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Network Modelling group

Thanks to great technological advances, regulatory networks are being uncovered that control cellular processes. Complementary to experimental approaches, mathematical models allow to get further insights into the functioning of these complex networks and to formulate hypotheses, e.g. identify proper strategies to enforce or prevent certain properties.
In this context, considering the dimensions and complexity of the networks at stake, we mainly rely on the logical framework, which can uncover the key characteristics of the dynamics of such large networks, as demonstrated by a growing number of published models. Our activity is mainly organised along three lines (see projects for details):
  • Methodological development to enhance the analysis of large models (properties in terms of attractors, reachability, etc.);
  • Implementation of new methods in the form of software tools;
  • Development of models to tackle specific applications, in close collaboration with experimentalists.
Network modelling group


News

September 2018

August 2018

  • Claudine is now member of PLOS ONE's Editorial Board.
  • Claudine is a speaker at the Discrete Models and Formal Verification in Biology meeting, 29-31 August 2018, Murray Edwards College Cambridge.
  • The paper Estimating attractor reachability in asynchronous logical models by ND Mendes, R Henrique, E Remy, J Carneiro, PT Monteiro & C Chaouiya has been accepted for publication in Frontiers in Physiology.

July 2018

  • The software tool article presenting EpiLog is now online: EpiLog: A software for the logical modelling of epithelial dynamics.
  • We´ll have 3 posters presented Monday, July 23th, at the poster session of the the 11th European Conference on Mathematical and Theoretical Biology, ECMTB 2018,
    • Poster P32 "Reconstruction and analysis of the global transcriptional regulatory network in yeast", presented by Pedro Monteiro
    • Poster P52 "Modelling approach to relate epithelial-to-mesenchymal transition and cancer stem cells", presented by Gianluca Selvaggio
    • Poster P55 "Logical Modelling To Explore Communication Network Features Influencing Pattern Formation" presented by Pedro Varela
  • Our mini-symposium Logical modelling of (multi)cellular networks during the 11th European Conference on Mathematical and Theoretical Biology, ECMTB 2018, which will be held on Friday, July 27th, 11:00 Room: C8.2.03 at Faculdade de Ciências da Universidade de Lisboa (see the program).

June 2018

  • The paper The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks has been published in Frontiers in Physiology, doi:10.3389/fphys.2018.00680.
  • The paper Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0 has been published in Frontiers in Physiology, doi:10.3389/fphys.2018.00646. This is a protocol paper presenting a GINsim tutorial.

May 2018

  • The paper Logical modelling uncovers developmental constraints for primary sex determination of chicken gonads in now online doi:10.1098/rsif.2018.0165.

April 2018

March 2018

February 2018

  • We are looking for a candidate with a BSc degree in Computer Science to work on the Ergodic project (Formal methods for the analysis of modular gEnetic ReGulatOry network DynamiCs), financed by the FCT. See the call for application to a fellowship of 9 month duration. Deadline for application: February 23, 2018.

January 2018

  • We are happy to welcome Mehran Piran, who is joining the lab to work on the CoMeDy project.
  • Our proposal for a mini-symposium Logical modelling of (multi)cellular networks has been accepted for the 11th European Conference on Mathematical and Theoretical Biology, ECMTB 2018, which will be held Lisbon, 23-27 July, 2018.

December 2017

  • We have extended the deadline of the application until December 29th for a fellowship to work on the Ergodic project (Formal methods for the analysis of modular gEnetic ReGulatOry network DynamiCs), financed by the FCT. See the call for application call for application.

November 2017

  • We are looking for a candidate with a BSc degree in Computer Science to work on the Ergodic project (Formal methods for the analysis of modular gEnetic ReGulatOry network DynamiCs), financed by the FCT. See the call for application.
  • Claudine is invited speaker at the 11ème Colloque sur la Modélisation des Systèmes Réactifs, Marseille 17 November.
  • We are organising the mid-term meeting for the CoMEDy project on November 2-3 (see project ).
  • Claudine joined the Editorial Board of BMC Bioinformatics.

