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For: Béal J, Montagud A, Traynard P, Barillot E, Calzone L. Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients. Front Physiol 2018;9:1965. [PMID: 30733688 DOI: 10.3389/fphys.2018.01965] [Cited by in Crossref: 41] [Cited by in F6Publishing: 42] [Article Influence: 10.3] [Reference Citation Analysis]
Number Citing Articles
1 He X, Liu X, Zuo F, Shi H, Jing J. Artificial intelligence-based multi-omics analysis fuels cancer precision medicine. Semin Cancer Biol 2023;88:187-200. [PMID: 36596352 DOI: 10.1016/j.semcancer.2022.12.009] [Reference Citation Analysis]
2 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. Comput Struct Biotechnol J 2022;20:5661-71. [PMID: 36284705 DOI: 10.1016/j.csbj.2022.10.003] [Reference Citation Analysis]
3 Bhavani GS, Palanisamy A. SNAIL driven by a feed forward loop motif promotes TGFβinduced epithelial to mesenchymal transition. Biomed Phys Eng Express 2022;8. [PMID: 35700712 DOI: 10.1088/2057-1976/ac7896] [Reference Citation Analysis]
4 Ponce-de-leon M, Montagud A, Noël V, Pradas G, Meert A, Barillot E, Calzone L, Valencia A. PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks.. [DOI: 10.1101/2022.01.06.468363] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
5 Réda C, Delahaye-duriez A. Prioritization of Candidate Genes Through Boolean Networks. Computational Methods in Systems Biology 2022. [DOI: 10.1007/978-3-031-15034-0_5] [Reference Citation Analysis]
6 Marazzi L, Shah M, Balakrishnan S, Patil A, Vera-licona P. NETISCE: A Network-Based Tool for Cell Fate Reprogramming.. [DOI: 10.1101/2021.12.30.474582] [Reference Citation Analysis]
7 Rocca A, Kholodenko BN. Can Systems Biology Advance Clinical Precision Oncology? Cancers (Basel) 2021;13:6312. [PMID: 34944932 DOI: 10.3390/cancers13246312] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
8 Gondal MN, Chaudhary SU. Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. Front Oncol 2021;11:712505. [PMID: 34900668 DOI: 10.3389/fonc.2021.712505] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.5] [Reference Citation Analysis]
9 Noël V, Ruscone M, Stoll G, Viara E, Zinovyev A, Barillot E, Calzone L. WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically. Front Mol Biosci 2021;8:754444. [PMID: 34888352 DOI: 10.3389/fmolb.2021.754444] [Cited by in Crossref: 2] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
10 Hall BA, Niarakis A. Data integration in logic-based models of biological mechanisms. Current Opinion in Systems Biology 2021;28:100386. [DOI: 10.1016/j.coisb.2021.100386] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
11 Montagud A, Ponce-de-leon M, Valencia A. Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems. Current Opinion in Systems Biology 2021;28:100385. [DOI: 10.1016/j.coisb.2021.100385] [Cited by in Crossref: 10] [Cited by in F6Publishing: 11] [Article Influence: 5.0] [Reference Citation Analysis]
12 Thobe K, Konrath F, Chapuy B, Wolf J. Patient-Specific Modeling of Diffuse Large B-Cell Lymphoma. Biomedicines 2021;9:1655. [PMID: 34829885 DOI: 10.3390/biomedicines9111655] [Reference Citation Analysis]
13 Kwon YW, Jo HS, Bae S, Seo Y, Song P, Song M, Yoon JH. Application of Proteomics in Cancer: Recent Trends and Approaches for Biomarkers Discovery. Front Med (Lausanne) 2021;8:747333. [PMID: 34631760 DOI: 10.3389/fmed.2021.747333] [Cited by in Crossref: 14] [Cited by in F6Publishing: 16] [Article Influence: 7.0] [Reference Citation Analysis]
14 Axenie C, Bauer R, Martínez MR. The Multiple Dimensions of Networks in Cancer: A Perspective. Symmetry 2021;13:1559. [DOI: 10.3390/sym13091559] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
