UMR 7238 CNRS - Sorbonne Université
About our Departement
The Laboratory of Computational, Quantitative and Synthetic Biology (CQSB), supported by the CNRS and Sorbonne Université and headed by Alessandra Carbone, is an interdisciplinary research department working at the interface of biology and quantitative sciences. The CQSB fosters a balanced integration of theoretical and experimental approaches to redefine biological questions, develop innovative experimental strategies, and enhance data analysis and modeling of complex biological systems. Our projects aim to explore the fundamental principles underlying biological structures and processes. We achieve this by integrating experimental data with computational models to uncover insights into genome evolution, molecular mechanisms, and cellular behavior. This includes generating in silico predictions for biological phenomena that remain inaccessible to direct experimentation. Statistical methods and AI approaches are developed and applied to analyze large-scale biological data and make precise predictions. In synthetic biology, we leverage computational and experimental frameworks to design novel biomolecular systems, including synthetic metabolic networks and programmable genetic circuits. These efforts aim to address key challenges in environmental sustainability, biotechnology, and medicine. With a strong foundation in collaboration and innovation, the CQSB advances both fundamental understanding and practical applications of biology in the quantitative and synthetic biological sciences.
NEWS
The HEAL group congratulates Léo Minglu Li, who has obtained a funded PhD position via Université Paris-Cité to explore the plastid proteome of the transformable dinoflagellate Amphidinium carterae.
The HEAL group congratulates Louis Graf on obtaining a JGI New Investigator Grant to sequence the genomes of four phylogenetically close, but geographically distant, members of the Chlamydomonadales from the Arctic and Antarctic Oceans.
New success for the iGEM team of Sorbonne Université: they received the Best Plant Synthetic Award! After one year of hard work in parallel of their classes and internships, our students (mostly from BMC and BIM master) received the Gold Medal for their project NAWI during the final conference (Grand Jamboree) held at the Paris Convention Center on October 26-28.
They were also nominated for Best Education and Best Presentation prizes out of 350 teams. Units implicated from IBPS: LCQB and LBD. Co-PIs: Frédérique Peronnet, Guillaume Garnier, Marco Da Costa, Pierre Crozet.
See article at SU here.
LAST PUBLICATIONS
Modeling Protein Evolution via Generative Inference From Monte Carlo Chains to Population Genetics
Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
Repeated losses of self-fertility shaped heterozygosity and polyploidy in yeast evolution
DOMAINS
TRANSVERSAL THEMES
Evolution of genomes, proteins and RNA molecules
We address questions on fundamental processes shaping the diversity and functionality of genomes, proteins, and RNA molecules evolving over time. Our research explores the mechanisms underlying genomic rearrangements, the co-evolution of biomolecular systems, and the adaptive evolution of molecular interactions. By combining computational modeling with experimental validation, these studies provide insights into how evolutionary forces drive structural and functional innovation and diversification.
Molecular mechanisms, structures and interactions
Understanding the molecular mechanisms underlying biological processes requires a detailed exploration of structural and interaction dynamics. Our research in this area focuses on predicting and modeling protein and RNA structures, deciphering interaction networks, and assessing the functional impact of mutations. These investigations integrate experimental data and computational tools to reveal the principles governing molecular architecture and function.
Human and environmental metagenomics
We investigate the genomic composition and functional dynamics of microbial communities in human and environmental contexts. Studies employ advanced computational and bioinformatics approaches to analyze metagenomic data, uncovering microbial diversity and their interactions with hosts or ecosystems. The research contributes to a deeper understanding of microbiota’s role in health, disease, and ecological balance.
Genomics of human diseases
We focus on elucidating the genetic and molecular basis of human diseases. Research explores genome dynamics, mutation patterns, and gene-environment interactions to identify the key genetic factors driving pathological conditions. These efforts inform the development of diagnostic tools and therapeutic strategies, contributing to advances in precision medicine and improved patient outcomes.
Biology of genomes
Computational Medicine
Functional Imaging Of Nuclear Architecture (FIONA)
Genetics Networks
Horizontal evolution of Algal Lifestyles
Mathematical Modeling in Biology
Proteome Diversification in Evolution
Statistical Genomics and Biological Physics
Telomere & Genome Stability
Cellular and multicellular behaviour
We investigate the regulatory and environmental factors influencing cellular and multicellular systems. By modeling gene networks and cellular responses, we analyze how cells adapt and interact in different contexts. These studies provide insights into the coordination and collective behavior of living systems, advancing our understanding of fundamental biological processes.
Synthetic biology
Synthetic biology focuses on the design and construction of engineered biological systems to address scientific and practical challenges. Research includes developing synthetic metabolic networks and optimizing their regulatory properties. This work advances the field by providing novel tools and frameworks for applications in medicine, biotechnology, and environmental solutions.
Education
As biology becomes increasingly data-driven, experts who can bridge experimental biology and computational sciences are in high demand. Our Master’s Program in Bioinformatics and Modeling (BIM) equips you with interdisciplinary skills by combining key biological concepts such as genetics, genomics, and evolution with advanced computational methods, including statistics, machine learning, artificial intelligence, and complex systems modeling. This integrated approach prepares you to tackle complex biological challenges through data analysis and computational tools.
The LCQB collaborates in international courses alongside Charles University, Heidelberg University, the University of Warsaw, and the University of Milan as part of the 4EU+ Alliance:
- Meet-U :Every year, teams of four students work on projects aligned with the year’s chosen scientific topic over the course of one semester. Each group is guided by a supervisor. A final workshop is held where both the students and invited keynote speakers present their work. The projects are evaluated by an international jury. To see more: http://www.lcqb.upmc.fr/laine/Documents/Meet-EU/meetEU_2021.html
- Deeplife: The course format comprises weekly online lecture and weekly hybrid (in-person/online) practical Python session. Lectures are given by teachers from 4EU+ members. Those content are centered on recent publication illustrating a specific application of deep learning to biology. The course ends with a 2-day workshop and hackathon meeting.To see more: https://deeplife4eu.github.io
The LCQB is seeking internship opportunities from research labs and industry partners for our M2 program. If you would like to share or promote internship openings, please contact Alessandra Carbone or Martin Weigt at [email protected] for dissemination.
PARTNERS
