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For: Barik D, Ball DA, Peccoud J, Tyson JJ. A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability. PLoS Comput Biol 2016;12:e1005230. [PMID: 27935947 DOI: 10.1371/journal.pcbi.1005230] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/01/2016] [Indexed: 12/14/2022]  Open
Number Cited by Other Article(s)
1
King CR, Berezin CT, Peccoud J. Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production. PLoS Comput Biol 2024;20:e1011373. [PMID: 38324583 PMCID: PMC10878530 DOI: 10.1371/journal.pcbi.1011373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 02/20/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024]  Open
2
Gligorovski V, Sadeghi A, Rahi SJ. Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor. Nat Commun 2023;14:3810. [PMID: 37369667 DOI: 10.1038/s41467-023-38959-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/24/2023] [Indexed: 06/29/2023]  Open
3
A continuous-time stochastic Boolean model provides a quantitative description of the budding yeast cell cycle. Sci Rep 2022;12:20302. [PMID: 36434030 PMCID: PMC9700812 DOI: 10.1038/s41598-022-24302-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022]  Open
4
Govindaraj V, Sarma S, Karulkar A, Purwar R, Kar S. Transcriptional Fluctuations Govern the Serum-Dependent Cell Cycle Duration Heterogeneities in Mammalian Cells. ACS Synth Biol 2022;11:3743-3758. [PMID: 36325971 DOI: 10.1021/acssynbio.2c00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
5
Tyson JJ, Csikasz-Nagy A, Gonze D, Kim JK, Santos S, Wolf J. Time-keeping and decision-making in living cells: Part II. Interface Focus 2022. [PMCID: PMC9184961 DOI: 10.1098/rsfs.2022.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
6
Pulsatile signaling of bistable switches reveal the distinct nature of pulse processing by mutual activation and mutual inhibition loop. J Theor Biol 2022;540:111075. [DOI: 10.1016/j.jtbi.2022.111075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/23/2022] [Indexed: 11/19/2022]
7
Dey A, Barik D. Emergent Bistable Switches from the Incoherent Feed-Forward Signaling of a Positive Feedback Loop. ACS Synth Biol 2021;10:3117-3128. [PMID: 34694110 DOI: 10.1021/acssynbio.1c00373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
8
Das S, Barik D. Scaling of intrinsic noise in an autocratic reaction network. Phys Rev E 2021;103:042403. [PMID: 34006004 DOI: 10.1103/physreve.103.042403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/16/2021] [Indexed: 11/07/2022]
9
Thomas P. Stochastic Modeling Approaches for Single-Cell Analyses. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11539-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]  Open
10
Katebi A, Kohar V, Lu M. Random Parametric Perturbations of Gene Regulatory Circuit Uncover State Transitions in Cell Cycle. iScience 2020;23:101150. [PMID: 32450514 PMCID: PMC7251928 DOI: 10.1016/j.isci.2020.101150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/05/2020] [Accepted: 05/05/2020] [Indexed: 02/03/2023]  Open
11
Gallegos JE, Adames NR, Rogers MF, Kraikivski P, Ibele A, Nurzynski-Loth K, Kudlow E, Murali TM, Tyson JJ, Peccoud J. Genetic interactions derived from high-throughput phenotyping of 6589 yeast cell cycle mutants. NPJ Syst Biol Appl 2020;6:11. [PMID: 32376972 PMCID: PMC7203125 DOI: 10.1038/s41540-020-0134-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/06/2020] [Indexed: 11/09/2022]  Open
12
Mondeel TDGA, Ivanov O, Westerhoff HV, Liebermeister W, Barberis M. Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs. NPJ Syst Biol Appl 2020;6:8. [PMID: 32245958 PMCID: PMC7125140 DOI: 10.1038/s41540-020-0125-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/20/2020] [Indexed: 12/13/2022]  Open
13
Das S, Barik D. Qualitative and quantitative nature of mutual interactions dictate chemical noise in a democratic reaction network. Phys Rev E 2020;101:042407. [PMID: 32422814 DOI: 10.1103/physreve.101.042407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
14
