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Items: 1 to 50 of 77

1.

Basic, simple and extendable kinetic model of protein synthesis.

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

Math Biosci Eng. 2019 Jul 17;16(6):6602-6622. doi: 10.3934/mbe.2019329.

2.

A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures.

Kondratova M, Czerwinska U, Sompairac N, Amigorena SD, Soumelis V, Barillot E, Zinovyev A, Kuperstein I.

Nat Commun. 2019 Oct 22;10(1):4808. doi: 10.1038/s41467-019-12270-x.

3.

ETS Proteins Bind with Glucocorticoid Receptors: Relevance for Treatment of Ewing Sarcoma.

Srivastava S, Nataraj NB, Sekar A, Ghosh S, Bornstein C, Drago-Garcia D, Roth L, Romaniello D, Marrocco I, David E, Gilad Y, Lauriola M, Rotkopf R, Kimchi A, Haga Y, Tsutsumi Y, Mirabeau O, Surdez D, Zinovyev A, Delattre O, Kovar H, Amit I, Yarden Y.

Cell Rep. 2019 Oct 1;29(1):104-117.e4. doi: 10.1016/j.celrep.2019.08.088.

4.

Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients.

Nazarov PV, Wienecke-Baldacchino AK, Zinovyev A, Czerwińska U, Muller A, Nashan D, Dittmar G, Azuaje F, Kreis S.

BMC Med Genomics. 2019 Sep 18;12(1):132. doi: 10.1186/s12920-019-0578-4.

5.

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets.

Sompairac N, Nazarov PV, Czerwinska U, Cantini L, Biton A, Molkenov A, Zhumadilov Z, Barillot E, Radvanyi F, Gorban A, Kairov U, Zinovyev A.

Int J Mol Sci. 2019 Sep 7;20(18). pii: E4414. doi: 10.3390/ijms20184414. Review.

6.

Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization.

Greco A, Sanchez Valle J, Pancaldi V, Baudot A, Barillot E, Caselle M, Valencia A, Zinovyev A, Cantini L.

Int J Mol Sci. 2019 Jun 26;20(13). pii: E3114. doi: 10.3390/ijms20133114.

7.

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM.

Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan GC, Pinello L.

Nat Commun. 2019 Apr 23;10(1):1903. doi: 10.1038/s41467-019-09670-4.

8.

Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer.

Sompairac N, Modamio J, Barillot E, Fleming RMT, Zinovyev A, Kuperstein I.

BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):140. doi: 10.1186/s12859-019-2682-z.

9.

Assessing reproducibility of matrix factorization methods in independent transcriptomes.

Cantini L, Kairov U, de Reyniès A, Barillot E, Radvanyi F, Zinovyev A.

Bioinformatics. 2019 Nov 1;35(21):4307-4313. doi: 10.1093/bioinformatics/btz225.

10.

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, Aurich MK, Clancy CM, Modamio J, Sauls JT, Noronha A, Bordbar A, Cousins B, El Assal DC, Valcarcel LV, Apaolaza I, Ghaderi S, Ahookhosh M, Ben Guebila M, Kostromins A, Sompairac N, Le HM, Ma D, Sun Y, Wang L, Yurkovich JT, Oliveira MAP, Vuong PT, El Assal LP, Kuperstein I, Zinovyev A, Hinton HS, Bryant WA, Aragón Artacho FJ, Planes FJ, Stalidzans E, Maass A, Vempala S, Hucka M, Saunders MA, Maranas CD, Lewis NE, Sauter T, Palsson BØ, Thiele I, Fleming RMT.

Nat Protoc. 2019 Mar;14(3):639-702. doi: 10.1038/s41596-018-0098-2.

PMID:
30787451
11.

Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer.

Cantini L, Bertoli G, Cava C, Dubois T, Zinovyev A, Caselle M, Castiglioni I, Barillot E, Martignetti L.

Nucleic Acids Res. 2019 Mar 18;47(5):2205-2215. doi: 10.1093/nar/gkz016.

12.

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease.

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Daníelsdóttir AD, Krecke M, Merten D, Haraldsdóttir HS, Heinken A, Heirendt L, Magnúsdóttir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Žagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I.

Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992.

13.

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.

14.

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.

15.

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.

16.

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.

Mazein A, Ostaszewski M, Kuperstein I, Watterson S, Le Novère N, Lefaudeux D, De Meulder B, Pellet J, Balaur I, Saqi M, Nogueira MM, He F, Parton A, Lemonnier N, Gawron P, Gebel S, Hainaut P, Ollert M, Dogrusoz U, Barillot E, Zinovyev A, Schneider R, Balling R, Auffray C.

NPJ Syst Biol Appl. 2018 Jun 2;4:21. doi: 10.1038/s41540-018-0059-y. eCollection 2018.

17.

Application of Atlas of Cancer Signalling Network in preclinical studies.

Monraz Gomez LC, Kondratova M, Ravel JM, Barillot E, Zinovyev A, Kuperstein I.

Brief Bioinform. 2019 Mar 25;20(2):701-716. doi: 10.1093/bib/bby031.

PMID:
29726961
18.

Signalling maps in cancer research: construction and data analysis.

Kondratova M, Sompairac N, Barillot E, Zinovyev A, Kuperstein I.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay036.

19.

Community-driven roadmap for integrated disease maps.

Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming RMT, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R.

Brief Bioinform. 2019 Mar 25;20(2):659-670. doi: 10.1093/bib/bby024.

20.

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 Mar 12;33(3):463-479.e10. doi: 10.1016/j.ccell.2018.01.011. Epub 2018 Feb 15.

21.

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.

22.

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.

23.

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
24.

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.

25.

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
26.

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.

27.

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.

28.

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.

29.

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
30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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
38.

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.

39.

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.

40.

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
41.

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.

42.

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
43.

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.

44.

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.

45.

[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
46.

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.

47.

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.

48.

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
49.

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
50.

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

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