Bruno Correia

Nationality: Portuguese

EPFL STI IBI-STI LPDI
AAB 0 44 (Bâtiment AAB)
Station 19
1015 Lausanne

Office: AAB 0 44
EPFLSTIIBI-STILPDI

Website: https://lpdi.epfl.ch

Expertise

Protein engineering, Computational design, Immunoengineering, Synthetic biology

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

Throughout my PhD and postdoctoral studies I was trained in world-renowned laboratories and institutions in the United States of America (University of Washington and The Scripps Research Institute). Very early in my scientific career I found out my fascination about protein structure and function. My PhD studies evolved in the direction of immunogen design and vaccine engineering which sparked my interest in the many needs and opportunities in vaccinology and translational research. My efforts resulted in an enlightening piece of work where for the first time, computationally designed immunogens elicited potent neutralizing antibodies. During my postdoctoral studies I joined a chemical biology laboratory at the Scripps Research Institute. In this stage I developed novel chemoproteomics methods for the identification of protein-small molecule interaction sites in complex proteomes. In March 2015, I joined the école Polytechnique Fédérale de Lausanne (EPFL) & Switzerland as a tenure track assistant professor. The focus of my research group is to develop computational tools for protein design with particular emphasis in applying these strategies to immunoengineering (e.g. vaccine and cancer immunotherapy). The activities in my laboratory focus on computational design methods development and experimental characterization of the designed proteins. Our laboratory has been awarded with 2 prestigious research grants from the European Research Council. Lastly, I have been awarded the prize for best teacher of Life sciences in 2019.

Education

PhD

| Computational Biology

2010 – 2010 Universidade Nova de Lisboa

B. S.

| Chemistry

2004 – 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

E. ElizarovaI. МоrozovaI. IgashovO. GamppD. R. P. Iosub  et al.

2025

Accurate single-domain scaffolding of three nonoverlapping protein epitopes using deep learning

K. M. CastroJ. WangS. GeorgeonB. E. Correia

Nature Chemical Biology. 2025. DOI : 10.1038/s41589-025-02083-z.

Mapping the latent CRBN-molecular glue degrader interactome

P. GalliS. XiaoY. MengA. HanzlA. M. Bendel  et al.

2025

Leveraging protein representations to explore uncharted fold spaces with generative models

B. CorreiaY. MiaoM. PacesaS. GeorgeonJ. Schmidt  et al.

2025

Structure-based Design of Chimeric Influenza Hemagglutinins to Elicit Cross-group Immunity

K. M. Castro GilabertR. AyardulabiS. WehrleH. CuiS. Georgeon  et al.

2025

Rational design of chemically responsive cytokines for cancer immunotherapy

L. BonatiS. M. BuckleyL. SchellerA. MinafraS. Georgeon  et al.

2025

Structures of a synthetic antibody selected against and bound to the C‐terminal domain of <i>Clostridium perfringens</i> enterotoxin

C. P. OgbuN. GoldbachM. PačesaS. KapoorB. E. Correia  et al.

Protein Science. 2025. DOI : 10.1002/pro.70281.

De novo design of phosphorylation-induced protein switches for synthetic signaling in cells

S. BuckleyY. MiaoM. IdrisP. LeeL. Scheller  et al.

2025

One-shot Design of Functional Protein Binders with Bindcraft

M. PacesaL. NickelC. SchellhaasJ. SchmidtE. Pyatova  et al.

NATURE. 2025. DOI : 10.1038/s41586-025-09429-6.

Molecular basis for anti-jumbo phage immunity by AVAST Type 5

A. MuralidharanA. R. CostaD. FierlierD. F. van den BergH. van den Bossche  et al.

2025

Humanized Caffeine-Inducible Systems for Controlling Cellular Functions

L. SchellerM. EliaL. BonatiC. KangP. Gaínza  et al.

2025

Mapping the Structural Landscape of Amyloid Fibrils to Guide Polymorph-Specific Therapeutics

A. SadekB. E. CorreiaH. A. Lashuel

2025

Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition

T.-S. CotetI. KrawczukM. PacesaL. NickelB. E. Correia  et al.

