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Items: 1 to 20 of 21

1.

System analysis of cross-talk between nuclear receptors reveals an opposite regulation of the cell cycle by LXR and FXR in human HepaRG liver cells.

Wigger L, Casals-Casas C, Baruchet M, Trang KB, Pradervand S, Naldi A, Desvergne B.

PLoS One. 2019 Aug 22;14(8):e0220894. doi: 10.1371/journal.pone.0220894. eCollection 2019.

2.

BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks.

Naldi A.

Front Physiol. 2018 Nov 19;9:1605. doi: 10.3389/fphys.2018.01605. eCollection 2018.

3.

Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial).

Levy N, Naldi A, Hernandez C, Stoll G, Thieffry D, Zinovyev A, Calzone L, Paulevé L.

Front Physiol. 2018 Jul 6;9:787. doi: 10.3389/fphys.2018.00787. eCollection 2018.

4.

GOATOOLS: A Python library for Gene Ontology analyses.

Klopfenstein DV, Zhang L, Pedersen BS, Ramírez F, Warwick Vesztrocy A, Naldi A, Mungall CJ, Yunes JM, Botvinnik O, Weigel M, Dampier W, Dessimoz C, Flick P, Tang H.

Sci Rep. 2018 Jul 18;8(1):10872. doi: 10.1038/s41598-018-28948-z.

5.

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.

6.

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.

7.

MaBoSS 2.0: an environment for stochastic Boolean modeling.

Stoll G, Caron B, Viara E, Dugourd A, Zinovyev A, Naldi A, Kroemer G, Barillot E, Calzone L.

Bioinformatics. 2017 Jul 15;33(14):2226-2228. doi: 10.1093/bioinformatics/btx123.

PMID:
28881959
8.

Erratum: The combination of the functionalities of feedback circuits is determinant for the attractors' number and size in pathway-like Boolean networks.

Azpeitia E, Muñoz S, González-Tokman D, Martínez-Sánchez ME, Weinstein N, Naldi A, Álvarez-Buylla ER, Rosenblueth DA, Mendoza L.

Sci Rep. 2017 Mar 22;7:44964. doi: 10.1038/srep44964. No abstract available.

9.

Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells.

Naldi A, Larive RM, Czerwinska U, Urbach S, Montcourrier P, Roy C, Solassol J, Freiss G, Coopman PJ, Radulescu O.

PLoS Comput Biol. 2017 Mar 17;13(3):e1005432. doi: 10.1371/journal.pcbi.1005432. eCollection 2017 Mar.

10.

The combination of the functionalities of feedback circuits is determinant for the attractors' number and size in pathway-like Boolean networks.

Azpeitia E, Muñoz S, González-Tokman D, Martínez-Sánchez ME, Weinstein N, Naldi A, Álvarez-Buylla ER, Rosenblueth DA, Mendoza L.

Sci Rep. 2017 Feb 10;7:42023. doi: 10.1038/srep42023. Erratum in: Sci Rep. 2017 Mar 22;7:44964.

11.

Geometric analysis of pathways dynamics: Application to versatility of TGF-β receptors.

Samal SS, Naldi A, Grigoriev D, Weber A, Théret N, Radulescu O.

Biosystems. 2016 Nov;149:3-14. doi: 10.1016/j.biosystems.2016.07.004. Epub 2016 Jul 21.

12.

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
13.

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.

14.

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
15.

Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals.

Gilardi F, Migliavacca E, Naldi A, Baruchet M, Canella D, Le Martelot G, Guex N, Desvergne B; CycliX Consortium.

PLoS Genet. 2014 Mar 6;10(3):e1004155. doi: 10.1371/journal.pgen.1004155. eCollection 2014 Mar.

16.

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.

17.

On circuit functionality in Boolean networks.

Comet JP, Noual M, Richard A, Aracena J, Calzone L, Demongeot J, Kaufman M, Naldi A, Snoussi el H, Thieffry D.

Bull Math Biol. 2013 Jun;75(6):906-19. doi: 10.1007/s11538-013-9829-2. Epub 2013 Mar 16.

PMID:
23504387
18.

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
19.

Diversity and plasticity of Th cell types predicted from regulatory network modelling.

Naldi A, Carneiro J, Chaouiya C, Thieffry D.

PLoS Comput Biol. 2010 Sep 2;6(9):e1000912. doi: 10.1371/journal.pcbi.1000912.

20.

Modular logical modelling of the budding yeast cell cycle.

Fauré A, Naldi A, Lopez F, Chaouiya C, Ciliberto A, Thieffry D.

Mol Biosyst. 2009 Dec;5(12):1787-96. doi: 10.1039/B910101m. Epub 2009 Jul 31.

PMID:
19763337

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