Bruno Correia
Nationality: Portuguese
+41 21 693 61 66
EPFL › SV › SV-SSV › SSV-ENS
Website: https://sv.epfl.ch/education
+41 21 693 61 66
EPFL › VPA › VPA-AVP-DLE › AVP-DLE-EDOC › EDBB-GE
Website: https://go.epfl.ch/phd-edbb
+41 21 693 61 66
EPFL › VPA › VPA-AVP-DLE › AVP-DLE-EDOC › CDOCT
Expertise
Current work
- Featuring molecular surface fingerprints to decipher protein functional properties
- Bottom-up de novo design of functional proteins
- Computational design of synthetic components for CAR T-cells
- Computational Design of Precision Vaccines
Education
PhD
| Computational Biology2010 – 2010 Universidade Nova de Lisboa
B. S.
| Chemistry2004 – 2004 Universidade de Coimbra
Professionals experiences
Assistant professor
Post-doctoral researcher
Awards
PhD scholarship
Fundação para a Ciência e Tecnologia
2006
ERC Starting grant
European Research Council
2016
Visiting scientist
Radcliffe Institute - Harvard
2018
Teaching award
EPFL - SV
2019
Protein Science Young Investigator Award from Protein Society
2021
Selected publications
De novo protein design enables precise induction of functional antibodies in vivo
Sesterhenn F*, Yang C*, Cramer JT, Bonet J, Wen X, Abriata LA, Kucharska I, Chiang CI, Wang Y, Castoro G, Vollers SS, Galloux M, Dheilly E, Richard CA, Rosset S, Corthesy P, Georgeon S, Villard M, Richard CA, Descamps D, Delgado T, Oricchio E, Rameix-Welti MA, Mas V, Ervin S, Eleouet JF, Riffault S, Bates JT, Julien JP, Li Y, Jardetzky T, Krey T, Correia BE
Published in Science, 2020 in
Computational design of anti-CRISPR proteins with improved inhibition potency and expanded specificity
Mathony J*, Harteveld Z*, Schmelas C*, Belzen JU, Aschenbrenner S, Hoffmann MD, Stengl C, Scheck A, Rosset S, Grimm D, Eils R, Correia BE*, Niopek D*
Published in Nature Chemical Biology, 2020 in
Macromolecular modeling and design in Rosetta: recent methods and frameworks
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R
Published in Nature Methods, 2020 in
Computationally designed STOP-CAR disrupted by small molecule confers on-command regulation of T-cell therapy
Giordano-Attianese G*, Gainza P*, Gray-Gaillard E*, Cribioli E, Shui S, Kim S, Kwak M, Vollers S, Osorio A, Reichenbach P, Bonet J, Oh B, Irving M*, Coukos G*, Correia BE*
Published in Nature Biotechnology, 2020 in
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
Gainza P, Sverrisson F, Monti F, Rodola E, Bronstein MM, Correia BE
Published in Nature Methods, 2020 in
rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics
Bonet J, Harteveld Z, Sesterhenn F, Scheck A, Correia BE
Published in BMC Bioinformatics, 2019 in
Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen
Sesterhenn F, Galloux M, Vollers S, Cspregi L, Yang C, Descamps D, Bonet J, Friedensohn S, Gainza P, Corthesy P, Chen M, Rosset S, Rameix-Welti MA, Elouet JF, Reddy ST, Graham B, Riffault S, Correia BE
Published in Plos Biology, 2019 in
Rosetta FunFolDes - a general framework for the computational design of functional proteins
Bonet J*, Wehrle S*, Schriever K*, Yang C*, Billet A, Sesterhenn F, Scheck A, Sverrisson F, Veselkova B, Vollers S, Lourman R, Villard M, Rosset S, Krey T, Correia BE
Published in Plos Computational Biology, 2018 in
Engineered anti-CRISPR proteins for optogenetic control of CRISPR/Cas9
Bubeck F, Hoffmann M, Harteveld Z, Aschenbrenner S, Bietz A, Waldhauer MC, Boerner K, Fakhiri J, Schmelas C, Dietz L, Grimm D, Correia BE, Eils R, Niopek D
Published in Nature Methods, 2018 in
Laboratory of Protein Design and Immunoengineering
FragmentScope - exploring the fragment space with learned surface representations
2025Accurate single-domain scaffolding of three nonoverlapping protein epitopes using deep learning
Nature Chemical Biology. 2025. DOI : 10.1038/s41589-025-02083-z.Mapping the latent CRBN-molecular glue degrader interactome
2025Leveraging protein representations to explore uncharted fold spaces with generative models
2025Structure-based Design of Chimeric Influenza Hemagglutinins to Elicit Cross-group Immunity
2025Rational design of chemically responsive cytokines for cancer immunotherapy
2025Structures of a synthetic antibody selected against and bound to the C‐terminal domain of <i>Clostridium perfringens</i> enterotoxin
Protein Science. 2025. DOI : 10.1002/pro.70281.De novo design of phosphorylation-induced protein switches for synthetic signaling in cells
2025One-shot Design of Functional Protein Binders with Bindcraft
