Research

General overview and Research Groups

The Turing Centre aims to stimulate a highly interdisciplinary community, especially physicists, mathematicians and computer scientists who, together with biologists, provide the means to base experimental studies on solid quantitative grounds, to identify new questions and conceptualize new ways of understanding the complexity of living systems.

Life is based on dynamic systems whose organizational principles remain unclear due to their complexity. Such complexity has different origins. Living systems are the product of a long evolutionary history and are intrinsically dynamic as they develop, renew their components, adapt to their physiological environments and are trained. This is illustrated for instance in the development of embryos and organs, and in the function of the immune and nervous systems.

Understanding biological complexity is one of the most significant challenges for the future. It will impact both basic research and medicine, since diseases emerge from anomalies in the organization and dynamics of living systems.

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The Turing Centre addresses the nature of the information underlying biological processes, and the organization and dynamics of biological structures. Five over-arching questions bringing together biologists interested in development, neuroscience and immunology along with physicists, computational biologists and mathematicians will underlie the research effort:

How does genetic information impact on cell fates?
How do signalling dynamics impact on cell differentiation?
How is information encoded in collective cellular dynamics?
How do networks of cell interactions form and function collectively?
How does mechanics impact on cell and tissue organization and dynamics?

CENTURI recruits researchers and post docs with backgrounds in computational biology, theoretical physics or biophysics, with a strong interest in working in a cross-disciplinary environment.

People and projects funded by CENTURI

Principal Investigators

Matthias Merkel (CPT)

Self-organization and collective effects in living systems

Hervé Rouault (CPT - INMED)

Neural networks for the representation of 3D environments

Jean-François Rupprecht (CPT)

Out-of-equilibrium Mechanics (OM)

Paul Villoutreix (LIS)

Learning Meaningful Representations of Life

Matthias Merkel (CPT) - Self-organization and collective effects in living systems

Hervé Rouault (CPT - INMED) Neural networks for the representation of 3D environments

Jean-François Rupprecht (CPT) - Out-of-equilibrium Mechanics (OM)

Paul Villoutreix (LIS) - Marseille Machine Learning Team

Postdoctoral fellow

Marie-Anne Burklein (Institut Fresnel - IBDM) - Smart-scans for live imaging of morphogenetic processes

Damien Courtine (LAI, CIML, LIS) - Deciphering chemical signals guiding T cells towards and in lymph node

Céline Dinet (IBDM, LCB)A Multiscale Analysis of Cell Polarity Transitions in a Bacterium

Stefan Harmansa (IBDM)Emergence and Dissipation of Mechanical Stress during Epithelial Growth

Maxime Lucas (IBDM, I2M, CPT) - A Multiscale Analysis of Cell Polarity Transitions in a Bacterium

Shao-Zhen Lin (CPT) - Hydrodynamic instabilities in curved environment

Fabio Manca (LAI, CINaM)Modeling mechanosensing of T cells: from ligand-receptor bonds to cytoskeleton dynamics

Olivier Mesdjian (M2P2, CINAM)Long-range collective dynamics of cilia

Maria Mandela Prünster (IBDM, IMBE)Evolution of protein interactions

Shrisha Rao Balappa (CPT, INMED)Study of the neural dynamics supporting internal spatial representations

Jain Rikesh (LCB - IBDM)Functional and bioinformatics analysis of predator prey interaction in bacteria

Charlotte Rulquin (IBDM) - Computational study of cell pattern emergence

Stefania Sarno (INMED, IRPHE) - Why animals learn the way they do?

Saswati Saha (TAGC) - Systems genetics: Developing new approaches integrating network analyses and modeling

Clara Sidor (IBDM, institut Fresnel) - Muscle building: Bridging molecular order to macroscopic morphogenesis

Solène Song (LAI, CIML, LIS) - Deciphering chemical signals guiding T cells towards and in lymph node

Nicolás Tizón-Escamilla (CPT)What can we learn from fluctuations in living active materials?

Sham Tlili (IBDM - CPT - LAI) - Mechanics of gastrulation in mammals using a minimal in vitro system

Marie-Anne Burklein (Institut Fresnel - IBDM)

Smart-scans for live imaging of morphogenetic processes

Damien Courtine (LAI, CIML, LIS)

Global and local genome sequence analysis to understand fungal virulence

Céline Dinet (IBDM, LCB)

A Multiscale Analysis of Cell Polarity Transitions in a Bacterium

Stefan Harmansa (IBDM)

Emergence and Dissipation of Mechanical Stress during Epithelial Growth

Maxime Lucas (IBDM, I2M, CPT)

A Multiscale Analysis of Cell Polarity Transitions

Shao-Zhen Lin (CPT)

Hydrodynamic instabilities in curved environment

Fabio Manca (LAI, CINaM)

Modeling mechanosensing of T cells: from ligand-receptor bonds to cytoskeleton dynamics

Olivier Mesdjian (M2P2, CINAM)

Long-range collective dynamics of cilia

Maria Mandela Prünster (IBDM, IMBE)

Evolution of protein interactions

Shrisha Rao Balappa (CPT, INMED)

Study of the neural dynamics supporting internal spatial representations

Jain Rikesh (LCB - IBDM)

Functional and bioinformatics analysis of predator prey interaction in bacteria

Charlotte Rulquin (IBDM)

Computational study of cell pattern emergence

Saswati Saha (TAGC)

Systems genetics

Stefania Sarno (INMED, IRPHE)

Why animals learn the way they do?

