Coffee + light bites 

Coffee Break
Sponsored by

• Welcome Remarks + Overview of meeting: Jose Ordovas-Montanes & Alexandra-Chloe Villani
• State of HCA: Vision and Community: ​​Aviv Regev
• State of HCA: The HCA 1.0 Atlases: Sarah Teichmann

Session Chair: Aviv Regev

• Roser Vento Tormo: Pan-organ atlas of the female reproductive system across the lifespan
• Margo Emont: Insights from Adipose Atlas 1.0
• Carla Cohen: Cartography of movement: assembling the human musculoskeletal atlas
• Maria Kasper: Consensus Human Skin Cell Atlas defines cutaneous cell type codex and unifying principles for transferable tissue references
• Matthias Kretzler: HCA Kidney Atlas: Defining Nephron Function and Failure as Foundation for Mechanistic Kidney Trials
• Q&A + Ask Me Anything

Coffee + light bites 

Meet-the-Editors

Barbara Cheifet
Editor, Nature Biotechnology
Madhura Mukhopadhyay
Senior Editor, Nature Methods
Sara Rohban
Scientific Editor, Cell Genomics (Cell Press) 

Coffee Break Sponsored by

Session Chair: Alexandra-Chloe Villani

• Alexandra-Chloe Villani: Introduction
• Gary Reynolds: Immune and Genetic Diversity Bionetworks
• Jose Ordovas-Montanes: A community-built gut cell atlas
• Michela Noseda: The human heart atlas: a community-built reference to understand health and disease
• Kevin Matthew Byrd: From Cell Atlases to Virtual Tissues: Integrating Archival and Living Human Tissue System
• Q&A + Ask Me Anything

Session Chair: Gary Bader

• Darren Segale (Illumina): Multiomics, Connected: A unified path from sample to insight across bulk, single‑cell, and spatial

Breakout Room - Bray

Session Description
Join HCA Civic Science Fellow, Krithika Venkataraman, over lunch to explore how the Human Cell Atlas is creating impact beyond scientific discoveries through social and infrastructural contributions—such as shared systems, capacity-strengthening initiatives, and trust networks—and how we can better surface and value these outcomes alongside traditional scientific metrics.

Please note that lunch will be provided in the room for all attendees.

Session Chair: Aviv Regev

Jure Leskovec: From Cells to Cures: Building AI Systems That Reason Across Biological Scales

Session Chair: Muzlifah Haniffa

• Muzlifah Haniffa: Introduction to 2.0 priorities
• Kai Kessenbrock: Breast Bionetwork
• Muzlifah Haniffa: Human Developmental Cell Atlas
• Martijn Nawijn: The integrated lung cell atlas (ILCA) - the version-2 atlas of the Lung Bionetwork
• Trygve Bakkan: Cross-species brain atlas for disease mapping and tools
• Q&A + Ask Me Anything

Coffee + light bites
 

Meet-the-Editors

Barbara Cheifet
Editor, Nature Biotechnology
Madhura Mukhopadhyay
Senior Editor, Nature Methods
Sara Rohban
Scientific Editor, Cell Genomics (Cell Press) 
 

Coffee Break  Sponsored by

Session Chair: Gary Bader

• Emily Martersteck (Biotechne Spatial): Transforming Tissue into Insight with Same-Section Spatial Multiomics
• George Emanuel (Vizgen): What's Next on MERSCOPE Ultra™: Roadmap Updates and Volumetric Tissue Mapping
• Jens Durruthy Durruthy (Element): High Dimensional Cell and Tissue Multiomics with AVITI24
• Charlie Roco (Parse Biosciences): Advances in Scalable Single Cell with Evercode Whole Transcriptome
• Zohar Shipony (Ultima Genomics): Unleash the power of genomics at scale
• Ozge Getkin (Takara): A transformative approach to single-cell spatial omics

1. Cross-Tissue integration and annotation to achieve a unified reference
2. From V1 Atlases to HCA Foundation Models
3. Building Reference Atlases across Lifespan
4. Building on and Leveraging V1 Atlases to Map Environmental Exposures

Breakout Session Leaders: Kevin Matthew Byrd & Gary Reynolds

This session will explore the importance of cross-tissue integration and annotation in advancing our understanding of how cell states and identities vary across tissues, developmental stages, and disease contexts. Participants will discuss landmark examples that have successfully established integrative frameworks for the field, similar to the role HCA Lung v1 played in shaping early atlas efforts, and consider how these models can inform future atlas-building initiatives. The discussion will also examine the major technical, computational, and social barriers that currently limit cross-tissue integration, including challenges related to data harmonization, annotation standards, collaboration, and infrastructure. Through this conversation, the session aims to identify the resources, community practices, and collaborative strategies needed to overcome these obstacles and enable more unified, scalable, and impactful atlas efforts across the HCA community.

