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For: Traynard P, Fauré A, Fages F, Thieffry D. Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation. Bioinformatics 2017;32:i772-i780. [PMID: 27587700 DOI: 10.1093/bioinformatics/btw457] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
Number Cited by Other Article(s)
1
Argyris GA, Lluch Lafuente A, Tribastone M, Tschaikowski M, Vandin A. Reducing Boolean networks with backward equivalence. BMC Bioinformatics 2023;24:212. [PMID: 37221494 DOI: 10.1186/s12859-023-05326-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/05/2023] [Indexed: 05/25/2023]  Open
2
Konur S, Gheorghe M, Krasnogor N. Verifiable biology. J R Soc Interface 2023;20:20230019. [PMID: 37160165 PMCID: PMC10169095 DOI: 10.1098/rsif.2023.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023]  Open
3
Lucas M, Morris A, Townsend-Teague A, Tichit L, Habermann B, Barrat A. Inferring cell cycle phases from a partially temporal network of protein interactions. CELL REPORTS METHODS 2023;3:100397. [PMID: 36936083 PMCID: PMC10014271 DOI: 10.1016/j.crmeth.2023.100397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/13/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
4
Thomas C, Cosme M, Gaucherel C, Pommereau F. Model-checking ecological state-transition graphs. PLoS Comput Biol 2022;18:e1009657. [PMID: 35666771 PMCID: PMC9203009 DOI: 10.1371/journal.pcbi.1009657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 06/16/2022] [Accepted: 05/08/2022] [Indexed: 11/18/2022]  Open
5
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 2022;11:e72626. [PMID: 35164900 PMCID: PMC9018074 DOI: 10.7554/elife.72626] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/27/2022] [Indexed: 11/22/2022]  Open
6
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 PMCID: PMC8651056 DOI: 10.3389/fmolb.2021.754444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022]  Open
7
SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models. Processes (Basel) 2021. [DOI: 10.3390/pr9101830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
8
Aghamiri SS, Delaplace F. TaBooN Boolean Network Synthesis Based on Tabu Search. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;PP:2499-2511. [PMID: 33661736 DOI: 10.1109/tcbb.2021.3063817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
9
Aghamiri SS, Singh V, Naldi A, Helikar T, Soliman S, Niarakis A. Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics 2021;36:4473-4482. [PMID: 32403123 PMCID: PMC7575051 DOI: 10.1093/bioinformatics/btaa484] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/17/2020] [Accepted: 05/06/2020] [Indexed: 12/16/2022]  Open
10
Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response. Cancers (Basel) 2020;12:cancers12123600. [PMID: 33276543 PMCID: PMC7761568 DOI: 10.3390/cancers12123600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023]  Open
11
Hernandez C, Thomas-Chollier M, Naldi A, Thieffry D. Computational Verification of Large Logical Models-Application to the Prediction of T Cell Response to Checkpoint Inhibitors. Front Physiol 2020;11:558606. [PMID: 33101049 PMCID: PMC7554341 DOI: 10.3389/fphys.2020.558606] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/19/2020] [Indexed: 12/31/2022]  Open
12
Paulevé L, Kolčák J, Chatain T, Haar S. Reconciling qualitative, abstract, and scalable modeling of biological networks. Nat Commun 2020;11:4256. [PMID: 32848126 PMCID: PMC7450094 DOI: 10.1038/s41467-020-18112-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/30/2020] [Indexed: 11/24/2022]  Open
13
Guttula PK, Monteiro PT, Gupta MK. A Boolean Logical model for Reprogramming of Testes-derived male Germline Stem Cells into Germline pluripotent stem cells. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020;192:105473. [PMID: 32305736 DOI: 10.1016/j.cmpb.2020.105473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 06/11/2023]
14
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 PMCID: PMC7291460 DOI: 10.1186/s12859-020-03548-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/18/2020] [Indexed: 12/02/2022]  Open
15
Réda C, Wilczyński B. Automated inference of gene regulatory networks using explicit regulatory modules. J Theor Biol 2020;486:110091. [PMID: 31790679 DOI: 10.1016/j.jtbi.2019.110091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/09/2019] [Accepted: 11/21/2019] [Indexed: 11/25/2022]
16
Ha S, Dimitrova E, Hoops S, Altarawy D, Ansariola M, Deb D, Glazebrook J, Hillmer R, Shahin H, Katagiri F, McDowell J, Megraw M, Setubal J, Tyler BM, Laubenbacher R. PlantSimLab - a modeling and simulation web tool for plant biologists. BMC Bioinformatics 2019;20:508. [PMID: 31638901 PMCID: PMC6805577 DOI: 10.1186/s12859-019-3094-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 09/10/2019] [Indexed: 11/10/2022]  Open
17
Gan X, Albert R. General method to find the attractors of discrete dynamic models of biological systems. Phys Rev E 2018;97:042308. [PMID: 29758614 DOI: 10.1103/physreve.97.042308] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Indexed: 12/31/2022]
18
Fages F, Martinez T, Rosenblueth DA, Soliman S. Influence Networks Compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:1138-1151. [PMID: 29994637 DOI: 10.1109/tcbb.2018.2805686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
19
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. Front Physiol 2018;9:680. [PMID: 29971009 PMCID: PMC6018415 DOI: 10.3389/fphys.2018.00680] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/15/2018] [Indexed: 01/07/2023]  Open
20
Naldi A, Hernandez C, Abou-Jaoudé W, Monteiro PT, Chaouiya C, Thieffry D. Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0. Front Physiol 2018;9:646. [PMID: 29971008 PMCID: PMC6018412 DOI: 10.3389/fphys.2018.00646] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/11/2018] [Indexed: 11/13/2022]  Open
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