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For: Marques-Pita M, Rocha LM. Canalization and control in automata networks: body segmentation in Drosophila melanogaster. PLoS One 2013;8:e55946. [PMID: 23520449 PMCID: PMC3592869 DOI: 10.1371/journal.pone.0055946] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 01/03/2013] [Indexed: 12/19/2022]  Open
Number Cited by Other Article(s)
1
Varley TF, Bongard J. Evolving higher-order synergies reveals a trade-off between stability and information-integration capacity in complex systems. CHAOS (WOODBURY, N.Y.) 2024;34:063127. [PMID: 38865092 DOI: 10.1063/5.0200425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024]
2
Mitra S, Sil P, Subbaroyan A, Martin OC, Samal A. Preponderance of generalized chain functions in reconstructed Boolean models of biological networks. Sci Rep 2024;14:6734. [PMID: 38509145 PMCID: PMC10954731 DOI: 10.1038/s41598-024-57086-y] [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: 01/02/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]  Open
3
Tung A, Sperry MM, Clawson W, Pavuluri A, Bulatao S, Yue M, Flores RM, Pai VP, McMillen P, Kuchling F, Levin M. Embryos assist morphogenesis of others through calcium and ATP signaling mechanisms in collective teratogen resistance. Nat Commun 2024;15:535. [PMID: 38233424 PMCID: PMC10794468 DOI: 10.1038/s41467-023-44522-2] [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: 06/22/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024]  Open
4
Parmer T, Radicchi F. Dynamical methods for target control of biological networks. ROYAL SOCIETY OPEN SCIENCE 2023;10:230542. [PMID: 37920567 PMCID: PMC10618059 DOI: 10.1098/rsos.230542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/29/2023] [Indexed: 11/04/2023]
5
Manicka S, Johnson K, Levin M, Murrugarra D. The nonlinearity of regulation in biological networks. NPJ Syst Biol Appl 2023;9:10. [PMID: 37015937 PMCID: PMC10073134 DOI: 10.1038/s41540-023-00273-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/23/2023] [Indexed: 04/06/2023]  Open
6
Costa FX, Rozum JC, Marcus AM, Rocha LM. Effective Connectivity and Bias Entropy Improve Prediction of Dynamical Regime in Automata Networks. ENTROPY (BASEL, SWITZERLAND) 2023;25:374. [PMID: 36832740 PMCID: PMC9955587 DOI: 10.3390/e25020374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
7
Brattig Correia R, Barrat A, Rocha LM. Contact networks have small metric backbones that maintain community structure and are primary transmission subgraphs. PLoS Comput Biol 2023;19:e1010854. [PMID: 36821564 PMCID: PMC9949650 DOI: 10.1371/journal.pcbi.1010854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 01/06/2023] [Indexed: 02/24/2023]  Open
8
An S, Jang SY, Park SM, Lee CK, Kim HM, Cho KH. Global stabilizing control of large-scale biomolecular regulatory networks. Bioinformatics 2023;39:6998201. [PMID: 36688702 PMCID: PMC9891247 DOI: 10.1093/bioinformatics/btad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023]  Open
9
Rocha LM. On the feasibility of dynamical analysis of network models of biochemical regulation. Bioinformatics 2022;38:3674-3675. [PMID: 35640987 PMCID: PMC9272802 DOI: 10.1093/bioinformatics/btac360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/20/2021] [Accepted: 05/27/2022] [Indexed: 11/12/2022]  Open
10
Parmer T, Rocha LM, Radicchi F. Influence maximization in Boolean networks. Nat Commun 2022;13:3457. [PMID: 35710639 PMCID: PMC9203747 DOI: 10.1038/s41467-022-31066-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 06/01/2022] [Indexed: 11/30/2022]  Open
11
Werle SD, Ikonomi N, Schwab JD, Kraus JM, Weidner FM, Lenhard Rudolph K, Pfister AS, Schuler R, Kühl M, Kestler HA. Identification of dynamic driver sets controlling phenotypical landscapes. Comput Struct Biotechnol J 2022;20:1603-1617. [PMID: 35465155 PMCID: PMC9010550 DOI: 10.1016/j.csbj.2022.03.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 11/03/2022]  Open
12
Çoban H, Kabakçıoğlu A. Proof for Minimum Sensitivity of Nested Canalizing Functions, a Fractal Bound, and Implications for Biology. PHYSICAL REVIEW LETTERS 2022;128:118101. [PMID: 35363011 DOI: 10.1103/physrevlett.128.118101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
13
Minimal Developmental Computation: A Causal Network Approach to Understand Morphogenetic Pattern Formation. ENTROPY 2022;24:e24010107. [PMID: 35052133 PMCID: PMC8774453 DOI: 10.3390/e24010107] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/22/2022]
