Matteo Dal Peraro
Nationalité: Italian
EPFL SV IBI-SV UPDALPE
AAB 0 48 (Bâtiment AAB)
Station 19
1015 Lausanne
+41 21 693 18 61
+41 21 693 21 52
Office:
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Site web: https://sv.epfl.ch/education
EPFL SV IBI-GE
AAB
Station 15
1015 Lausanne
+41 21 693 18 61
EPFL › SV › IBI-SV › IBI-SV-GE
Site web: https://bioengineering.epfl.ch/
EPFL STI IBI-GE
AAB
Station 15
1015 Lausanne
+41 21 693 18 61
EPFL › STI › IBI-STI › IBI-STI-GE
Site web: https://bioengineering.epfl.ch/
+41 21 693 18 61
EPFL › STI › STI-DEC › STI-DIR
+41 21 693 18 61
EPFL › VPA › VPA-AVP-DLE › AVP-DLE-EDOC › EDCB-GE
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EPFL › SV › SV-DEC › SV-DIR
Formation
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2000 – 2000 University of Padua
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2004 – 2004 International School for Advanced Studies (SISSA)
Journal Articles
2026
Asymmetric envelope surface disposition of secreted protein YjbI controls bimodal antibiotic susceptibilities in C. crescentus
The EMBO Journal. 2026. DOI : 10.1038/s44318-025-00668-x.ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models
Journal of molecular biology. 2026. DOI : 10.1016/j.jmb.2026.169658.2025
Wide-field fluorescence lifetime imaging of single molecules with a gated single-photon camera
Light, science & applications. 2025. DOI : 10.1038/s41377-025-01901-2.Cardiolipin dynamics promote membrane remodeling by mitochondrial OPA1
Nature Communications. 2025. DOI : 10.1038/s41467-025-63813-4.Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization
Science Advances. 2025. DOI : 10.1126/sciadv.adw4124.Exploring New Nanopore Sensors from the Aerolysin Family
Small. 2025. DOI : 10.1002/smll.202501219.Aerolysin Nanopore Structures Revealed at High Resolution in a Lipid Environment
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2025. DOI : 10.1021/jacs.4c14288.BPS2025 - Identification of cyanotoxins with a biological nanopore
Biophysical Journal. 2025. DOI : 10.1016/j.bpj.2024.11.156.ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism
Nature Structural & Molecular Biology. 2025. DOI : 10.1038/s41594-025-01596-4.2024
Virus adaptation to heparan sulfate comes with capsid stability tradeoff
eLife. 2024. DOI : 10.7554/eLife.98441.OXA β-lactamases from Acinetobacter spp. are membrane bound and secreted into outer membrane vesicles
MBIO. 2024. DOI : 10.1128/mbio.03343-24.G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction
Computational and Structural Biotechnology Journal. 2024. DOI : 10.1016/j.csbj.2024.06.029.Missense variants in CMS22 patients reveal that PREPL has both enzymatic and nonenzymatic functions
JCI Insight. 2024. DOI : 10.1172/jci.insight.179276.A look beyond the QR code of SNARE proteins
Protein science : a publication of the Protein Society. 2024. DOI : 10.1002/pro.5158.PeSTo-Carbs: Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces
Journal of Chemical Theory and Computation. 2024. DOI : 10.1021/acs.jctc.3c01145.A humoral stress response protects Drosophila tissues from antimicrobial peptides
Current Biology. 2024. DOI : 10.1016/j.cub.2024.02.049.2023
Bicc1 ribonucleoprotein complexes specifying organ laterality are licensed by ANKS6-induced structural remodeling of associated ANKS3
Plos Biology. 2023. DOI : 10.1371/journal.pbio.3002302.2022
Article Structure and functionality of a multimeric human COQ7:COQ9 complex
Molecular Cell. 2022. DOI : 10.1016/j.molcel.2022.10.003.Ultrasensitive Label-Free Detection of Protein–Membrane Interaction Exemplified by Toxin-Liposome Insertion
The Journal of Physical Chemistry Letters. 2022. DOI : 10.1021/acs.jpclett.1c04011.Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using moleculARweb's Virtual Modeling Kits
Chimia. 2022. DOI : 10.2533/chimia.2022.145.2021
BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy
EMBO Molecular Medicine. 2021. DOI : 10.15252/emmm.202013787.S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity
Developmental Cell. 2021. DOI : 10.1016/j.devcel.2021.09.016.Democratizing interactive, immersive experiences for science education with WebXR
Nature Computational Science. 2021. DOI : 10.1038/s43588-021-00142-8.Specific Protein-Membrane Interactions Promote Packaging of Metallo-beta-Lactamases into Outer Membrane Vesicles
Antimicrobial Agents and Chemotherapy. 2021. DOI : 10.1128/AAC.00507-21.Investigating Crosstalk Among PTMs Provides Novel Insight Into the Structural Basis Underlying the Differential Effects of Nt17 PTMs on Mutant Httex1 Aggregation
Frontiers in Molecular Biosciences. 2021. DOI : 10.3389/fmolb.2021.686086.MoleculARweb: A Web Site for Chemistry and Structural Biology Education through Interactive Augmented Reality out of the Box in Commodity Devices
Journal Of Chemical Education. 2021. DOI : 10.1021/acs.jchemed.1c00179.Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains
Nature Chemical Biology. 2021. DOI : 10.1038/s41589-021-00753-2.CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles
Bioinformatics. 2021. DOI : 10.1093/bioinformatics/btaa742.2020
Aerolysin nanopores decode digital information stored in tailored macromolecular analytes
Science Advances. 2020. DOI : 10.1126/sciadv.abc2661.Molecular Bases of the Membrane Association Mechanism Potentiating Antibiotic Resistance by New Delhi Metallo-beta-lactamase 1
Acs Infectious Diseases. 2020. DOI : 10.1021/acsinfecdis.0c00341.The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain
Structure. 2020. DOI : 10.1016/j.str.2020.06.008.Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations
Frontiers In Molecular Biosciences. 2020. DOI : 10.3389/fmolb.2020.00194.Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms
Nature Communications. 2020. DOI : 10.1038/s41467-020-16128-5.About the need to make computational models of biological macromolecules available and discoverable
