| Year |
Citation |
Score |
| 2024 |
Najm M, Cornet M, Albergante L, Zinovyev A, Sermet-Gaudelus I, Stoven V, Calzone L, Martignetti L. Representation and quantification of module activity from omics data with rROMA. Npj Systems Biology and Applications. 10: 8. PMID 38242871 DOI: 10.1038/s41540-024-00331-x |
0.656 |
|
| 2023 |
Ruscone M, Montagud A, Chavrier P, Destaing O, Bonnet I, Zinovyev A, Barillot E, Noël V, Calzone L. Multiscale model of the different modes of cancer cell invasion. Bioinformatics (Oxford, England). PMID 37289551 DOI: 10.1093/bioinformatics/btad374 |
0.8 |
|
| 2022 |
Captier N, Merlevede J, Molkenov A, Seisenova A, Zhubanchaliyev A, Nazarov PV, Barillot E, Kairov U, Zinovyev A. BIODICA: a computational environment for Independent Component Analysis of omics data. Bioinformatics (Oxford, England). 38: 2963-2964. PMID 35561190 DOI: 10.1093/bioinformatics/btac204 |
0.508 |
|
| 2022 |
Captier N, Merlevede J, Molkenov A, Seisenova A, Zhubanchaliyev A, Nazarov PV, Barillot E, Kairov U, Zinovyev A. BIODICA: a computational environment for Independent Component Analysis of omics data. Bioinformatics (Oxford, England). PMID 35462395 DOI: 10.1093/bioinformatics/btac204 |
0.508 |
|
| 2022 |
Captier N, Merlevede J, Molkenov A, Seisenova A, Zhubanchaliyev A, Nazarov PV, Barillot E, Kairov U, Zinovyev A. BIODICA: a computational environment for Independent Component Analysis. Bioinformatics (Oxford, England). PMID 35385067 DOI: 10.1093/bioinformatics/btac204 |
0.505 |
|
| 2022 |
Zinovyev A, Sadovsky M, Calzone L, Fouché A, Groeneveld CS, Chervov A, Barillot E, Gorban AN. Modeling Progression of Single Cell Populations Through the Cell Cycle as a Sequence of Switches. Frontiers in Molecular Biosciences. 8: 793912. PMID 35178429 DOI: 10.3389/fmolb.2021.793912 |
0.713 |
|
| 2021 |
Noël V, Ruscone M, Stoll G, Viara E, Zinovyev A, Barillot E, Calzone L. WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically. Frontiers in Molecular Biosciences. 8: 754444. PMID 34888352 DOI: 10.3389/fmolb.2021.754444 |
0.722 |
|
| 2021 |
Seisenova A, Daniyarov A, Molkenov A, Sharip A, Zinovyev A, Kairov U. Meta-Analysis of Esophageal Cancer Transcriptomes Using Independent Component Analysis. Frontiers in Genetics. 12: 683632. PMID 34795689 DOI: 10.3389/fgene.2021.683632 |
0.309 |
|
| 2021 |
Núñez-Carpintero I, Petrizzelli M, Zinovyev A, Cirillo D, Valencia A. The multilayer community structure of medulloblastoma. Iscience. 24: 102365. PMID 33889829 DOI: 10.1016/j.isci.2021.102365 |
0.458 |
|
| 2021 |
Petrizzelli M, Merlevede J, Zinovyev A. Systems Biology Analysis for Ewing Sarcoma. Methods in Molecular Biology (Clifton, N.J.). 2226: 303-333. PMID 33326111 DOI: 10.1007/978-1-0716-1020-6_23 |
0.311 |
|
| 2020 |
Albergante L, Mirkes E, Bac J, Chen H, Martin A, Faure L, Barillot E, Pinello L, Gorban A, Zinovyev A. Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph. Entropy (Basel, Switzerland). 22. PMID 33286070 DOI: 10.3390/e22030296 |
0.475 |
|
| 2020 |
Kondratova M, Barillot E, Zinovyev A, Calzone L. Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response. Cancers. 12. PMID 33276543 DOI: 10.3390/cancers12123600 |
0.692 |
|
| 2020 |
Golovenkin SE, Bac J, Chervov A, Mirkes EM, Orlova YV, Barillot E, Gorban AN, Zinovyev A. Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data. Gigascience. 9. PMID 33241287 DOI: 10.1093/gigascience/giaa128 |
0.464 |
|
| 2020 |
Balaur I, Roy L, Mazein A, Karaca SG, Dogrusoz U, Barillot E, Zinovyev A. cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinformatics (Oxford, England). PMID 33146381 DOI: 10.1093/bioinformatics/btaa528 |