14
Manicka S, Marques-Pita M, Rocha LM. Effective connectivity determines the critical dynamics of biochemical networks. J R Soc Interface 2022;19:20210659. [PMID: 35042384 PMCID: PMC8767216 DOI: 10.1098/rsif.2021.0659] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/02/2021] [Indexed: 11/12/2022]  Open
15
Gates AJ, Brattig Correia R, Wang X, Rocha LM. The effective graph reveals redundancy, canalization, and control pathways in biochemical regulation and signaling. Proc Natl Acad Sci U S A 2021;118:e2022598118. [PMID: 33737396 PMCID: PMC8000424 DOI: 10.1073/pnas.2022598118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
16
Gene regulatory networks exhibit several kinds of memory: quantification of memory in biological and random transcriptional networks. iScience 2021;24:102131. [PMID: 33748699 PMCID: PMC7970124 DOI: 10.1016/j.isci.2021.102131] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/09/2020] [Accepted: 01/26/2021] [Indexed: 02/08/2023]  Open
17
Kim H, Muñoz S, Osuna P, Gershenson C. Antifragility Predicts the Robustness and Evolvability of Biological Networks through Multi-Class Classification with a Convolutional Neural Network. ENTROPY 2020;22:e22090986. [PMID: 33286756 PMCID: PMC7597304 DOI: 10.3390/e22090986] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/02/2020] [Indexed: 12/28/2022]
18
Deritei D, Rozum J, Ravasz Regan E, Albert R. A feedback loop of conditionally stable circuits drives the cell cycle from checkpoint to checkpoint. Sci Rep 2019;9:16430. [PMID: 31712566 PMCID: PMC6848090 DOI: 10.1038/s41598-019-52725-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022]  Open
19
Manicka S, Levin M. The Cognitive Lens: a primer on conceptual tools for analysing information processing in developmental and regenerative morphogenesis. Philos Trans R Soc Lond B Biol Sci 2019;374:20180369. [PMID: 31006373 PMCID: PMC6553590 DOI: 10.1098/rstb.2018.0369] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2018] [Indexed: 12/31/2022]  Open
20
Pentzien T, Puniya BL, Helikar T, Matache MT. Identification of Biologically Essential Nodes via Determinative Power in Logical Models of Cellular Processes. Front Physiol 2018;9:1185. [PMID: 30233390 PMCID: PMC6127445 DOI: 10.3389/fphys.2018.01185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 08/07/2018] [Indexed: 12/15/2022]  Open
21
Correia RB, Gates AJ, Wang X, Rocha LM. CANA: A Python Package for Quantifying Control and Canalization in Boolean Networks. Front Physiol 2018;9:1046. [PMID: 30154728 PMCID: PMC6102667 DOI: 10.3389/fphys.2018.01046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/13/2018] [Indexed: 01/11/2023]  Open
22
Control of complex networks requires both structure and dynamics. Sci Rep 2016;6:24456. [PMID: 27087469 PMCID: PMC4834509 DOI: 10.1038/srep24456] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/21/2016] [Indexed: 12/22/2022]  Open
23
Palma E, Salinas L, Aracena J. Enumeration and extension of non-equivalent deterministic update schedules in Boolean networks. Bioinformatics 2016;32:722-9. [DOI: 10.1093/bioinformatics/btv628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 10/25/2015] [Indexed: 11/13/2022]  Open
24
Chen J, Nolte V, Schlötterer C. Temperature stress mediates decanalization and dominance of gene expression in Drosophila melanogaster. PLoS Genet 2015;11:e1004883. [PMID: 25719753 PMCID: PMC4342254 DOI: 10.1371/journal.pgen.1004883] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/10/2014] [Indexed: 11/18/2022]  Open
25
Kim MC, Jeong YK, Song M. Investigating the integrated landscape of the intellectual topology of bioinformatics. Scientometrics 2014. [DOI: 10.1007/s11192-014-1417-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
26
Kim J, Vandamme D, Kim JR, Munoz AG, Kolch W, Cho KH. Robustness and evolvability of the human signaling network. PLoS Comput Biol 2014;10:e1003763. [PMID: 25077791 PMCID: PMC4117429 DOI: 10.1371/journal.pcbi.1003763] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 06/20/2014] [Indexed: 11/18/2022]  Open
27
Smythies J, Edelstein L, Ramachandran V. Molecular mechanisms for the inheritance of acquired characteristics-exosomes, microRNA shuttling, fear and stress: Lamarck resurrected? Front Genet 2014;5:133. [PMID: 24860599 PMCID: PMC4030137 DOI: 10.3389/fgene.2014.00133] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 04/24/2014] [Indexed: 12/17/2022]  Open
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