Human Cell Atlas

The Human Cell Atlas (HCA) is a global collaboration to map and characterize all cells in a healthy human body: cell types, numbers, locations, relationships, and molecular components. It will require advances in single-cell RNA sequencing, image-based transcriptomics and proteomics, tissue handling protocols, data analysis, and more. Once complete, it will be a fundamental resource for scientists, allowing them to better understand how healthy cells work, and what goes wrong when disease strikes.

The idea for the HCA grew from an enthusiastic scientific community, and represents a collaborative effort to increase the impact of single-cell biology by federating results from different organs, cell types, experimental approaches, and countries, without suppressing the dynamism of individual communities and projects. The HCA project welcomes participation by scientists, physicians, and engineers around the world. CZI joins groups such as the Wellcome Trust, the European Bioinformatics Institute (EMBL-EBI), the Broad Institute, the Sanger Institute, and UC Santa Cruz to support this work. We are supporting the HCA through a variety of mechanisms, including:

1. Helping to build a data coordination platform

We are working together with international genomics leaders to formulate, fund, and jointly build a unified data coordination platform that will enable data sharing across researchers and research institutes. The size and scope of this project requires collaboration between bioinformatics and genomics experts in academia, as well as the software expertise of CZI engineers. Collaborations are underway regarding this element of the HCA with EMBL-EBI, the Broad Institute, and UC Santa Cruz. Partnership with EMBL-EBI will ensure that all data standards meet the exacting international criteria for data access and data sharing that EBI must follow, such as permanent maintenance of data through EBI and deposition of all data into the European Nucleotide Archive or the European Genome-phenome Archive, as appropriate.

Learn more about the Data Coordination Platform

2. Helping to build computational tools

Our computational biologists and software engineers are working collaboratively with the scientific community to develop tools for analyzing sequencing and imaging data. In all cases, we work closely with scientists and computational researchers to identify bottlenecks in current approaches, and identify opportunities for improving existing tools. This may include developing new tools, or building consensus around formats, standards, or benchmark datasets. An example of an open-source repository reflecting current work around standardizing analysis pipelines for image-based transcriptomics can be found here.

3. Grantmaking

We are funding 38 pilot projects to help build new technologies, best practices, and data analysis techniques for the Human Cell Atlas. These individuals and organizations will further the goal of the HCA by accelerating our understanding in key areas including the brain, immune system, tissue handling and processing, gastrointestinal, skin, and technological development.

Read the original Request for Applications

View each project in detail

We are funding 85 one-year projects to develop computational tools, algorithms, visualizations, and benchmark datasets in support of the Human Cell Atlas. Participants in this project will collaborate with each other and with us to accelerate progress, facilitate communications, and maximize open dissemination of the resulting tools.

Read the original Request for Applications

View each project in detail

We are supporting the continued progress of the Human Cell Atlas through the creation of Seed Networks that will enable growth, solidify collaborations, and help generate valuable data and tools for the first draft of the Human Cell Atlas. Seed Networks consist of at least three principal investigators, including at least one computational biologist or software engineer, together with additional computational biologists, engineers, experimental biologists, and/or physicians.

Read the original Request for Applications

View each project in detail

The CZI Science team would like to thank the following people for their contributions to the peer review process for the Human Cell Atlas grants program:

Zhirong Bao, Memorial Sloan Kettering Cancer Center

Josh Batson, Chan Zuckerberg Biohub

Ewan Birney, European Bioinformatics Institute

Bernd Bodenmiller, University of Zurich

Richard Bonneau, New York University

Titus Brown, University of California, Davis

Carlos Bustamante, Stanford University

Thomas Caswell, Brookhaven National Laboratory

Susan E. Celniker, Lawrence Berkeley National Laboratory

Vivian Cheung, University of Michigan

Bruce Conklin, University of California, San Francisco Gladstone Institutes

Ian Dunham, European Bioinformatics Institute

Joe Ecker, Salk Institute for Biological Studies

Michael Eisen, Lawrence Berkeley National Laboratory

Mark Ellisman, Lawrence Berkeley National Laboratory

Scott Fraser, University of Southern California

Kelly Frazer, University of California, San Diego

Lars Fugger, University of Oxford

Chris Gorgolewski, Stanford University

Tom Gingeras, Cold Spring Harbor Laboratory

Robert Glaeser, Lawrence Berkeley National Laboratory

Joe Gleeson, University of California, San Deigo

Berthold Gottgens, University of Cambridge

Nick Grishin, University of Texas Southwestern Medical Center

David Haussler, University of California, San Diego

Nat Heintz, The Rockefeller University

James Hicks, University of Southern California

Viren Jain, Google

Jim Karkanias, Chan Zuckerberg Biohub

Manolis Kellis, Massachusetts Institute of Technology

Purvesh Khatri, Stanford University

Paul Klenerman, University of Oxford

Leonid Kruglyak, University of California, Los Angeles

Peter Kuhn, University of Southern California

Patrick La Riviere, University of Chicago

Manuel Leonetti, Chan Zuckerberg Biohub

Jure Leskovec, Stanford University

Loren Looger, Janelia Research Campus

Susan Mango, Harvard University

Vilas Menon, Janelia Research Campus

Sayan Mukherjee, Duke University

Dyche Mullins, University of California, San Francisco

Max Ogden, Dat

Uwe Ohler, Max Delbrück Center for Molecular Medicine

Matteo Pellegrini, University of California, Los Angeles

Katie Pollard, University of California, San Francisco, Gladstone Institutes

Chris Ponting, The University of Edinburgh

Rickard Sandberg, Karolinska Institutet

Mark B. Schnitzer, Stanford University

Ehud Shapiro, Weizmann Institute of Science

Padmanee Sharma, MD Anderson Cancer Center

Robert Singer, Albert Einstein College of Medicine

Paul Sternberg, California Institute of Technology

Scott Sternson, Janelia Research Campus

J Seth Strattan, Stanford University

Susan Strome, University of California, Santa Cruz

Saeed Tavazoie, Columbia University

Robert Tijan, University of California, Berkeley

Laura Waller, University of California, Berkeley

Jonathan Weissman, University of California, San Francisco

Jake VanDerPlas, University of Washington

Ramnik Xavier, Harvard University

Plus other anonymous reviewers