0.411 |
|
| 2020 |
Koltai M, Noel V, Zinovyev A, Calzone L, Barillot E. Exact solving and sensitivity analysis of stochastic continuous time Boolean models. Bmc Bioinformatics. 21: 241. PMID 32527218 DOI: 10.1186/S12859-020-03548-9 |
0.685 |
|
| 2020 |
Ravel JM, Monraz Gomez LC, Sompairac N, Calzone L, Zhivotovsky B, Kroemer G, Barillot E, Zinovyev A, Kuperstein I. Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases. Cancers. 12. PMID 32316560 DOI: 10.3390/Cancers12040990 |
0.763 |
|
| 2020 |
Zinovyev A, Czerwinska U, Cantini L, Barillot E, Frahm KM, Shepelyansky DL. Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network. Plos Computational Biology. 16: e1007652. PMID 32069277 DOI: 10.1371/Journal.Pcbi.1007652 |
0.525 |
|
| 2020 |
Aynaud MM, Mirabeau O, Gruel N, Grossetête S, Boeva V, Durand S, Surdez D, Saulnier O, Zaïdi S, Gribkova S, Fouché A, Kairov U, Raynal V, Tirode F, Grünewald TGP, ... ... Zinovyev A, et al. Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution. Cell Reports. 30: 1767-1779.e6. PMID 32049009 DOI: 10.1016/J.Celrep.2020.01.049 |
0.575 |
|
| 2020 |
Balaur I, Roy L, Mazein A, Karaca SG, Dogrusoz U, Barillot E, Zinovyev A. cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinformatics (Oxford, England). PMID 31904823 DOI: 10.1093/Bioinformatics/Btz969 |
0.522 |
|
| 2020 |
Colaprico A, Olsen C, Bailey MH, Odom GJ, Terkelsen T, Silva TC, Olsen AV, Cantini L, Zinovyev A, Barillot E, Noushmehr H, Bertoli G, Castiglioni I, Cava C, Bontempi G, et al. Interpreting pathways to discover cancer driver genes with Moonlight. Nature Communications. 11: 69. PMID 31900418 DOI: 10.1038/S41467-019-13803-0 |
0.527 |
|
| 2019 |
Gorban AN, Harel-Bellan A, Morozova N, Zinovyev A. Basic, simple and extendable kinetic model of protein synthesis. Mathematical Biosciences and Engineering : Mbe. 16: 6602-6622. PMID 31698578 DOI: 10.3934/Mbe.2019329 |
0.333 |
|
| 2019 |
Kondratova M, Czerwinska U, Sompairac N, Amigorena SD, Soumelis V, Barillot E, Zinovyev A, Kuperstein I. A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures. Nature Communications. 10: 4808. PMID 31641119 DOI: 10.1038/S41467-019-12270-X |
0.604 |
|
| 2019 |
Nazarov PV, Wienecke-Baldacchino AK, Zinovyev A, Czerwińska U, Muller A, Nashan D, Dittmar G, Azuaje F, Kreis S. Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients. Bmc Medical Genomics. 12: 132. PMID 31533822 DOI: 10.1186/S12920-019-0578-4 |
0.377 |
|
| 2019 |
Sompairac N, Nazarov PV, Czerwinska U, Cantini L, Biton A, Molkenov A, Zhumadilov Z, Barillot E, Radvanyi F, Gorban A, Kairov U, Zinovyev A. Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets. International Journal of Molecular Sciences. 20. PMID 31500324 DOI: 10.3390/Ijms20184414 |
0.584 |
|
| 2019 |
Greco A, Sanchez Valle J, Pancaldi V, Baudot A, Barillot E, Caselle M, Valencia A, Zinovyev A, Cantini L. Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization. International Journal of Molecular Sciences. 20. PMID 31247897 DOI: 10.3390/Ijms20133114 |
0.635 |
|
| 2019 |
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. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nature Communications. 10: 1903. PMID 31015418 DOI: 10.1038/S41467-019-09670-4 |
0.35 |
|
| 2019 |
Sompairac N, Modamio J, Barillot E, Fleming RMT, Zinovyev A, Kuperstein I. Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer. Bmc Bioinformatics. 20: 140. PMID 30999838 DOI: 10.1186/S12859-019-2682-Z |
0.525 |
|
| 2019 |