2025

Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning

R. A. SilversteinN. KimA.-S. KroellR. T. WaltonJ. Delano  et al.

Nature. 2025. DOI : 10.1038/s41586-025-09021-y.

Boltzdesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design

Y. ChoM. PacesaZ. ZhangB. E. CorreiaS. Ovchinnikov

2025

Computationally designed stem-epitope mimetics elicit broadly reactive antibodies

S. WehrleA. ScheckL. ReuschF. L. MatassoliS. Georgeon  et al.

2025

Targeting protein-ligand neosurfaces with a generalizable deep learning tool

A. MarchandS. BuckleyA. SchneuingM. PacesaM. Elia  et al.

NATURE. 2025. DOI : 10.1038/s41586-024-08435-4.

AtomSurf: Surface Representation for Learning on Protein Structures

V. MalletS. AttaikiY. MiaoB. CorreiaM. Ovsjanikov

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

P. GuoB. Ferreira de Sousa CorreiaP. VandergheynstD. Probst

2025. 42nd International Conference on Machine Learning, Vancouver, Canada, 2025-07-13 - 2025-07-19.

Computational Design of Protein Switches

S. M. Buckley

Lausanne, EPFL, 2025. DOI : 10.5075/epfl-thesis-11419.

Towards Conformational Targeting of Alpha-Synuclein Fibrils

A. S. S. Z. M. Sadek

Lausanne, EPFL, 2025. DOI : 10.5075/epfl-thesis-10710.

Computational design of complex protein folds and soluble analogs of membrane proteins

C. A. Goverde

Lausanne, EPFL, 2025. DOI : 10.5075/epfl-thesis-11287.

The physiological landscape and specificity of antibody repertoires are consolidated by multiple immunizations

L. CsepregiK. HoehnD. NeumeierJ. M. TaftS. Friedensohn  et al.

eLife. 2024. DOI : 10.7554/eLife.92718.

Mapping targetable sites on the human surfaceome for the design of novel binders

P. E. M. BalbiA. K. SadekA. MarchandT.-Y. YuJ. Damjanovic  et al.

2024

A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins

T. StadelmannD. HeidM. JendruschJ. MathonyS. Aschenbrenner  et al.

Nucleic acids research. 2024. DOI : 10.1093/nar/gkae1052.

Structure-based drug design with equivariant diffusion models

A. SchneuingC. HarrisY. DuK. DidiA. Jamasb  et al.

NATURE COMPUTATIONAL SCIENCE. 2024. DOI : 10.1038/s43588-024-00737-x.

Epitope-focused immunogens targeting the hepatitis C virus glycoproteins induce broadly neutralizing antibodies

K. NagarathinamA. ScheckM. LabuhnL. J. StroehE. Herold  et al.

SCIENCE ADVANCES. 2024. DOI : 10.1126/sciadv.ado2600.

FSscore: A Personalized Machine Learning-Based Synthetic Feasibility Score

R. M. NeeserB. CorreiaP. Schwaller

Chemistry-Methods. 2024. DOI : 10.1002/cmtd.202400024.

Dual ON/OFF-switch chimeric antigen receptor controlled by two clinically approved drugs

G. M. P. G. AttianeseaS. ShuiE. CribioliM. TribouletL. Scheller  et al.

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

Z. HarteveldA. Van Hall-BeauvaisI. MorozovaJ. SouthernC. Goverde  et al.

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

I. FernándezF. BontemsD. BrunY. CoquinC. Goverde  et al.

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

D. ChenX. ZhangA. A. VorobievaR. TachibanaA. Stein  et al.

Nature chemistry. 2024. DOI : 10.1038/s41557-024-01562-5.

