Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

Sanjay Jain; Liming Pei; Jeffrey M Spraggins; Michael Angelo; James P Carson; Nils Gehlenborg; Fiona Ginty; Joana P Gonçalves; James S Hagood; John W Hickey; Neil L Kelleher; Louise C Laurent; Shin Lin; Yiing Lin; Huiping Liu; Alexandra Naba; Ernesto S Nakayasu; Wei-Jun Qian; Andrea Radtke; Paul Robson; Brent R Stockwell; Raf Van de Plas; Ioannis S Vlachos; Mowei Zhou; HuBMAP Consortium; Katy Börner; Michael P Snyder

doi:10.1038/s41556-023-01194-w

Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

Nat Cell Biol. 2023 Aug;25(8):1089-1100. doi: 10.1038/s41556-023-01194-w. Epub 2023 Jul 19.

Authors

Sanjay Jain^#^{1

2

3}, Liming Pei^#⁴, Jeffrey M Spraggins^#⁵, Michael Angelo⁶, James P Carson⁷, Nils Gehlenborg⁸, Fiona Ginty⁹, Joana P Gonçalves¹⁰, James S Hagood¹¹, John W Hickey¹², Neil L Kelleher¹³, Louise C Laurent¹⁴, Shin Lin¹⁵, Yiing Lin¹⁶, Huiping Liu¹⁷, Alexandra Naba¹⁸, Ernesto S Nakayasu¹⁹, Wei-Jun Qian¹⁹, Andrea Radtke²⁰, Paul Robson²¹, Brent R Stockwell²², Raf Van de Plas²³, Ioannis S Vlachos^{24