Cantini L, Kairov U, de Reyniès A, Barillot E, Radvanyi F, Zinovyev A. Assessing reproducibility of matrix factorization methods in independent transcriptomes. Bioinformatics (Oxford, England). PMID 30938767 DOI: 10.1093/Bioinformatics/Btz225 |
0.452 |
|
| 2019 |
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, ... ... Zinovyev A, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols. PMID 30787451 DOI: 10.1038/S41596-018-0098-2 |
0.415 |
|
| 2019 |
Cantini L, Bertoli G, Cava C, Dubois T, Zinovyev A, Caselle M, Castiglioni I, Barillot E, Martignetti L. Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer. Nucleic Acids Research. PMID 30657980 DOI: 10.1093/Nar/Gkz016 |
0.532 |
|
| 2018 |
Letort G, Montagud A, Stoll G, Heiland R, Barillot E, Macklin P, Zinovyev A, Calzone L. PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. Bioinformatics (Oxford, England). PMID 30169736 DOI: 10.1093/Bioinformatics/Bty766 |
0.784 |
|
| 2018 |
Levy N, Naldi A, Hernandez C, Stoll G, Thieffry D, Zinovyev A, Calzone L, Paulevé L. Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial). Frontiers in Physiology. 9: 787. PMID 30034343 DOI: 10.1101/319780 |
0.694 |
|
| 2018 |
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. The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. Frontiers in Physiology. 9: 680. PMID 29971009 DOI: 10.3389/Fphys.2018.00680 |
0.684 |
|
| 2018 |
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, ... ... Zinovyev A, et al. Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. Npj Systems Biology and Applications. 4: 21. PMID 29872544 DOI: 10.1038/s41540-018-0059-y |
0.493 |
|
| 2018 |
Monraz Gomez LC, Kondratova M, Ravel JM, Barillot E, Zinovyev A, Kuperstein I. Application of Atlas of Cancer Signalling Network in preclinical studies. Briefings in Bioinformatics. PMID 29726961 DOI: 10.1093/Bib/Bby031 |
0.583 |
|
| 2018 |
Kondratova M, Sompairac N, Barillot E, Zinovyev A, Kuperstein I. Signalling maps in cancer research: construction and data analysis. Database : the Journal of Biological Databases and Curation. 2018. PMID 29688383 DOI: 10.1093/Database/Bay036 |
0.528 |
|
| 2018 |
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, et al. Community-driven roadmap for integrated disease maps. Briefings in Bioinformatics. PMID 29688273 DOI: 10.1093/Bib/Bby024 |
0.522 |
|
| 2018 |
Lages J, Shepelyansky DL, Zinovyev A. Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks. Plos One. 13: e0190812. PMID 29370181 DOI: 10.1371/Journal.Pone.0190812 |
0.383 |
|
| 2018 |
Cantini L, Calzone L, Martignetti L, Rydenfelt M, Blüthgen N, Barillot E, Zinovyev A. Classification of gene signatures for their information value and functional redundancy. Npj Systems Biology and Applications. 4: 2. PMID 29263798 DOI: 10.1038/s41540-017-0038-8 |
0.71 |
|
| 2018 |
Calzone L, Barillot E, Zinovyev A. Logical versus kinetic modeling of biological networks: applications in cancer research Current Opinion in Chemical Engineering. 21: 22-31. DOI: 10.1016/J.Coche.2018.02.005 |
0.64 |
|
| 2017 |
Montagud A, Traynard P, Martignetti L, Bonnet E, Barillot E, Zinovyev A, Calzone L. Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. Briefings in Bioinformatics. PMID 29237040 DOI: 10.1093/Bib/Bbx163 |
0.811 |
|
| 2017 |
Kairov U, Cantini L, Greco A, Molkenov A, Czerwinska U, Barillot E, Zinovyev A. Determining the optimal number of independent components for reproducible transcriptomic data analysis. Bmc Genomics. 18: 712. PMID 28893186 DOI: 10.1186/S12864-017-4112-9 |
0.551 |
|
| 2017 |
