Year |
Citation |
Score |
2024 |
Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, ... ... Calzone L, et al. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology. 14: 1282859. PMID 38414974 DOI: 10.3389/fimmu.2023.1282859 |
0.415 |
|
2024 |
Tsirvouli E, Noël V, Flobak Å, Calzone L, Kuiper M. Dynamic Boolean modeling of molecular and cellular interactions in psoriasis predicts drug target candidates. Iscience. 27: 108859. PMID 38303723 DOI: 10.1016/j.isci.2024.108859 |
0.333 |
|
2023 |
Ponce-de-Leon M, Montagud A, Noël V, Meert A, Pradas G, Barillot E, Calzone L, Valencia A. PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks. Npj Systems Biology and Applications. 9: 54. PMID 37903760 DOI: 10.1038/s41540-023-00314-4 |
0.821 |
|
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 |
0.795 |
|
2023 |
Calzone L, Noël V, Barillot E, Kroemer G, Stoll G. Corrigendum to "Modeling signaling pathways in biology with MaBoSS: From one single cell to a dynamic population of heterogeneous interacting cells" [Comput. Struct. Biotechnol. 20 (2022) 5661-5671]. Computational and Structural Biotechnology Journal. 21: 3158. PMID 37287810 DOI: 10.1016/j.csbj.2023.05.021 |
0.744 |
|
2022 |
Calzone L, Noël V, Barillot E, Kroemer G, Stoll G. Modeling signaling pathways in biology with MaBoSS: From one single cell to a dynamic population of heterogeneous interacting cells. Computational and Structural Biotechnology Journal. 20: 5661-5671. PMID 36284705 DOI: 10.1016/j.csbj.2022.10.003 |
0.795 |
|
2022 |
Niarakis A, Waltemath D, Glazier J, Schreiber F, Keating SM, Nickerson D, Chaouiya C, Siegel A, Noël V, Hermjakob H, Helikar T, Soliman S, Calzone L. Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings in Bioinformatics. PMID 35671510 DOI: 10.1093/bib/bbac212 |
0.683 |
|
2022 |
Stoll G, Naldi A, Noël V, Viara E, Barillot E, Kroemer G, Thieffry D, Calzone L. UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling. Frontiers in Molecular Biosciences. 9: 800152. PMID 35309516 DOI: 10.3389/fmolb.2022.800152 |
0.762 |
|
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 |
|
2022 |
Montagud A, Béal J, Tobalina L, Traynard P, Subramanian V, Szalai B, Alföldi R, Puskás L, Valencia A, Barillot E, Saez-Rodriguez J, Calzone L. Patient-specific Boolean models of signalling networks guide personalised treatments. Elife. 11. PMID 35164900 DOI: 10.7554/eLife.72626 |
0.794 |
|
2021 |
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, ... ... Calzone L, et al. COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology. 17: e10851. PMID 34939300 DOI: 10.15252/msb.202110851 |
0.747 |
|
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 |
0.808 |
|
2021 |
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, ... ... Calzone L, et al. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology. 17: e10387. PMID 34664389 DOI: 10.15252/msb.202110387 |
0.787 |
|
2021 |
Béal J, Pantolini L, Noël V, Barillot E, Calzone L. Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers. Plos Computational Biology. 17: e1007900. PMID 33507915 DOI: 10.1371/journal.pcbi.1007900 |
0.777 |
|
2020 |
Checcoli A, Pol JG, Naldi A, Noel V, Barillot E, Kroemer G, Thieffry D, Calzone L, Stoll G. Dynamical Boolean Modeling of Immunogenic Cell Death. Frontiers in Physiology. 11: 590479. PMID 33281620 DOI: 10.3389/fphys.2020.590479 |
0.764 |
|
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 |
0.676 |
|
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 |
0.774 |
|
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 |
0.727 |
|
2020 |
Niarakis A, Kuiper M, Ostaszewski M, Malik Sheriff RS, Casals-Casas C, Thieffry D, Freeman TC, Thomas P, Touré V, Noël V, Stoll G, Saez-Rodriguez J, Naldi A, Oshurko E, Xenarios I, ... ... Calzone L, et al. Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. Briefings in Bioinformatics. PMID 32313939 DOI: 10.1093/Bib/Bbaa046 |
0.735 |
|
2019 |
Vanacker H, Angevin E, Hollebecque A, Sun R, Deutsch E, Zynovyev A, Calzone L, Barillot E, Massard C, Verlingue L. Enhanced performance of prognostic estimation from TCGA RNAseq data using transfer learning Annals of Oncology. 30: v52. DOI: 10.1093/Annonc/Mdz239.073 |
0.474 |
|
2018 |
Béal J, Montagud A, Traynard P, Barillot E, Calzone L. Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients. Frontiers in Physiology. 9: 1965. PMID 30733688 DOI: 10.3389/Fphys.2018.01965 |
0.809 |
|
2018 |
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, et al. Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling. Cancer Cell. 34: 379-395.e7. PMID 30205043 DOI: 10.1016/J.Ccell.2018.08.002 |
0.761 |
|
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 |
0.799 |
|
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 |
0.661 |
|
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 |
0.66 |
|
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 |
0.669 |
|
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 |
0.819 |
|
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 |
0.736 |
|
2017 |
