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Items: 39


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.


Transcranial Color-Coded Sonography for Monitoring Idiopathic Intracranial Hypertension.

Naldi A, Lochner P, Canu P, Settembre R, Alessi S, Sanguigni S.

Ultraschall Med. 2018 Nov 20. doi: 10.1055/a-0783-2541. [Epub ahead of print]


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.


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.


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.


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.


Neuronal erythropoietin overexpression is protective against kanamycin-induced hearing loss in mice.

Bächinger D, Horvath L, Eckhard A, Goosmann MM, Honegger T, Gassmann M, Vogel J, Naldi AM.

Toxicol Lett. 2018 Jul;291:121-128. doi: 10.1016/j.toxlet.2018.04.007. Epub 2018 Apr 11.


Longitudinal Assessment of Transorbital Sonography, Visual Acuity, and Biomarkers for Inflammation and Axonal Injury in Optic Neuritis.

Lochner P, Cantello R, Fassbender K, Lesmeister M, Nardone R, Siniscalchi A, Clemente N, Naldi A, Coppo L, Brigo F, Comi C.

Dis Markers. 2017;2017:5434310. doi: 10.1155/2017/5434310. Epub 2017 Sep 11.


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.


The measuring of substantia nigra hyperechogenicity in an Italian cohort of Parkinson disease patients: a case/control study (NOBIS Study).

Prati P, Bignamini A, Coppo L, Naldi A, Comi C, Cantello R, Gusmaroli G, Walter U.

J Neural Transm (Vienna). 2017 Jul;124(7):869-879. doi: 10.1007/s00702-017-1724-9. Epub 2017 Apr 27.


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.


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.


Can neuroimaging differentiate PFO and AF-related cardioembolic stroke from the other embolic sources? Clinical-radiological correlation on a retrospective study.

Stecco A, Quagliozzi M, Soligo E, Naldi A, Cassarà A, Coppo L, Rosso R, Bongo AS, Amatuzzo P, Buemi F, Guenzi E, Carriero A.

Radiol Med. 2017 Jun;122(6):412-418. doi: 10.1007/s11547-017-0738-6. Epub 2017 Feb 21.


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.


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.


Erratum to: Feasibility and usefulness of ultrasonography in idiopathic intracranial hypertension or secondary intracranial hypertension.

Lochner P, Brigo F, Zedde ML, Sanguigni S, Coppo L, Nardone R, Naldi A, Sola D, Stolz E.

BMC Neurol. 2016 Jul 1;16(1):94. No abstract available.


Feasibility and usefulness of ultrasonography in idiopathic intracranial hypertension or secondary intracranial hypertension.

Lochner P, Brio F, Zedde ML, Sanguigni S, Coppo L, Nardone R, Naldi A, Sola D, Stolz E.

BMC Neurol. 2016 Jun 2;16:85. doi: 10.1186/s12883-016-0594-3. Erratum in: BMC Neurol. 2016;16:94.


Analysis of steroid hormones and their conjugated forms in water and urine by on-line solid-phase extraction coupled to liquid chromatography tandem mass spectrometry.

Naldi AC, Fayad PB, Prévost M, Sauvé S.

Chem Cent J. 2016 May 6;10:30. doi: 10.1186/s13065-016-0174-z. eCollection 2016.


Intra- and interobserver reliability of transorbital sonographic assessment of the optic nerve sheath diameter and optic nerve diameter in healthy adults.

Lochner P, Coppo L, Cantello R, Nardone R, Naldi A, Leone MA, Brigo F.

J Ultrasound. 2014 Nov 20;19(1):41-5. doi: 10.1007/s40477-014-0144-z. eCollection 2016 Mar.


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.


All Akt isoforms (Akt1, Akt2, Akt3) are involved in normal hearing, but only Akt2 and Akt3 are involved in auditory hair cell survival in the mammalian inner ear.

Brand Y, Levano S, Radojevic V, Naldi AM, Setz C, Ryan AF, Pak K, Hemmings BA, Bodmer D.

PLoS One. 2015 Mar 26;10(3):e0121599. doi: 10.1371/journal.pone.0121599. eCollection 2015.


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.


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.


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.


Detection and grading of endolymphatic hydrops in Menière disease using MR imaging.

Baráth K, Schuknecht B, Naldi AM, Schrepfer T, Bockisch CJ, Hegemann SC.

AJNR Am J Neuroradiol. 2014 Jul;35(7):1387-92. doi: 10.3174/ajnr.A3856. Epub 2014 Feb 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.


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.


Liver iron modulates hepcidin expression during chronically elevated erythropoiesis in mice.

Díaz V, Gammella E, Recalcati S, Santambrogio P, Naldi AM, Vogel J, Gassmann M, Cairo G.

Hepatology. 2013 Dec;58(6):2122-32. doi: 10.1002/hep.26550. Epub 2013 Oct 21.


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.


Central neuropathic itch as the presenting symptom of an intramedullary cavernous hemangioma: case report and review of literature.

Lanotte M, Panciani PP, Magistrello M, Naldi A, Fontanella M, Ducati A, Giordana MT.

Clin Neurol Neurosurg. 2013 Apr;115(4):454-6. doi: 10.1016/j.clineuro.2012.05.028. Epub 2012 Jun 17. No abstract available.


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.


Dementia and cognitive impairment in amyotrophic lateral sclerosis: a review.

Giordana MT, Ferrero P, Grifoni S, Pellerino A, Naldi A, Montuschi A.

Neurol Sci. 2011 Feb;32(1):9-16. doi: 10.1007/s10072-010-0439-6. Epub 2010 Oct 16. Review.


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.


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.


Logical modelling of regulatory networks with GINsim 2.3.

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

Biosystems. 2009 Aug;97(2):134-9. doi: 10.1016/j.biosystems.2009.04.008. Epub 2009 May 6.


Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.

Fauré A, Naldi A, Chaouiya C, Thieffry D.

Bioinformatics. 2006 Jul 15;22(14):e124-31.


GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks.

Gonzalez AG, Naldi A, Sánchez L, Thieffry D, Chaouiya C.

Biosystems. 2006 May;84(2):91-100. Epub 2006 Jan 24.


[Biometric evaluation of the use of a battery of tests for studying the rheumatoid factor].

Ferri S, Gaiardi M, Procicchiani D, Marsigli R, Naldi A.

Quad Sclavo Diagn. 1983 Mar;19(1):47-54. Italian.


[Pectus carinatum: diagnosis and bloodless therapy].

Bilotta TW, Manuelli L, Mazzanti U, Naldi A, Prioli L.

Chir Organi Mov. 1982 May-Jun;68(3):351-9. Italian. No abstract available.


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