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Understanding and exploiting evolvability of biological systems


Thesis topic details

General information

Organisation

The French Alternative Energies and Atomic Energy Commission (CEA) is a key player in research, development and innovation in four main areas :
• defence and security,
• nuclear energy (fission and fusion),
• technological research for industry,
• fundamental research in the physical sciences and life sciences.

Drawing on its widely acknowledged expertise, and thanks to its 16000 technicians, engineers, researchers and staff, the CEA actively participates in collaborative projects with a large number of academic and industrial partners.

The CEA is established in ten centers spread throughout France
  

Reference

SL-DRF-26-0785  

Direction

DRF

Thesis topic details

Category

Life Sciences

Thesis topics

Understanding and exploiting evolvability of biological systems

Contract

Thèse

Job description

Directed evolution is a cornerstone of synthetic biology, yet its outcome is heavily constrained by the starting genotype. This latent capacity to innovate—termed evolvability—varies drastically across closely related proteins and microbial strains due to biophysical trade-offs and historical contingency. Financed by the ANR ProtEvol project, this thesis aims to systematically decipher and engineer the determinants of evolvability across two biological scales. At the macromolecular level, we will develop a novel, plasmid-free genomic diversification strategy to map the adaptive pathways of diverse ROK kinase homologs, leveraging AI and machine learning collaborations to extract predictive sequence features of functional promiscuity. Simultaneously, at the organismal scale, we will utilize the automated continuous-culture GM3 platform to evaluate how Escherichia coli strains with divergent pyruvate assimilation backgrounds evolve toward synthetic C1-formatotrophy. By combining high-throughput sequence diversification, machine learning, and automated evolution, this work will transform evolvability from an abstract evolutionary concept into a predictable, steerable parameter for industrial bioproduction.

University / doctoral school

Structure et Dynamique des Systèmes Vivants (SDSV)
Paris-Saclay

Thesis topic location

Site

Fontenay-aux-Roses

Requester

Person to be contacted by the applicant

CHOUDHURY Alaksh achoudhu@genoscope.cns.fr
CEA
DRF/JACOB/Genoscope/L2BMS
2 Rue Gaston Crémieux, 91000 Évry-Courcouronnes

Tutor / Responsible thesis director

Doring Volker vdoring@genoscope.cns.fr
CEA
DRF/JACOB/GEN/LA
2 rue Gaston Crémieux

91057 EVRY CEDEX
0160874586

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