NATURE. 2025. DOI : 10.1038/s41586-025-09429-6.Molecular basis for anti-jumbo phage immunity by AVAST Type 5
2025Humanized Caffeine-Inducible Systems for Controlling Cellular Functions
2025Mapping the Structural Landscape of Amyloid Fibrils to Guide Polymorph-Specific Therapeutics
2025Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition
2025Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning
Nature. 2025. DOI : 10.1038/s41586-025-09021-y.Boltzdesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design
2025Computationally designed stem-epitope mimetics elicit broadly reactive antibodies
2025Targeting protein-ligand neosurfaces with a generalizable deep learning tool
NATURE. 2025. DOI : 10.1038/s41586-024-08435-4.AtomSurf: Surface Representation for Learning on Protein Structures
2025. 13th International Conference on Learning Representations (ICLR 2025), Singapore, 2025-04-24 - 2025-04-28. p. 19779 - 19804.Boosting Protein Graph Representations through Static-Dynamic Fusion
2025. 42nd International Conference on Machine Learning, Vancouver, Canada, 2025-07-13 - 2025-07-19.Computational Design of Protein Switches
Lausanne, EPFL, 2025. DOI : 10.5075/epfl-thesis-11419.Towards Conformational Targeting of Alpha-Synuclein Fibrils
Lausanne, EPFL, 2025. DOI : 10.5075/epfl-thesis-10710.Computational design of complex protein folds and soluble analogs of membrane proteins
Lausanne, EPFL, 2025. DOI : 10.5075/epfl-thesis-11287.The physiological landscape and specificity of antibody repertoires are consolidated by multiple immunizations
eLife. 2024. DOI : 10.7554/eLife.92718.Mapping targetable sites on the human surfaceome for the design of novel binders
2024A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins
Nucleic acids research. 2024. DOI : 10.1093/nar/gkae1052.Structure-based drug design with equivariant diffusion models
NATURE COMPUTATIONAL SCIENCE. 2024. DOI : 10.1038/s43588-024-00737-x.Epitope-focused immunogens targeting the hepatitis C virus glycoproteins induce broadly neutralizing antibodies
SCIENCE ADVANCES. 2024. DOI : 10.1126/sciadv.ado2600.FSscore: A Personalized Machine Learning-Based Synthetic Feasibility Score
Chemistry-Methods. 2024. DOI : 10.1002/cmtd.202400024.Dual ON/OFF-switch chimeric antigen receptor controlled by two clinically approved drugs
Proceedings of the National Academy of Sciences of the United States of America. 2024. DOI : 10.1073/pnas.2405085121.Exploring “dark-matter” protein folds using deep learning
Cell systems. 2024. DOI : 10.1016/j.cels.2024.09.006.Structures of the Foamy virus fusion protein reveal an unexpected link with the F protein of paramyxo- and pneumoviruses
Science Advances. 2024. DOI : 10.1126/sciadv.ado7035.An evolved artificial radical cyclase enables the construction of bicyclic terpenoid scaffolds via an H-atom transfer pathway
Nature chemistry. 2024. DOI : 10.1038/s41557-024-01562-5.BindCraft: one-shot design of functional protein binders
2024V-111.4: PD-1 stimulation of human regulatory T cells using stimulating de novo miniprotein in vitro increased Foxp3/Helios expression
Transplantation. 2024. DOI : 10.1097/01.tp.0001066704.93068.a5.Drug-controlled CAR-T cells through the regulation of cell-cell interactions
2024Computational design of soluble and functional membrane protein analogues
Nature. 2024. DOI : 10.1038/s41586-024-07601-y.Antibody-peptide conjugates deliver covalent inhibitors blocking oncogenic cathepsins
Nature Chemical Biology. 2024. DOI : 10.1038/s41589-024-01627-z.Accurate single domain scaffolding of three non-overlapping protein epitopes using deep learning
2024Opportunities and challenges in design and optimization of protein function
Nature Reviews Molecular Cell Biology. 2024. DOI : 10.1038/s41580-024-00718-y.Equivariant 3D-conditional diffusion model for molecular linker design
Nature Machine Intelligence. 2024. DOI : 10.1038/s42256-024-00815-9.Targeting protein-ligand neosurfaces using a generalizable deep learning approach
2024A Synthetic Multivalent Lipopeptide Derived from Pam3CSK4 with Irreversible Influenza Inhibition and Immuno-Stimulating Effects
Small. 2024. DOI : 10.1002/smll.202307709.An atlas of protein homo-oligomerization across domains of life
Cell. 2024. DOI : 10.1016/j.cell.2024.01.022.DiffTopo: Fold exploration using coarse grained protein topology representations
2024Multi-motif scaffolding for de novo pathogen antigen mimetics by deep generative learning