Bioinformatics. 2020. DOI : 10.1093/bioinformatics/btaa086.Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces
Journal of Virology. 2020. DOI : 10.1128/JVI.02176-19.2019
An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in beta-lactam resistance
Scientific Reports. 2019. DOI : 10.1038/s41598-019-55923-z.Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores
Nature Communications. 2019. DOI : 10.1038/s41467-019-12690-9.Editorial overview: The future after the cryo-EM resolution revolution
Current Opinion In Structural Biology. 2019. DOI : 10.1016/j.sbi.2019.07.007.KAP1 is an antiparallel dimer with a functional asymmetry
Life Science Alliance. 2019. DOI : 10.26508/lsa.201900349.Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes
Molecular Biology and Evolution. 2019. DOI : 10.1093/molbev/msz096.An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis
Molecular Cell. 2019. DOI : 10.1016/j.molcel.2018.11.033.2017
Evolution of Acid-Sensing Olfactory Circuits in Drosophilids
Neuron. 2017. DOI : 10.1016/j.neuron.2016.12.024.Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies
Scientific Reports. 2017. DOI : 10.1038/s41598-017-00266-w.2016
Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-eta
Nucleic Acids Research. 2016. DOI : 10.1093/nar/gkw128.Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer
The Journal of Physical Chemistry Letters. 2016. DOI : 10.1021/acs.jpclett.6b01721.Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity
Molecular Cell. 2016. DOI : 10.1016/j.molcel.2016.06.030.Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server
Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1124-4.A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria
Nature Communications. 2016. DOI : 10.1038/ncomms12527.Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics
Biophysical Journal. 2016. DOI : 10.1016/j.bpj.2016.07.011.Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server(vol 1, 242, 2016)
Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1315-z.Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2016. DOI : 10.1073/pnas.1608349113.2015
GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis
Journal of Bacteriology. 2015. DOI : 10.1128/Jb.00628-15.The importance of dynamics in integrative modeling of supramolecular assemblies
Current Opinion In Structural Biology. 2015. DOI : 10.1016/j.sbi.2015.02.018.Lipid Builder: A Framework To Build Realistic Models for Biological Membranes
Journal Of Chemical Information And Modeling. 2015. DOI : 10.1021/acs.jcim.5b00501.How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme
Plos One. 2015. DOI : 10.1371/journal.pone.0118684.A coiled coil switch mediates cold sensing by the thermosensory protein DesK
Molecular Microbiology. 2015. DOI : 10.1111/mmi.13118.Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
Scientific Reports. 2015. DOI : 10.1038/srep10549.Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519
Biochemistry. 2015. DOI : 10.1021/bi501227b.2014
Perturbations of the Straight Transmembrane alpha-Helical Structure of the Amyloid Precursor Protein Affect Its Processing by gamma-Secretase
Journal of Biological Chemistry. 2014. DOI : 10.1074/jbc.M113.470781.Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics
The Journal of Physical Chemistry B. 2014. DOI : 10.1021/jp4126705.A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP
Journal Of Inorganic Biochemistry. 2014. DOI : 10.1016/j.jinorgbio.2014.07.022.ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells
PLoS Genetics. 2014. DOI : 10.1371/journal.pgen.1004066.Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control
JBIC Journal of Biological Inorganic Chemistry. 2014. DOI : 10.1007/s00775-014-1108-7.Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase
The Journal of Physical Chemistry B. 2014. DOI : 10.1021/jp411786z.Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2014. DOI : 10.1073/pnas.1321165111.2013
In situ structural analysis of the Yersinia enterocolitica injectisome
Elife. 2013. DOI : 10.7554/eLife.00792.Arranged Sevenfold: Structural Insights into the C-Terminal Oligomerization Domain of Human C4b-Binding Protein
Journal of Molecular Biology. 2013. DOI : 10.1016/j.jmb.2012.12.017.In-depth analysis of hyaline fibromatosis syndrome frameshift mutations at the same site reveal the necessity of personalized therapy
Human mutation. 2013. DOI : 10.1002/humu.22324.Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase
Journal of Chemical Theory and Computation. 2013. DOI : 10.1021/ct300691u.Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling
Structure. 2013. DOI : 10.1016/j.str.2013.05.014.Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism
Nature Chemical Biology. 2013. DOI : 10.1038/Nchembio.1312.Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations
PLoS Computational Biology. 2013. DOI : 10.1371/journal.pcbi.1002878.Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes
Journal of Chemical Theory and Computation. 2013. DOI : 10.1021/ct300590v.2012
On the active site of mononuclear B1 metallo beta-lactamases: a computational study
Journal Of Computer-Aided Molecular Design. 2012. DOI : 10.1007/s10822-012-9571-0.Palmitoylated calnexin is a key component of the ribosome-translocon complex
Embo Journal. 2012. DOI : 10.1038/emboj.2012.15.2011
Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis
Molecular Microbiology. 2011. DOI : 10.1111/j.1365-2958.2011.07813.x.Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin
PLoS Pathogens. 2011. DOI : 10.1371/journal.ppat.1002135.Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus
Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011. DOI : 10.1016/j.bbamem.2010.03.025.An introduction to quantum chemical methods applied to drug design
Frontiers in Bioscience. 2011. DOI : 10.2741/311.2010
Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis?