BindCraft: one-shot design of functional protein binders

M. PacesaL. NickelC. SchellhaasJ. SchmidtE. Pyatova  et al.

2024

V-111.4: PD-1 stimulation of human regulatory T cells using stimulating de novo miniprotein in vitro increased Foxp3/Helios expression

Q. Y. HoH. HashimotoE. VossX. ZhengA. Marchand  et al.

Transplantation. 2024. DOI : 10.1097/01.tp.0001066704.93068.a5.

Drug-controlled CAR-T cells through the regulation of cell-cell interactions

L. SchellerG. M. P. G. AttianeseR. Castellanos-RuedaR. B. Di RobertoM. Barden  et al.

2024

Computational design of soluble and functional membrane protein analogues

C. A. GoverdeM. PacesaN. GoldbachL. J. DornfeldP. E. Balbi  et al.

Nature. 2024. DOI : 10.1038/s41586-024-07601-y.

Antibody-peptide conjugates deliver covalent inhibitors blocking oncogenic cathepsins

A. S. PetruzzellaM. BruandA. Santamaria-MartinezN. KatanayevaL. Reymond  et al.

Nature Chemical Biology. 2024. DOI : 10.1038/s41589-024-01627-z.

Accurate single domain scaffolding of three non-overlapping protein epitopes using deep learning

K. M. CastroJ. L. WatsonJ. WangJ. SouthernR. Ayardulabi  et al.

2024

Opportunities and challenges in design and optimization of protein function

D. ListovC. A. GoverdeB. E. CorreiaS. J. Fleishman

Nature Reviews Molecular Cell Biology. 2024. DOI : 10.1038/s41580-024-00718-y.

Equivariant 3D-conditional diffusion model for molecular linker design

I. IgashovH. StärkC. VignacA. SchneuingV. G. Satorras  et al.

Nature Machine Intelligence. 2024. DOI : 10.1038/s42256-024-00815-9.

Targeting protein-ligand neosurfaces using a generalizable deep learning approach

A. MarchandS. M. BuckleyA. SchneuingM. PacesaP. Gaínza  et al.

2024

A Synthetic Multivalent Lipopeptide Derived from Pam3CSK4 with Irreversible Influenza Inhibition and Immuno-Stimulating Effects

Y. ZhuL. WeiA. C.-A. ZwygartP. GainzaQ. O. Khac  et al.

Small. 2024. DOI : 10.1002/smll.202307709.

An atlas of protein homo-oligomerization across domains of life

H. SchwekeM. PacesaT. LevinC. A. GoverdeP. Kumar  et al.

Cell. 2024. DOI : 10.1016/j.cell.2024.01.022.

DiffTopo: Fold exploration using coarse grained protein topology representations

Y. MiaoB. Correia

2024

Multi-motif scaffolding for de novo pathogen antigen mimetics by deep generative learning

K. M. Castro Gilabert

Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10640.

Chemically disruptable molecule switch and use thereof

P. Gainza CirauquiB. E. CorreiaL. TangA. MarchandL. Bonati  et al.

WO2024133630 . 2024.

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

A. Marchand

Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10799.

Predicting protein interactions using geometric deep learning on protein surfaces

F. Sverrisson

Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10271.

A new age in protein design empowered by deep learning

H. KhakzadI. IgashovA. SchneuingC. GoverdeM. Bronstein  et al.

Cell Systems. 2023. DOI : 10.1016/j.cels.2023.10.006.

Protein-based bandpass filters for controlling cellular signaling with chemical inputs

S. ShuiL. SchellerB. E. Correia

Nature Chemical Biology. 2023. DOI : 10.1038/s41589-023-01463-7.

Rational design of small-molecule responsive protein switches

S. ShuiS. BuckleyL. SchellerB. E. Correia

Protein Science. 2023. DOI : 10.1002/pro.4774.

Rules and mechanisms governing G protein coupling selectivity of GPCRs

I. MasuhoR. KiseP. GainzaE. Von MooX. Li  et al.

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

H. SchwekeQ. XuG. TaurielloL. PantoliniT. Schwede  et al.

PROTEOMICS. 2023. DOI : 10.1002/pmic.202200323.

