Developing novel immunogens, vaccines and other biotherapeutics using deep learning-guided protein design. Our work places a special emphasis on viral glycoproteins and pathogens targeting mucosal sites.

PI of the Protein Design for Biotherapeutics team – PD4Bio

Yoann Aldon is a CNRS Professeur Junior at AFMB, where he leads the Protein Design for Biotherapeutics (PD4Bio) team. He obtained his PhD in 2019 at Imperial College London in the laboratory of Prof. Robin J. Shattock, focusing on vaccine design, adjuvantation, and the development of HIV-1 Envelope immunogens that progressed to a Phase I clinical trial. He subsequently carried out postdoctoral research with Prof. Rogier W. Sanders at the University of Amsterdam on the design of HIV-1 Env germline-targeting, shaping and polishing immunogens (currently under clinical evaluation), as well as on antibodies for therapeutic purposes. He further broadened his expertise to AI-based protein design methods in the laboratory of Dr. Neil P. King at the Institute for Protein Design (IPD), University of Washington.

His work now focuses on the development of next-generation immunogens, vaccines, and other biotherapeutics through AI-guided protein engineering, with a special interest in viral glycoproteins and other mucosa-targeting pathogens.

Publications

2026

2026
Differential contributions of human oligosaccharyltransferase complexes OST-A and OST-B to HIV-1 envelope glycoprotein glycosylation

Tugba Atabey, Ronald Derking, Maddy Newby, Joey Bouhuijs, Jonne Snitselaar, Monique Vink, Yoann Aldon, Joel Allen, Max Crispin, Rogier Sanders

Journal of Virology 100 (2026)10.1128/jvi.01481-25

2025

2025
Germline-targeting Strategies to Induce bNAbs against HIV-1

Tugba Atabey, Rogier Sanders, Yoann Aldon

Current HIV Research 23 (2025)10.2174/011570162X365229250527111140

2023

2023
Profound structural conservation of chemically cross-linked HIV-1 envelope glycoprotein experimental vaccine antigens

Gregory Martin, Rebecca Russell, Philip Mundsperger, Scarlett Harris, Lu Jovanoska, Luiza Farache Trajano, Torben Schiffner, Katalin Fabian, Monica Tolazzi, Gabriella Scarlatti, Leon Mcfarlane, Hannah Cheeseman, Yoann Aldon, Edith Schermer, Marielle Breemen, Kwinten Sliepen, Dietmar Katinger, Renate Kunert, Rogier Sanders, Robin Shattock, Andrew Ward, Quentin Sattentau

NPJ vaccines 8:101 (2023)10.1038/s41541-023-00696-w

2023
Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions

Tom Caniels, Max Medina-Ramírez, Jinsong Zhang, Anita Sarkar, Sonu Kumar, Alex Labranche, Ronald Derking, Joel Allen, Jonne Snitselaar, Joan Capella-Pujol, Iván del Moral Sánchez, Anila Yasmeen, Marilyn Diaz, Yoann Aldon, Tom P.L. Bijl, Sravani Venkatayogi, Joshua Martin Beem, Amanda Newman, Chuancang Jiang, Wen-Hsin Lee, Maarten Pater, Judith Burger, Mariëlle van Breemen, Steven de Taeye, Kimmo Rantalainen, Celia Labranche, Kevin Saunders, David Montefiori, Gabriel Ozorowski, Andrew Ward, Max Crispin, John Moore, Per Johan Klasse, Barton Haynes, Ian Wilson, Kevin Wiehe, Laurent Verkoczy, Rogier Sanders

Cell Reports Medicine 4:101003 (2023)10.1016/j.xcrm.2023.101003

2022

2022
Innate cell markers that predict anti-HIV neutralizing antibody titers in vaccinated macaques

Matthieu van Tilbeurgh, Pauline Maisonnasse, Jean-Louis Palgen, Monica Tolazzi, Yoann Aldon, Nathalie Dereuddre-Bosquet, Mariangela Cavarelli, Anne-Sophie Beignon, Ernesto Marcos-Lopez, Anne-Sophie Gallouet, Emmanuel Gilson, Gabriel Ozorowski, Andrew Ward, Ilja Bontjer, Paul Mckay, Robin Shattock, Gabriella Scarlatti, Rogier Sanders, Roger Le Grand