Stoll G, Caron B, Viara E, Dugourd A, Zinovyev A, Naldi A, Kroemer G, Barillot E, Calzone L. MaBoSS 2.0: an environment for stochastic Boolean modeling. Bioinformatics (Oxford, England). 33: 2226-2228. PMID 28881959 DOI: 10.1093/Bioinformatics/Btx123 |
0.726 |
|
| 2017 |
Dorel M, Viara E, Barillot E, Zinovyev A, Kuperstein I. NaviCom: a web application to create interactive molecular network portraits using multi-level omics data. Database : the Journal of Biological Databases and Curation. 2017. PMID 28415074 DOI: 10.1093/Database/Bax026 |
0.577 |
|
| 2017 |
Cantini L, Caselle M, Forget A, Zinovyev A, Barillot E, Martignetti L. A review of computational approaches detecting microRNAs involved in cancer. Frontiers in Bioscience (Landmark Edition). 22: 1774-1791. PMID 28410145 DOI: 10.2741/4571 |
0.533 |
|
| 2016 |
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. Drug Driven Synthetic Lethality: bypassing tumor cell genetics with a combination of Dbait and PARP inhibitors. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 27559053 DOI: 10.1158/1078-0432.Ccr-16-1193 |
0.531 |
|
| 2016 |
Martignetti L, Calzone L, Bonnet E, Barillot E, Zinovyev A. ROMA: Representation and Quantification of Module Activity from Target Expression Data. Frontiers in Genetics. 7: 18. PMID 26925094 DOI: 10.3389/Fgene.2016.00018 |
0.719 |
|
| 2016 |
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, ... ... Zinovyev A, et al. The second European interdisciplinary Ewing sarcoma research summit - A joint effort to deconstructing the multiple layers of a complex disease. Oncotarget. PMID 26802024 DOI: 10.18632/Oncotarget.6937 |
0.37 |
|
| 2016 |
Cantini L, Barillot E, Radvanyi F, Zinovyev A. Independent component analysis (ICA) unveils the landscape of multi-omics pancancer data F1000research. 5. DOI: 10.7490/F1000Research.1112804.1 |
0.529 |
|
| 2016 |
Czerwińska U, Barillot E, Soumelis V, Zinovyev A. Deconvolution of cell and environment specific signals and their interactions from complex mixtures in biological samples F1000research. 5. DOI: 10.7490/F1000Research.1112649.1 |
0.547 |
|
| 2016 |
Deveau P, Barillot E, Boeva V, Zinovyev A, Bonnet E. Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages The R Journal. 8: 293. DOI: 10.32614/Rj-2016-047 |
0.485 |
|
| 2016 |
Dutreix M, Jdey W, Thierry S, Devun F, Kuperstein I, Zinovyev A, Barillot E. Drugs driven synthetic lethality: getting rid of tumor genetics with combination of Dbait and PARP inhibitors European Journal of Cancer. 61: S115. DOI: 10.1016/S0959-8049(16)61407-7 |
0.5 |
|
| 2015 |
Cohen DP, Martignetti L, Robine S, Barillot E, Zinovyev A, Calzone L. Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration. Plos Computational Biology. 11: e1004571. PMID 26528548 DOI: 10.1371/Journal.Pcbi.1004571 |
0.739 |
|
| 2015 |
Czerwinska U, Calzone L, Barillot E, Zinovyev A. DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. Bmc Systems Biology. 9: 46. PMID 26271256 DOI: 10.1186/S12918-015-0189-4 |
0.715 |
|
| 2015 |
Remy E, Rebouissou S, Chaouiya C, Zinovyev A, Radvanyi F, Calzone L. A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis. Cancer Research. 75: 4042-52. PMID 26238783 DOI: 10.1158/0008-5472.Can-15-0602 |
0.678 |
|
| 2015 |
Dorel M, Barillot E, Zinovyev A, Kuperstein I. Network-based approaches for drug response prediction and targeted therapy development in cancer. Biochemical and Biophysical Research Communications. 464: 386-91. PMID 26086105 DOI: 10.1016/J.Bbrc.2015.06.094 |
0.597 |
|
| 2015 |
Kuperstein I, Robine S, Zinovyev A. Network biology elucidates metastatic colon cancer mechanisms. Cell Cycle (Georgetown, Tex.). 14: 2189-90. PMID 26083805 DOI: 10.1080/15384101.2015.1060816 |