Rational Design of Chemically Controlled Antibodies and Protein Therapeutics

A. MarchandL. BonatiS. ShuiL. SchellerP. Gainza Cirauqui  et al.

ACS Chemical Biology. 2023. DOI : 10.1021/acschembio.3c00012.

De novo protein design by inversion of the AlphaFold structure prediction network

C. GoverdeB. WolfH. KhakzadS. RossetB. Correia

Protein Science. 2023. DOI : 10.1002/pro.4653.

De novo design of protein interactions with learned surface fingerprints

P. Gainza CirauquiS. WehrleA. K. Van Hall-BeauvaisA. MarchandA. Scheck  et al.

Nature. 2023. DOI : 10.1038/s41586-023-05993-x.

De novo designed proteins: a study in engineering novel folds and functions

A. K. Van Hall-Beauvais

Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-11556.

Computational design of vaccine immunogens

K. M. CastroA. ScheckS. XiaoB. E. Correia

Current Opinion In Biotechnology. 2022. DOI : 10.1016/j.copbio.2022.102821.

A generic framework for hierarchical de novo protein design

Z. HarteveldJ. BonetS. RossetC. YangF. Sesterhenn  et al.

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

D. ListovR. Lipsh-SokolikS. RossetC. YangB. E. Correia  et al.

Protein Science. 2022. DOI : 10.1002/pro.4400.

Antibodies to combat viral infections: development strategies and progress

G. PantaleoB. CorreiaC. FenwickV. S. JooL. Perez

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

A. MarchandA. K. Van Hall-BeauvaisB. Correia

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

M. BronsteinF. SverrissonJ. Pierre FeydyP. GainzaB. Ferreira De Sousa Correia

WO2022152478 . 2022.

Novel chemically controlled cellular switches

B. E. CorreiaS. ShuiP. Gainza Cirauqui

WO2022156885 . 2022.

Targeting molecular surfaces to engineer novel protein-based immunogens and inhibitors

S. Wehrle

Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-9141.

Rational design of protein switches: applications in synthetic biology and cancer immunotherapy

S. Shui

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

Z. Harteveld

Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-9195.

Computational design of bioactive protein switches with multi-logics for cell-based therapeutics

S. ShuiP. GainzaL. SchellerC. YangB. Correia

2021. p. 37 - 37.

A Nanoscaffolded Spike-RBD Vaccine Provides Protection against SARS-CoV-2 with Minimal Anti-Scaffold Response

D. LainščekT. FinkV. ForstneričI. Hafner-BratkovičS. Orehek  et al.

Vaccines. 2021. DOI : 10.3390/vaccines9050431.

Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning

D. M. MasonS. FriedensohnC. R. WeberC. JordiB. Wagner  et al.

Nature Biomedical Engineering. 2021. DOI : 10.1038/s41551-021-00699-9.

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

C. T. SchoederS. SchmitzJ. Adolf-BryfogleA. M. SevyJ. A. Finn  et al.

Biochemistry. 2021. DOI : 10.1021/acs.biochem.0c00912.

Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein

M. D. HoffmannJ. MathonyJ. U. Zu BelzenZ. HarteveldS. Aschenbrenner  et al.

Nucleic Acids Research. 2021. DOI : 10.1093/nar/gkaa1198.

Bottom-up de novo design of functional proteins with complex structural features

C. YangF. SesterhennJ. BonetE. A. van AalenL. Scheller  et al.

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

A. Scheck

Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8752.

Fast end-to-end learning on protein surfaces

F. SverrissonJ. FeydyB. E. CorreiaM. M. Bronstein

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

A. FrangolhoB. CorreiaD. C. VazZ. L. AlmeidaR. M. M. Brito

Molecules. 2020. DOI : 10.3390/molecules25235698.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

J. K. LemanB. D. WeitznerS. M. LewisJ. Adolf-BryfogleN. Alam  et al.

Nature Methods. 2020. DOI : 10.1038/s41592-020-0848-2.

