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

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, Christian Schellhaas, Tian Zhu, Ekaterina Pyatova, Lennart Nickel, 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, Ilia Igashov, Arne Schneuing

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.

Synthetic biology

BIOENG-320

This advanced Bachelor/Master level course will cover fundamentals and approaches at the interface of biology, chemistry, engineering and computer science for diverse fields of synthetic biology. This class requires critical and analytical thinking at the frontiers of multiple disciplines

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.