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Items: 1 to 50 of 58

1.

Fibroblast Heterogeneity and Immunosuppressive Environment in Human Breast Cancer.

Costa A, Kieffer Y, Scholer-Dahirel A, Pelon F, Bourachot B, Cardon M, Sirven P, Magagna I, Fuhrmann L, Bernard C, Bonneau C, Kondratova M, Kuperstein I, Zinovyev A, Givel AM, Parrini MC, Soumelis V, Vincent-Salomon A, Mechta-Grigoriou F.

Cancer Cell. 2018 Feb 12. pii: S1535-6108(18)30011-4. doi: 10.1016/j.ccell.2018.01.011. [Epub ahead of print]

PMID:
29455927
2.

Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks.

Lages J, Shepelyansky DL, Zinovyev A.

PLoS One. 2018 Jan 25;13(1):e0190812. doi: 10.1371/journal.pone.0190812. eCollection 2018.

3.

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.

4.

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. 2017 Dec 8. doi: 10.1093/bib/bbx163. [Epub ahead of print]

PMID:
29237040
5.

Determining the optimal number of independent components for reproducible transcriptomic data analysis.

Kairov U, Cantini L, Greco A, Molkenov A, Czerwinska U, Barillot E, Zinovyev A.

BMC Genomics. 2017 Sep 11;18(1):712. doi: 10.1186/s12864-017-4112-9.

6.

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
7.

NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis.

Le Morvan M, Zinovyev A, Vert JP.

PLoS Comput Biol. 2017 Jun 26;13(6):e1005573. doi: 10.1371/journal.pcbi.1005573. eCollection 2017 Jun.

8.

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.

Dorel M, Viara E, Barillot E, Zinovyev A, Kuperstein I.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax026.

9.

A review of computational approaches detecting microRNAs involved in cancer.

Cantini L, Caselle M, Forget A, Zinovyev A, Barillot E, Martignetti L.

Front Biosci (Landmark Ed). 2017 Jun 1;22:1774-1791. Review.

PMID:
28410145
10.

Piece-wise quadratic approximations of arbitrary error functions for fast and robust machine learning.

Gorban AN, Mirkes EM, Zinovyev A.

Neural Netw. 2016 Dec;84:28-38. doi: 10.1016/j.neunet.2016.08.007. Epub 2016 Aug 30.

PMID:
27639721
11.

Drug-Driven Synthetic Lethality: Bypassing Tumor Cell Genetics with a Combination of AsiDNA and PARP Inhibitors.

Jdey W, Thierry S, Russo C, Devun F, Al Abo M, Noguiez-Hellin P, Sun JS, Barillot E, Zinovyev A, Kuperstein I, Pommier Y, Dutreix M.

Clin Cancer Res. 2017 Feb 15;23(4):1001-1011. doi: 10.1158/1078-0432.CCR-16-1193. Epub 2016 Aug 24.

12.

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.

13.

The second European interdisciplinary Ewing sarcoma research summit--A joint effort to deconstructing the multiple layers of a complex disease.

Kovar H, Amatruda J, Brunet E, Burdach S, Cidre-Aranaz F, de Alava E, Dirksen U, van der Ent W, Grohar P, Grünewald TG, Helman L, Houghton P, Iljin K, Korsching E, Ladanyi M, Lawlor E, Lessnick S, Ludwig J, Meltzer P, Metzler M, Mora J, Moriggl R, Nakamura T, Papamarkou T, Radic Sarikas B, Rédini F, Richter GH, Rossig C, Schadler K, Schäfer BW, Scotlandi K, Sheffield NC, Shelat A, Snaar-Jagalska E, Sorensen P, Stegmaier K, Stewart E, Sweet-Cordero A, Szuhai K, Tirado OM, Tirode F, Toretsky J, Tsafou K, Üren A, Zinovyev A, Delattre O.

Oncotarget. 2016 Feb 23;7(8):8613-24. doi: 10.18632/oncotarget.6937. Review.

14.

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.

15.

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.

16.

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.

17.

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.

18.

Network-based approaches for drug response prediction and targeted therapy development in cancer.

Dorel M, Barillot E, Zinovyev A, Kuperstein I.

Biochem Biophys Res Commun. 2015 Aug 21;464(2):386-91. doi: 10.1016/j.bbrc.2015.06.094. Epub 2015 Jun 15. Review.

PMID:
26086105
19.

Network biology elucidates metastatic colon cancer mechanisms.

Kuperstein I, Robine S, Zinovyev A.

Cell Cycle. 2015;14(14):2189-90. doi: 10.1080/15384101.2015.1060816. No abstract available.

20.

Detection of miRNA regulatory effect on triple negative breast cancer transcriptome.

Martignetti L, Tesson B, Almeida A, Zinovyev A, Tucker GC, Dubois T, Barillot E.

BMC Genomics. 2015;16:S4. doi: 10.1186/1471-2164-16-S6-S4. Epub 2015 Jun 1.

21.

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
22.

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.

23.

The shortest path is not the one you know: application of biological network resources in precision oncology research.

Kuperstein I, Grieco L, Cohen DP, Thieffry D, Zinovyev A, Barillot E.

Mutagenesis. 2015 Mar;30(2):191-204. doi: 10.1093/mutage/geu078. Review.

PMID:
25688112
24.

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes.

Biton A, Bernard-Pierrot I, Lou Y, Krucker C, Chapeaublanc E, Rubio-Pérez C, López-Bigas N, Kamoun A, Neuzillet Y, Gestraud P, Grieco L, Rebouissou S, de Reyniès A, Benhamou S, Lebret T, Southgate J, Barillot E, Allory Y, Zinovyev A, Radvanyi F.

