International PhD Program

Marta Kwapisz

Chargé de Recherche, CNRS
05 61 33 58 10

Team members

  Administrative staff  --
  • Julie BATUT
  • Frederic Beckouet
  • Kerstin Bystricky
  • Thomas CLOUAIRE
  • Jean-Marc DEVAUD
  • Pascale DUFOURCQ
  • Christian JOST
  • Gaëlle LEGUBE
  • Andreas MERDES
  • Marie-Christine MIQUEL
  • François PAYRE
  • Philippe Rousseau


The CBI PhD International program was initiated in 2016 with the creation of the CBI and integrated all PhD students. Ambition of the program is to create the community of well-trained, highly motivated and dynamic young researchers. The CBI PhD program committee, framing the program, is composed of stuff scientist representing all Institutes composing the CBI and supported by its direction. Our aim is to help our PhD students to become a part of a scientific community, to guide them in their career choices and to participate in their training. Based on stimulating and dynamic environment offered by the CBI, the program proposes an in-house training courses, seminars and social events.

Planning of the CBI's year:


To read and meditate : Twenty things I wish I’d known when I started my PhD...


The CBI International PhD Program - PhD recruitment

Thesis in molecular and bacterial genetics M/F

Titre :  Nucleation mechanism for the auto-assembly of a large nucleoprotein complex on supercoiled DNA

In bacteria, faithful DNA segregation relies essentially on active partition by dedicated minimal systems, namely ParABS systems. Formation of the partition complexes on centromere sites, parS, is a key step to ensure the displacement and the subsequent accurate positioning of DNA molecules within the cells (Baxter & Funnell, 2014; Bouet & Funnell, 2019). We have recently proposed and tested a new model for the auto-assembly of this large nucleoprotein complex (Debaugny et al, 2018; Sanchez et al, 2015). This Ph.D. project now aims at (i) further characterizing the nucleation step and (ii) testing the effect of variation of DNA supercoiling. By a combination of genetics, biochemistry and fluorescence microscopy, gain of function mutants for a parS-independent assembly of the partition complex will be uncovered and fully characterized. This will allow for the molecular understanding of the strict parS-specific control for the partition complex assembly. Dedicated plasmids and strains will also be genetically constructed and characterized for variation of the DNA supercoiling level. Their effect on the ParB binding profiles will be analyzed by high resolution ChIP-sequencing. These studies will permit to test and validate the implementation of DNA supercoiling by physical modeling in collaboration with theoretical physicists.

The Ph.D. will be carried out in the team of Jean-Yves Bouet “active segregation of bacterial genome: mechanisms and diversity” at the Centre of Integrative Biology in Toulouse (CBI) in the Molecular Microbiology and Genetics Laboratory (LMGM). The CBI (5 laboratories, 40 teams, 400 people) is an international institute which provided a rich and stimulating scientific environment. The CBI is a multidisciplinary center that combines a wide range of research fields from genetics to epigenetics, including microbiology, cell biology, chromatin / chromosome dynamics, RNA biology, developmental biology, neurobiology, collective animal behavior, as well as computer biology and systems. The whole being supported by quality platforms (imagery ...)

The PhD will be hold within the doctoral school BSB (Biologie Santé Biotechnologie) of the University of Toulouse III Paul Sabatier. It will be supported by the AO80Prime program of the CNRS, with a collaboration with a network of theoretical physicists coordinated by Jean-Charles Walter (L2C, Montpellier).

The candidate must have a Masters degree in biology. The position requires sound knowledge of bacterial genetics, molecular biology, fluorescence microscopy, a high level of communication skills, both oral and written (French and English required). Sound knowledge of R software would be highly appreciated. We are looking for a PhD fellow who will be able to become fully involved with the project, with a thirst for knowledge, a certain independence of thought and strong motivation to develop skills in the field of bacterial DNA segregation. In addition, the candidate must be able to work in a team on multi-disciplinary projects.
Applications must be fill on the CNRS website:

The closing date for sending applications is 05/08/2019.