0.435 |
|
| 2015 |
Martignetti L, Tesson B, Almeida A, Zinovyev A, Tucker GC, Dubois T, Barillot E. Detection of miRNA regulatory effect on triple negative breast cancer transcriptome. Bmc Genomics. 16: S4. PMID 26046581 DOI: 10.1186/1471-2164-16-S6-S4 |
0.543 |
|
| 2015 |
Calzone L, Barillot E, Zinovyev A. Predicting genetic interactions from Boolean models of biological networks. Integrative Biology : Quantitative Biosciences From Nano to Macro. 7: 921-9. PMID 25958956 DOI: 10.1039/C5Ib00029G |
0.749 |
|
| 2015 |
Bonnet E, Viara E, Kuperstein I, Calzone L, Cohen DP, Barillot E, Zinovyev A. NaviCell Web Service for network-based data visualization. Nucleic Acids Research. 43: W560-5. PMID 25958393 DOI: 10.1093/Nar/Gkv450 |
0.713 |
|
| 2015 |
Kuperstein I, Grieco L, Cohen DP, Thieffry D, Zinovyev A, Barillot E. The shortest path is not the one you know: application of biological network resources in precision oncology research. Mutagenesis. 30: 191-204. PMID 25688112 DOI: 10.1093/Mutage/Geu078 |
0.645 |
|
| 2015 |
Zinovyev A. Overcoming Complexity of Biological Systems: from Data Analysis to Mathematical Modeling Mathematical Modelling of Natural Phenomena. 10: 186-205. DOI: 10.1051/Mmnp/201510314 |
0.385 |
|
| 2014 |
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, ... ... Zinovyev A, et al. Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes. Cell Reports. 9: 1235-45. PMID 25456126 DOI: 10.1016/J.Celrep.2014.10.035 |
0.575 |
|
| 2014 |
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, ... ... Zinovyev A, et al. Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut. Nature Communications. 5: 5005. PMID 25295490 DOI: 10.1038/Ncomms6005 |
0.577 |
|
| 2014 |
Calzone L, Kuperstein I, Cohen D, Grieco L, Bonnet E, Servant N, Hupé P, Zinovyev A, Barillot E. [Biological network modelling and precision medicine in oncology]. Bulletin Du Cancer. 101: S18-21. PMID 24966078 DOI: 10.1684/Bdc.2014.1973 |
0.745 |
|
| 2013 |
Kuperstein I, Cohen DP, Pook S, Viara E, Calzone L, Barillot E, Zinovyev A. NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. Bmc Systems Biology. 7: 100. PMID 24099179 DOI: 10.1186/1752-0509-7-100 |
0.701 |
|
| 2013 |
Stoll G, Surdez D, Tirode F, Laud K, Barillot E, Zinovyev A, Delattre O. Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis. Nucleic Acids Research. 41: 8853-71. PMID 23935076 DOI: 10.1093/Nar/Gkt678 |
0.629 |
|
| 2013 |
Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A. Practical use of BiNoM: a biological network manager software. Methods in Molecular Biology (Clifton, N.J.). 1021: 127-46. PMID 23715983 DOI: 10.1007/978-1-62703-450-0_7 |
0.742 |
|
| 2013 |
Cohen D, Kuperstein I, Barillot E, Zinovyev A, Calzone L. From a biological hypothesis to the construction of a mathematical model. Methods in Molecular Biology (Clifton, N.J.). 1021: 107-25. PMID 23715982 DOI: 10.1007/978-1-62703-450-0_6 |
0.739 |
|
| 2013 |
Vera-Licona P, Bonnet E, Barillot E, Zinovyev A. OCSANA: optimal combinations of interventions from network analysis. Bioinformatics (Oxford, England). 29: 1571-3. PMID 23626000 DOI: 10.1093/Bioinformatics/Btt195 |
0.491 |
|
| 2013 |
Zinovyev A, Kuperstein I, Barillot E, Heyer WD. Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps. Plos Computational Biology. 9: e1003016. PMID 23592964 DOI: 10.1371/Journal.Pcbi.1003016 |
0.545 |
|
| 2013 |
Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A. BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. Bmc Systems Biology. 7: 18. PMID 23453054 DOI: 10.1186/1752-0509-7-18 |
0.728 |
|
| 2013 |
