Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

The Extended Polydimensional Immunome Characterization (EPIC) web-based reference and discovery tool for cytometry data

A Publisher Correction to this article was published on 28 May 2020

This article has been updated

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: EPIC bio-informatics toolkit.
Fig. 2: Exploration of EPIC data and user-generated data.
Fig. 3: EPIC data analytics using an elderly cohort and user uploaded data.

Data availability

The EPIC web portal and its associated database and analytic tools will be made available for investigation as described in the manuscript to researchers who do not belong to a for-profit entity.

Code availability

The web applications Sci-Atlas Miner and Discovery Tool can be freely accessed on all modern web browsers at The source code of the R Shiny applications and R scripts for the creation of Immune Atlas data files are available on request for academic use.

Change history

  • 28 May 2020

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.


  1. 1.

    Gibbons, D. et al. Nat. Med. 20, 1206–1210 (2014).

    CAS  Article  Google Scholar 

  2. 2.

    van den Broek, T., Borghans, J. A. M. & van Wijk, F. Nat. Rev. Immunol. 18, 363–373 (2018).

    Article  Google Scholar 

  3. 3.

    Reen, D. J. Vaccine 16, 1401–1408 (1998).

    CAS  Article  Google Scholar 

  4. 4.

    Beck, R. & Lam-Po-Tang, P. R. Immunol. Cell Biol. 72, 440–444 (1994).

    CAS  Article  Google Scholar 

  5. 5.

    van der Maaten, L. & Hinton, G. J. Mach. Learn. Res. 9, 2579–2605 (2008).

    Google Scholar 

  6. 6.

    Blanco, E. et al. J. Allergy Clin. Immunol. 141, 2208–2219.e16 (2018).

    CAS  Article  Google Scholar 

  7. 7.

    Van Gassen, S. et al. Cytometry A 87, 636–645 (2015).

    Article  Google Scholar 

  8. 8.

    Ritchie, M. E. et al. Nucleic Acids Res. 43, e47 (2015).

    Article  Google Scholar 

  9. 9.

    Johnson, W. E., Li, C. & Rabinovic, A. Biostatistics 8, 118–127 (2007).

    Article  Google Scholar 

  10. 10.

    Bhattacharya, S. et al. Immunol. Res. 58, 234–239 (2014).

    CAS  Article  Google Scholar 

  11. 11.

    Zalocusky, K. A. et al. Cell Rep. 25, 513–522.e3 (2018).

    CAS  Article  Google Scholar 

  12. 12.

    Hu, Z. et al. Cell Rep. 24, 1377–1388 (2018).

    CAS  Article  Google Scholar 

Download references


This research is supported by the National Research Foundation Singapore under its NMRC Centre Grant Programme (NMRC/CG/M003/2017) and administered by the Singapore Ministry of Health’s National Medical Research Council. Other grant support from NMRC (NMRC/TA/0059/2017, NMRC/STaR/020/2013, NMRC/MOHIAFCAT2/2/08, MOHIAFCAT2/0001/2014, NMRC MOHIAFCAT1-6003, TCR15Jun006, NMRC/CIRG/ 1460/2016, MH 095:003\016-0002), Duke-NUS, A*STAR-BMRC (IAF311020) and BMRC (SPF2014/005) is gratefully acknowledged. The pediatric patients were recruited with the strong support of Yew Nam Siow and the Department of Anaesthesia, KK Women’s and Children’s Hospital. Testing of EPIC and feedback by Antonio La Cava, Femke van Wijk, Eveline Delemarre, Antonio Bertoletti, Michelle Hong Li Wen, Matthew Kirkey and Rosa Bacchetta are greatly appreciated. We also acknowledge Loshinidevi Thana Bathi for processing the large number of samples used in EPIC.

Author information




S.A. conceived and oversaw the study. E.S.C.L., K.T.Y., A.Y.J.T., S.Y.L., A.L., T.A., M.S.Z.N., T.P.N., S.C., M.G., A.M., S.P.T., S.K.N. and C.F.Y. oversaw the ethics approval, patients screening and recruitment. J.G.Y., S.L.P., F.A., L.L., A.J.M.L. and K.N.Y. performed the experiments. S.L.P. oversaw and coordinated all the mass cytometry staining. P.L. and J.G.Y. performed the initial bioinformatics analysis with input from J.C., F.G., C.-A.D., B.S.P. and J.L. M.W. developed the R-Shiny-based Sci-Atlas Miner tool and P.K. developed the Discovery tool. P.K. and C.J.H.C. constructed the web-based interface and server system. S.A., J.G.Y., M.W. and P.K. wrote the manuscript with input from all other authors.

Corresponding author

Correspondence to Salvatore Albani.

Ethics declarations

Competing interests

The authors declare no competing interests.

Supplementary information

Supplementary information

Supplementary Methods

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Yeo, J.G., Wasser, M., Kumar, P. et al. The Extended Polydimensional Immunome Characterization (EPIC) web-based reference and discovery tool for cytometry data. Nat Biotechnol 38, 679–684 (2020).

Download citation

Further reading

  • A Virus-Specific Immune Rheostat in the Immunome of Patients Recovering From Mild COVID-19

    • Joo Guan Yeo
    • , Jing Yao Leong
    • , Shi Huan Tay
    • , Karen Donceras Nadua
    • , Danielle E. Anderson
    • , Amanda Jin Mei Lim
    • , Xiang Wen Ng
    • , Su Li Poh
    • , Dianyan Guo
    • , Katherine Nay Yaung
    • , Pavanish Kumar
    • , Martin Wasser
    • , Sharifah Nur Hazirah
    • , Nursyuhadah Sutamam
    • , Camillus Jian Hui Chua
    • , Martin Qui
    • , Randy Foo
    • , Akshamal Mihiranga Gamage
    • , Kee Thai Yeo
    • , Lakshmi Ramakrishna
    • , Thaschawee Arkachaisri
    • , Barnaby E. Young
    • , David Chien Lye
    • , Lin-Fa Wang
    • , Chia Yin Chong
    • , Natalie Woon Hui Tan
    • , Jiahui Li
    • , Kai-Qian Kam
    • , Florent Ginhoux
    • , Koh Cheng Thoon
    • , Jerry Kok Yen Chan
    • , Chee Fu Yung
    •  & Salvatore Albani

    Frontiers in Immunology (2021)


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing