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Items: 1 to 20 of 33

1.

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.

Naldi A, Hernandez C, Levy N, Stoll G, Monteiro PT, Chaouiya C, Helikar T, Zinovyev A, Calzone L, Cohen-Boulakia S, Thieffry D, Paulevé L.

Front Physiol. 2018 Jun 19;9:680. doi: 10.3389/fphys.2018.00680. eCollection 2018.

2.

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0.

Naldi A, Hernandez C, Abou-Jaoudé W, Monteiro PT, Chaouiya C, Thieffry D.

Front Physiol. 2018 Jun 19;9:646. doi: 10.3389/fphys.2018.00646. eCollection 2018.

3.

Logical modelling uncovers developmental constraints for primary sex determination of chicken gonads.

Sánchez L, Chaouiya C.

J R Soc Interface. 2018 May;15(142). pii: 20180165. doi: 10.1098/rsif.2018.0165.

4.

Logical Modeling and Dynamical Analysis of Cellular Networks.

Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C.

Front Genet. 2016 May 31;7:94. doi: 10.3389/fgene.2016.00094. eCollection 2016. Review.

5.
6.

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel MP, Le Novère N, Helikar T.

J Integr Bioinform. 2015 Sep 4;12(2):270. doi: 10.2390/biecoll-jib-2015-270.

PMID:
26528568
7.

A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis.

Remy E, Rebouissou S, Chaouiya C, Zinovyev A, Radvanyi F, Calzone L.

Cancer Res. 2015 Oct 1;75(19):4042-52. doi: 10.1158/0008-5472.CAN-15-0602. Epub 2015 Aug 3. Erratum in: Cancer Res. 2016 Jan 15;76(2):505.

8.

Model checking to assess T-helper cell plasticity.

Abou-Jaoudé W, Monteiro PT, Naldi A, Grandclaudon M, Soumelis V, Chaouiya C, Thieffry D.

Front Bioeng Biotechnol. 2015 Jan 28;2:86. doi: 10.3389/fbioe.2014.00086. eCollection 2014.

9.

Cooperative development of logical modelling standards and tools with CoLoMoTo.

Naldi A, Monteiro PT, Müssel C; Consortium for Logical Models and Tools, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C.

Bioinformatics. 2015 Apr 1;31(7):1154-9. doi: 10.1093/bioinformatics/btv013. Epub 2015 Jan 25.

PMID:
25619997
10.

Modelling the onset of senescence at the G1/S cell cycle checkpoint.

Mombach JC, Bugs CA, Chaouiya C.

BMC Genomics. 2014;15 Suppl 7:S7. doi: 10.1186/1471-2164-15-S7-S7. Epub 2014 Oct 27.

11.

A discrete model of Drosophila eggshell patterning reveals cell-autonomous and juxtacrine effects.

Fauré A, Vreede BM, Sucena E, Chaouiya C.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003527. doi: 10.1371/journal.pcbi.1003527. eCollection 2014 Mar.

12.

Bringing dicynodonts back to life: paleobiology and anatomy of a new emydopoid genus from the Upper Permian of Mozambique.

Castanhinha R, Araújo R, Júnior LC, Angielczyk KD, Martins GG, Martins RM, Chaouiya C, Beckmann F, Wilde F.

PLoS One. 2013 Dec 4;8(12):e80974. doi: 10.1371/journal.pone.0080974. eCollection 2013. Erratum in: PLoS One. 2014;9(4):e94720.

13.

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T.

BMC Syst Biol. 2013 Dec 10;7:135. doi: 10.1186/1752-0509-7-135.

14.

Path2Models: large-scale generation of computational models from biochemical pathway maps.

Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.

BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.

15.

Majority rules with random tie-breaking in Boolean gene regulatory networks.

Chaouiya C, Ourrad O, Lima R.

PLoS One. 2013 Jul 26;8(7):e69626. doi: 10.1371/journal.pone.0069626. Print 2013.

16.

Dynamical modeling and analysis of large cellular regulatory networks.

Bérenguier D, Chaouiya C, Monteiro PT, Naldi A, Remy E, Thieffry D, Tichit L.

Chaos. 2013 Jun;23(2):025114. doi: 10.1063/1.4809783.

PMID:
23822512
17.

Logical modelling of regulatory networks, methods and applications.

Chaouiya C, Remy E.

Bull Math Biol. 2013 Jun;75(6):891-5. doi: 10.1007/s11538-013-9863-0. No abstract available.

PMID:
23722297
18.

Composition and abstraction of logical regulatory modules: application to multicellular systems.

Mendes ND, Lang F, Le Cornec YS, Mateescu R, Batt G, Chaouiya C.

Bioinformatics. 2013 Mar 15;29(6):749-57. doi: 10.1093/bioinformatics/btt033. Epub 2013 Jan 22.

PMID:
23341501
19.

Logical modelling of gene regulatory networks with GINsim.

Chaouiya C, Naldi A, Thieffry D.

Methods Mol Biol. 2012;804:463-79. doi: 10.1007/978-1-61779-361-5_23.

PMID:
22144167
20.

Mapping multivalued onto Boolean dynamics.

Didier G, Remy E, Chaouiya C.

J Theor Biol. 2011 Feb 7;270(1):177-84. doi: 10.1016/j.jtbi.2010.09.017. Epub 2010 Sep 22.

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