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

Creators: Jain, Sanjay; Pei, Liming; Spraggins, Jeffrey M.; Angelo, Michael; Carson, James P.; Gehlenborg, Nils; Ginty, Fiona; Gonçalves, Joana P.; Hagood, James S.; Hickey, John W.; Kelleher, Neil L.; Laurent, Louise C.; Lin, Shin; Lin, Yiing; Liu, Huiping; Naba, Alexandra; Nakayasu, Ernesto S.; Qian, Wei-Jun; Radtke, Andrea; Robson, Paul; Stockwell, Brent R.; Van de Plas, Raf; Vlachos, Ioannis S.; Zhou, Mowei; Ahn, Kyung Jin; Allen, Jamie; Anderson, David M.; Anderton, Christopher R.; Curcio, Christine; Angelin, Alessia; Arvanitis, Constadina; Atta, Lyla; Awosika-Olumo, Demi; Bahmani, Amir; Bai, Huajun; Balderrama, Karol; Balzano, Leandro; Bandyopadhyay, Gautam; Bandyopadhyay, Shovik; Bar-Joseph, Ziv; Barnhart, Kurt; Barwinska, Daria; Becich, Michael; Becker, Laren; Becker, Winston; Bedi, Kenneth; Bendall, Sean; Benninger, Kathy; Betancur, David; Bettinger, Keith; Billings, Sunteasja; Blood, Philip; Bolin, Daniel; Border, Samuel; Bosse, Marc; Bramer, Lisa; Brewer, Maya; Brusko, Maigan; Bueckle, Andreas; Burke, Karl; Burnum-Johnson, Kristin; Butcher, Eugene; Butterworth, Elizabeth; Cai, Long¹; Calandrelli, Riccardo; Caldwell, Michael; Campbell-Thompson, Martha; Cao, Dongfeng; Cao-Berg, Ivan; Caprioli, Richard; Caraccio, Chiara; Caron, Anita; Carroll, Megan; Chadwick, Chrystal; Chen, Angela; Chen, Derek; Chen, Fei; Chen, Haoran; Chen, Jing; Chen, Li; Chen, Lu; Chiacchia, Kenneth; Cho, Sanghee; Chou, Peter; Choy, Lisa; Cisar, Cecilia; Clair, Geremy; Clarke, Laura; Clouthier, Kelly A.; Colley, Madeline E.; Conlon, Kristin; Conroy, John; Contrepois, Kevin; Corbett, Anthony; Corwin, Alex; Cotter, Daniel; Courtois, Elise; Cruz, Aaron; Csonka, Christopher; Czupil, Kimberley; Daiya, Vicky; Dale, Kali; Davanagere, Shakeel Ahamed; Dayao, Monica; de Caestecker, Mark P.; Decker, Aubrianna; Deems, Stephen; Degnan, David; Desai, Tushar; Deshpande, Vikrant; Deutsch, Gail; Devlin, Michelle; Diep, Dinh¹; Dodd, Carla; Donahue, Sean; Dong, Weixiu; dos Santos Peixoto, Rafael; Duffy, Michael; Dufresne, Martin; Duong, Thu Elizabeth; Dutra, Jennifer; Eadon, Michael T.; El-Achkar, Tarek M.; Enninful, Archibald; Eraslan, Gokcen; Eshelman, Diane; Espin-Perez, Almudena; Esplin, Edward D.; Esselman, Allison; Falo, Louis D.; Falo, Louis; Fan, Jean; Fan, Rong; Farrow, Melissa A.; Farzad, Negin; Favaro, Patricia; Fermin, Jamie; Filiz, Ferda; Filus, Shane; Fisch, Kathleen; Fisher, Eyal; Fisher, Stephen; Flowers, Katelyn; Flynn, William F.; Fogo, Agnes B.; Fu, Dongtao; Fulcher, James; Fung, Anthony; Furst, Derek; Gallant, Michael; Gao, Fu; Gao, Yu; Gaulton, Kyle; Gaut, Joseph