15 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 signaling networks guide personalized treatments.. [DOI: 10.1101/2021.07.28.454126] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
16 Cesareni G, Sacco F, Perfetto L. Assembling Disease Networks From Causal Interaction Resources. Front Genet 2021;12:694468. [PMID: 34178043 DOI: 10.3389/fgene.2021.694468] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
17 Gondal MN, Chaudhary SU. Navigating Multi-scale Cancer Systems Biology towards Model-driven Personalized Therapeutics.. [DOI: 10.1101/2021.05.17.444410] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.5] [Reference Citation Analysis]
18 Selvaggio G, Chaouiya C, Janody F. In Silico Logical Modelling to Uncover Cooperative Interactions in Cancer. Int J Mol Sci 2021;22:4897. [PMID: 34063110 DOI: 10.3390/ijms22094897] [Cited by in F6Publishing: 1] [Reference Citation Analysis]
19 Sherekar S, Viswanathan GA. Boolean dynamic modeling of cancer signaling networks: Prognosis, progression, and therapeutics. Comp Sys Onco 2021;1. [DOI: 10.1002/cso2.1017] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 2.0] [Reference Citation Analysis]
20 Tognetti M, Gabor A, Yang M, Cappelletti V, Windhager J, Rueda OM, Charmpi K, Esmaeilishirazifard E, Bruna A, de Souza N, Caldas C, Beyer A, Picotti P, Saez-Rodriguez J, Bodenmiller B. Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell Syst 2021;12:401-418.e12. [PMID: 33932331 DOI: 10.1016/j.cels.2021.04.002] [Cited by in Crossref: 9] [Cited by in F6Publishing: 10] [Article Influence: 4.5] [Reference Citation Analysis]
21 Selvaggio G, Chaouiya C, Janody F. In silico logical modelling to uncover cooperative interactions in cancer.. [DOI: 10.1101/2021.03.11.434958] [Reference Citation Analysis]
22 Vlachavas EI, Bohn J, Ückert F, Nürnberg S. A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research. Int J Mol Sci 2021;22:2822. [PMID: 33802234 DOI: 10.3390/ijms22062822] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 2.0] [Reference Citation Analysis]
23 Palma A, Iannuccelli M, Rozzo I, Licata L, Perfetto L, Massacci G, Castagnoli L, Cesareni G, Sacco F. Integrating Patient-Specific Information into Logic Models of Complex Diseases: Application to Acute Myeloid Leukemia. J Pers Med 2021;11:117. [PMID: 33578936 DOI: 10.3390/jpm11020117] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
24 Saez-Rodriguez J, Blüthgen N. Personalized signaling models for personalized treatments. Mol Syst Biol 2020;16:e9042. [PMID: 32129942 DOI: 10.15252/msb.20199042] [Cited by in Crossref: 25] [Cited by in F6Publishing: 24] [Article Influence: 12.5] [Reference Citation Analysis]
25 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 Comput Biol 2021;17:e1007900. [PMID: 33507915 DOI: 10.1371/journal.pcbi.1007900] [Cited by in Crossref: 15] [Cited by in F6Publishing: 17] [Article Influence: 7.5] [Reference Citation Analysis]
26 Tsirvouli E, Touré V, Niederdorfer B, Vázquez M, Flobak Å, Kuiper M. A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines. Front Mol Biosci 2020;7:502573. [PMID: 33195403 DOI: 10.3389/fmolb.2020.502573] [Cited by in Crossref: 7] [Cited by in F6Publishing: 8] [Article Influence: 2.3] [Reference Citation Analysis]
27 Niederdorfer B, Touré V, Vazquez M, Thommesen L, Kuiper M, Lægreid A, Flobak Å. Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction. Front Physiol 2020;11:862. [PMID: 32848834 DOI: 10.3389/fphys.2020.00862] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 1.7] [Reference Citation Analysis]
