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Items: 41

1.

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.

Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R.

iScience. 2019 Oct 31;21:664-680. doi: 10.1016/j.isci.2019.10.059. [Epub ahead of print]

2.

Integrative proteomic and phosphoproteomic profiling of prostate cell lines.

Katsogiannou M, Boyer JB, Valdeolivas A, Remy E, Calzone L, Audebert S, Rocchi P, Camoin L, Baudot A.

PLoS One. 2019 Nov 1;14(11):e0224148. doi: 10.1371/journal.pone.0224148. eCollection 2019.

3.

Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients.

Béal J, Montagud A, Traynard P, Barillot E, Calzone L.

Front Physiol. 2019 Jan 24;9:1965. doi: 10.3389/fphys.2018.01965. eCollection 2018.

4.

Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling.

Forget A, Martignetti L, Puget S, Calzone L, Brabetz S, Picard D, Montagud A, Liva S, Sta A, Dingli F, Arras G, Rivera J, Loew D, Besnard A, Lacombe J, Pagès M, Varlet P, Dufour C, Yu H, Mercier AL, Indersie E, Chivet A, Leboucher S, Sieber L, Beccaria K, Gombert M, Meyer FD, Qin N, Bartl J, Chavez L, Okonechnikov K, Sharma T, Thatikonda V, Bourdeaut F, Pouponnot C, Ramaswamy V, Korshunov A, Borkhardt A, Reifenberger G, Poullet P, Taylor MD, Kool M, Pfister SM, Kawauchi D, Barillot E, Remke M, Ayrault O.

Cancer Cell. 2018 Sep 10;34(3):379-395.e7. doi: 10.1016/j.ccell.2018.08.002.

5.

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling.

Letort G, Montagud A, Stoll G, Heiland R, Barillot E, Macklin P, Zinovyev A, Calzone L.

Bioinformatics. 2019 Apr 1;35(7):1188-1196. doi: 10.1093/bioinformatics/bty766.

6.

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.

7.

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.

8.

Classification of gene signatures for their information value and functional redundancy.

Cantini L, Calzone L, Martignetti L, Rydenfelt M, Blüthgen N, Barillot E, Zinovyev A.

NPJ Syst Biol Appl. 2017 Dec 19;4:2. doi: 10.1038/s41540-017-0038-8. eCollection 2018.

9.

Conceptual and computational framework for logical modelling of biological networks deregulated in diseases.

Montagud A, Traynard P, Martignetti L, Bonnet E, Barillot E, Zinovyev A, Calzone L.

Brief Bioinform. 2019 Jul 19;20(4):1238-1249. doi: 10.1093/bib/bbx163.

PMID:
29237040
10.

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
11.

Logic Modeling in Quantitative Systems Pharmacology.

Traynard P, Tobalina L, Eduati F, Calzone L, Saez-Rodriguez J.

CPT Pharmacometrics Syst Pharmacol. 2017 Aug;6(8):499-511. doi: 10.1002/psp4.12225. Epub 2017 Jul 29.

12.

A comprehensive approach to the molecular determinants of lifespan using a Boolean model of geroconversion.

Verlingue L, Dugourd A, Stoll G, Barillot E, Calzone L, Londoño-Vallejo A.

Aging Cell. 2016 Dec;15(6):1018-1026. doi: 10.1111/acel.12504. Epub 2016 Sep 9.

13.

Qualitative dynamics semantics for SBGN process description.

Rougny A, Froidevaux C, Calzone L, Paulevé L.

BMC Syst Biol. 2016 Jun 16;10(1):42. doi: 10.1186/s12918-016-0285-0.

14.

ROMA: Representation and Quantification of Module Activity from Target Expression Data.

Martignetti L, Calzone L, Bonnet E, Barillot E, Zinovyev A.

Front Genet. 2016 Feb 19;7:18. doi: 10.3389/fgene.2016.00018. eCollection 2016.

15.

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration.

Cohen DP, Martignetti L, Robine S, Barillot E, Zinovyev A, Calzone L.

PLoS Comput Biol. 2015 Nov 3;11(11):e1004571. doi: 10.1371/journal.pcbi.1004571. eCollection 2015 Nov.

16.

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts.

Czerwinska U, Calzone L, Barillot E, Zinovyev A.

BMC Syst Biol. 2015 Aug 14;9:46. doi: 10.1186/s12918-015-0189-4.

17.

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.

18.

Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps.

Kuperstein I, Bonnet E, Nguyen HA, Cohen D, Viara E, Grieco L, Fourquet S, Calzone L, Russo C, Kondratova M, Dutreix M, Barillot E, Zinovyev A.

Oncogenesis. 2015 Jul 20;4:e160. doi: 10.1038/oncsis.2015.19.

19.

Predicting genetic interactions from Boolean models of biological networks.

Calzone L, Barillot E, Zinovyev A.

Integr Biol (Camb). 2015 Aug;7(8):921-9. doi: 10.1039/c5ib00029g. Epub 2015 May 11.

PMID:
25958956
20.

NaviCell Web Service for network-based data visualization.

Bonnet E, Viara E, Kuperstein I, Calzone L, Cohen DP, Barillot E, Zinovyev A.

Nucleic Acids Res. 2015 Jul 1;43(W1):W560-5. doi: 10.1093/nar/gkv450. Epub 2015 May 9.

