E. Tonello, E. Farcot, and C. Chaouiya , Local Negative Circuits and Cyclic Attractors in Boolean Networks with at most Five Components , SIAM J. Appl. Dyn. Syst. 18-1, pp. 68-79, 2019 (DOI)
A. Naldi, C. Hernandez, N. Levy, G. Stoll, P.T. Monteiro, C. Chaouiya, T. Helikar, A. Zinovyev, L. Calzone, S. Cohen-Boulakia, D. Thieffry, L. Paulevé, The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks, Front. Physiol., 9, pp. 680, 2018 (DOI)
A. Naldi, C. Hernandez, W. Abou-Jaoudé, P.T. Monteiro, C. Chaouiya, D. Thieffry, Logical modelling and analysis of cellular regulatory networks with GINsim 3.0, Front. Physiol., 9, pp. 646, 2018 (DOI)
L. Sánchez, C. Chaouiya, Logical modelling uncovers developmental constraints for primary sex determination of chicken gonads, Journal of The Royal Society Interface, 15(142), 2018 (DOI)
ND Mendes, R Henriques, E Remy, J Carneiro, PT Monteiro, C Chaouiya, Estimating Attractor Reachability in Asynchronous Logical Models, Front. Physiol., 9, pp. 1161, 2018 (DOI)
P.L. Varela, I. Lynce, V. Manquinho, C. Chaouiya, P.T. Monteiro, Stable States of Boolean Regulatory Networks Composed Over Hexagonal Grids, Proc. 7th Int. Workshop on Static Analysis and Systems Biology (SASB 2016), ENTCS, 335: 113-130, 2018 (DOI)
Pedro L. Varela, Camila V. Ramos, Pedro T. Monteiro, Claudine Chaouiya, EpiLog: A software for the logical modelling of epithelial dynamics, F1000Research, 7:1145 , 2018 (DOI)
Network Modelling group - latest news
Pedro Monteiro starts his 6 month sabbatical leave with us. Welcome Pedro!
We are looking for a motivated candidate to work on the CoMEDy project (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 (in PT and UK).
We are happy to welcome Ana Fonseca who joins our group to work on the MIXEDUP research project.
Ricardo Pais defended his PhD on December, 15th. Parabéns to Ricardo, and may thanks to the jury for the great discussion!
Claudine is giving the "Computational Biology" course at the University Saint Joseph in Beyrouth, for the master in Functional Genomics and Proteomics (December 3-7)
We are looking for a highly motivated candidate to work on the Mixed-up project (Targeting pathogenesis and engineering cell factories: by developing mixed regulatory metabolic genomic models in yeasts), financed by the FCT. The candidate should hold a Masters in Computer Sciences, Bioinformatics or related disciplines. See the call for application (in Portuguese and English) for a fellowship of 12 month duration. Deadline for application: November 15, 2018 December 15, 2018.
Claudine joins the group of coordinators of the SysMod COSI (Community of Special Interest of the International Society for Computational Biology (ISCB)).
Elisa's paper "Local negative circuits and cyclic attractors in Boolean networks with at most five components" is now ready for publication in SIAM Journal on Applied Dynamical Systems.
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.
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).
CompSysBio 3rd Advanced Lecture Course on Computational Systems Biology, Aussois ski resort, France, March 31st- April 6th, 2019.
JOBIM (Journées Ouvertes Biologie, Informatique et Mathématiques), Nantes, France, 2-5 July 2019
ISMB-ECCM 27th Conference on Intelligent Systems for Molecular Biology and 18th European Conference on Computational Biology, Basel, Switzerland, July 21-25 2019. Call for abstracts is open, submit to the 4th SysMod COSI !
[BC]2 2019 will take place September 9-11 in Basel, and there will be a CoLoMoTo workshop "Annotation and curation of computational models in biology" (further detail soon).
CMSB 17th International Conference on Computational Methods in Systems Biology, Trieste, Italy 18-20 September 2019.
8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE 2019), 15-18 October 2019, Valencia, Spain.