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10640.Chemically disruptable molecule switch and use thereof
WO2024133630 . 2024.Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10799.Predicting protein interactions using geometric deep learning on protein surfaces
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10271.A new age in protein design empowered by deep learning
Cell Systems. 2023. DOI : 10.1016/j.cels.2023.10.006.Protein-based bandpass filters for controlling cellular signaling with chemical inputs
Nature Chemical Biology. 2023. DOI : 10.1038/s41589-023-01463-7.Rational design of small-molecule responsive protein switches
Protein Science. 2023. DOI : 10.1002/pro.4774.Rules and mechanisms governing G protein coupling selectivity of GPCRs
Cell Reports. 2023. DOI : 10.1016/j.celrep.2023.113173.Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study
PROTEOMICS. 2023. DOI : 10.1002/pmic.202200323.Rational Design of Chemically Controlled Antibodies and Protein Therapeutics
ACS Chemical Biology. 2023. DOI : 10.1021/acschembio.3c00012.De novo protein design by inversion of the AlphaFold structure prediction network
Protein Science. 2023. DOI : 10.1002/pro.4653.De novo design of protein interactions with learned surface fingerprints
Nature. 2023. DOI : 10.1038/s41586-023-05993-x.De novo designed proteins: a study in engineering novel folds and functions
Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-11556.Computational design of vaccine immunogens
Current Opinion In Biotechnology. 2022. DOI : 10.1016/j.copbio.2022.102821.A generic framework for hierarchical de novo protein design
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2022. DOI : 10.1073/pnas.2206111119.Assessing and enhancing foldability in designed proteins
Protein Science. 2022. DOI : 10.1002/pro.4400.Antibodies to combat viral infections: development strategies and progress
Nature Reviews Drug Discovery. 2022. DOI : 10.1038/s41573-022-00495-3.Computational design of novel protein–protein interactions – An overview on methodological approaches and applications
Current Opinion in Structural Biology. 2022. DOI : 10.1016/j.sbi.2022.102370.A method and system for fast end-to-end learning on protein surfaces
WO2022152478 . 2022.Novel chemically controlled cellular switches
WO2022156885 . 2022.Targeting molecular surfaces to engineer novel protein-based immunogens and inhibitors
Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-9141.Rational design of protein switches: applications in synthetic biology and cancer immunotherapy
Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-9246.Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions
Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-9195.Computational design of bioactive protein switches with multi-logics for cell-based therapeutics
2021. p. 37 - 37.A Nanoscaffolded Spike-RBD Vaccine Provides Protection against SARS-CoV-2 with Minimal Anti-Scaffold Response
Vaccines. 2021. DOI : 10.3390/vaccines9050431.Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning
Nature Biomedical Engineering. 2021. DOI : 10.1038/s41551-021-00699-9.Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design
Biochemistry. 2021. DOI : 10.1021/acs.biochem.0c00912.Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein
Nucleic Acids Research. 2021. DOI : 10.1093/nar/gkaa1198.Bottom-up de novo design of functional proteins with complex structural features
Nature Chemical Biology. 2021. DOI : 10.1038/s41589-020-00699-x.On the exploration of novel methodological approaches for immunogen design: case studies in influenza and hepatitis C
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8752.Fast end-to-end learning on protein surfaces
2021. IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), ELECTR NETWORK, Jun 19-25, 2021. p. 15267 - 15276. DOI : 10.1109/CVPR46437.2021.01502.Oligomerization Profile of Human Transthyretin Variants with Distinct Amyloidogenicity
Molecules. 2020. DOI : 10.3390/molecules25235698.Macromolecular modeling and design in Rosetta: recent methods and frameworks
Nature Methods. 2020. DOI : 10.1038/s41592-020-0848-2.De novo protein design enables the precise induction of RSV-neutralizing antibodies
Science. 2020. DOI : 10.1126/science.aay5051.Computational design of anti-CRISPR proteins with improved inhibition potency