25}, Mowei Zhou²⁶; HuBMAP Consortium; Katy Börner^#²⁷, Michael P Snyder^#²⁸

Collaborators

HuBMAP Consortium:
Kyung Jin Ahn, Jamie Allen, David M Anderson, Christopher R Anderton, Christine Curcio, Alessia Angelin, Constadina Arvanitis, Lyla Atta, Demi Awosika-Olumo, Amir Bahmani, Huajun Bai, Karol Balderrama, Leandro Balzano, Gautam Bandyopadhyay, Shovik Bandyopadhyay, Ziv Bar-Joseph, Kurt Barnhart, Daria Barwinska, Michael Becich, Laren Becker, Winston Becker, Kenneth Bedi, Sean Bendall, Kathy Benninger, David Betancur, Keith Bettinger, Sunteasja Billings, Philip Blood, Daniel Bolin, Samuel Border, Marc Bosse, Lisa Bramer, Maya Brewer, Maigan Brusko, Andreas Bueckle, Karl Burke, Kristin Burnum-Johnson, Eugene Butcher, Elizabeth Butterworth, Long Cai, Riccardo Calandrelli, Michael Caldwell, Martha Campbell-Thompson, Dongfeng Cao, Ivan Cao-Berg, Richard Caprioli, Chiara Caraccio, Anita Caron, Megan Carroll, Chrystal Chadwick, Angela Chen, Derek Chen, Fei Chen, Haoran Chen, Jing Chen, Li Chen, Lu Chen, Kenneth Chiacchia, Sanghee Cho, Peter Chou, Lisa Choy, Cecilia Cisar, Geremy Clair, Laura Clarke, Kelly A Clouthier, Madeline E Colley, Kristin Conlon, John Conroy, Kevin Contrepois, Anthony Corbett, Alex Corwin, Daniel Cotter, Elise Courtois, Aaron Cruz, Christopher Csonka, Kimberley Czupil, Vicky Daiya, Kali Dale, Shakeel Ahamed Davanagere, Monica Dayao, Mark P de Caestecker, Aubrianna Decker, Stephen Deems, David Degnan, Tushar Desai, Vikrant Deshpande, Gail Deutsch, Michelle Devlin, Dinh Diep, Carla Dodd, Sean Donahue, Weixiu Dong, Rafael Dos Santos Peixoto, Michael Duffy, Martin Dufresne, Thu Elizabeth Duong, Jennifer Dutra, Michael T Eadon, Tarek M El-Achkar, Archibald Enninful, Gokcen Eraslan, Diane Eshelman, Almudena Espin-Perez, Edward D Esplin, Allison Esselman, Louis D Falo, Louis Falo, Jean Fan, Rong Fan, Melissa A Farrow, Negin Farzad, Patricia Favaro, Jamie Fermin, Ferda Filiz, Shane Filus, Kathleen Fisch, Eyal Fisher, Stephen Fisher, Katelyn Flowers, William F Flynn, Agnes B Fogo, Dongtao Ann Fu, James Fulcher, Anthony Fung, Derek Furst, Michael Gallant, Fu Gao, Yu Gao, Kyle Gaulton, Joseph P Gaut, James Gee, Reetika R Ghag, Shila Ghazanfar, Soumya Ghose, Debora Gisch, Ilan Gold, Aashay Gondalia, Brittney Gorman, William Greenleaf, Noah Greenwald, Brian Gregory, Rong Guo, Rajat Gupta, Hunter Hakimian, Jeff Haltom, Marc Halushka, Kyu Sang Han, Casey Hanson, Pehr Harbury, Josef Hardi, Linda Harlan, Raymond C Harris, Austin Hartman, Elyas Heidari, Jesse Helfer, David Helminiak, Martin Hemberg, Nathaniel Henning, Bruce W Herr 2nd, Jonhan Ho, Jeanne Holden-Wiltse, Seung-Hyun Hong, Young-Kwon Hong, Brendan Honick, Greg Hood, Po Hu, Qiwen Hu, Molly Huang, Heidie Huyck, Tamjid Imtiaz, Olof Gerdur Isberg, Maxim Itkin, Dana Jackson, Marni Jacobs, Yashvardhan Jain, David Jewell, Lihua Jiang, Zhenghui G Jiang, Sarah Johnston, Pujan Joshi, Yingnan Ju, Audra Judd, Adam Kagel, Ari Kahn, Nikolaos Kalavros, Kian Kalhor, Dimitra Karagkouni, Thomas Karathanos, Arivarasan Karunamurthy, Suhas Katari, Heather Kates, Madhurima Kaushal, Nicholas Keener, Mark Keller, Mariah Kenney, Colin Kern, Peter Kharchenko, Junhyong Kim, Carl Kingsford, Jessica Kirwan, Vladimir Kiselev, Jocelyn Kishi, Reta Birhanu Kitata, Amanda Knoten, Charles Kollar, Praveen Krishnamoorthy, Angela R S Kruse, Kuang Da, Anshul Kundaje, Eric Kutschera, Yumi Kwon, Blue B Lake, Samuel Lancaster, Jonah Langlieb, Roy Lardenoije, Monica Laronda, Julia Laskin, Ken Lau, Hayan Lee, Maria Lee, Mejeong Lee, Yulia Levites Strekalova, Dongshunyi Li, Jennifer Li, Jilong Li, Xiangtang Li, Zhi Li, Yen-Chen Liao, Tiffany Liaw, Pei Lin, Yulieh Lin, Scott Lindsay, Chunjie Liu, Yang Liu, Yuan Liu, Marie Lott, Martin Lotz, Lisa Lowery, Peiran Lu, Xinyue Lu, Nicholas Lucarelli, Xiaokang Lun, Zhifei Luo, Jian Ma, Evan Macosko, Mayank Mahajan, Libby Maier, Danika Makowski, Morad Malek, David Manthey, Trevor Manz, Kenneth Margulies, John Marioni, Matthew Martindale, Cayla Mason, Clayton Mathews, Peter Maye, Chuck McCallum, Elizabeth McDonough, Liz McDonough, Hannah Mcdowell, Morgan Meads, Miguel Medina-Serpas, Ricardo Melo Ferreira, Jeffrey Messinger, Kay Metis, Lukasz G Migas, Brendan Miller, Sayat Mimar, Brittany Minor, Ravi Misra, Alsu Missarova, Christopher Mistretta, Roger Moens, Eric Moerth, Jeffrey Moffitt, Gesmira Molla, Matthew Monroe, Emma Monte, Mike Morgan, Daniele Muraro, Bob Robert Murphy, Evan Murray, Mark A Musen, Ahmed Naglah, Chanond Nasamran, Taruna Neelakantan, Stephanie Nevins, Hieu Nguyen, Nam Nguyen, Tram Nguyen, Tri Nguyen, Deb Nigra, Michel Nofal, Garry Nolan, Gerald Nwanne, Martin O'Connor, Kenichi Okuda, Merissa Olmer, Kathleen O'Neill, Nancy Otaluka, Minxing Pang, Mana Parast, Ljiljana Pasa-Tolic, Benedict Paten, Nathan Heath Patterson, Ting Peng, Gesina Phillips, Mina Pichavant, Paul Piehowski, Hannah Pilner, Ellie Pingry, Yered Pita-Juarez, Sylvia Plevritis, Athanasios Ploumakis, Alison Pouch, Gloria Pryhuber, Juan Puerto, Danial Qaurooni, Ling Qin, Ellen M Quardokus, Presha Rajbhandari, Rebecca Rakow-Penner, Ramalakshmi Ramasamy, David Read, Elizabeth G Record, David Reeves, Allyson Ricarte, Ana Rodríguez-Soto, Alexander Ropelewski, Jean Rosario, Morla-Adames Roselkis, David Rowe, Tarun Kanti Roy, Matt Ruffalo, Nancy Ruschman, Angela Sabo, Nina Sachdev, Sinem Saka, Diane Salamon, Pinaki Sarder, Hiroshi Sasaki, Rahul Satija, Diane Saunders, Riley Sawka, Kevin Schey, Heidi Schlehlein, David Scholten, Sarah Schultz, Lauren Schwartz, Melissa Schwenk, Robin Scibek, Ayellet Segre, Matthew Serrata, Walter Shands, Xiaotao Shen, Jay Shendure, Holly Shephard, Lingyan Shi, Tujin Shi, Dong-Guk Shin, Bill Shirey, Max Sibilla, Michal Silber, Jonathan Silverstein, Derek Simmel, Alan Simmons, Dhruv Singhal, Santhosh Sivajothi, Thomas Smits, Francesca Soncin, Qi Song, Valentina Stanley, Tim Stuart, Hanquan Su, Pei Su, Xin Sun, Christine Surrette, Hannah Swahn, Kai Tan, Sarah Teichmann, Abhiroop Tejomay, George Tellides, Kathleen Thomas, Tracey Thomas, Marissa Thompson, Hua Tian, Leonoor Tideman, Cole Trapnell, Albert G Tsai, Chia-Feng Tsai, Leo Tsai, Elizabeth Tsui, Tina Tsui, Jason Tung, Morgan Turner, Jackie Uranic, Eeshit Dhaval Vaishnav, Sricharan Reddy Varra, Vasyl Vaskivskyi, Dusan Velickovic, Marija Velickovic, Jamie Verheyden, Jessica Waldrip, Douglas Wallace, Xueyi Wan, Allen Wang, Fusheng Wang, Meng Wang, Shuoshuo Wang, Xuefei Wang, Clive Wasserfall, Leonard Wayne, James Webber, Griffin M Weber, Bei Wei, Jian-Jun Wei, Annika Weimer, Joel Welling, Xingzhao Wen, Zishen Wen, MacKenzie Williams, Seth Winfree, Nicholas Winograd, Abashai Woodard, Devin Wright, Fan Wu, Pei-Hsun Wu, Qiuyang Wu, Xiaodong Wu, Yi Xing, Tianyang Xu, Manxi Yang, Mingyu Yang, Joseph Yap, Dong Hye Ye, Peng Yin, Zhou Yuan, Chi Jina Yun, Ali Zahraei, Kevin Zemaitis, Bo Zhang, Caibin Zhang, Chenyu Zhang, Chi Zhang, Kun Zhang, Shiping Zhang, Ted Zhang, Yida Zhang, Bingqing Zhao, Wenxin Zhao, Jia Wen Zheng, Sheng Zhong, Bokai Zhu, Chenchen Zhu, Diming Zhu, Quan Zhu, Ying Zhu