P.; Gee, James; Ghag, Reetika R.; Ghazanfar, Shila; Ghose, Soumya; Gisch, Debora; Gold, Ilan; Gondalia, Aashay; Gorman, Brittney; Greenleaf, William; Greenwald, Noah; Gregory, Brian; Guo, Rong; Gupta, Rajat; Hakimian, Hunter; Haltom, Jeff; Halushka, Marc; Han, Kyu Sang; Hanson, Casey; Harbury, Pehr; Hardi, Josef; Harlan, Linda; Harris, Raymond C.; Hartman, Austin; Heidari, Elyas; Helfer, Jesse; Helminiak, David; Hemberg, Martin; Henning, Nathaniel; Herr, Bruce W.; Ho, Jonhan; Holden-Wiltse, Jeanne; Hong, Seung-Hyun; Hong, Young-Kwon; Honick, Brendan; Hood, Greg; Hu, Po; Hu, Qiwen; Huang, Molly; Huyck, Heidie; Imtiaz, Tamjid; Isberg, Olof Gerdur; Itkin, Maxim; Jackson, Dana; Jacobs, Marni; Jain, Yashvardhan; Jewell, David; Jiang, Lihua; Jiang, Zhenghui G.; Johnston, Sarah; Joshi, Pujan; Ju, Yingnan; Judd, Audra; Kagel, Adam; Kahn, Ari; Kalavros, Nikolaos; Kalhor, Kian; Karagkouni, Dimitra; Karathanos, Thomas; Karunamurthy, Arivarasan; Katari, Suhas; Kates, Heather; Kaushal, Madhurima; Keener, Nicholas; Keller, Mark; Kenney, Mariah; Kern, Colin; Kharchenko, Peter; Kim, Junhyong; Kingsford, Carl; Kirwan, Jessica; Kiselev, Vladimir; Kishi, Jocelyn; Kitata, Reta Birhanu; Knoten, Amanda; Kollar, Charles; Krishnamoorthy, Praveen; Kruse, Angela R. S.; Kuang, Da; Kundaje, Anshul; Kutschera, Eric; Kwon, Yumi; Lake, Blue B.; Lancaster, Samuel; Langlieb, Jonah; Lardenoije, Roy; Laronda, Monica; Laskin, Julia; Lau, Ken; Lee, Hayan; Lee, Maria; Lee, Mejeong; Levites Strekalova, Yulia; Li, Dongshunyi; Li, Jennifer; Li, Jilong; Li, Xiangtang; Li, Zhi; Liao, Yen-Chen; Liaw, Tiffany; Lin, Pei; Lin, Yulieh; Lindsay, Scott; Liu, Chunjie; Liu, Yang; Liu, Yuan; Lott, Marie; Lotz, Martin; Lowery, Lisa; Lu, Peiran; Lu, Xinyue; Lucarelli, Nicholas; Lun, Xiaokang; Luo, Zhifei; Ma, Jian; Macosko, Evan; Mahajan, Mayank; Maier, Libby; Makowski, Danika; Malek, Morad; Manthey, David; Manz, Trevor; Margulies, Kenneth; Marioni, John; Martindale, Matthew; Mason, Cayla; Mathews, Clayton; Maye, Peter; McCallum, Chuck; McDonough, Elizabeth; McDonough, Liz; Mcdowell, Hannah; Meads, Morgan; Medina-Serpas, Miguel; Melo Ferreira, Ricardo; Messinger, Jeffrey; Metis, Kay; Migas, Lukasz G.; Miller, Brendan; Mimar, Sayat; Minor, Brittany; Misra, Ravi; Missarova, Alsu; Mistretta, Christopher; Moens, Roger; Moerth, Eric; Moffitt, Jeffrey; Molla, Gesmira; Monroe, Matthew; Monte, Emma; Morgan, Mike; Muraro, Daniele; Murphy, Bob; Murray, Evan; Musen, Mark A.; Naglah, Ahmed; Nasamran, Chanond; Neelakantan, Taruna; Nevins, Stephanie; Nguyen, Hieu; Nguyen, Nam; Nguyen, Tram; Nguyen, Tri; Nigra, Deb; Nofal, Michel; Nolan, Garry; Nwanne, Gerald; O'Connor, Martin; Okuda, Kenichi; Olmer, Merissa; O'Neill, Kathleen; Otaluka, Nancy; Pang, Minxing; Parast, Mana; Pasa-Tolic, Ljiljana; Paten, Benedict; Patterson, Nathan