Zinovyev A, Calzone L, Fourquet S, Barillot E. How cell decides between life and death: Mathematical modeling of epigenetic landscapes of cellular fates Springer Proceedings in Mathematics. 15: 191-204. DOI: 10.1007/978-3-642-20164-6_16 |
0.696 |
|
| 2013 |
Calzone L, Zinovyev A, Zhivotovsky B. Understanding different types of cell death using systems biology Systems Biology of Apoptosis. 125-143. DOI: 10.1007/978-1-4614-4009-3_6 |
0.604 |
|
| 2012 |
Kairov U, Karpenyuk T, Ramanculov E, Zinovyev A. Network analysis of gene lists for finding reproducible prognostic breast cancer gene signatures. Bioinformation. 8: 773-6. PMID 23055628 DOI: 10.6026/97320630008773 |
0.356 |
|
| 2012 |
Morozova N, Zinovyev A, Nonne N, Pritchard LL, Gorban AN, Harel-Bellan A. Kinetic signatures of microRNA modes of action. Rna (New York, N.Y.). 18: 1635-55. PMID 22850425 DOI: 10.1261/Rna.032284.112 |
0.307 |
|
| 2012 |
Martignetti L, Laud-Duval K, Tirode F, Pierron G, Reynaud S, Barillot E, Delattre O, Zinovyev A. Antagonism pattern detection between microRNA and target expression in Ewing's sarcoma. Plos One. 7: e41770. PMID 22848594 DOI: 10.1371/Journal.Pone.0041770 |
0.508 |
|
| 2012 |
Martignetti L, Zinovyev A, Barillot E. Identification of shortened 3' untranslated regions from expression arrays. Journal of Bioinformatics and Computational Biology. 10: 1241001. PMID 22809337 DOI: 10.1142/S0219720012410016 |
0.52 |
|
| 2012 |
Zinovyev A, Fourquet S, Tournier L, Calzone L, Barillot E. Cell death and life in cancer: mathematical modeling of cell fate decisions. Advances in Experimental Medicine and Biology. 736: 261-74. PMID 22161334 DOI: 10.1007/978-1-4419-7210-1_15 |
0.742 |
|
| 2012 |
Radulescu O, Gorban AN, Zinovyev A, Noel V. Reduction of dynamical biochemical reactions networks in computational biology Frontiers in Genetics. 3. DOI: 10.3389/Fgene.2012.00131 |
0.412 |
|
| 2012 |
Martignetti L, Laud-Duval K, Tirode F, Pierron G, Reynaud S, Barillot E, Delattre O, Zinovyev A. Two different relationships can be distinguished between the expression of a given miRNA and a target. Plos One. DOI: 10.1371/Journal.Pone.0041770.G001 |
0.485 |
|
| 2012 |
Vera-Licona P, Zinovyev A, Bonnet E, Kupperstein I, Kel-Margoulis O, Kel-Margoulis A, Dubois T, Tucker G, Barillot E. Abstract A13: A signaling pathway rationale for the design of combination therapies for cancer Cancer Research. 72. DOI: 10.1158/1538-7445.Csb12-A13 |
0.619 |
|
| 2012 |
Pinna G, Zinovyev A, Araujo N, Morozova N, Harel-Bellan A. Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells Mathematical Modelling of Natural Phenomena. 7: 337-368. DOI: 10.1051/Mmnp/20127115 |
0.444 |
|
| 2012 |
Calzone L, Remy E, Coffin F, Radvanyi F, Rebouissou S, Zinovyev A, Barillot E, Chaouiya C. 656 Mathematical Modeling of Bladder Tumorigenesis European Journal of Cancer. 48: S155-S156. DOI: 10.1016/S0959-8049(12)71303-5 |
0.548 |
|
| 2012 |
Vera-Licona P, Zinovyev A, Bonnet E, Kuperstein I, Kel O, Kel A, Dubois T, Tucker G, Barillot E. 650 A Pathway-based Design of Rational Combination Therapies for Cancer European Journal of Cancer. 48: S154. DOI: 10.1016/S0959-8049(12)71297-2 |
0.535 |
|
| 2012 |
Martignetti L, Laud-Duval K, Tirode F, Barillot E, Delattre O, Zinovyev A. 648 Identification of Shortened 3 Untranslated Regions and Impact on MicroRNA Regulation European Journal of Cancer. 48. DOI: 10.1016/S0959-8049(12)71296-0 |
0.484 |
|
| 2012 |
Kuperstein I, Zinovyev A, Cohen D, Fourquet S, Calzone L, Pook S, Vera-Licona P, Bonnet E, Rovera D, Barillot E. 640 Towards of Atlas of Cancer Signaling Networks – Basis for the Institut Curie Systems Biology Platform for Data Analysis and Interpretation European Journal of Cancer. 48: S152. DOI: 10.1016/S0959-8049(12)71288-1 |