21.

Integrative multi-omics module network inference with Lemon-Tree.

Bonnet E, Calzone L, Michoel T.

PLoS Comput Biol. 2015 Feb 13;11(2):e1003983. doi: 10.1371/journal.pcbi.1003983. eCollection 2015 Feb.

22.

[Biological network modelling and precision medicine in oncology].

Calzone L, Kuperstein I, Cohen D, Grieco L, Bonnet E, Servant N, Hupé P, Zinovyev A, Barillot E.

Bull Cancer. 2014 Jun;101 Suppl 1:S18-21. doi: 10.1684/bdc.2014.1973. Review. French.

PMID:
24966078
23.

Integrative modelling of the influence of MAPK network on cancer cell fate decision.

Grieco L, Calzone L, Bernard-Pierrot I, Radvanyi F, Kahn-Perlès B, Thieffry D.

PLoS Comput Biol. 2013 Oct;9(10):e1003286. doi: 10.1371/journal.pcbi.1003286. Epub 2013 Oct 24. Erratum in: PLoS Comput Biol. 2013 Nov;9(11). doi:10.1371/annotation/90e5e4be-952b-42b8-b56d-46baae3479ed.

24.

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.

Kuperstein I, Cohen DP, Pook S, Viara E, Calzone L, Barillot E, Zinovyev A.

BMC Syst Biol. 2013 Oct 7;7:100. doi: 10.1186/1752-0509-7-100.

25.

Practical use of BiNoM: a biological network manager software.

Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.

Methods Mol Biol. 2013;1021:127-46. doi: 10.1007/978-1-62703-450-0_7.

PMID:
23715983
26.

From a biological hypothesis to the construction of a mathematical model.

Cohen D, Kuperstein I, Barillot E, Zinovyev A, Calzone L.

Methods Mol Biol. 2013;1021:107-25. doi: 10.1007/978-1-62703-450-0_6.

PMID:
23715982
27.

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
28.

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.

Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.

BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18.

29.

Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm.

Stoll G, Viara E, Barillot E, Calzone L.

BMC Syst Biol. 2012 Aug 29;6:116. doi: 10.1186/1752-0509-6-116.

30.

Cell death and life in cancer: mathematical modeling of cell fate decisions.

Zinovyev A, Fourquet S, Tournier L, Calzone L, Barillot E.

Adv Exp Med Biol. 2012;736:261-74. doi: 10.1007/978-1-4419-7210-1_15.

PMID:
22161334
31.

Mathematical modelling of cell-fate decision in response to death receptor engagement.

Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A.

PLoS Comput Biol. 2010 Mar 5;6(3):e1000702. doi: 10.1371/journal.pcbi.1000702.

32.

Cow's milk protein allergy in children: a practical guide.

Caffarelli C, Baldi F, Bendandi B, Calzone L, Marani M, Pasquinelli P; EWGPAG.

Ital J Pediatr. 2010 Jan 15;36:5. doi: 10.1186/1824-7288-36-5. Review.

33.

The Systems Biology Graphical Notation.

Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H.

Nat Biotechnol. 2009 Aug;27(8):735-41. doi: 10.1038/nbt.1558. Epub 2009 Aug 7. Erratum in: Nat Biotechnol. 2009 Sep;27(9):864.

PMID:
19668183
34.

[Systems biology of cancer].

Barillot E, Calzone L, Zinovyev A.

Med Sci (Paris). 2009 Jun-Jul;25(6-7):601-7. doi: 10.1051/medsci/2009256-7601. French.

35.

Egg sensitization caused by immediate hypersensitivity reaction to drug-containing lysozyme.

Artesani MC, Donnanno S, Cavagni G, Calzone L, D'Urbano L.

Ann Allergy Asthma Immunol. 2008 Jul;101(1):105. doi: 10.1016/S1081-1206(10)60843-5. No abstract available.

PMID:
18681093
36.

A comprehensive modular map of molecular interactions in RB/E2F pathway.

Calzone L, Gelay A, Zinovyev A, Radvanyi F, Barillot E.

Mol Syst Biol. 2008;4:173. doi: 10.1038/msb.2008.7. Epub 2008 Mar 4.

37.

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks.

Zinovyev A, Viara E, Calzone L, Barillot E.

Bioinformatics. 2008 Mar 15;24(6):876-7. Epub 2007 Nov 16.

PMID:
18024474
38.

Dynamical modeling of syncytial mitotic cycles in Drosophila embryos.

Calzone L, Thieffry D, Tyson JJ, Novak B.

Mol Syst Biol. 2007;3:131. Epub 2007 Jul 31.

39.

BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge.

Calzone L, Fages F, Soliman S.

Bioinformatics. 2006 Jul 15;22(14):1805-7. Epub 2006 May 3.

PMID:
16672256
40.

Integrative analysis of cell cycle control in budding yeast.

Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ.

Mol Biol Cell. 2004 Aug;15(8):3841-62. Epub 2004 May 28.

41.

Modeling regulatory networks at Virginia Tech.

Allen NA, Calzone L, Chen KC, Ciliberto A, Ramakrishnan N, Shaffer CA, Sible JC, Tyson JJ, Vass MT, Watson LT, Zwolak JW.

OMICS. 2003 Fall;7(3):285-99.

PMID:
14583117

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