 - Breakout Session: Spatial methods (experimental) - introduction and presentation (Xiao Wang, Kazumasa Kanemaru)

00:08:23 - 01:17:12 - Group discussion

[P10] Breakout session 2.3?

00:00:00 - 00:03:36 - Breakout Session: New dimensions to enable new questions introduction (John Marioni)

00:03:36 - 00:09:38 - Panel (John Marioni, Dana Pe'er, Aviv Regev)

00:09:38 - 01:11:35 - Group discussion

[P11] Day 2 PM

00:00:00 - 00:00:50 - Keynote introduction (Philip Awadalla)

00:00:50 - 00:38:32 - Keynote: Stem cell-derived human embryo models- are they close to becoming functional embryos? (Janet Rossant)

00:38:32 - 00:44:54 - Audience Q&A

00:45:01 - 00:45:08 - Lightning Talks introduction (Sergio Triana)

00:45:08 - 00:54:17 - Perspective Learning Continuous Dynamics from Time-lapsed Single-cell Data (Alexander Tong)

00:54:17 - 01:06:36 - Towards Causal Modeling of Single-cell Perturbation Data (Romain Lopez)

01:06:36 - 01:17:07 - Neural Optimal Transport for Single-Cell Biology (Charlotte Bunne)

01:17:18 - 01:17:42 - Frontiers in Deep Learning and the Human Cell Atlas introduction (Jinmiao Chen)

01:17:42 - 01:35:26 - scGPT: towards building a foundation model for single-cell multi-omics using generative AI (Bo Wang)

01:35:26 - 01:53:10 - Leveraging machine-learning paradigms towards single-subject prediction (Danilo Bzdok)

01:53:10 - 02:10:56 - Deep learning for cell type discovery (Maria Brbic)

02:10:56 - 02:14:01 - Session closing (Gary Bader)

[P12] Breakout session 3.1

00:00:00 - 00:13:52 - Breakout Session: Spatial methods (computational) introduction & presentation

00:13:52 - 00:13:52 - Group discussion

[P13] Breakout session 3.2

00:00:00 - 00:03:23 - Deep learning and machine learning for single cell mapping - introduction & presentation (Kieran Campbell, Amin Emad)

00:03:23 - 01:01:57 - Group discussion

[P14] Breakout session 3.3

00:00:00 - 00:04:06 - Breakout Session: Cross tissue integration/analysis introduction (Alexandra-Chloé Villani)

00:04:06 - 01:04:00 - Panel & group discussion (Kerstin Meyer, Shyam Prabhakar)

----------- Day 3 ------------

[P15] Day 3 AM

00:00:00 - 00:00:38 - Welcoming Remarks (Sophia George)

00:00:38 - 00:44:27 - Keynote: Making the most of large cohorts:?tools, thoughts and applications (Nir Yosef)

00:44:27 - 00:52:30 - Audience Q&A

00:52:37 - 00:52:30 - How should we think about cell function? introduction (Kristin Ardlie)

00:53:20 - 00:58:03 - Functional Tissue Units (Katy B?rner)

00:58:03 - 01:08:42 - Annotating cell function (David Osumi-Sutherland)

01:08:42 - 01:25:16 - Towards Integrative Human Organoid Atlases (Gray Camp)

01:25:16 - 01:41:20 - Investigating cancer cell control of their local cell environment (Brian Brown)

01:41:20 - 01:54:23 - Atlas of Transcribed Cis-Regulatory Elements Reveals Disease-Associated Regulatory Modules in Distinct Cell Populations (Jay Shin)

[P16] Breakout session 4.1

00:00:00 - 00:17:35 - Breakout Session: How should we think about, discover and validate cell function? introduction (Jesse Gillis, Sarah Crome)

00:17:35 - 00:58:38 - Group discussion

[P17] Breakout session 4.2

00:00:00 - 00:56:17 - Breakout Session: Emerging Ethical Issues introduction (Bartha Maria Knoppers) & group discussion

[P18] Breakout session 4.3

00:00:00 - 00:03:22 - Breakout Session: How will the atlas be used? introduction (Patricia Severino, Graham Heimberg)

00:03:22 - 01:01:20 - Group discussion

[P19] Day 3 Closing Sessions

00:00:00 - 00:32:34 - Closing Panel Discussion: What comes next? (Alexandra Chloé-Villani, Mariana Boroni, Aviv Regev, Maria Brbic, Fei Chen, Sarah Teichmann, Jay Shin)

00:32:45 - 00:44:25 - Closing Remarks (Gary Bader, Aviv Regev)