Journal of the American Chemical Society. 2010. DOI : 10.1021/ja102933y.A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements
Journal of Chemical Theory and Computation. 2010. DOI : 10.1021/ct900457z.Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP)
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2010. DOI : 10.1073/pnas.1006985107.2009
Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation
Journal of Chemical Theory and Computation. 2009. DOI : 10.1021/ct8004722.Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2009. DOI : 10.1073/pnas.0811720106.The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome
Molecular microbiology. 2009. DOI : 10.1111/j.1365-2958.2008.06556.x.Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling
CHIMIA. 2009. DOI : 10.2533/chimia.2009.14.2008
Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement
Structure. 2008. DOI : 10.1016/j.str.2007.11.011.Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism
Journal of the American Chemical Society. 2008. DOI : 10.1021/ja8005786.2007
Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations
Current Opinion in Structural Biology. 2007. DOI : 10.1016/j.sbi.2007.03.018.The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site
Journal of Biological Chemistry. 2007. DOI : 10.1074/jbc.M700467200.Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations
J Struct Biol. 2007. DOI : 10.1016/j.jsb.2006.10.019.Proton shuttles and phosphatase activity in soluble epoxide hydrolase
J Am Chem Soc. 2007. DOI : 10.1021/ja066150c.2006
Polarization effects and charge transfer in the KcsA potassium channel
Biophysical Chemistry. 2006. DOI : 10.1016/j.bpc.2006.04.008.2004
Water-Assisted Reaction Mechanism of Monozinc b-Lactamases
Journal of the American Chemical Society. 2004. DOI : 10.1021/ja048071b.Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus
Proteins. 2004. DOI : 10.1002/prot.10554.2002
Structural determinants and hydrogen-bond network of the mononuclear zinc(II)-beta-lactamase active site
J Biol Inorg Chem. 2002. DOI : 10.1007/s00775-002-0346-2.2001
Ser133 phosphate-KIX interactions in the CREB-CBP complex: an ab initio molecular dynamics study
Eur Biophysical Journal. 2001. DOI : 10.1007/s002490000112.Conference Papers
2025
Lumen Charge Governs Memristive Ion Transport in Β-barrel Nanopores
2025. 15th EBSA European Biophysics Congress, Rome, ITALY, 2025-06-30 - 2025-07-04. p. S250 - S251.Unveiling the Architecture of the Rna Helicase Ddx21 and 7sk Ribonucleoprotein Complex
2025. 15th EBSA European Biophysics Congress, Rome, ITALY, 2025-06-30 - 2025-07-04. p. S230 - S231.2023
Structural characterization of Prolyl endopeptidase-like, a mitochondrial protein involved in congenital myasthenic syndrome-22
2023. p. S109 - S109.Using integrative structural biology for the identification of novel aerolysin-like pore forming toxins for nanopore sensing
2023. p. S116 - S116.2022
The role of PTM crosstalks in Httex1 structure, aggregation and membrane interaction
2022. p. 38 - 38. DOI : 10.1016/j.bpj.2021.11.2495.Bacterial nanopores open the future of data storage
2022. International Electron Devices Meeting (IEDM), San Francisco, CA, Dec 03-07, 2022. DOI : 10.1109/IEDM45625.2022.10019421.2019
Molecular Simulations Give Insights into the NDM-1/Membrane Interaction that Causes Rise of a Super-Bacterium
2019. 63rd Annual Meeting of the Biophysical-Society, Baltimore, MD, Mar 02-06, 2019. p. 205A - 205A. DOI : 10.1016/j.bpj.2018.11.1132.2013
Intrinsic Transmembrane Flexibility of the Amyloid Precursor Protein Explored by Molecular Simulations
2013. 57th Annual Meeting of the Biophysical-Society, Philadelphia, PA, FEB 02-06, 2013. p. 226A - 226A. DOI : 10.1016/j.bpj.2012.11.1278.2011
Development of a chemical-detailed coarse-grained force field for proteins
2011. 242nd National Meeting of the American-Chemical-Society (ACS), Denver, CO, Aug 28-Sep 01, 2011. p. 28 - COMP.2010
Assembly and function of large Gram-negative bacterial machines studied by molecular simulation integrated with experimental data
2010. p. 425 - COMP.A model for the assembly and activation process of the pore-forming toxin Aerolysin
2010. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, SWEDEN, Jun 26-Jul 01, 2010. p. 194 - 194.Conformational coupling between LOV and kinase domains in phototropins: A computational perspective
2010. p. 436 - COMP.Shedding a new light on photolyases: Accurate molecular modeling as a tool for undestanding DNA repairing enzymes
2010. p. 20 - PHYS.Coarse-graining electrostatics in multiscale molecular simulations
2010. p. 391 - COMP.2008
Topologically-based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins
2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 57 - COMP.Unraveling the enzymatic mechanism of the protein farnesyltransferase: A QM/MM study
2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 258 - COMP.Reviews
2022
Biological nanopores for single-molecule sensing
iScience. 2022. DOI : 10.1016/j.isci.2022.104145.2021
State-of-the-art web services for de novo protein structure prediction
Briefings In Bioinformatics. 2021. DOI : 10.1093/bib/bbaa139.2016