Heath; Peng, Ting; Phillips, Gesina; Pichavant, Mina; Piehowski, Paul; Pilner, Hannah; Pingry, Ellie; Pita-Juarez, Yered; Plevritis, Sylvia; Ploumakis, Athanasios; Pouch, Alison; Pryhuber, Gloria; Puerto, Juan; Qaurooni, Danial; Qin, Ling; Quardokus, Ellen M.; Rajbhandari, Presha; Rakow-Penner, Rebecca; Ramasamy, Ramalakshmi; Read, David; Record, Elizabeth G.; Reeves, David; Ricarte, Allyson; Rodríguez-Soto, Ana; Ropelewski, Alexander; Rosario, Jean; Roselkis, Morla-Adames; Rowe, David; Roy, Tarun Kanti; Ruffalo, Matt; Ruschman, Nancy; Sabo, Angela; Sachdev, Nina; Saka, Sinem; Salamon, Diane; Sarder, Pinaki; Sasaki, Hiroshi; Satija, Rahul; Saunders, Diane; Sawka, Riley; Schey, Kevin; Schlehlein, Heidi; Scholten, David; Schultz, Sarah; Schwartz, Lauren; Schwenk, Melissa; Scibek, Robin; Segre, Ayellet; Serrata, Matthew; Shands, Walter; Shen, Xiaotao; Shendure, Jay; Shephard, Holly; Shi, Lingyan; Shi, Tujin; Shin, Dong-Guk; Shirey, Bill; Sibilla, Max; Silber, Michal; Silverstein, Jonathan; Simmel, Derek; Simmons, Alan; Singhal, Dhruv; Sivajothi, Santhosh; Smits, Thomas; Soncin, Francesca; Song, Qi; Stanley, Valentina; Stuart, Tim; Su, Hanquan; Su, Pei; Sun, Xin; Surrette, Christine; Swahn, Hannah; Tan, Kai; Teichmann, Sarah; Tejomay, Abhiroop; Tellides, George; Thomas, Kathleen; Thomas, Tracey; Thompson, Marissa; Tian, Hua; Tideman, Leonoor; Trapnell, Cole; Tsai, Albert G.; Tsai, Chia-Feng; Tsai, Leo; Tsui, Elizabeth; Tsui, Tina; Tung, Jason; Turner, Morgan; Uranic, Jackie; Vaishnav, Eeshit Dhaval; Varra, Sricharan Reddy; Vaskivskyi, Vasyl; Velickovic, Dusan; Velickovic, Marija; Verheyden, Jamie; Waldrip, Jessica; Wallace, Douglas; Wan, Xueyi; Wang, Allen; Wang, Fusheng; Wang, Meng; Wang, Shuoshuo; Wang, Xuefei¹; Wasserfall, Clive; Wayne, Leonard; Webber, James; Weber, Griffin M.; Wei, Bei; Wei, Jian-Jun; Weimer, Annika; Welling, Joel; Wen, Xingzhao; Wen, Zishen; Williams, MacKenzie; Winfree, Seth; Winograd, Nicholas; Woodard, Abashai; Wright, Devin; Wu, Fan; Wu, Pei-Hsun; Wu, Qiuyang; Wu, Xiaodong; Xing, Yi; Xu, Tiangyang; Yang, Manxi; Yang, Mingyu; Yap, Joseph; Ye, Dong Hye; Yin, Peng; Yuan, Zhou; Yun, Chi (Jina)¹; Zahraei, Ali; Zemaitis, Kevin; Zhang, Bo; Zhang, Caibin; Zhang, Chenyu; Zhang, Chi; Zhang, Kun; Zhang, Shiping; Zhang, Ted; Zhang, Yida; Zhao, Bingqing; Zhao, Wenxin; Zheng, Jia Wen; Zhong, Sheng; Zhu, Bokai; Zhu, Chenchen; Zhu, Diming; Zhu, Quan; Zhu, Ying; Börner, Katy; Snyder, Michael P.; HuBMAP Consortium