Affiliations

¹ Department of Medicine, Washington University School of Medicine, St Louis, MO, USA. sanjayjain@wustl.edu.
² Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA. sanjayjain@wustl.edu.
³ Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA. sanjayjain@wustl.edu.
⁴ Center for Mitochondrial and Epigenomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. lpei@pennmedicine.upenn.edu.
⁵ Department of Cell and Developmental Biology and the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA. jeff.spraggins@vanderbilt.edu.
⁶ Department of Pathology, Stanford School of Medicine, Stanford, CA, USA.
⁷ Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA.
⁸ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
⁹ GE Research Center, Niskayuna, NY, USA.
¹⁰ Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands.
¹¹ Department of Pediatrics (Pulmonology) and Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
¹² Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
¹³ Departments of Medicine, Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA.
¹⁴ Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
¹⁵ Division of Cardiology, University of Washington School of Medicine, Seattle, WA, USA.
¹⁶ Department of Surgery, Washington University School of Medicine, St Louis, MO, USA.
¹⁷ Departments of Pharmacology, Medicine (Hematology and Oncology), Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
¹⁸ Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA.
¹⁹ Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
²⁰ Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
²¹ The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
²² Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA.
²³ Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands.
²⁴ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
²⁵ Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA, USA.
²⁶ Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
²⁷ Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA. katy@indiana.edu.
²⁸ Department of Genetics, Stanford School of Medicine, Stanford, CA, USA. mpsnyder@stanford.edu.

^# Contributed equally.

Abstract

The Human BioMolecular Atlas Program (HuBMAP) aims to create a multi-scale spatial atlas of the healthy human body at single-cell resolution by applying advanced technologies and disseminating resources to the community. As the HuBMAP moves past its first phase, creating ontologies, protocols and pipelines, this Perspective introduces the production phase: the generation of reference spatial maps of functional tissue units across many organs from diverse populations and the creation of mapping tools and infrastructure to advance biomedical research.

Publication types

Review

Abstract

Publication types

Grants and funding