Cell Reports Medicine 3:100751 (2022)10.1016/j.xcrm.2022.100751

2022
A public antibody class recognizes an S2 epitope exposed on open conformations of SARS-CoV-2 spike

Mathieu Claireaux, Tom Caniels, Marlon de Gast, Julianna Han, Denise Guerra, Gius Kerster, Barbera van Schaik, Aldo Jongejan, Angela Schriek, Marloes Grobben, Philip Brouwer, Karlijn van der Straten, Yoann Aldon, Joan Capella-Pujol, Jonne Snitselaar, Wouter Olijhoek, Aafke Aartse, Mitch Brinkkemper, Ilja Bontjer, Judith Burger, Meliawati Poniman, Tom Bijl, Jonathan Torres, Jeffrey Copps, Isabel Cuella Martin, Steven de Taeye, Godelieve de Bree, Andrew Ward, Kwinten Sliepen, Antoine van Kampen, Perry Moerland, Rogier Sanders, Marit van Gils

Nature Communications 13:4539 (2022)10.1038/s41467-022-32232-0

2022
Persistent immunogenicity of integrase defective lentiviral vectors delivering membrane-tethered native-like HIV-1 envelope trimers

Alessandra Gallinaro, Maria Franca Pirillo, Yoann Aldon, Serena Cecchetti, Zuleika Michelini, Antonella Tinari, Martina Borghi, Andrea Canitano, Paul Mckay, Roberta Bona, Maria Fenicia Vescio, Felicia Grasso, Maria Blasi, Silvia Baroncelli, Gabriella Scarlatti, Celia Labranche, David Montefiori, Mary Klotman, Rogier Sanders, Robin Shattock, Donatella Negri, Andrea Cara

NPJ vaccines 7:44 (2022)10.1038/s41541-022-00465-1

2022
Computed tomography and [18F]-FDG PET imaging provide additional readouts for COVID-19 pathogenesis and therapies evaluation in non-human primates

Thibaut Naninck, Nidhal Kahlaoui, Julien Lemaitre, Pauline Maisonnasse, Antoine de Mori, Quentin Pascal, Vanessa Contreras, Romain Marlin, Francis Relouzat, Benoît Delache, Cécile Hérate, Yoann Aldon, Marit van Gils, Nerea Zabaleta, Raphaël Ho Tsong Fang, Nathalie Bosquet, Rogier Sanders, Luk Vandenberghe, Catherine Chapon, Roger Le Grand

iScience 25:104101 (2022)10.1016/j.isci.2022.104101

2021

2021
Probing Affinity, Avidity, Anticooperativity, and Competition in Antibody and Receptor Binding to the SARS-CoV-2 Spike by Single Particle Mass Analyses

Victor Yin, Szu-Hsueh Lai, Tom Caniels, Philip Brouwer, Mitch Brinkkemper, Yoann Aldon, Hejun Liu, Meng Yuan, Ian Wilson, Rogier Sanders, Marit van Gils, Albert Heck

ACS Central Science 7:1863-1873 (2021)10.1021/acscentsci.1c00804

2021
Defining variant-resistant epitopes targeted by SARS-CoV-2 antibodies: A global consortium study

Kathryn Hastie, Haoyang Li, Daniel Bedinger, Sharon Schendel, S. Moses Dennison, Kan Li, Vamseedhar Rayaprolu, Xiaoying Yu, Colin Mann, Michelle Zandonatti, Ruben Diaz Avalos, Dawid Zyla, Tierra Buck, Sean Hui, Kelly Shaffer, Chitra Hariharan, Jieyun Yin, Eduardo Olmedillas, Adrian Enriquez, Diptiben Parekh, Milite Abraha, Elizabeth Feeney, Gillian Horn, Yoann Aldon, Hanif Ali, Sanja Aracic, Ronald Cobb, Ross Federman, Joseph Fernandez, Jacob Glanville, Robin Green, Gevorg Grigoryan, Ana Lujan Hernandez, David Ho, Kuan-Ying Huang, John Ingraham, Weidong Jiang, Paul Kellam, Cheolmin Kim, Minsoo Kim, Hyeong Mi Kim, Chao Kong, Shelly Krebs, Fei Lan, Guojun Lang, Sooyoung Lee, Cheuk Lun Leung, Junli Liu, Yanan Lu, Anna Maccamy, Andrew Mcguire, Anne Palser, Terence Rabbitts, Zahra Rikhtegaran Tehrani, Mohammad Sajadi, Rogier Sanders, Aaron Sato, Liang Schweizer, Jimin Seo, Bingqing Shen, Jonne Snitselaar, Leonidas Stamatatos, Yongcong Tan, Milan Tomic, Marit van Gils, Sawsan Youssef, Jian Yu, Tom Yuan, Qian Zhang, Bjoern Peters, Georgia Tomaras, Timothy Germann, Erica Ollmann Saphire