Solène Song (LAI, CIML, LIS)

Deciphering chemical signals guiding T cells towards and in lymph node

Nicolás Tizón-Escamilla (CPT)

What can we learn from fluctuations in living active materials?

Sham Tlili (IBDM - CPT - LAI)

Mechanics of gastrulation in mammals 

PhD students

Achyuth Acharya (IBDM, LAI)Instructing myofibrillogenesis in human muscle

Athullya Baby (IBDM, CINaM, M2P2) - Quantitative analysis and simulation of fluid flows powered by cilia in vivo

Anthony Baptista (TAGC, MMG)Genetic and phenotypic comorbidities between Mendelian and common diseases

Katia Barret (IBDM, LAI, CPT)Mechanical environment and fate specification during mammalian morphogenesis

Ammar Sabir Cheema (CIML, CPT)Deciphering the activation states of plasmacytoid dendritic cells

Sébastien Choteau (CIML - TAGC) - Understanding uORF functions through dendritic cells biology and computational approaches

Naveen Gajendra Kumar (INMED, Institut Fresnel)Visualizing deep hippocampus neuronal functional activity

Niels Gouirand (IBDM, CPT) - Deciphering the interplay between cell polarity and inter-cellular forces in epithelial 3D organization

Muhamet Ibrahimi (IBDM, CPT) Conditions for self-organized oriented deformation of biological tissue

Mathieu Loizeau (IBDM, CPT)Functional transformations of sensory information in the brain

Thomas Morvan (INMED, IRPHE) - Studying algorithm(s) for decision making and confidence in an ethological framework

Varun Puthumana (CIML, M2P2) - Modeling T cell plasma membrane phase separation

Alla Solod (INMED, CPT)Understanding large-scale spatial navigation using virtual reality

Achyuth Acharya (IBDM, LAI)

Instructing myofibrillogenesis in human muscle

Athullya Baby (IBDM, CINaM, M2P2)

Quantitative analysis and simulation of fluid flows powered by cilia in vivo

Anthony Baptista (TAGC, MMG)

Genetic and phenotypic comorbidities

Katia Barret (IBDM, LAI, CPT)

Mechanical environment and fate specification during mammalian morphogenesis

Ammar Sabir Cheema (CIML, CPT)

Deciphering the activation states of plasmacytoid dendritic cells

Sébastien Choteau (CIML - TAGC)

Understanding uORF functions 

Naveen Gajendra Kumar (INMED, Institut Fresnel)

Visualizing deep hippocampus neuronal functional activity

Niels Gouirand (IBDM, CPT)

Interplay between cell polarity and inter-cellular forces

Muhamet Ibrahimi (IBDM, CPT)

Conditions for self-organized oriented deformation of biological tissue

Mathieu Loizeau (IBDM, CPT)

Functional transformations of sensory information in the brain

Thomas Morvan (INMED, IRPHE)

Studying algorithm(s) for decision making and confidence in an ethological framework

Varun Puthumana (CIML, M2P2)

Modeling T cell plasma membrane phase separation

Alla Solod (INMED, CPT)

Understanding large-scale spatial navigation using virtual reality

Engineers

Sophie Brustlein - Optics & Biophotonics

Benoit Dehapiot - Image processing & data analysis

Guillaume Gay - Database management and data curation

Mathias Lechelon - Mechatronics

Qingzong Tseng - Image processing & data analysis

Thomas Vannier - Bioinformatics Data Analyst

Sophie Brustlein

Optics & Biophotonics

Benoit Dehapiot

Image processing & data analysis

Guillaume Gay

Database management and data curation

Mathias Lechelon

Mechatronics

Qingzong Tseng

Image processing & data analysis

Thomas Vannier

Bioinformatics Data Analyst

Publications

2020

  • Assembly of a persistent apical actin network by the formin Frl/Fmnl tunes epithelial cell deformability. Dehapiot, B., Clément, R., Alégot, H. et al.  Nat Cell Biol (2020). https://doi.org/10.1038/s41556-020-0524-x
  • Turning the body into a clock: Accurate timing is facilitated by simple stereotyped interactions with the environment. Mostafa SafaieMaria-Teresa Jurado-Parras, Stefania SarnoJordane LouisCorane KaroutchiLudovic F. PetitMatthieu O. Pasquet, Christophe Eloy, and David Robbe.