Cell Rep. 2014 Nov 20;9(4):1235-45. doi: 10.1016/j.celrep.2014.10.035. Epub 2014 Nov 13.

25.

Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut.

Chanrion M, Kuperstein I, Barrière C, El Marjou F, Cohen D, Vignjevic D, Stimmer L, Paul-Gilloteaux P, Bièche I, Tavares Sdos R, Boccia GF, Cacheux W, Meseure D, Fre S, Martignetti L, Legoix-Né P, Girard E, Fetler L, Barillot E, Louvard D, Zinovyev A, Robine S.

Nat Commun. 2014 Oct 8;5:5005. doi: 10.1038/ncomms6005.

26.

[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
27.

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.

28.

Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis.

Stoll G, Surdez D, Tirode F, Laud K, Barillot E, Zinovyev A, Delattre O.

Nucleic Acids Res. 2013 Oct;41(19):8853-71. doi: 10.1093/nar/gkt678. Epub 2013 Aug 8.

29.

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
30.

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
31.

OCSANA: optimal combinations of interventions from network analysis.

Vera-Licona P, Bonnet E, Barillot E, Zinovyev A.

Bioinformatics. 2013 Jun 15;29(12):1571-3. doi: 10.1093/bioinformatics/btt195. Epub 2013 Apr 26.

PMID:
23626000
32.

Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps.

Zinovyev A, Kuperstein I, Barillot E, Heyer WD.

PLoS Comput Biol. 2013 Apr;9(4):e1003016. doi: 10.1371/journal.pcbi.1003016. Epub 2013 Apr 4.

33.

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.

34.

Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways.

Kutumova E, Zinovyev A, Sharipov R, Kolpakov F.

BMC Syst Biol. 2013 Feb 15;7:13. doi: 10.1186/1752-0509-7-13.

35.

Mathematical modeling of microRNA-mediated mechanisms of translation repression.

Zinovyev A, Morozova N, Gorban AN, Harel-Belan A.

Adv Exp Med Biol. 2013;774:189-224. doi: 10.1007/978-94-007-5590-1_11. Review.

PMID:
23377975
36.

Blind source separation methods for deconvolution of complex signals in cancer biology.

Zinovyev A, Kairov U, Karpenyuk T, Ramanculov E.

Biochem Biophys Res Commun. 2013 Jan 18;430(3):1182-7. doi: 10.1016/j.bbrc.2012.12.043. Epub 2012 Dec 19. Review.

PMID:
23261450
37.

Network analysis of gene lists for finding reproducible prognostic breast cancer gene signatures.

Kairov U, Karpenyuk T, Ramanculov E, Zinovyev A.

Bioinformation. 2012;8(16):773-6. doi: 10.6026/97320630008773. Epub 2012 Aug 24.

38.

Kinetic signatures of microRNA modes of action.

Morozova N, Zinovyev A, Nonne N, Pritchard LL, Gorban AN, Harel-Bellan A.

RNA. 2012 Sep;18(9):1635-55. doi: 10.1261/rna.032284.112. Epub 2012 Jul 31.

39.

Antagonism pattern detection between microRNA and target expression in Ewing's sarcoma.

Martignetti L, Laud-Duval K, Tirode F, Pierron G, Reynaud S, Barillot E, Delattre O, Zinovyev A.

PLoS One. 2012;7(7):e41770. doi: 10.1371/journal.pone.0041770. Epub 2012 Jul 25.

40.

Reduction of dynamical biochemical reactions networks in computational biology.

Radulescu O, Gorban AN, Zinovyev A, Noel V.

Front Genet. 2012 Jul 19;3:131. doi: 10.3389/fgene.2012.00131. eCollection 2012.

41.

Identification of shortened 3' untranslated regions from expression arrays.

Martignetti L, Zinovyev A, Barillot E.

J Bioinform Comput Biol. 2012 Apr;10(2):1241001. doi: 10.1142/S0219720012410016.

PMID:
22809337
42.

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
43.

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.

Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, Barillot E.

Bioinformatics. 2011 Jan 15;27(2):268-9. doi: 10.1093/bioinformatics/btq635. Epub 2010 Nov 15.

44.

Principal manifolds and graphs in practice: from molecular biology to dynamical systems.

Gorban AN, Zinovyev A.

Int J Neural Syst. 2010 Jun;20(3):219-32.

PMID:
20556849
45.

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.

46.

Dynamical modeling of microRNA action on the protein translation process.

Zinovyev A, Morozova N, Nonne N, Barillot E, Harel-Bellan A, Gorban AN.

BMC Syst Biol. 2010 Feb 24;4:13. doi: 10.1186/1752-0509-4-13.

47.

[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.

48.

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008).

Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B.

Mol Oncol. 2009 Feb;3(1):9-17. doi: 10.1016/j.molonc.2008.11.003. Epub 2008 Dec 9.

49.

Robust simplifications of multiscale biochemical networks.

Radulescu O, Gorban AN, Zinovyev A, Lilienbaum A.

BMC Syst Biol. 2008 Oct 14;2:86. doi: 10.1186/1752-0509-2-86.

50.

How much non-coding DNA do eukaryotes require?

Ahnert SE, Fink TM, Zinovyev A.

J Theor Biol. 2008 Jun 21;252(4):587-92. doi: 10.1016/j.jtbi.2008.02.005. Epub 2008 Feb 14.

PMID:
18384817

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