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Items: 23

1.

EpiLog: A software for the logical modelling of epithelial dynamics.

Varela PL, Ramos CV, Monteiro PT, Chaouiya C.

F1000Res. 2018 Jul 27;7:1145. doi: 10.12688/f1000research.15613.1. eCollection 2018.

2.

Estimating Attractor Reachability in Asynchronous Logical Models.

Mendes ND, Henriques R, Remy E, Carneiro J, Monteiro PT, Chaouiya C.

Front Physiol. 2018 Sep 7;9:1161. doi: 10.3389/fphys.2018.01161. eCollection 2018.

3.

Large-Scale Simulations of Bacterial Populations Over Complex Networks.

Teixeira AS, Monteiro PT, Carriço JA, Santos FC, Francisco AP.

J Comput Biol. 2018 Aug;25(8):850-861. doi: 10.1089/cmb.2018.0083. Epub 2018 Jul 9.

PMID:
29985650
4.

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.

5.

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.

6.

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae.

Teixeira MC, Monteiro PT, Palma M, Costa C, Godinho CP, Pais P, Cavalheiro M, Antunes M, Lemos A, Pedreira T, Sá-Correia I.

Nucleic Acids Res. 2018 Jan 4;46(D1):D348-D353. doi: 10.1093/nar/gkx842.

7.

The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts.

Monteiro PT, Pais P, Costa C, Manna S, Sá-Correia I, Teixeira MC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D597-D603. doi: 10.1093/nar/gkw817. Epub 2016 Sep 12.

8.

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.

9.

Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step-by-Step Guided Analysis.

Teixeira MC, Monteiro PT, Sá-Correia I.

Methods Mol Biol. 2016;1361:391-404. doi: 10.1007/978-1-4939-3079-1_22.

PMID:
26483034
10.

Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis.

Teixeira AS, Monteiro PT, Carriço JA, Ramirez M, Francisco AP.

PLoS One. 2015 Mar 23;10(3):e0119315. doi: 10.1371/journal.pone.0119315. eCollection 2015.

11.

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.

12.

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
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.

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae.

Teixeira MC, Monteiro PT, Guerreiro JF, Gonçalves JP, Mira NP, dos Santos SC, Cabrito TR, Palma M, Costa C, Francisco AP, Madeira SC, Oliveira AL, Freitas AT, Sá-Correia I.

Nucleic Acids Res. 2014 Jan;42(Database issue):D161-6. doi: 10.1093/nar/gkt1015. Epub 2013 Oct 28.

15.

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
16.

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods.

Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carriço JA.

BMC Bioinformatics. 2012 May 8;13:87. doi: 10.1186/1471-2105-13-87.

17.

Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks.

Batt G, Besson B, Ciron PE, de Jong H, Dumas E, Geiselmann J, Monte R, Monteiro PT, Page M, Rechenmann F, Ropers D.

Methods Mol Biol. 2012;804:439-62. doi: 10.1007/978-1-61779-361-5_22.

PMID:
22144166
18.

Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae.

Monteiro PT, Dias PJ, Ropers D, Oliveira AL, Sá-Correia I, Teixeira MC, Freitas AT.

IET Syst Biol. 2011 Sep;5(5):308-16. doi: 10.1049/iet-syb.2011.0001.

PMID:
22010757
19.

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface.

Abdulrehman D, Monteiro PT, Teixeira MC, Mira NP, Lourenço AB, dos Santos SC, Cabrito TR, Francisco AP, Madeira SC, Aires RS, Oliveira AL, Sá-Correia I, Freitas AT.

Nucleic Acids Res. 2011 Jan;39(Database issue):D136-40. doi: 10.1093/nar/gkq964. Epub 2010 Oct 23.

20.

Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches.

Teixeira MC, Dias PJ, Monteiro PT, Sala A, Oliveira AL, Freitas AT, Sá-Correia I.

Mol Biosyst. 2010 Dec;6(12):2471-81. doi: 10.1039/c004881j. Epub 2010 Oct 11.

PMID:
20938527
21.

A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks.

Monteiro PT, Dumas E, Besson B, Mateescu R, Page M, Freitas AT, de Jong H.

BMC Bioinformatics. 2009 Dec 30;10:450. doi: 10.1186/1471-2105-10-450.

22.

Temporal logic patterns for querying dynamic models of cellular interaction networks.

Monteiro PT, Ropers D, Mateescu R, Freitas AT, de Jong H.

Bioinformatics. 2008 Aug 15;24(16):i227-33. doi: 10.1093/bioinformatics/btn275.

PMID:
18689830
23.

YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae.

Monteiro PT, Mendes ND, Teixeira MC, d'Orey S, Tenreiro S, Mira NP, Pais H, Francisco AP, Carvalho AM, Lourenço AB, Sá-Correia I, Oliveira AL, Freitas AT.

Nucleic Acids Res. 2008 Jan;36(Database issue):D132-6. Epub 2007 Nov 21.

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