Team's members

Juliette Martin (DR2 CNRS, co-team leader)

I am full-time CNRS researcher in structural bioinformatics.

I obtained my PhD in Bioinformatics in 2005 from University Paris 7, with as topic the assignment and prediction of local protein structures using Hidden Markov Models (co-supervision of J-F Gibrat  and F. Rodolphe at the INRA center at Jouy-en-Josas). For my first post-doc, I joined the laboratory of C. Etchebest (University of Paris) to study protein structures with structural alphabets. For my second post-doc, I joined the laboratory of N. Srinivasan (Indian Institute of Science Bangalore) to study protein kinase superfamilies. I obtained a permanent position at CNRS (Research Associate) in 2008 at the Institute of Biology and Chemistry of Proteins (IBCP) in Lyon. My main research topic is protein-protein interactions. In 2023, I was promoted Senior Researcher (DR) by CNRS and moved to the LBMC to integrate my research activity within a biology institute and to develop new projects on macromolecular machines. My full list of publications can be found here.  

Riccardo Pellarin (CRCN CNRS, co-team leader)

I am a computational structural biologist.

I did my physics master thesis in 2002, in Rome. Back in the time, I studied statistical mechanics of confined liquids. Then I moved to the Department of Biochemistry of the University of Zurich for my PhD, in the group of Amedeo Caflisch. Here I did molecular dynamics simulations of membrane proteins, amyloid aggregation, and protein folding. In 2010 I decided to move to the US with a postdoc fellowship from the Swiss National Science Foundation. I  settled at UCSF in the group of Andrej Sali, where I started to work on structural biology of large macromolecular complexes, and designed strategies for integrative modeling. I collaborated with Brian Chait, on the Nuclear Pore complex, with Roger Kornberg, on the transcription mediator complex, and with Nenad Ban on translation initiation. I've got more and more interested in the modeling of cross-linking and cryoEM to build models of these systems. In 2014 I decided to move back to Europe, to the Institut Pasteur, in the group of Michael Nilges. Here I reinforced my expertise on data modeling using bayesian inference. In 2015 I’ve got my CR position at CNRS, and since then I'm enthusiastically interested in large macromolecular machines in bacteria. I started a long and fruitful collaboration with Eric Durand and Eric Cascales studying different aspects of the type 6 secretion system. 

Paulo C. T. Souza

After earning a chemistry technician diploma and gaining industry experience at Saint Gobain, I pursued my passion for science with Bachelor's and Licentiate degrees in Chemistry at the University of Campinas (Brazil). Since my undergraduate studies, I delved into Physical Chemistry and Molecular Biophysics during my Masters and PhD, focusing on learning and using computational approaches to study biological and medical problems. As a postdoc at the University of Groningen (Netherlands) I specialized in molecular simulations of biomolecules and materials, leading to the development of the Martini force-field, a popular coarse-grained model worldwide used for biomolecular simulations. After a short but intense period in a pharma company in South Korea, I became a CR at CNRS-Lyon, where I continue to explore molecular interactions, with a keen interest in advancing scientific knowledge in biology and chemistry, but also in collaborating with industry in (bio)molecular design of drugs and vaccines. Excitedly, I recently joined LBMC to establish a new team with many colleagues, embarking on a promising new journey at ENS de Lyon.

Guillaume Launay

I received my phD training from the Biochemistry Lab of Ecole Polytechnique(Palaiseau) working on the in silico modeling of protein-protein interactions at the molecular level.
I did a fist post-doc in a computer science institute (IRISA:Rennes) working on the prediction of protein folding. During my second post doc at INIRAE, I developed methods to predict the action of a broad range of ligands on a family of GPCRs. Since my appointment as associate Professor in the Biosciences Dpt of Lyon, I have been working on methods to predict and study protein-protein interactions networks and use them in the context of experimental omics data.

Kai Stroh

Kai Stroh joined the dynamics and control of biological assemblies and macromolecular machines (DAMM) team in February 2024. During his doctoral studies at the Institute for Theoretical Physics in Goettingen and as a post-doc at TU Dortmund, Kai worked on phase space and parameter space sampling in realistic protein-lipid environments, employing coarse-grained molecular dynamics simulations and global optimization methods. At LBMC Kai will work on protein design with the goal of inhibiting type 6 secretion system activity.

Mariana Valerio

I am originally from Portugal, where I completed my undergraduate studies in Biochemistry at the University of Lisbon. For my PhD, I shifted to Computational Biophysics, specializing in the use of molecular dynamics to explore the mechanisms of viral fusion. During my doctoral research, I had the privilege of visiting the DAMM team in Lyon, where I acquired expertise in employing coarse-grain Martini models to investigate my viral fusion systems. Thanks to this amazing experience, in February of 2024 I joined the LBMC lab as a Post-Doc. I am thrilled to continue my academic journey here!

Gilberto Pereira

I started out as a biologist, graduating in 2016 from the Technical University of Lisbon. As a follow-up, I attended a masters’ degree in medical biochemistry in the University of Lisbon, during which I carried out computational and experimental work with the aim of identifying ligands targeting potassium voltage-gated ion channels.

I decided to then move towards a PhD in computational chemistry and protein-ligand binding, which was completed at the University of Strasbourg in 2021.
I am currently a post-doc in the Martin-Pellarin group at LBMC, where I work with protein-protein interactions and molecular modeling using multi-scale techniques.

Luis Borges

I wrapped up my BSc. and MSc. in Biochemistry at the Faculty of Sciences, University of Lisbon. Rather than attending my lectures, I spent most of my time in the Physics department, where I discovered the beautiful world of applying physics-based methodologies to answer biology-centered questions. I obtained my PhD in Chemistry from Instituto Superior Tecnico, University of Lisbon, specializing in molecular biophysics. I leveraged advanced fluorescence methods and molecular dynamics to investigate the function and dynamics of lipids and proteins. In June 2022, I joined the Institute of Biology and Chemistry of Proteins in Lyon, under the supervision of Dr. Paulo C. T. Souza. My current focus revolves around the development of next- generation Martini coarse-grained models for proteins, lipids, and everything in between. In November 2023, I joined LBMC with the rest of the team.

Qin Zhang

My name is Qin Zhang, a doctoral student from the University of Electronic Science and Technology of China (UESTC). I am currently doing a one-year internship at LBMC. My research topic is the terahertz electromagnetic biological effects. Specifically, We will use coarse-grained simulation to study the influence and mechanism of terahertz electromagnetic waves on the aggregation or phase separation of RNA. I am honored to join this big family!

Nicoletta Ceres

Nicoletta Ceres is a pharmacist, a computational biologist, and a computational pharmacologist with over a decade of experience across both academia and industry. She is passionate about employing computational modeling at different scales to unravel the complexities of fundamental biology and its applications in pharmacology.Before joining the DAMM team, she acquired expertise in model- informed drug development at Novadiscovery, focusing on physiologically-based pharmacokinetic modeling to streamline drug development and enhance decision- making processes.Nicoletta received her PharmD from the University of Naples in 2006 and her PhD in Computational Structural Biology from Université Claude Bernard Lyon II in 2012, where she specialized in coarse-grained modeling of protein mechanics. Her post-doctoral research further explored the potential of coarse-grained models in the screening and prediction of protein-protein interactions.Within the DAMM team, Nicoletta is set to merge her diverse interests and skill set, applying a variety of computational strategies to illuminate the structural dynamics of multidrug-resistance transmembrane exporters. Her work promises to offer valuable insights into the mechanisms underlying multidrug resistance, potentially paving the way for novel therapeutic strategies.

The DAMM team in March 2024