Références bibliographiques
- Baxter JC, Funnell BE (2014) Plasmid Partition Mechanisms. Microbiology spectrum 2: PLAS-0023-2014
- Bouet JY, Funnell BE (2019) Plasmid Localization and Partition in Enterobacteriaceae. EcoSal Plus 8(2)
- Bouet JY, Lane D (2009) Molecular basis of the supercoil deficit induced by the mini-F plasmid partition complex. J Biol Chem 284: 165-173
- Debaugny RE, Sanchez A, Rech J, Labourdette D, Dorignac J, Geniet F, Palmeri J, Parmeggiani A, Boudsocq F, Anton Leberre V, Walter JC, Bouet JY (2018) A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids. Mol Syst Biol 14: e8516
- Sanchez A, Cattoni DI, Walter JC, Rech J, Parmeggiani A, Nollmann M, Bouet JY (2015) Stochastic Self-Assembly of ParB Proteins Builds the Bacterial DNA Segregation Apparatus. Cell Syst 1: 163-173


Detailed description of the CBI PhD program program here, any questions: 


The CBI PhD Mentoring!    created by Julie Batut

Do not hesitate to contact Julie if you would like to become a mentor or you need advice. It became doctoral school's module entitled  "Module Mentoring CBI PhD programme" and could be found via Adum!

Our mentoring program includes:

1. Individual meetings and discussions (at least monthly)
2. Round table sessions
Program for 2018/19
3. Career Workshop

Mentoring is a timeless concept with roots in ancient history. The word “mentor” comes from The Odyssey by the Greek poet Homer. When Odysseus, King of Ithaca, sailed off with his army to fight in the Trojan War, he entrusted his friend Mentor to care for and educate his son, Telemachus. The word “mentor” eventually came to mean a trusted advisor, counselor, and friend.

The CBI Mentoring pairs new students with faculty mentors that match student interests and needs.

Mentors are: • Advisors, who have career experience and are willing to share their knowledge,
                      • Supporters, who provide emotional and moral encouragement,
                      • Tutors, who give specific feedback on one’s performance,
                      • Supervisors, who monitor their students’ academic and professional progress,
                      • Trainers, who teach students about professional responsibility,
                      • Sponsors, who are sources of information about opportunities and assist students in obtaining them, and
                      • Role models, who exhibit the qualities and ethical values that academics should posses. 

                                                                                                                                                                                                                                  (The National Institutes of Health,1999; Zelditch, 2001).



Two CBI students are regional finalists of MT180 (Ma Thèse en 180 secondes)
Coline MONCHANIN from Martin Giurfa & Jean-Marc Devaud's group
Clair CHAIGNE from Patrick Blader's group


The CBI PhD Integration Day 2018!  19/10/2018 in Toulouse

The whole day was devoted to welcoming of our new PhD students, to have fun and to discuss science and beyond! PROGRAM

THANK YOU ALL for coming and participating! Special acknowledgement for the Organizing Committee!

Emma, Cyril, Matthias, Alexandre, Christophe, David and Maxime


The CBI International PhD Program - PhD recruitment

Detailed description of the CBI PhD program program here, questions: 


   in Toulouse, at the Paul Sabatier University and in the CBI...

                                                                                                                                                                                                                                     Ma thèse en 180 secondes  c'est :                                               Only for French-speaking students


• Un véritable défi : intéresser un auditoire profane et diversifié en présentant votre sujet de thèse en seulement 3 minutes chrono !
• Une occasion unique de parfaire vos aptitudes en communication, tout en vous donnant la possibilité de diffuser votre recherche dans l’espace public.


Tentez de décrocher votre place pour la finale nationale organisée par la CPU et le CNRS, et peut-être représenter la France au concours international francophone qui rassemblera les finalistes québécois, français, marocains et belges le 26 septembre 2019 à Dakar.

Le concours « Ma thèse en 180 secondes » vise à informer le grand public de la richesse et de l’intérêt des recherches scientifiques, tout en développant les compétences communicationnelles des doctorants avec le grand public. Le but ? Chaque participant présente, en 3 minutes, un exposé de vulgarisation en français, clair, concis et convaincant sur son projet de recherche. Le tout avec l’appui d’une seule diapositive !

De présentation de MT180 ici
Pour s'inscrire sur ADUM à MT180 ici


Alpha T  association of PhD biology students in Toulouse. Do not hesitate to viist their website and participate in upcoming events!






  • Mourad R, Ginalski K, Legube G, Cuvier O.
    Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution
    Genome Biology
    2018 Mar
  • Mourad R, Ginalski K, Legube G, Cuvier O.
    Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution
    Genome Biology
    2018 Mar
  • Mourad R, Ginalski K, Legube G, Cuvier O.
    Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution
    Genome Biology
    2018 Mar

Université Paul Sabatier
118 Route de Narbonne

31062 TOULOUSE Cedex

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