Science 374:472-478 (2021)10.1126/science.abh2315

2021
COVA1-18 neutralizing antibody protects against SARS-CoV-2 in three preclinical models

Pauline Maisonnasse, Yoann Aldon, Aurélien Marc, Romain Marlin, Nathalie Dereuddre-Bosquet, Natalia Kuzmina, Alec Freyn, Jonne Snitselaar, Antonio Gonçalves, Tom Caniels, Judith Burger, Meliawati Poniman, Ilja Bontjer, Virginie Chesnais, Ségolène Diry, Anton Iershov, Adam Ronk, Sonia Jangra, Raveen Rathnasinghe, Philip Brouwer, Tom Bijl, Jelle van Schooten, Mitch Brinkkemper, Hejun Liu, Meng Yuan, Chad Mire, Mariëlle van Breemen, Vanessa Contreras, Thibaut Naninck, Julien Lemaître, Nidhal Kahlaoui, Francis Relouzat, Catherine Chapon, Raphaël Ho Tsong Fang, Charlene Mcdanal, Mary Osei-Twum, Natalie St-Amant, Luc Gagnon, David Montefiori, Ian Wilson, Eric Ginoux, Godelieve de Bree, Adolfo García-Sastre, Michael Schotsaert, Lynda Coughlan, Alexander Bukreyev, Sylvie van der Werf, Jérémie Guedj, Rogier Sanders, Marit van Gils, Roger Le Grand

Nature Communications 12:6097 (2021)10.1038/s41467-021-26354-0

2021
The entry inhibitor DS003 (BMS-599793): a BMS-806 analogue, provides superior activity as a pre-exposure prophylaxis candidate

Carolina Herrera, Sarah Harman, Yoann Aldon, Paul Rogers, Naomi Armanasco, Paul Ziprin, Daniel Stieh, Jeremy Nuttall, Robin Shattock

AIDS. Official journal of the international AIDS Society 35:1907-1917 (2021)10.1097/QAD.0000000000002974

2021
Immunogenicity of stabilized HIV-1 Env trimers delivered by self-amplifying mRNA

Yoann Aldon, Paul Mckay, Jorge Moreno Herrero, Annette Vogel, Réka Lévai, Pauline Maisonnasse, Nathalie Dereuddre-Bosquet, Heinrich Haas, Katalin Fábián, Roger Le Grand, Ugur Sahin, Robin Shattock

Molecular Therapy - Nucleic Acids 25:483-493 (2021)10.1016/j.omtn.2021.06.008

2021
Enhancing glycan occupancy of soluble HIV-1 envelope trimers to mimic the native viral spike

Ronald Derking, Joel Allen, Christopher Cottrell, Kwinten Sliepen, Gemma Seabright, Wen-Hsin Lee, Yoann Aldon, Kimmo Rantalainen, Aleksandar Antanasijevic, Jeffrey Copps, Anila Yasmeen, Albert Cupo, Victor Cruz Portillo, Meliawati Poniman, Niki Bol, Patricia van der Woude, Steven de Taeye, Tom L.G.M. van den Kerkhof, P.J. Klasse, Gabriel Ozorowski, Marit van Gils, John Moore, Andrew Ward, Max Crispin, Rogier Sanders

Cell Reports 35:108933 (2021)10.1016/j.celrep.2021.108933

2021
Two-component spike nanoparticle vaccine protects macaques from SARS-CoV-2 infection

Philip J.M. Brouwer, Mitch Brinkkemper, Pauline Maisonnasse, Nathalie Dereuddre-Bosquet, Marloes Grobben, Mathieu Claireaux, Marlon de Gast, Romain Marlin, Virginie Chesnais, Ségolène Diry, Joel Allen, Yasunori Watanabe, Julia Giezen, Gius Kerster, Hannah Turner, Karlijn van der Straten, Cynthia van der Linden, Yoann Aldon, Thibaut Naninck, Ilja Bontjer, Judith Burger, Meliawati Poniman, Anna Mykytyn, Nisreen M.A. Okba, Edith Schermer, Marielle van Breemen, Rashmi Ravichandran, Tom Caniels, Jelle van Schooten, Nidhal Kahlaoui, Vanessa Contreras, Julien Lemaître, Catherine Chapon, Raphaël Ho Tsong Fang, Julien Villaudy, Kwinten Sliepen, Yme van der Velden, Bart Haagmans, Godelieve de Bree, Eric Ginoux, Andrew Ward, Max Crispin, Neil King, Sylvie van der Werf, Marit van Gils, Roger Le Grand, Rogier Sanders

Cell 184:1188-1200.e19 (2021)10.1016/j.cell.2021.01.035

2021
The effect of spike mutations on SARS-CoV-2 neutralization

Chloe Rees-Spear, Luke Muir, Sarah Griffith, Judith Heaney, Yoann Aldon, Jonne Snitselaar, Peter Thomas, Carl Graham, Jeffrey Seow, Nayung Lee, Annachiara Rosa, Chloe Roustan, Catherine Houlihan, Rogier Sanders, Ravindra Gupta, Peter Cherepanov, Hans Stauss, Eleni Nastouli, Katie Doores, Marit van Gils, Laura Mccoy