0.606 |
|
| 2012 |
Kuperstein I, Zinovyev A, Barillot E, Heyer W. 639 Mathematical Modeling of Synthetic Lethality With Applications to DNA Repair European Journal of Cancer. 48: S151-S152. DOI: 10.1016/S0959-8049(12)71287-X |
0.513 |
|
| 2012 |
Stoll G, Surdez D, Barillot E, Delattre O, Zinovyev A. 463 Constructing Therapeutic Strategies for Ewing Sarcoma by Systems Biology Approach European Journal of Cancer. 48: S111. DOI: 10.1016/S0959-8049(12)71136-X |
0.525 |
|
| 2011 |
Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, Barillot E. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics (Oxford, England). 27: 268-9. PMID 21081509 DOI: 10.1093/Bioinformatics/Btq635 |
0.547 |
|
| 2011 |
Boeva V, Zeitouni B, Bleakley K, Zinovyev A, Vert J, Janoueix-Lerosey I, Delattre O, Barillot E. Getting maximum information from your paired-end reads: A package for accurate detection of copy number alterations F1000research. 2. DOI: 10.7490/F1000Research.1933.1 |
0.491 |
|
| 2010 |
Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A. Mathematical modelling of cell-fate decision in response to death receptor engagement. Plos Computational Biology. 6: e1000702. PMID 20221256 DOI: 10.1371/Journal.Pcbi.1000702 |
0.729 |
|
| 2010 |
Zinovyev A, Morozova N, Nonne N, Barillot E, Harel-Bellan A, Gorban AN. Dynamical modeling of microRNA action on the protein translation process. Bmc Systems Biology. 4: 13. PMID 20181238 DOI: 10.1186/1752-0509-4-13 |
0.489 |
|
| 2010 |
Zinovyev A. BiNoM Cytoscape Plugin for constructing, querying and analyzing biological networks, using systems biology standards Nature Precedings. 1-1. DOI: 10.1038/Npre.2010.5120.1 |
0.366 |
|
| 2010 |
Kuperstein I, Vera-Licona P, Zinovyev A, Tucker G, Dubois T, Barillot E. 826 Integrated cell cycle and DNA repair signalling network modelling for identification of key molecular regulators in basal-like breast cancer European Journal of Cancer Supplements. 8: 208-209. DOI: 10.1016/S1359-6349(10)71622-0 |
0.593 |
|
| 2009 |
Barillot E, Calzone L, Zinovyev A. [Systems biology of cancer]. MéDecine Sciences : M/S. 25: 601-7. PMID 19602357 DOI: 10.1051/Medsci/2009256-7601 |
0.757 |
|
| 2009 |
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, ... ... Zinovyev A, et al. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Molecular Oncology. 3: 9-17. PMID 19383362 DOI: 10.1016/J.Molonc.2008.11.003 |
0.603 |
|
| 2009 |
Surdez D, Stoll G, Tirode F, Laud K, Zinovyev A, Barillot E, Delattre O. Abstract B71: A systems biology approach to study Ewing's sarcoma Cancer Research. 69. DOI: 10.1158/0008-5472.Fbcr09-B71 |
0.637 |
|
| 2008 |
Calzone L, Gelay A, Zinovyev A, Radvanyi F, Barillot E. A comprehensive modular map of molecular interactions in RB/E2F pathway. Molecular Systems Biology. 4: 173. PMID 18319725 DOI: 10.1038/Msb.2008.7 |
0.757 |
|
| 2008 |
Zinovyev A, Viara E, Calzone L, Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics (Oxford, England). 24: 876-7. PMID 18024474 DOI: 10.1093/Bioinformatics/Btm553 |
0.716 |
|
| 2007 |
Rapaport F, Zinovyev A, Dutreix M, Barillot E, Vert JP. Classification of microarray data using gene networks. Bmc Bioinformatics. 8: 35. PMID 17270037 DOI: 10.1186/1471-2105-8-35 |
0.547 |
|
| 2006 |
Gorban A, Karlin I, Zinovyev A. Invariant grids: Method of complexity reduction in reaction networks Complexus. 2: 110-127. DOI: 10.1159/000093684 |
0.314 |
|
| Show low-probability matches. |