1. California Institute of Technology

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.

Copyright and License

Errata

An Author Correction to this article was published on 01 March 2024

Code Availability

The HuBMAP Consortium GitHub at https://github.com/hubmapconsortium has 120 repositories that support data ingest, analysis, visualization and search plus HRA construction and usage. Documentation is available at https://software.docs.hubmapconsortium.org/apis.html.

Acknowledgement

We thank L. M. McGuire, SciStories, F. Goncalves, H. Schlehlein and V. A. Deshpande for their efforts in designing and creating graphics. We thank A. Honkala for assistance with manuscript formatting. We thank Z. Galis from the National Heart, Lung, and Blood Institute for many useful comments. Support for title page creation and format was provided by AuthorArranger, a tool developed at the National Cancer Institute. The authors gratefully acknowledge NIH HuBMAP grants U54HL165442 and U01HL166058 (L.P.); U54DK134301 and OT2OD033753 (S.J.); U54EY032442, U54DK120058 and U54DK134302 (J.M.S.); OT2OD033756 and OT2OD026671 (K.B.); UH3CA246635 (N.L.K.); UG3CA256967 (H.L.); U54HG010426 (M.P.S.); UH3CA246633 (M.A.); U54HD104393 (L.C.L. and P.R.); U54DK127823 (E.S.N., J.P.C. and W.-J.Q.); OT2OD033758 (N.G.); UH3CA246594 (F.G.); U54EY032442 and U54DK134302 (J.P.G.); U54HL145611 (S.L. and Y.L.); U01HG012680 (A.N.); U54DK120058, U54EY032442 and U54DK134302 (B.R.S.); UG3CA256959 (M.Z.); and U54HL165440 (I.S.V.). The authors are also supported by these grants: 2U01DK114933, P50DK133943 and U24DK135157 (S.J.); U54HL145608 and U54HL165443 (J.S.H.); U24CA268108 and U2CDK114886 (K.B.); Department of Defense W81XWH-22-1-0058 and Additional Ventures (L.P.). J.W.H. was supported by an NIH T32 Fellowship (T32CA196585) and an American Cancer Society: Roaring Fork Valley Postdoctoral Fellowship (PF-20-032-01-CSM). This work was supported, in part, by the Intramural Research Program of the NIH, National Institute of Allergy and Infectious Diseases (NIAID) and National Cancer Institute (NCI) (A.J.R.).

Conflict of Interest

The authors declare the following competing interests. F.G. is an employee of GE Research. B.R.S. is an inventor on patents and patent applications involving small-molecule-drug discovery and the 3F3 anti-Ferroptotic Membrane (3F3-FMA) antibody; co-founded and serves as a consultant to Inzen Therapeutics, Nevrox, Exarta Therapeutics and ProJenX; and serves as a consultant to Weatherwax Biotechnologies and Akin Gump Strauss Hauer and Feld. M.P.S. is a co-founder and an advisory board member of Personalis, Qbio, January AI, Mirvie, Filtricine, Fodsel, Lollo and Protos. I.S.V. consults for Guidepoint Global, Cowen, Mosaic and NextRNA. N.G. is a co-founder and an equity owner of Datavisyn. H.L. is a co-founder and an equity owner of ExoMira Medicine. The remaining authors declare no competing interests.

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