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Title: The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Journal Article · · Nature (London)
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  1. Stanford University
  2. University of Washington
  3. University of Florida
  4. Broad Institute
  5. Broad Institute of MIT and Harvard
  6. New York Genome Center
  7. Harvard Medical School
  8. Purdue University
  9. University of Pittsburgh
  10. Carnegie Mellon University
  11. University of California, San Diego
  12. Indiana University-Bloomington
  13. Washington University In Saint Louis
  14. National Institute of Health
  15. California Institute of Technology
  16. University of Rochester
  17. Institute of Molecular Life Sciences
  18. VISITORS
  19. Vanderbilt University
  20. Delft University of Technology
  21. Dana-Farber Cancer Institute
  22. Harvard University
  23. Marquette University,
  24. BATTELLE (PACIFIC NW LAB)
  25. Wellcome Sanger Institute
  26. Jack Baskin School of Engineering
  27. Opto-Knowledge Systems, Inc
  28. Pittsburgh Supercomputing Center
  29. University of South Dakota
  30. University of North Carolina at Chapel Hill
  31. Knowinnovation Inc
  32. University of Cambridge
  33. Massachusetts Institute of Technology
  34. National Heart, Lung, and Blood Institute
  35. National Institute of Diabetes and Digestive and Kidney Diseases
+ Show Author Affiliations

Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) aims to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, and the biomedical research community at large towards the shared vision of a comprehensive, accessible 3D molecular and cellular atlas of the human body, in health and various disease settings.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE
Contributing Organization:
HuBMAP Consortium
Grant/Contract Number:
AC05-76RL01830
OSTI ID:
1577443
Report Number(s):
PNNL-SA--146510
Journal Information:
Nature (London), Journal Name: Nature (London) Journal Issue: 7777 Vol. 574; ISSN 0028-0836
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

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An Immune Atlas of Clear Cell Renal Cell Carcinoma journal May 2017
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility journal August 2018
Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry journal April 2018
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seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus journal May 2017
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High Spatial Resolution Imaging of Mouse Pancreatic Islets Using Nanospray Desorption Electrospray Ionization Mass Spectrometry journal April 2018
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Integrating single-cell transcriptomic data across different conditions, technologies, and species journal April 2018
Ultrasensitive optical imaging with lanthanide lumiphores journal November 2017
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Image fusion of mass spectrometry and microscopy: a multimodality paradigm for molecular tissue mapping journal February 2015
Single-cell epigenomics: techniques and emerging applications journal October 2015
Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells journal February 2018
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+ journal March 2019
The Cardiac Atlas Project—an imaging database for computational modeling and statistical atlases of the heart journal July 2011
Principles of metadata organization at the ENCODE data coordination center journal January 2016
Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants journal October 2015
Factors That Influence the Quality of RNA From the Pancreas of Organ Donors journal January 2017
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing journal May 2015
Comprehensive single-cell transcriptional profiling of a multicellular organism journal August 2017
Single-cell ATAC-seq: strength in numbers journal August 2015
A benchmark for RNA-seq quantification pipelines journal April 2016
The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows journal January 2017
CellCycleTRACER accounts for cell cycle and volume in mass cytometry data text January 2018
Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry text January 2018
Network for Pancreatic Organ Donors with Diabetes (nPOD): developing a tissue biobank for type 1 diabetes: Tissue Biobank for Diabetes journal October 2012
Next-generation technologies for spatial proteomics: Integrating ultra-high speed MALDI-TOF and high mass resolution MALDI FTICR imaging mass spectrometry for protein analysis journal May 2016
An Immune Atlas of Clear Cell Renal Cell Carcinoma journal May 2017
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility journal August 2018
Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging journal August 2018
Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry journal January 2018
Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry journal May 2018
Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry journal April 2018
In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus journal October 2016
seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus journal May 2017
The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas journal November 2017
High Spatial Resolution Imaging of Mouse Pancreatic Islets Using Nanospray Desorption Electrospray Ionization Mass Spectrometry journal April 2018
Next Generation Histology-Directed Imaging Mass Spectrometry Driven by Autofluorescence Microscopy journal October 2018
Analysis of Tissue Specimens by Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry in Biological and Clinical Research journal February 2013
Single-cell chromatin accessibility reveals principles of regulatory variation journal June 2015
Scaling single-cell genomics from phenomenology to mechanism journal January 2017
Genetic effects on gene expression across human tissues journal October 2017
Toil enables reproducible, open source, big biomedical data analyses journal April 2017
Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors journal April 2018
Integrating single-cell transcriptomic data across different conditions, technologies, and species journal April 2018
Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data journal October 2018
Ultrasensitive optical imaging with lanthanide lumiphores journal November 2017
Single-cell in situ RNA profiling by sequential hybridization journal March 2014
Image fusion of mass spectrometry and microscopy: a multimodality paradigm for molecular tissue mapping journal February 2015
Power analysis of single-cell RNA-sequencing experiments journal March 2017
histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data journal August 2017
Single-cell epigenomics: techniques and emerging applications journal October 2015
CellCycleTRACER accounts for cell cycle and volume in mass cytometry data journal February 2018
Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells journal February 2018
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+ journal March 2019
Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues journal August 2019
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues journal May 2019
An interactive framework for whole-brain maps at cellular resolution journal December 2017
The FAIR Guiding Principles for scientific data management and stewardship journal March 2016
The Cardiac Atlas Project—an imaging database for computational modeling and statistical atlases of the heart journal July 2011
Principles of metadata organization at the ENCODE data coordination center journal January 2016
Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants journal October 2015
Factors That Influence the Quality of RNA From the Pancreas of Organ Donors journal January 2017
A probabilistic atlas and reference system for the human brain: International Consortium for Brain Mapping (ICBM)
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Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing journal May 2015
Comprehensive single-cell transcriptional profiling of a multicellular organism journal August 2017
A benchmark for RNA-seq quantification pipelines journal April 2016
Erratum to: A benchmark for RNA-seq quantification pipelines journal May 2016
Erratum to: A benchmark for RNA-seq quantification pipelines journal September 2016
The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows journal January 2017
Genetic effects on gene expression across human tissues text January 2017
Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry dataset January 2017
Compensation of signal spillover in suspension and imaging mass cytometry dataset January 2018
The Human Cell Atlas. text January 2017
Power analysis of single-cell RNA-sequencing experiments text January 2017
The FAIR Guiding Principles for scientific data management and stewardship. other January 2016
Genetic effects on gene expression across human tissues text January 2017
An Immune Atlas of Clear Cell Renal Cell Carcinoma text January 2017
CellCycleTRACER accounts for cell cycle and volume in mass cytometry data text January 2018
Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry text January 2018
histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data text January 2017
Simultaneous multiplexed imaging of mRNA and proteins with subcellular resolution in breast cancer tissue samples by mass cytometry text January 2018
Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry text January 2018
CellCycleTRACER accounts for cell cycle and volume in mass cytometry data text January 2018
The Human Cell Atlas text January 2017
The Human Cell Atlas journal December 2017

Cited By (9)

Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body journal March 2020
A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs journal January 2020
Key challenges facing data-driven multicellular systems biology text January 2018
3DPro: Querying Complex Three-Dimensional Data with Progressive Compression and Refinement dataset January 2022
Additional file 3 of Bi-order multimodal integration of single-cell data dataset January 2022
A brief history of human disease genetics journal January 2020
Key challenges facing data-driven multicellular systems biology journal October 2019
Cellular diversity and lineage trajectory: insights from mouse single cell transcriptomes journal January 2020
Key challenges facing data-driven multicellular systems biology text January 2018

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