A hybrid stochastic model of the budding yeast cell cycle. NPJ Syst Biol Appl 2020;6:7. [PMID: 32221305 PMCID: PMC7101447 DOI: 10.1038/s41540-020-0126-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 02/14/2020] [Indexed: 12/17/2022]  Open
15
Das S, Barik D. Investigation of chemical noise in multisite phosphorylation chain using linear noise approximation. Phys Rev E 2019;100:052402. [PMID: 31870028 DOI: 10.1103/physreve.100.052402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Indexed: 06/10/2023]
16
Dey A, Barik D. Dichotomous Nature of Bistability Generated by Negative Cooperativity in Receptor-Ligand Binding. ACS Synth Biol 2019;8:1294-1302. [PMID: 31132851 DOI: 10.1021/acssynbio.8b00517] [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] [Indexed: 11/29/2022]
17
Ahmadian M, Tyson JJ, Cao Y. A stochastic model of size control in the budding yeast cell cycle. BMC Bioinformatics 2019;20:322. [PMID: 31216979 PMCID: PMC6584508 DOI: 10.1186/s12859-019-2839-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
18
Clarke R, Tyson JJ, Tan M, Baumann WT, Jin L, Xuan J, Wang Y. Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers. Endocr Relat Cancer 2019;26:R345-R368. [PMID: 30965282 PMCID: PMC7045974 DOI: 10.1530/erc-18-0309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022]
19
A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle. Sci Rep 2019;9:3343. [PMID: 30833602 PMCID: PMC6399449 DOI: 10.1038/s41598-019-39850-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 01/30/2019] [Indexed: 12/11/2022]  Open
20
Contribution of RNA Degradation to Intrinsic and Extrinsic Noise in Gene Expression. Cell Rep 2019;26:3752-3761.e5. [DOI: 10.1016/j.celrep.2019.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 11/26/2018] [Accepted: 02/27/2019] [Indexed: 12/29/2022]  Open
21
Comparison of Deterministic and Stochastic Regime in a Model for Cdc42 Oscillations in Fission Yeast. Bull Math Biol 2019;81:1268-1302. [PMID: 30756233 DOI: 10.1007/s11538-019-00573-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/29/2019] [Indexed: 01/13/2023]
22
Tyson JJ, Laomettachit T, Kraikivski P. Modeling the dynamic behavior of biochemical regulatory networks. J Theor Biol 2018;462:514-527. [PMID: 30502409 DOI: 10.1016/j.jtbi.2018.11.034] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/12/2018] [Accepted: 11/27/2018] [Indexed: 12/11/2022]
23
Arulraj T, Barik D. Mathematical modeling identifies Lck as a potential mediator for PD-1 induced inhibition of early TCR signaling. PLoS One 2018;13:e0206232. [PMID: 30356330 PMCID: PMC6200280 DOI: 10.1371/journal.pone.0206232] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/09/2018] [Indexed: 12/27/2022]  Open
24
Accuracy Analysis of Hybrid Stochastic Simulation Algorithm on Linear Chain Reaction Systems. Bull Math Biol 2018;81:3024-3052. [PMID: 29992454 DOI: 10.1007/s11538-018-0461-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/29/2018] [Indexed: 01/06/2023]
25
Gonze D, Gérard C, Wacquier B, Woller A, Tosenberger A, Goldbeter A, Dupont G. Modeling-Based Investigation of the Effect of Noise in Cellular Systems. Front Mol Biosci 2018;5:34. [PMID: 29707543 PMCID: PMC5907451 DOI: 10.3389/fmolb.2018.00034] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/26/2018] [Indexed: 12/14/2022]  Open
26
Dey A, Barik D. Parallel arrangements of positive feedback loops limit cell-to-cell variability in differentiation. PLoS One 2017;12:e0188623. [PMID: 29186174 PMCID: PMC5706692 DOI: 10.1371/journal.pone.0188623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/10/2017] [Indexed: 02/04/2023]  Open
27
Correction: A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability. PLoS Comput Biol 2017;13:e1005323. [PMID: 28081212 PMCID: PMC5230745 DOI: 10.1371/journal.pcbi.1005323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
28
Vargas-Garcia CA, Soltani M, Singh A. Conditions for Cell Size Homeostasis: A Stochastic Hybrid System Approach. ACTA ACUST UNITED AC 2016. [DOI: 10.1109/lls.2016.2646383] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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