October 2017

  • Claudine is member of the jury of Samuel Collombet PhD defense (Oct. 30) at Ecole Normale Supérieure de Paris. A workshop Computational approaches for the study of blood cell specification will follow.
  • We are looking for a highly motivated candidate to join the group and work on the CoMEDy project. The candidate should hold a Masters in Bioinformatics or related disciplines. See the call for application (in Portuguese and English), and contact for further information. Deadline for application October 30, 2017.
  • Welcome to Mohieddin Jafari and Mehdi Mirzaie, from Institut Pasteur and Tarbiat Modares University in Teheran, who are visiting our group for two weeks.
  • Claudine participates to the COMBINE meeting in Milan, 9-13 October.

September 2017

July 2017

  • We are happy to welcome Gianluca who will work on the CANCEL STEM project!
  • Claudine & Pedro Monteiro attend the 4th CoLoMoTo meeting held at Ecole Normale Supérieure in Paris (17-19 July).
  • Claudine gives a talk at the SysMod track session (computational modelling of biological systems) of the ISMB/ECCB 2017 conference (21-25 July, Prague).

June 2017

May 2017

  • We are looking for highly motivated candidates to join the group. Deadline for application to a Postdoctoral position 17 May 2017.

March 2017

  • Advanced Lecture Course on Computational Systems Biology, held in the Aussois ski resort (France) between March 19-25, 2017, where
    • Claudine is giving a "Blackboard teaching and Computer practical" on Logical Modelling.
    • Ana is presenting a poster A systems biology approach to the maintenance and evolution of haemocyte proportions in the Drosophila larva,
    • Jorge is presenting a poster Identification of strategies for improving salt stress response in Arabidopsis thaliana through integration of omics data and mathematical modeling

February 2017

January 2017

  • January 26th - Claudine is at I3S in Porto, for the kickoff meeting of the CANCEL STEM project (news local media).

  • We are still looking for highly motivated candidates to join the group!!
    • Deadline for application to the Postdoctoral position has been extended to 20 January 2017. See call for application.
    • Master research fellowship, project COMeDy .(A COmputational Modelling platform for Epithelial DYnamics to explore the role of epithelial to mesenchymal transition and stemness acquisition in cancer recurrence.). See the advert in English or in Portuguese, deadline January, 17 2017.
  • Claudine is elected as an SBML Editor!

December 2016

We are looking for highly motivated candidates to join the group!!
  • Master research fellowship, project COMeDy .(A COmputational Modelling platform for Epithelial DYnamics to explore the role of epithelial to mesenchymal transition and stemness acquisition in cancer recurrence.). Please see the advert in English or in Portuguese, deadline January, 17 .
  • Twelve months post-doctoral contract (renewable up to 36 months) to join the CANCEL STEM research program. deadline December, 30 .

November 2016

  • November 21, Claudine is visiting J. Cury (former visiting scientist in the group), at the Departamento de automação e sistema at Universidade Federal de Santa Catarina (Florianópolis, Brasil), with financial support of the CAPES.
  • Claudine gives a course at the pre-doctoral program of PSL-ITI, Paris.
  • November 3-4, we organise with Elisabeth Remy a workshop in Marseille Asynchronous dynamics of logical models: assessing biologically relevant properties.

October 2016

  • October 1st, great open day at IGC! We present our device illustrating the regulatory control of the cell cycle. See some photos here.

September 2016

August 2016

  • We are looking for motivated candidates to join the group!!
    • Research fellowship(Master), project COMeDy (A COmputational Modelling platform for Epithelial DYnamics to explore the role of epithelial to mesenchymal transition and stemness acquisition in cancer recurrence.) see the call for application deadline September, 23
    • Research fellowship(Master), project CANTROL (Deciphering the mechanisms of transcriptional regulation that control antifungal drug resistance in the pathogenic yeast Candida glabrata: aiming the development of improved diagnosis and therapeutic approaches) see the call for application deadline August, 31

July 2016

  • Camila defends her Master thesis on July, 28th. Congratulations Camila!
  • We attend the European Conference on Mathematical and Theoretical Biology (ECMTB), in Nottingham. Claudine \& Pedro give talks there.

May, 2016

  • Our paper Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells has been published in BMC Systems Biology and is available online
  • Our paper Logical modeling and dynamical analysis of cellular networks has been accepted for publication in Frontiers in Genetics, available online

April, 2016

  • We are happy to welcome Sébastien Fueyo, master student in Discrete Math and Fundamental Informatics, from Aix-Marseille University, for an internship of 2 months.

 

 

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