Pore-forming toxins: ancient, but never really out of fashion
Nature Reviews Microbiology. 2016. DOI : 10.1038/nrmicro.2015.3.2015
Catalytic Metal Ions and Enzymatic Processing of DNA and RNA
Accounts Of Chemical Research. 2015. DOI : 10.1021/ar500314j.Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Structure. 2015. DOI : 10.1016/j.str.2015.05.013.2014
HCV E2 core structures and mAbs: something is still missing
Drug Discovery Today. 2014. DOI : 10.1016/j.drudis.2014.08.011.2013
Peptide-Based Vaccinology: Experimental and Computational Approaches to Target Hypervariable Viruses through the Fine Characterization of Protective Epitopes Recognized by Monoclonal Antibodies and the Identification of T-Cell-Activating Peptides
Clinical & Developmental Immunology. 2013. DOI : 10.1155/2013/521231.Theses
2024
Exploring ion and analyte transport in beta-barrel forming biological nanopores
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10672.Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10530.Label-Efficient Deep Learning Methods for Event Detection, Object Segmentation and Cell Tracking in Biological Microscopy Images
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-11163.2023
A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer
Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-10309.2021
New Methods for the Integrative Dynamic Modeling of Biomolecular Structures
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8284.2020
Beneficial axis of the renin-angiotensin system: from applications to drug discovery
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10223.2019
Exploring on Protein-DNA interactions
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9426.Characterization of Coenzyme Q Biosynthesis Proteins through Integrative Modeling at the Protein-Membrane Interface
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9641.2018
Structural and functional analysis of host attachment proteins from contractile injection systems
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8267.2017
Studying membrane-protein interplay by modeling realistic conditions
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7934.2015
Modeling and Engineering Proteins Thermostability
Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6637.2014
New models and techniques to simulate realistic biological membranes
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6310.2013
Molecular Modeling of Membrane Embedded Proteins
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5695.Multiscale simulations of protein dynamics
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5841.Book Chapters
2014
New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
Biomolecular Modelling And Simulations; San Diego: Elsevier Academic Press Inc, 2014. p. 77 - 111.Working Papers
2025
MolecularWeb Democratizes Web-Based, Immersive, Multiuser Molecular Graphics And Modeling
2025Sub-Nanomolar Detection and Discrimination of Microcystin Congeners Using Aerolysin Nanopores
2025Molecular Regulation and Physiological Role of GOLPH3-mediated Golgi retention
2025Practical outcomes from CASP16 for users in need of biomolecular structure prediction
2025Context-aware geometric deep learning for RNA sequence design
2025Posters
2022
Identification of single amino acid with engineered aerolysin nanopores
Single-Molecule Protein Sequencing 3 (SMPS3), Delft, The Netherlands, October 31-November 3, 2022.Talks
2022
Bacterial proteolytic enzymes as biological scissors in the fate of enteroviruses in natural ecosystems
Swiss Society for Microbiology Annual Meeting - SMM 2022, Lausanne, Switzerland, August 30 - September 1, 2022.Mechanisms of inactivation of non-enveloped viruses in natural ecosystems: bacterial proteolytic enzymes as biological scissors in the fate of enteroviruses
7th International Society for Food and Environmental Virology Conference - ISFEV2020, Santiago de Compostela, Spain, May 16-20, 2022.2018
Structural characterization of thermoresistant enteroviruses
ISFEV 2018 - 6th Food and Environmental Virology Conference, Tempe, Arizona, USA, October 7-10, 2018.Patents
2025
Uses of aerolysin nanopores
WO2025003492 . 2025.2024
Mutant aerolysin and uses thereof
EP4362028 . 2024.2022
Systems and methods for digital information decoding and data storage in hybrid macromolecules
US2023377649 ; EP4222742 ; WO2022069022 . 2022.2024
Dissecting the membrane association mechanism of aerolysin pore at femtomolar concentrations using water as a probe
2024.Journal Articles
2026
Asymmetric envelope surface disposition of secreted protein YjbI controls bimodal antibiotic susceptibilities in C. crescentus
The EMBO Journal. 2026. DOI : 10.1038/s44318-025-00668-x.ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models
Journal of molecular biology. 2026. DOI : 10.1016/j.jmb.2026.169658.2025
Wide-field fluorescence lifetime imaging of single molecules with a gated single-photon camera
Light, science & applications. 2025. DOI : 10.1038/s41377-025-01901-2.Cardiolipin dynamics promote membrane remodeling by mitochondrial OPA1