Cell Reports 34:108890 (2021)10.1016/j.celrep.2021.108890

2020

2020
Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability

Philip Brouwer, Tom Caniels, Karlijn van der Straten, Jonne Snitselaar, Yoann Aldon, Sandhya Bangaru, Jonathan Torres, Nisreen Okba, Mathieu Claireaux, Gius Kerster, Arthur Bentlage, Marlies van Haaren, Denise Guerra, Judith Burger, Edith Schermer, Kirsten Verheul, Niels van der Velde, Alex van der Kooi, Jelle van Schooten, Mariëlle van Breemen, Tom Bijl, Kwinten Sliepen, Aafke Aartse, Ronald Derking, Ilja Bontjer, Neeltje Kootstra, W. Joost Wiersinga, Gestur Vidarsson, Bart Haagmans, Andrew Ward, Godelieve de Bree, Rogier Sanders, Marit van Gils

Science 369:643-650 (2020)10.1126/science.abc5902

2019

2019
Inside out: optimization of lipid nanoparticle formulations for exterior complexation and in vivo delivery of saRNA

Anna Blakney, Paul Mckay, Bárbara Ibarzo Yus, Yoann Aldon, Robin Shattock

Gene Therapy 26:363-372 (2019)10.1038/s41434-019-0095-2

2019
Effects of cationic adjuvant formulation particle type, fluidity and immunomodulators on delivery and immunogenicity of saRNA

Anna Blakney, Paul Mckay, Dennis Christensen, Bárbara Ibarzo Yus, Yoann Aldon, Frank Follmann, Robin Shattock

Journal of Controlled Release 304:65-74 (2019)10.1016/j.jconrel.2019.04.043

2019
Identification of potential biomarkers of vaccine inflammation in mice

Paul Mckay, Deniz Cizmeci, Yoann Aldon, Jeroen Maertzdorf, January Weiner, Stefan He Kaufmann, David Jm Lewis, Robert van den Berg, Giuseppe del Giudice, Robin Shattock

eLife 8 (2019)10.7554/eLife.46149

2018

2018
Rational Design of DNA-Expressed Stabilized Native-Like HIV-1 Envelope Trimers

Yoann Aldon, Paul Mckay, Joel Allen, Gabriel Ozorowski, Réka Felfödiné Lévai, Monica Tolazzi, Paul Rogers, Linling He, Natalia de Val, Katalin Fábián, Gabriella Scarlatti, Jiang Zhu, Andrew Ward, Max Crispin, Robin Shattock

Cell Reports 24:3324-3338.e5 (2018)10.1016/j.celrep.2018.08.051

2017

2017
A Phase 1 Human Immunodeficiency Virus Vaccine Trial for Cross-Profiling the Kinetics of Serum and Mucosal Antibody Responses to CN54gp140 Modulated by Two Homologous Prime-Boost Vaccine Regimens

Sven Kratochvil, Paul Mckay, Jakub Kopycinski, Cynthia Bishop, Peter John Hayes, Luke Muir, Christopher Pinder, Deniz Cizmeci, Deborah King, Yoann Aldon, Bruce Wines, P. Mark Hogarth, Amy Chung, Stephen Kent, Kathrin Held, Christof Geldmacher, Len Dally, Nelson Santos, Tom Cole, Jill Gilmour, Sarah Fidler, Robin Shattock

Frontiers in Immunology 8 (2017)10.3389/fimmu.2017.00595

2017
Intravaginal immunisation using a novel antigen-releasing ring device elicits robust vaccine antigen-specific systemic and mucosal humoral immune responses

Paul Mckay, Jamie F.S. Mann, Aditya Pattani, Vicky Kett, Yoann Aldon, Deborah King, R. Karl Malcolm, Robin Shattock

Journal of Controlled Release 249:74-83 (2017)10.1016/j.jconrel.2017.01.018

2016

2016
CD71 targeting boosts immunogenicity of sublingually delivered influenza haemagglutinin antigen and protects against viral challenge in mice

Jamie F.S. Mann, John Tregoning, Yoann Aldon, Robin Shattock, Paul Mckay

Journal of Controlled Release 232:75-82 (2016)10.1016/j.jconrel.2016.04.022

2015

2015
Discrete partitioning of HIV-1 Env forms revealed by viral capture

Daniel Stieh, Deborah King, Katja Klein, Yoann Aldon, Paul Mckay, Robin Shattock

Retrovirology 12:81 (2015)10.1186/s12977-015-0207-z