Zhong Q, Guo T, Toussaint N, Wagner U, Charmpi K, Calzone L, Beyer A, Aebersold R, Wild PJ. Abstract 5565: Multi-omic profiling of prostate cancer evolution in 39 patients Cancer Research. 77: 5565-5565. DOI: 10.1158/1538-7445.Am2017-5565 |
0.326 |
|
2017 |
Forget A, Loredana M, Brabetz S, Picard D, Puget S, Calzone L, Poullet P, Montagud A, Liva S, Dingli F, Arras G, Yu H, Mercier A, Pouponnot C, Loew D, et al. CSIG-15. PROTEOMIC AND PHOSPHOPROTEOMIC ANALYSIS OF HUMAN MEDULLOBLASTOMA REVEALS DISTINCT ACTIVATED PATHWAYS BETWEEN SUBGROUPS Neuro-Oncology. 19: vi52-vi53. DOI: 10.1093/Neuonc/Nox168.209 |
0.752 |
|
2016 |
Verlingue L, Dugourd A, Stoll G, Barillot E, Calzone L, Londoño-Vallejo A. A comprehensive approach to the molecular determinants of lifespan using a Boolean model of geroconversion. Aging Cell. PMID 27613445 DOI: 10.1111/Acel.12504 |
0.58 |
|
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 |
0.692 |
|
2016 |
Verlingue L, Calzone L, Kamal M, Servant N, Belin L, Barillot E, Tourneau CL. Abstract 1509:In silicoprediction of the clinical response to the mTOR inhibitor everolimus using a Boolean model: validation from a cohort of the SHIVA trial Cancer Research. 76: 1509-1509. DOI: 10.1158/1538-7445.Am2016-1509 |
0.617 |
|
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 |
0.755 |
|
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 |
0.704 |
|
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 |
0.617 |
|
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 |
0.752 |
|
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 |
0.706 |
|
2015 |
Bonnet E, Calzone L, Michoel T. Integrative multi-omics module network inference with Lemon-Tree. Plos Computational Biology. 11: e1003983. PMID 25679508 DOI: 10.1371/Journal.Pcbi.1003983 |
0.384 |
|
2015 |
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. Atlas of Cancer Signalling Network: A systems biology resource for integrative analysis of cancer data with Google Maps Oncogenesis. 4. DOI: 10.1038/oncsis.2015.19 |
0.554 |
|
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 |
0.73 |
|
2013 |
Grieco L, Calzone L, Bernard-Pierrot I, Radvanyi F, Kahn-Perlès B, Thieffry D. Integrative modelling of the influence of MAPK network on cancer cell fate decision. Plos Computational Biology. 9: e1003286. PMID 24250280 DOI: 10.1371/Journal.Pcbi.1003286 |
0.499 |
|
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 |
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 |
0.718 |
|
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 |
0.748 |
|
2013 |
Comet JP, Noual M, Richard A, Aracena J, Calzone L, Demongeot J, Kaufman M, Naldi A, Snoussi el H, Thieffry D. On circuit functionality in Boolean networks. Bulletin of Mathematical Biology. 75: 906-19. PMID 23504387 DOI: 10.1007/S11538-013-9829-2 |
0.32 |
|
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 |
0.723 |
|
2013 |
Grieco L, Calzone L, Bernard-Pierrot I, Radvanyi F, Kahn-Perlès B, Thieffry D. Correction: Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision Plos Computational Biology. 9. DOI: 10.1371/Annotation/90E5E4Be-952B-42B8-B56D-46Baae3479Ed |
0.369 |
|
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 |
0.69 |
|
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 |
0.554 |
|
2012 |
Stoll G, Viara E, Barillot E, Calzone L. Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm. Bmc Systems Biology. 6: 116. PMID 22932419 DOI: 10.1186/1752-0509-6-116 |
0.631 |
|
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 |
0.739 |
|
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 |
0.756 |
|
2009 |
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, ... ... Calzone L, et al. The Systems Biology Graphical Notation. Nature Biotechnology. 27: 735-41. PMID 19668183 DOI: 10.1038/Nbt.1558 |
0.372 |
|
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 |
0.735 |
|
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 |
0.744 |
|
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 |
0.708 |
|
2007 |
Calzone L, Thieffry D, Tyson JJ, Novak B. Dynamical modeling of syncytial mitotic cycles in Drosophila embryos. Molecular Systems Biology. 3: 131. PMID 17667953 DOI: 10.1038/Msb4100171 |
0.692 |
|
2007 |
Calzone L, Chabrier-Rivier N, Fages F, Fosse L, Soliman S. Langages formels dans la machine abstraite biochimique BIOCHAM Technique Et Science Informatiques. 26: 47-72. DOI: 10.3166/Tsi.26.47-72 |
0.306 |
|
2006 |
Calzone L, Fages F, Soliman S. BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics (Oxford, England). 22: 1805-7. PMID 16672256 DOI: 10.1093/Bioinformatics/Btl172 |
0.474 |
|
2004 |
Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ. Integrative analysis of cell cycle control in budding yeast. Molecular Biology of the Cell. 15: 3841-62. PMID 15169868 DOI: 10.1091/Mbc.E03-11-0794 |
0.809 |
|
2003 |
Allen NA, Calzone L, Chen KC, Ciliberto A, Ramakrishnan N, Shaffer CA, Sible JC, Tyson JJ, Vass MT, Watson LT, Zwolak JW. Modeling regulatory networks at Virginia Tech. Omics : a Journal of Integrative Biology. 7: 285-99. PMID 14583117 DOI: 10.1089/153623103322452404 |
0.821 |
|
Show low-probability matches. |