Nature Communications. 2025. DOI : 10.1038/s41467-025-63813-4.Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization
Science Advances. 2025. DOI : 10.1126/sciadv.adw4124.Exploring New Nanopore Sensors from the Aerolysin Family
Small. 2025. DOI : 10.1002/smll.202501219.Aerolysin Nanopore Structures Revealed at High Resolution in a Lipid Environment
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2025. DOI : 10.1021/jacs.4c14288.BPS2025 - Identification of cyanotoxins with a biological nanopore
Biophysical Journal. 2025. DOI : 10.1016/j.bpj.2024.11.156.ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism
Nature Structural & Molecular Biology. 2025. DOI : 10.1038/s41594-025-01596-4.2024
Virus adaptation to heparan sulfate comes with capsid stability tradeoff
eLife. 2024. DOI : 10.7554/eLife.98441.OXA β-lactamases from Acinetobacter spp. are membrane bound and secreted into outer membrane vesicles
MBIO. 2024. DOI : 10.1128/mbio.03343-24.G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction
Computational and Structural Biotechnology Journal. 2024. DOI : 10.1016/j.csbj.2024.06.029.Missense variants in CMS22 patients reveal that PREPL has both enzymatic and nonenzymatic functions
JCI Insight. 2024. DOI : 10.1172/jci.insight.179276.A look beyond the QR code of SNARE proteins
Protein science : a publication of the Protein Society. 2024. DOI : 10.1002/pro.5158.PeSTo-Carbs: Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces
Journal of Chemical Theory and Computation. 2024. DOI : 10.1021/acs.jctc.3c01145.A humoral stress response protects Drosophila tissues from antimicrobial peptides
Current Biology. 2024. DOI : 10.1016/j.cub.2024.02.049.2023
Bicc1 ribonucleoprotein complexes specifying organ laterality are licensed by ANKS6-induced structural remodeling of associated ANKS3
Plos Biology. 2023. DOI : 10.1371/journal.pbio.3002302.2022
Article Structure and functionality of a multimeric human COQ7:COQ9 complex
Molecular Cell. 2022. DOI : 10.1016/j.molcel.2022.10.003.Ultrasensitive Label-Free Detection of Protein–Membrane Interaction Exemplified by Toxin-Liposome Insertion
The Journal of Physical Chemistry Letters. 2022. DOI : 10.1021/acs.jpclett.1c04011.Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using moleculARweb's Virtual Modeling Kits
Chimia. 2022. DOI : 10.2533/chimia.2022.145.2021
BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy
EMBO Molecular Medicine. 2021. DOI : 10.15252/emmm.202013787.S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity
Developmental Cell. 2021. DOI : 10.1016/j.devcel.2021.09.016.Democratizing interactive, immersive experiences for science education with WebXR
Nature Computational Science. 2021. DOI : 10.1038/s43588-021-00142-8.Specific Protein-Membrane Interactions Promote Packaging of Metallo-beta-Lactamases into Outer Membrane Vesicles
Antimicrobial Agents and Chemotherapy. 2021. DOI : 10.1128/AAC.00507-21.Investigating Crosstalk Among PTMs Provides Novel Insight Into the Structural Basis Underlying the Differential Effects of Nt17 PTMs on Mutant Httex1 Aggregation
Frontiers in Molecular Biosciences. 2021. DOI : 10.3389/fmolb.2021.686086.MoleculARweb: A Web Site for Chemistry and Structural Biology Education through Interactive Augmented Reality out of the Box in Commodity Devices
Journal Of Chemical Education. 2021. DOI : 10.1021/acs.jchemed.1c00179.Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains
Nature Chemical Biology. 2021. DOI : 10.1038/s41589-021-00753-2.CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles
Bioinformatics. 2021. DOI : 10.1093/bioinformatics/btaa742.2020
Aerolysin nanopores decode digital information stored in tailored macromolecular analytes
Science Advances. 2020. DOI : 10.1126/sciadv.abc2661.Molecular Bases of the Membrane Association Mechanism Potentiating Antibiotic Resistance by New Delhi Metallo-beta-lactamase 1
Acs Infectious Diseases. 2020. DOI : 10.1021/acsinfecdis.0c00341.The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain
Structure. 2020. DOI : 10.1016/j.str.2020.06.008.Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations
Frontiers In Molecular Biosciences. 2020. DOI : 10.3389/fmolb.2020.00194.Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms
Nature Communications. 2020. DOI : 10.1038/s41467-020-16128-5.About the need to make computational models of biological macromolecules available and discoverable
Bioinformatics. 2020. DOI : 10.1093/bioinformatics/btaa086.Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces
Journal of Virology. 2020. DOI : 10.1128/JVI.02176-19.2019
An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in beta-lactam resistance
Scientific Reports. 2019. DOI : 10.1038/s41598-019-55923-z.Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores
Nature Communications. 2019. DOI : 10.1038/s41467-019-12690-9.Editorial overview: The future after the cryo-EM resolution revolution
Current Opinion In Structural Biology. 2019. DOI : 10.1016/j.sbi.2019.07.007.KAP1 is an antiparallel dimer with a functional asymmetry
Life Science Alliance. 2019. DOI : 10.26508/lsa.201900349.Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes
Molecular Biology and Evolution. 2019. DOI : 10.1093/molbev/msz096.An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis
Molecular Cell. 2019. DOI : 10.1016/j.molcel.2018.11.033.2017
Evolution of Acid-Sensing Olfactory Circuits in Drosophilids
Neuron. 2017. DOI : 10.1016/j.neuron.2016.12.024.Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies
Scientific Reports. 2017. DOI : 10.1038/s41598-017-00266-w.2016
Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-eta
Nucleic Acids Research. 2016. DOI : 10.1093/nar/gkw128.Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer
The Journal of Physical Chemistry Letters. 2016. DOI : 10.1021/acs.jpclett.6b01721.Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity
Molecular Cell. 2016. DOI : 10.1016/j.molcel.2016.06.030.Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server
Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1124-4.A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria
Nature Communications. 2016. DOI : 10.1038/ncomms12527.Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics
Biophysical Journal. 2016. DOI : 10.1016/j.bpj.2016.07.011.Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server(vol 1, 242, 2016)
Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-016-1315-z.Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2016. DOI : 10.1073/pnas.1608349113.2015
GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis
Journal of Bacteriology. 2015. DOI : 10.1128/Jb.00628-15.The importance of dynamics in integrative modeling of supramolecular assemblies
Current Opinion In Structural Biology. 2015. DOI : 10.1016/j.sbi.2015.02.018.Lipid Builder: A Framework To Build Realistic Models for Biological Membranes
Journal Of Chemical Information And Modeling. 2015. DOI : 10.1021/acs.jcim.5b00501.How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme
Plos One. 2015. DOI : 10.1371/journal.pone.0118684.A coiled coil switch mediates cold sensing by the thermosensory protein DesK
Molecular Microbiology. 2015. DOI : 10.1111/mmi.13118.Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
Scientific Reports. 2015. DOI : 10.1038/srep10549.Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519
Biochemistry. 2015. DOI : 10.1021/bi501227b.2014
Perturbations of the Straight Transmembrane alpha-Helical Structure of the Amyloid Precursor Protein Affect Its Processing by gamma-Secretase
Journal of Biological Chemistry. 2014. DOI : 10.1074/jbc.M113.470781.Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics
The Journal of Physical Chemistry B. 2014. DOI : 10.1021/jp4126705.A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP
Journal Of Inorganic Biochemistry. 2014. DOI : 10.1016/j.jinorgbio.2014.07.022.ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells
PLoS Genetics. 2014. DOI : 10.1371/journal.pgen.1004066.Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control
JBIC Journal of Biological Inorganic Chemistry. 2014. DOI : 10.1007/s00775-014-1108-7.Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase
The Journal of Physical Chemistry B. 2014. DOI : 10.1021/jp411786z.Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2014. DOI : 10.1073/pnas.1321165111.2013
In situ structural analysis of the Yersinia enterocolitica injectisome
Elife. 2013. DOI : 10.7554/eLife.00792.Arranged Sevenfold: Structural Insights into the C-Terminal Oligomerization Domain of Human C4b-Binding Protein
Journal of Molecular Biology. 2013. DOI : 10.1016/j.jmb.2012.12.017.In-depth analysis of hyaline fibromatosis syndrome frameshift mutations at the same site reveal the necessity of personalized therapy
Human mutation. 2013. DOI : 10.1002/humu.22324.Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase
Journal of Chemical Theory and Computation. 2013. DOI : 10.1021/ct300691u.Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling
Structure. 2013. DOI : 10.1016/j.str.2013.05.014.Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism
Nature Chemical Biology. 2013. DOI : 10.1038/Nchembio.1312.Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations
PLoS Computational Biology. 2013. DOI : 10.1371/journal.pcbi.1002878.Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes
Journal of Chemical Theory and Computation. 2013. DOI : 10.1021/ct300590v.2012
On the active site of mononuclear B1 metallo beta-lactamases: a computational study
Journal Of Computer-Aided Molecular Design. 2012. DOI : 10.1007/s10822-012-9571-0.Palmitoylated calnexin is a key component of the ribosome-translocon complex
Embo Journal. 2012. DOI : 10.1038/emboj.2012.15.2011
Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis
Molecular Microbiology. 2011. DOI : 10.1111/j.1365-2958.2011.07813.x.Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin
PLoS Pathogens. 2011. DOI : 10.1371/journal.ppat.1002135.Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus
Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011. DOI : 10.1016/j.bbamem.2010.03.025.An introduction to quantum chemical methods applied to drug design
Frontiers in Bioscience. 2011. DOI : 10.2741/311.2010
Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis?