  • Active mucus–cilia hydrodynamic coupling drives self-organization of human bronchial epithelium.Loiseau, E., Gsell, S., Nommick, A. et al.  Nat. Phys. (2020). https://doi.org/10.1038/s41567-020-0980-z

2019

  • Self-organization of red blood cell suspensions under confined 2D flows. C. Iss, D. Midou, A. Moreau, D. Held, A. Charrier, S. Mendez, A. Viallat#, Helfer#. Soft Matter 15, 2971 (2019)
  • White blood cells dynamics in micro-flows. A. Viallat, J. Dupire, Helfer. In : Blood Cells Suspension Dynamics in Microflows, CRC Press (2019)
  • Are Conventional Type 1 Dendritic Cells Critical for Protective Antitumor Immunity and How? Cancel JC, Crozat K, Dalod M, Mattiuz R.  Front Immunol. 2019;10:9. doi: 10.3389/fimmu.2019.00009.
  • NK cells orchestrate splenic cDC1 migration to potentiate antiviral protective CD8+ T cell responses. Ghilas S, Ambrosini M, Cancel JC, Massé M, Lelouard H, Dalod M, Crozat K.  bioRxiv 2020.04.23.057463; doi: https://doi.org/10.1101/2020.04.23.057463
  • A minimal-length approach unifies rigidity in underconstrained materials. Matthias Merkel, Karsten Baumgarten, Brian P. Tighe, M. Lisa Manning. Proceedings of the National Academy of Sciences Apr 2019, 116 (14) 6560-6568; DOI: 10.1073/pnas.1815436116
  • Matrix metalloproteinase 1 modulates invasive behavior of tracheal branches during entry into Drosophila flight muscles. Sauerwald J, Backer W, Matzat T, Schnorrer F, Luschnig S. eLife. pii: e48857. doi: 10.7554/eLife.48857.
  • A small proportion of Talin molecules transmit forces at developing muscle attachments in vivo. Lemke SB, Weidemann T, Cost AL, Grashoff C, and Schnorrer F. (2019). PLoS Biology. 17(3):e3000057. doi: 10.1371/journal.pbio.3000057
  • 1 contributes to a rapid homeostatic plasticity of intrinsic excitability in CA1 pyramidal neurons in vivo. Morgan PJ, Bourboulou R, Filippi C, Koenig-Gambini J, Epsztein J. Elife. 2019 Nov 27;8.
  • Dynamic control of hippocampal spatial coding resolution by local visual cues. Bourboulou R, Marti G, Michon FX, El Feghaly E, Nouguier M, Robbe D, Koenig J, Epsztein J. Elife. 2019 Mar 1;8
  • Genetic induction and mechanochemical propagation of a morphogenetic wave; Bailles A, et al. Nature 2019. PMID 31413363
  • Experimental validation of force inference in epithelia from cell to tissue scale; Kong W, et al. Sci Rep 2019. PMID 31601854
  • Mechanical Stiffness of Reconstituted Actin Patches Correlates Tightly with Endocytosis Efficiency. PLANADE J, BELBAHRI R, BOEIRO SANDERS M, GUILLOTIN A, DU ROURE O, MICHELOT A*, HEUVINGH J. PLoS Biol. 2019 Oct 25 ;17(10) :e3000500
  • Sizes of actin networks sharing a common environment are determined by the relative rates of assembly. ANTKOWIAK A, GUILLOTIN A, BOEIRO SANDERS M, COLOMBO J, VINCENTELLI R, MICHELOT A*. PLoS Biol. 2019 Jun 10 ;17(6) :e3000317
  • Internal representation of hippocampal neuronal population spans a time-distance continuum. Haimerl C, Angulo-Garcia D, Villette V, Reichinnek S, Torcini A, Cossart R, Malvache A. Proc Natl Acad Sci U S A. 2019 Apr 9;116(15):7477-7482. doi: 10.1073/pnas.1718518116
  • Distinct RhoGEFs activate apical and junctional actomyosin contractility under control of G proteins during epithelial morphogenesis. Alain Garcia De Las Bayonas, Jean-Marc Philippe, Annemarie C. Lellouch, Thomas Lecuit. Current Biology. 2019 Oct 21;29(20):3370-3385.e7. DOI: 10.1016/j.cub.2019.08.017

2018

  • Distinct contributions of tensile and shear stress on E-cadherin levels during morphogenesis.Kale GR, Yang X, Philippe JM, Mani M, Lenne PF, Lecuit T. Nat Commun. 2018 Nov 27;9(1):5021. doi: 10.1038/s41467-018-07448-8. PMID: 30479400
  • Novel Cre-Expressing Mouse Strains Permitting to Selectively Track and Edit Type 1 Conventional Dendritic Cells Facilitate Disentangling Their Complexity in vivo. Mattiuz R, Wohn C, Ghilas S, Ambrosini M, Alexandre YO, Sanchez C, Fries A, Vu Manh TP, Malissen B, Dalod M, Crozat K.  Front Immunol. 2018;9:2805. doi: 10.3389/fimmu.2018.02805.
  • Quantitative Control of GPCR Organization and Signaling by Endocytosis in Epithelial Morphogenesis. Jha A, van Zanten TS, Philippe JM, Mayor S, Lecuit T., Curr Biol. 2018 May 21;28(10):1570-1584.e6. doi: 10.1016/j.cub.2018.03.068. Epub 2018 May 3.
 
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