De novo protein design enables the precise induction of RSV-neutralizing antibodies

F. SesterhennC. YangJ. BonetJ. T. CramerX. Wen  et al.

Science. 2020. DOI : 10.1126/science.aay5051.

Computational design of anti-CRISPR proteins with improved inhibition potency

J. MathonyZ. HarteveldC. SchmelasJ. U. zu BelzenS. Aschenbrenner  et al.

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

K. M. GeigerD. GuignardC. YangJ.-P. BikorimanaB. E. Correia  et al.

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

G. Giordano-AttianeseP. GainzaE. Gray-GaillardE. CribioliS. Shui  et al.

Nature Biotechnology. 2020. DOI : 10.1038/s41587-019-0403-9.

Immunogen

B. CorreiaF. SesterhennC. YangJ. Bonet

JP2022542003 ; US2022249649 ; EP3758004 ; CA3145336 ; WO2020260910 . 2020.

Immunogen

B. CorreiaF. Sesterhenn

WO2020065033 ; EP3628678 . 2020.

Functional de novo Protein Design for Targeted Vaccines and Synthetic Biology Applications

C. Yang

Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7545.

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

P. GainzaF. SverrissonF. MontiE. RodolàD. Boscaini  et al.

Nature Methods. 2019. DOI : 10.1038/s41592-019-0666-6.

Decrypting interaction fingerprints in protein molecular surfaces

P. GainzaF. SverrissonF. MontiM. BronsteinB. Correia

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

J. BonetZ. HarteveldF. SesterhennA. ScheckB. E. Correia

BMC Bioinformatics. 2019. DOI : 10.1186/s12859-019-2796-3.

Engineered Anti-CRISPR Proteins for Precision Control of CRISPR-Cas9

F. BubeckM. D. HoffmannZ. HarteveldS. AschenbrennerA. Bietz  et al.

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

G. CoukosM. IrvingB. CorreiaP. Gainza-CirauquiG. Giordano Attianese

US2021113615 ; EP3774866 ; WO2019197676 . 2019.

Expanding beyond the natural protein repertoire to engineer targeted vaccines and diagnostics

F. Sesterhenn

Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-7515.

Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen

J. MunroF. SesterhennM. GallouxS. S. VollersL. Csepregi  et al.

PLoS Biology. 2019. DOI : 10.1371/journal.pbio.3000164.

Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9

F. BubeckM. D. HoffmannZ. HarteveldS. AschenbrennerA. Bietz  et al.

Nature Methods. 2018. DOI : 10.1038/s41592-018-0178-9.

Rosetta FunFolDes - A general framework for the computational design of functional proteins

J. BonetS. WehrleK. SchrieverC. YangA. Billet  et al.

PLoS Computational Biology. 2018. DOI : 10.1371/journal.pcbi.1006623.

Design and characterization of near-native Ebola GP vaccine candidates: implications for immunogenicity

V. AgnolonI. AyadiJ. P. BikorimanaD. KiseljakV. De Vaux  et al.

2018. p. 6S - 7S.

Expanding the druggable proteome: Ligand and target discovery by fragment-based screening in cells

C. ParkerA. GalmozziY. WangB. CorreiaE. Saez  et al.

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

F. SesterhennJ. BonetB. E. Correia

Current Opinion In Structural Biology. 2018. DOI : 10.1016/j.sbi.2018.06.002.

OFF-switch CAR T cell for safety-enhanced cancer immunotherapy

E. F. Gray-GaillardG. G. AttianeseP. Gainza-CirauquiS. VollersS. Shui  et al.

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

E. SartiI. GladichS. ZamunerB. E. CorreiaA. Laio

Proteins-Structure Function And Bioinformatics. 2016. DOI : 10.1002/prot.25079.

Proof of principle for epitope-focused vaccine design

B. CorreiaJ. BatesR. LoomisC. CarricoJ. Jardine  et al.

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

M. IrvingM. HafeziG. CoukosB. CorreiaL. Scheller

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.