Translational Biomedical Data Science

This group is led by Prof. Raphael Gottardo, center Director and Full Professor in the Faculty of Biology and Medicine at the University of Lausanne. It focuses on developing and applying novel computational tools, statistical methods, and machine learning algorithms to solve significant biological problems using high-dimensional modeling and multimodal data integration.

Professor Gottardo is a worldwide expert in this field with more than 20 years of experience. His research interests cover a wide range of areas, including the evaluation of vaccine immunogenicity, cancer immunotherapy, and the characterization of immune responses to infectious diseases.

This group extensively collaborates with researchers and clinicians within the Division of Immunology and Allergy, the Department of Oncology and the Department of Dermatology (to name a few).

Similar collaborations are currently being established with other departments/services in which high-dimensional data is generated.

• Tian Y, Carpp LN, Miller HER, Zager M, Newell EW, Gottardo R. “Single-cell immunology of SARS-CoV-2 infection”. Nat. Biotechnol. 2022 Jan 40(1): 30–41.
• Moncunill G, Carnes J, Chad Young W, Carpp L, De Rosa S, Campo JJ, Nhabomba A, Mpina M, Jairoce C, Finak G, Haas P, Muriel C, Van P, Sanz H, Dutta S, Mordmüller B, Agnandji ST, Díez-Padrisa N, Williams NA, Aponte JJ, Valim C., Neafsey DE, Daubenberger C, McElrath MJ, Dobaño C, Stuart K, Gottardo R. “Transcriptional correlates of malaria in RTS,S/AS01-vaccinated African children: a matched case–control study”. Elife. 2022 Jan 21; 11:e70393.
• Zhao E, Stone MR, Ren X, Guenthoer J, Smythe KS, Pulliam T, Williams SR, Uytingco CR, Taylor SEB, Nghiem P, Bielas JH, Gottardo R. 2021. “Spatial transcriptomics at subspot resolution with BayesSpace”. Nat. Biotechnol. 2021 Nov 39(11):1375-1384.
• Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC. “Orchestrating single-cell analysis with Bioconductor”. Nat. Methods. 2020 Feb 17(2); 137–145.
• Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, Slichter CK, Miller HW, McElrath MJ, Prlic M, Linsley PS, Gottardo R. “MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data”. Genome Biol. 2015 Dec 10; 16:278.

- CoVICIS : To address the emergence of variants of concern (VOCs) that threaten gains achieved against SARS-CoV-2, this multi-center research program represents a broad virologic and immunologic surveillance platform with 14 partners from 7 countries. It will leverage data from national genomic surveillance programs and from targeted cohort and children studies, including immunocompromised cohorts, in Europe and in Sub-Saharan Africa. Our aim is to gain an in-depth understanding of the risk and protective factors to SARS-CoV-2 infection, as well as of the evolution of the virus in different risk, gender and age cohorts across a range of geographic and vaccination contexts.

- Human Immunology Project Consortium (HIPC) : This program was established in 2010 by the Division of Allergy, Immunology and Transplantation of the National Institute of Allergy and Infectious Diseases (NIAID) as part of NIAID’s focus on human immunology. Through this program, well-characterized human cohorts are studied using a variety of multi-parametric tests and modern analytical tools. This data is shared on the ImmuneSpace portal and analysis engine, which was developed in part by Professor Raphael Gottardo and his team.