Breakout Session Leaders: Malte Luecken & Maria Brbic

This session will examine the opportunities and challenges involved in developing an HCA foundation model capable of supporting a broad range of biological and translational applications. Participants will discuss the key tasks and benchmarks such models should be evaluated against, as well as the standards for robustness, interpretability, scalability, and long-term utility that the HCA community should expect. The conversation will also explore how to balance scientific rigor and real-world applicability, including questions around when data quality is “good enough” to support model development versus waiting for more complete or ideal datasets. In addition, the session will consider whether the HCA should focus on creating a shared base model alone or also support fine-tuned models optimized for specific downstream tasks and community needs. Finally, participants will discuss strategies to encourage large-scale data sharing and re-use, recognizing that successful foundation models will require unprecedented levels of interoperable, high-quality data contributed across the HCA ecosystem.
 

Breakout Session Leaders: Deanne Taylor & Rui Chen

This session will focus on the integration of pediatric, developmental, and aging atlases with existing HCA v1 atlases to create a more comprehensive view of human biology across the lifespan. Participants will discuss the need for analytical frameworks that enable integration across individual studies, institutions, and age groups, while also considering how future study designs can more intentionally incorporate lifespan diversity from the outset. The session will examine key data gaps within current atlases and explore opportunities to incorporate complementary consortium datasets that could expand demographic, developmental, and longitudinal representation. In addition, the discussion will address the technical, computational, and social barriers that currently limit these efforts, including challenges related to interoperability, metadata harmonization, coordination across communities, and infrastructure. Participants will also consider whether the current HCA Biological Network structure adequately supports lifespan-focused integration and identify potential organizational or collaborative changes needed to advance this area of research.

Breakout Session Leader: Sophia George & Yesid Cuesta Astroz

This session will explore how the HCA and broader scientific community can better integrate exposome research into atlas-building efforts to understand how chronic and acute environmental exposures influence human health across populations and contexts. Participants will discuss emerging worldwide exposome initiatives and the opportunities they present for connecting environmental, socioeconomic, clinical, and single-cell datasets at scale. A major focus of the session will be on the challenges of data harmonization, including the standardization and alignment of datasets collected across institutions, countries, and disciplines. The discussion will also address how advances in environmental genomics can be translated into frameworks that are meaningful for environmental governance and public health decision-making. Finally, the session will consider strategies for effective community engagement and collaboration across government, academia, industry and biotechnology, and lay communities to ensure that exposome-focused atlas efforts are impactful, inclusive, and broadly actionable.

Light bites + drinks to be served

Coffee + Light Bites provided

Coffee Break
Sponsored by

Speaker: Alexandra-Chloe Villani

• Michael Schnall-Levin (10x Genomics): From the Beginning, For Years to Come

• Shyam Prabhakar
• Holger Heyn
• Gary Bader
• Kondwani Jambo
• Session Q&A

This session is sponsored by 10x Genomics.

Coffee + light bites 

Meet-the-Editors

Barbara Cheifet
Editor, Nature Biotechnology
Madhura Mukhopadhyay
Senior Editor, Nature Methods
Sara Rohban
Scientific Editor, Cell Genomics (Cell Press) 
 

Coffee Break Sponsored by

Session Chair: Patricia Severino

Speakers:
Maria Brbic
Eric Lander
John Tsang
Faisal Mahmood
 

Session Chair: Holger Heyn

• Patrick Bogard (Roche): The Power of One: AXELIOS 1

Session Chair: Holger Heyn

• Stellaromics: TBD
• Amos Lee (Meteor Biotech): Decoding Cellular Networks: The Synergy of AI and SLACS in Spatial Omics
• Pixelgen: TBD
• Patrick Murphy (Oxford Nanopore Technologies): Expanding Spatial and Single Cell Transcriptomics Discovery with Full-Length Transcript Sequencing
• BD Bioscience: TBD
• Michael Kubal (Singleron Bioscience): Single-Cell Multi-Omics to Precision Medicine 2.0
   

Session Chair: Aviv Regev

David Altshuler: Humanizing Drug Discovery

Session Chair: Eric Lander

Panelists:
David Altshuler
Muzlifah Haniffa
Aviv Regev
Sarah Teichmann
Alexandra-Chloe Villani

1. The Future of Spatial Technology: Breakthroughs, Challenges, and Opportunities
2. Integrating Atlases for Human Disease
3. Expanding Diversity in Contributors and Data
4. Serving the Community with the HCA Spatial Data Portal

Coffee + light bites 

Meet-the-Editors

Barbara Cheifet
Editor, Nature Biotechnology
Madhura Mukhopadhyay
Senior Editor, Nature Methods
Sara Rohban
Scientific Editor, Cell Genomics (Cell Press) 
 

Coffee Break Sponsored by

Breakout Session Leaders: Sami Farhi & Holger Heyn

This session will examine the challenges and opportunities associated with generating and integrating highly heterogeneous large-scale spatial datasets, particularly in the context of the 30 Billion Cells spatial program and related initiatives. Participants will discuss how additional modalities, including advanced imaging approaches, proteomics, and other emerging technologies, could be incorporated into the existing program and through complementary future efforts to create richer, multidimensional atlases. The session will also highlight immediate technical barriers that could benefit from focused community collaboration through future workshops, hackathons, and method-development efforts, including challenges such as cell segmentation, data standardization, and computational scalability. Finally, the discussion will explore strategies for integrating and harmonizing data across platforms and modalities to enable more unified, interoperable, and biologically meaningful spatial atlas resources.

Breakout Session Leaders: Musa Mhlanga &  Shyam Prabhakar 

This session will explore how longitudinal patient studies, integrated with genetic and molecular data, can advance understanding of disease mechanisms and cellular pathogenesis within HCA 2.0. Participants will discuss the importance of collecting whole genome sequencing (WGS) and histopathology data in parallel with single-cell datasets, and how these complementary data layers can strengthen the identification of disease-associated cell states while helping distinguish correlation from causation in single-cell analyses. The conversation will also examine how approaches such as single-cell eQTL mapping, longitudinal sampling, and multimodal integration can provide deeper insight into disease progression, treatment response, and inter-individual variability. In addition, the session will consider what additional layers of information, including clinical, imaging, environmental, and functional data, may be necessary to build more comprehensive and mechanistic models of human disease across the HCA ecosystem.
 

Breakout Sessions Leaders: Kian Hong Kock & Patricia Severino

This session will focus on strategies to broaden participation and representation across the HCA ecosystem by expanding cohort diversity, increasing access to spatial technologies, and engaging a wider community in data analysis and interpretation. Participants will discuss barriers that currently limit equitable participation in atlas generation and analysis, including disparities in infrastructure, funding, training, and access to technology across regions and institutions. The conversation will explore approaches for diversifying cohorts and datasets to ensure more globally representative atlases, while also identifying opportunities to democratize access to emerging spatial and multimodal technologies. In addition, the session will consider how to move beyond a relatively small circle of data contributors by developing more accessible analytical tools, training initiatives, collaborative frameworks, and community-driven models that enable broader participation in computational analysis and biological discovery.

Breakout Session Leaders: Muzlifah Haniffa & Nils Gehlenborg
 

This discussion will focus on defining the future of the HCA Portal by identifying the primary user communities it should serve, prioritizing the essential features required for the initial release, and exploring opportunities for community engagement in its ongoing development. Participants will be invited to share their perspectives on user needs, critical functionality, and how they would like to help shape the design, implementation, and long-term evolution of the portal to ensure it effectively supports the goals of the Human Cell Atlas community.

Session Chair: Jose Ordovas-Montanes

Panelists:
Alexandra-Chloe Villani
Holger Heyn
Shyam Prabhakar
Muzlifah Haniffa

Coffee + Light Bites

Location: Zambezi Room (75 Ames-3rd floor)

9am - 11am: Bionetwork Coordinators Meeting (By Invitation Only)

11:30am - 1:00pm: DEO Meeting (By Invitation Only) (Lunch meeting, Bionetwork Coordinators welcome to attend)

Location: Auditorium (415M-Ground floor)

Session Chair: Musa Mhlanga

9am - 9:45am: Global Exposome Seminar (Open Session)

Session description: This seminar will feature scientific presentations highlighting current research and emerging opportunities in the field. Building on these talks, a panel discussion will explore potential next steps for future collaborations, focusing on areas with strong scientific momentum, funding interest, and a critical mass of engaged researchers. The discussion will be informed by insights from the June 16 Breakout Session led by Sophie George and Yesid Cuesta Astorz.

9:45am - 10:15am: Break

10:15am - 11:15am: Global Exposome Seminar Panel/Discussion (Open Session)

1pm - 2pm:  Equity Working Group + Diversity Task Force Discussion (Open Session)

Session description: This interactive session will discuss (HCA) 2.0 roadmap and Diversity Task Force (DTF) recommendations for enhancing equity and plans for implementation. Participants will help shape strategies to ensure global representation across the consortium, democratize access to spatial technologies and resources, and expand opportunities for involvement in leadership, decision-making, and scientific impact. The discussion will focus on identifying actionable steps and metrics to foster a more inclusive, accessible, and globally representative community. 
 

Location: Monadnock Room (415M-1st floor)

9am - 12:30pm: Immune Cross-Tissue Jamboree, Part I (By Invitation Only)

12:30pm - 2pm: Lunch Break

2pm - 4pm: Immune Cross-Tissue Jamboree, Part II (By Invitation Only)

Location: Joshua Tree Room (75A-M1 floor)

10:30am - 1pm: Ethics Session

Session Description: We will have consultative ethics sessions covering emerging challenges in human cell atlas research, from developmental and pediatric studies to the opportunities and responsibilities of HCA 2.0.

• Ma'n Zawati: EWG consultative session: AI and HCA 2.0 (Open Session)
• Deanne Taylor: EWG consultative session: Development/Pediatric (Open Session)
• EWG Working Lunch Meeting (By Invitation Only)