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Laurence Calzone, Ph.D. - Publications

Affiliations: 
2003 Virginia Polytechnic Institute and State University, Blacksburg, VA, United States 
Area:
cell cycle modeling
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62 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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
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