Journal of the American Chemical Society. 2010. DOI : 10.1021/ja102933y.A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements
Journal of Chemical Theory and Computation. 2010. DOI : 10.1021/ct900457z.Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP)
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2010. DOI : 10.1073/pnas.1006985107.2009
Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation
Journal of Chemical Theory and Computation. 2009. DOI : 10.1021/ct8004722.Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2009. DOI : 10.1073/pnas.0811720106.The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome
Molecular microbiology. 2009. DOI : 10.1111/j.1365-2958.2008.06556.x.Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling
CHIMIA. 2009. DOI : 10.2533/chimia.2009.14.2008
Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement
Structure. 2008. DOI : 10.1016/j.str.2007.11.011.Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism
Journal of the American Chemical Society. 2008. DOI : 10.1021/ja8005786.2007
Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations
Current Opinion in Structural Biology. 2007. DOI : 10.1016/j.sbi.2007.03.018.The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site
Journal of Biological Chemistry. 2007. DOI : 10.1074/jbc.M700467200.Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations
J Struct Biol. 2007. DOI : 10.1016/j.jsb.2006.10.019.Proton shuttles and phosphatase activity in soluble epoxide hydrolase
J Am Chem Soc. 2007. DOI : 10.1021/ja066150c.2006
Polarization effects and charge transfer in the KcsA potassium channel
Biophysical Chemistry. 2006. DOI : 10.1016/j.bpc.2006.04.008.2004
Water-Assisted Reaction Mechanism of Monozinc b-Lactamases
Journal of the American Chemical Society. 2004. DOI : 10.1021/ja048071b.Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus
Proteins. 2004. DOI : 10.1002/prot.10554.2002
Structural determinants and hydrogen-bond network of the mononuclear zinc(II)-beta-lactamase active site
J Biol Inorg Chem. 2002. DOI : 10.1007/s00775-002-0346-2.2001
Ser133 phosphate-KIX interactions in the CREB-CBP complex: an ab initio molecular dynamics study
Eur Biophysical Journal. 2001. DOI : 10.1007/s002490000112.Conference Papers
2025
Lumen Charge Governs Memristive Ion Transport in Β-barrel Nanopores
2025. 15th EBSA European Biophysics Congress, Rome, ITALY, 2025-06-30 - 2025-07-04. p. S250 - S251.Unveiling the Architecture of the Rna Helicase Ddx21 and 7sk Ribonucleoprotein Complex
2025. 15th EBSA European Biophysics Congress, Rome, ITALY, 2025-06-30 - 2025-07-04. p. S230 - S231.2023
Structural characterization of Prolyl endopeptidase-like, a mitochondrial protein involved in congenital myasthenic syndrome-22
2023. p. S109 - S109.Using integrative structural biology for the identification of novel aerolysin-like pore forming toxins for nanopore sensing
2023. p. S116 - S116.2022
The role of PTM crosstalks in Httex1 structure, aggregation and membrane interaction
2022. p. 38 - 38. DOI : 10.1016/j.bpj.2021.11.2495.Bacterial nanopores open the future of data storage
2022. International Electron Devices Meeting (IEDM), San Francisco, CA, Dec 03-07, 2022. DOI : 10.1109/IEDM45625.2022.10019421.2019
Molecular Simulations Give Insights into the NDM-1/Membrane Interaction that Causes Rise of a Super-Bacterium
2019. 63rd Annual Meeting of the Biophysical-Society, Baltimore, MD, Mar 02-06, 2019. p. 205A - 205A. DOI : 10.1016/j.bpj.2018.11.1132.2013
Intrinsic Transmembrane Flexibility of the Amyloid Precursor Protein Explored by Molecular Simulations
2013. 57th Annual Meeting of the Biophysical-Society, Philadelphia, PA, FEB 02-06, 2013. p. 226A - 226A. DOI : 10.1016/j.bpj.2012.11.1278.2011
Development of a chemical-detailed coarse-grained force field for proteins
2011. 242nd National Meeting of the American-Chemical-Society (ACS), Denver, CO, Aug 28-Sep 01, 2011. p. 28 - COMP.2010
Assembly and function of large Gram-negative bacterial machines studied by molecular simulation integrated with experimental data
2010. p. 425 - COMP.A model for the assembly and activation process of the pore-forming toxin Aerolysin
2010. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, SWEDEN, Jun 26-Jul 01, 2010. p. 194 - 194.Conformational coupling between LOV and kinase domains in phototropins: A computational perspective
2010. p. 436 - COMP.Shedding a new light on photolyases: Accurate molecular modeling as a tool for undestanding DNA repairing enzymes
2010. p. 20 - PHYS.Coarse-graining electrostatics in multiscale molecular simulations
2010. p. 391 - COMP.2008
Topologically-based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins
2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 57 - COMP.Unraveling the enzymatic mechanism of the protein farnesyltransferase: A QM/MM study
2008. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, Aug 17-21, 2008. p. 258 - COMP.Reviews
2022
Biological nanopores for single-molecule sensing
iScience. 2022. DOI : 10.1016/j.isci.2022.104145.2021
State-of-the-art web services for de novo protein structure prediction
Briefings In Bioinformatics. 2021. DOI : 10.1093/bib/bbaa139.2016
Pore-forming toxins: ancient, but never really out of fashion
Nature Reviews Microbiology. 2016. DOI : 10.1038/nrmicro.2015.3.2015
Catalytic Metal Ions and Enzymatic Processing of DNA and RNA
Accounts Of Chemical Research. 2015. DOI : 10.1021/ar500314j.Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Structure. 2015. DOI : 10.1016/j.str.2015.05.013.2014
HCV E2 core structures and mAbs: something is still missing
Drug Discovery Today. 2014. DOI : 10.1016/j.drudis.2014.08.011.2013
Peptide-Based Vaccinology: Experimental and Computational Approaches to Target Hypervariable Viruses through the Fine Characterization of Protective Epitopes Recognized by Monoclonal Antibodies and the Identification of T-Cell-Activating Peptides