Nature Chemical Biology. 2020. DOI : 10.1038/s41589-020-0518-9.Epitope Mapping and Fine Specificity of Human T and B Cell Responses for Novel Candidate Blood-Stage Malaria Vaccine P27A
Frontiers In Immunology. 2020. DOI : 10.3389/fimmu.2020.00412.A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy
Nature Biotechnology. 2020. DOI : 10.1038/s41587-019-0403-9.Immunogen
JP2022542003 ; US2022249649 ; EP3758004 ; CA3145336 ; WO2020260910 . 2020.Immunogen
WO2020065033 ; EP3628678 . 2020.Functional de novo Protein Design for Targeted Vaccines and Synthetic Biology Applications
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7545.Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
Nature Methods. 2019. DOI : 10.1038/s41592-019-0666-6.Decrypting interaction fingerprints in protein molecular surfaces
2019. Joint 12th EBSA European Biophysics Congress / 10th IUPAP International Conference on Biological Physics (ICBP), Madrid, SPAIN, Jul 20-24, 2019. p. S224 - S224.rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics
BMC Bioinformatics. 2019. DOI : 10.1186/s12859-019-2796-3.Engineered Anti-CRISPR Proteins for Precision Control of CRISPR-Cas9
2019. 22nd Annual Meeting of the American-Society-of-Gene-and-Cell-Therapy (ASGCT), Washington, DC, Apr 29-May 02, 2019. p. 297 - 297.Heterodimeric inactivatable chimeric antigen receptors
US2021113615 ; EP3774866 ; WO2019197676 . 2019.Expanding beyond the natural protein repertoire to engineer targeted vaccines and diagnostics
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-7515.Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen
PLoS Biology. 2019. DOI : 10.1371/journal.pbio.3000164.Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9
Nature Methods. 2018. DOI : 10.1038/s41592-018-0178-9.Rosetta FunFolDes - A general framework for the computational design of functional proteins
PLoS Computational Biology. 2018. DOI : 10.1371/journal.pcbi.1006623.Design and characterization of near-native Ebola GP vaccine candidates: implications for immunogenicity
2018. p. 6S - 7S.Expanding the druggable proteome: Ligand and target discovery by fragment-based screening in cells
2018. 256th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nanoscience, Nanotechnology and Beyond, Boston, MA, Aug 19-23, 2018.Structure-based immunogen design - leading the way to the new age of precision vaccines
Current Opinion In Structural Biology. 2018. DOI : 10.1016/j.sbi.2018.06.002.OFF-switch CAR T cell for safety-enhanced cancer immunotherapy
2018. Annual Meeting of the American-Association-for-Cancer-Research (AACR), Chicago, IL, Apr 14-18, 2018. DOI : 10.1158/1538-7445.AM2018-2570.Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses
Proteins-Structure Function And Bioinformatics. 2016. DOI : 10.1002/prot.25079.Proof of principle for epitope-focused vaccine design
2015. 29th Annual Symposium of the Protein-Society, Barcelona, SPAIN, JUL 22-25, 2015. p. 181 - 184.Heterodimeric proteins comprising dimerization motifs and methods of using
WO2025133340 .Teaching & PhD
PhD Students
Shuhao Xiao, Irina Morozova, Yangyang Miao, Pengkang Guo, Mubarak Olanrewaju Idris, Adrian Wolfgang Dobbelstein, Julius Wenckstern, Flávia Mayumi Odahara de Abreu, Marin Paul Geoffroy Marie Ollagnon, Evgenia Elizarova, Ilia Igashov, Christian Schellhaas, Tian Zhu, Ekaterina Pyatova, Lennart Nickel, Arne Schneuing, Petra Elisabeth Marilena Balbi, Nicolas Manuel Goldbach, Maddalena Elia, Rebecca Manuela Neeser
Past EPFL PhD Students
Fabian Sesterhenn, Che Yang, Andreas Scheck, Zander Harteveld, Sailan Shui, Sarah Wehrle, Alexandra Krina Van Hall-Beauvais, Anthony Marchand, Freyr Sverrisson, Karla Montserrat Castro Gilabert, Ahmed Sadek, Casper Goverde, Stephen Michael Buckley
Past EPFL PhD Students as codirector
Mathieu Girardin, Lucia Bonati
Courses
Bio-organic chemistry
BIO-110
The aim of the course is to provide a chemical understanding and intuition to decipher and predict chemical processes in living systems.
Monthly IBI-EDBB Mini-symposia
BIOENG-600
To expose EDBB students to research in Bioengineering through attendance of lecture series given by EDBB students and external speakers. The objectives are to broaden the knowledge of students in the field of Bioengineering and expose them to the diversity of studies in the IBI community.
Trends in chemical biology and drug discovery
BIOENG-510
In this course we will cover the scientific basis behind chemical biology approaches for drug development.