28 Smaïl-Tabbone M, Rance B; Section Editors for the IMIA Yearbook Section on Bioinformatics and Translational Informatics. Contributions from the 2019 Literature on Bioinformatics and Translational Informatics. Yearb Med Inform 2020;29:188-92. [PMID: 32823315 DOI: 10.1055/s-0040-1702002] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 0.3] [Reference Citation Analysis]
29 Nicora G, Vitali F, Dagliati A, Geifman N, Bellazzi R. Integrated Multi-Omics Analyses in Oncology: A Review of Machine Learning Methods and Tools. Front Oncol. 2020;10:1030. [PMID: 32695678 DOI: 10.3389/fonc.2020.01030] [Cited by in Crossref: 69] [Cited by in F6Publishing: 77] [Article Influence: 23.0] [Reference Citation Analysis]
30 Lapuente-Santana Ó, Eduati F. Toward Systems Biomarkers of Response to Immune Checkpoint Blockers. Front Oncol 2020;10:1027. [PMID: 32670886 DOI: 10.3389/fonc.2020.01027] [Cited by in Crossref: 11] [Cited by in F6Publishing: 12] [Article Influence: 3.7] [Reference Citation Analysis]
31 Koltai M, Noel V, Zinovyev A, Calzone L, Barillot E. Exact solving and sensitivity analysis of stochastic continuous time Boolean models. BMC Bioinformatics 2020;21:241. [PMID: 32527218 DOI: 10.1186/s12859-020-03548-9] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.3] [Reference Citation Analysis]
32 John A, Qin B, Kalari KR, Wang L, Yu J. Patient-specific multi-omics models and the application in personalized combination therapy. Future Oncol 2020;16:1737-50. [PMID: 32462937 DOI: 10.2217/fon-2020-0119] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 0.7] [Reference Citation Analysis]
33 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.. [DOI: 10.1101/2020.05.27.119016] [Reference Citation Analysis]
34 Stalidzans E, Zanin M, Tieri P, Castiglione F, Polster A, Scheiner S, Pahle J, Stres B, List M, Baumbach J, Lautizi M, Van Steen K, Schmidt HH. Mechanistic Modeling and Multiscale Applications for Precision Medicine: Theory and Practice. Network and Systems Medicine 2020;3:36-56. [DOI: 10.1089/nsm.2020.0002] [Cited by in Crossref: 7] [Cited by in F6Publishing: 8] [Article Influence: 2.3] [Reference Citation Analysis]
35 Tognetti M, Gabor A, Yang M, Cappelletti V, Windhager J, Charmpi K, de Souza N, Beyer A, Picotti P, Saez-rodriguez J, Bodenmiller B. Deciphering the Signaling Network Landscape of Breast Cancer Improves Drug Sensitivity Prediction.. [DOI: 10.1101/2020.01.21.907691] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
36 Ge R, Zhang R, Wang P. Prediction of Chronic Diseases With Multi-Label Neural Network. IEEE Access 2020;8:138210-6. [DOI: 10.1109/access.2020.3011374] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 1.7] [Reference Citation Analysis]
37 Salvucci M, Zakaria Z, Carberry S, Tivnan A, Seifert V, Kögel D, Murphy BM, Prehn JHM. System-based approaches as prognostic tools for glioblastoma. BMC Cancer 2019;19:1092. [PMID: 31718568 DOI: 10.1186/s12885-019-6280-2] [Cited by in Crossref: 8] [Cited by in F6Publishing: 8] [Article Influence: 2.0] [Reference Citation Analysis]
38 Koltai M, Noel V, Zinovyev A, Calzone L, Barillot E. Exact calculation of stationary solution and parameter sensitivity analysis of stochastic continuous time Boolean models.. [DOI: 10.1101/794230] [Reference Citation Analysis]
39 Salem I, Kimak M, Conic R, Bragazzi NL, Watad A, Adawi M, Bridgewood C, Pacifico A, Santus P, Rizzi M, Petrou S, Colombo D, Fiore M, Pigatto PDM, Damiani G. Neutrophilic Dermatoses and Their Implication in Pathophysiology of Asthma and Other Respiratory Comorbidities: A Narrative Review. Biomed Res Int 2019;2019:7315274. [PMID: 31281845 DOI: 10.1155/2019/7315274] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 1.3] [Reference Citation Analysis]