Clinical & Developmental Immunology. 2013. DOI : 10.1155/2013/521231.Theses
2024
Exploring ion and analyte transport in beta-barrel forming biological nanopores
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10672.Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10530.Label-Efficient Deep Learning Methods for Event Detection, Object Segmentation and Cell Tracking in Biological Microscopy Images
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-11163.2023
A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer
Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-10309.2021
New Methods for the Integrative Dynamic Modeling of Biomolecular Structures
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8284.2020
Beneficial axis of the renin-angiotensin system: from applications to drug discovery
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10223.2019
Exploring on Protein-DNA interactions
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9426.Characterization of Coenzyme Q Biosynthesis Proteins through Integrative Modeling at the Protein-Membrane Interface
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9641.2018
Structural and functional analysis of host attachment proteins from contractile injection systems
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8267.2017
Studying membrane-protein interplay by modeling realistic conditions
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7934.2015
Modeling and Engineering Proteins Thermostability
Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6637.2014
New models and techniques to simulate realistic biological membranes
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6310.2013
Molecular Modeling of Membrane Embedded Proteins
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5695.Multiscale simulations of protein dynamics
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5841.Book Chapters
2014
New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
Biomolecular Modelling And Simulations; San Diego: Elsevier Academic Press Inc, 2014. p. 77 - 111.Working Papers
2025
MolecularWeb Democratizes Web-Based, Immersive, Multiuser Molecular Graphics And Modeling
2025Sub-Nanomolar Detection and Discrimination of Microcystin Congeners Using Aerolysin Nanopores
2025Molecular Regulation and Physiological Role of GOLPH3-mediated Golgi retention
2025Practical outcomes from CASP16 for users in need of biomolecular structure prediction
2025Context-aware geometric deep learning for RNA sequence design
2025Posters
2022
Identification of single amino acid with engineered aerolysin nanopores
Single-Molecule Protein Sequencing 3 (SMPS3), Delft, The Netherlands, October 31-November 3, 2022.Talks
2022
Bacterial proteolytic enzymes as biological scissors in the fate of enteroviruses in natural ecosystems
Swiss Society for Microbiology Annual Meeting - SMM 2022, Lausanne, Switzerland, August 30 - September 1, 2022.Mechanisms of inactivation of non-enveloped viruses in natural ecosystems: bacterial proteolytic enzymes as biological scissors in the fate of enteroviruses
7th International Society for Food and Environmental Virology Conference - ISFEV2020, Santiago de Compostela, Spain, May 16-20, 2022.2018
Structural characterization of thermoresistant enteroviruses
ISFEV 2018 - 6th Food and Environmental Virology Conference, Tempe, Arizona, USA, October 7-10, 2018.Patents
2025
Uses of aerolysin nanopores
WO2025003492 . 2025.2024
Mutant aerolysin and uses thereof
EP4362028 . 2024.2022
Systems and methods for digital information decoding and data storage in hybrid macromolecules
US2023377649 ; EP4222742 ; WO2022069022 . 2022.2024
Dissecting the membrane association mechanism of aerolysin pore at femtomolar concentrations using water as a probe
2024.Enseignement et PhD
Doctorant·es actuel·les
Verena Rukes, Parth Bibekar, Arthur Samurkas, Fernando Augusto Teixeira Pinto Meireles, Benedikt Singer, Artemiy Burov, Ekaterina Pyatova, Edoardo Cavani, Alissa Agerova, Marianna Mitsioni, Jana Susanne Anton, Roxana Ghasemi
A dirigé les thèses EPFL de
Matteo Thomas Degiacomi, Thomas Lemmin, Enrico Spiga, Christophe Bovigny, Hasan Pezeshgi Modarres, Martina Audagnotto, Giorgio Elikem Tamo, Alexandra Styliani Kalantzi, Deniz Aydin, Giulia Fonti, Alessio Prunotto, Sylvain Träger, Lucien Fabrice Krapp, Zhidian Zhang, Simon Finn Mayer, Anastasia Theodoropoulou, Benjamin Gallusser
A co-dirigé les thèses EPFL de
Michel Plattner, Maiia Bragina
Cours
Biological chemistry I
BIO-212
La biochimie est une discipline clé dans les sciences de la vie. La chimie biologique I et II sont deux cours étroitement interconnectés qui visent à comprendre en termes moléculaires les processus qui rendent la vie possible.
Scientific literature analysis in computational molecular biology
BIO-468
But: apprendre à analyser un article scientifique de manière critique, c'est-à-dire d'étudier le bien fondé des questions scientifiques posées et des conclusions tirées. Cette analyse est présentée sous la forme d'un résumé écrit critique mais constructif, dans le style d'un `referee report'.
Structural biology
BIO-315
Ce cours est axé sur les interactions moléculaires qui définissent la structure, la dynamique et la fonction des systèmes biologiques. Les principales techniques expérimentales et computationnelles utilisées en biologie structurale seront présentées et mises en pratique.
Synthetic biology
BIOENG-320
Ce cours avancé de niveau Bachelor/Master couvrira les principes fondamentaux et les approches à l'interface de la biologie, la chimie, l'ingénierie et l'informatique pour la biologie synthétique. Ce cours requiert une pensée critique et analytique aux frontières de plusieurs disciplines.