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Volumn 3, Issue SEP, 2015, Pages

Designing experiments to discriminate families of logic models

Author keywords

Answer set programming; Boolean logic models; Experimental design; Phosphoproteomic; Signaling networks

Indexed keywords

COMPUTER CIRCUITS; COMPUTER PROGRAMMING; DESIGN OF EXPERIMENTS; LOGIC PROGRAMMING; MEAN SQUARE ERROR; RECONFIGURABLE HARDWARE; SIGNALING; STATISTICS;

EID: 84971011351     PISSN: None     EISSN: 22964185     Source Type: Journal    
DOI: 10.3389/fbioe.2015.00131     Document Type: Article
Times cited : (7)

References (28)
  • 1
    • 77956554551 scopus 로고    scopus 로고
    • Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes
    • Alexopoulos, L. G., Saez-Rodriguez, J., Cosgrove, B., Lauffenburger, D. A., and Sorger, P. (2010). Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. Mol. Cell. Proteomics 9, 1849-1865. doi: 10.1074/mcp.M110.000406
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 1849-1865
    • Alexopoulos, L.G.1    Saez-Rodriguez, J.2    Cosgrove, B.3    Lauffenburger, D.A.4    Sorger, P.5
  • 2
    • 84907024690 scopus 로고    scopus 로고
    • Experimental design schemes for learning Boolean network models
    • Atias, N., Gershenzon, M., Labazin, K., and Sharan, R. (2014). Experimental design schemes for learning Boolean network models. Bioinformatics 30, i445-i452. doi:10.1093/bioinformatics/btu451
    • (2014) Bioinformatics , vol.30 , pp. i445-i452
    • Atias, N.1    Gershenzon, M.2    Labazin, K.3    Sharan, R.4
  • 3
    • 33646920070 scopus 로고    scopus 로고
    • Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach
    • Barrett, C. L., and Palsson, B. Ø (2006). Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput. Biol. 2:e52. doi:10.1371/journal.pcbi.0020052
    • (2006) PLoS Comput. Biol , vol.2
    • Barrett, C.L.1    Palsson, B.Ø.2
  • 4
    • 84885615538 scopus 로고    scopus 로고
    • Near-optimal experimental design for model selection in systems biology
    • Busetto, A. G., Hauser, A., Krummenacher, G., Sunnåker, M., Dimopoulos, S., Ong, C. S., et al. (2013). Near-optimal experimental design for model selection in systems biology. Bioinformatics 29, 2625-2632. doi:10.1093/bioinformatics/btt436
    • (2013) Bioinformatics , vol.29 , pp. 2625-2632
    • Busetto, A.G.1    Hauser, A.2    Krummenacher, G.3    Sunnåker, M.4    Dimopoulos, S.5    Ong, C.S.6
  • 5
    • 84872075045 scopus 로고    scopus 로고
    • Synthesis Lectures on Artificial Intelligence and Machine Learning. Morgan and Claypool Publishers
    • Gebser, M., Kaminski, R., Kaufmann, B., and Schaub, T. (2012). Answer Set Solving in Practice. Synthesis Lectures on Artificial Intelligence and Machine Learning. Morgan and Claypool Publishers.
    • (2012) Answer Set Solving in Practice
    • Gebser, M.1    Kaminski, R.2    Kaufmann, B.3    Schaub, T.4
  • 6
    • 84883476230 scopus 로고    scopus 로고
    • Exhaustively characterizing feasible logic models of a signaling network using answer set programming
    • Guziolowski, C., Videla, S., Eduati, F., Thiele, S., Cokelaer, T., Siegel, A., et al. (2013). Exhaustively characterizing feasible logic models of a signaling network using answer set programming. Bioinformatics 29, 2320-2326. doi:10.1093/bioinformatics/btt393
    • (2013) Bioinformatics , vol.29 , pp. 2320-2326
    • Guziolowski, C.1    Videla, S.2    Eduati, F.3    Thiele, S.4    Cokelaer, T.5    Siegel, A.6
  • 7
    • 0033642067 scopus 로고    scopus 로고
    • "Discovery of regulatory interactions through perturbation: inference and experimental design,"
    • eds R. B. Altman, A. K. Dunker, L. Hunter, and T. E. Klein
    • Ideker, T. E., Thorsson, V., and Karp, R. M. (2000). "Discovery of regulatory interactions through perturbation: inference and experimental design," in Pacific Symposium on Biocomputing, Vol. 5, eds R. B. Altman, A. K. Dunker, L. Hunter, and T. E. Klein 305-316.
    • (2000) Pacific Symposium on Biocomputing , vol.5 , pp. 305-316
    • Ideker, T.E.1    Thorsson, V.2    Karp, R.M.3
  • 8
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • Kauffman, S. (1969). Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22, 437-467. doi:10.1016/0022-5193(69)90015-0
    • (1969) J. Theor. Biol , vol.22 , pp. 437-467
    • Kauffman, S.1
  • 9
    • 4644301730 scopus 로고    scopus 로고
    • A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions
    • Kremling, A., Fischer, S., Gadkar, K., Doyle, F., Sauter, T., Bullinger, E., et al. (2004). A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions. Genome Res. 14, 1773-1785. doi:10.1101/gr.1226004
    • (2004) Genome Res , vol.14 , pp. 1773-1785
    • Kremling, A.1    Fischer, S.2    Gadkar, K.3    Doyle, F.4    Sauter, T.5    Bullinger, E.6
  • 10
    • 58849137994 scopus 로고    scopus 로고
    • Systems biology: experimental design
    • Kreutz, C., and Timmer, J. (2009). Systems biology: experimental design. FEBS J. 276, 923-942. doi:10.1111/j.1742-4658.2008.06843.x
    • (2009) FEBS J , vol.276 , pp. 923-942
    • Kreutz, C.1    Timmer, J.2
  • 12
    • 2442535151 scopus 로고    scopus 로고
    • Survey of multi-objective optimization methods for engineering
    • Marler, R. T., and Arora, J. S. (2004). Survey of multi-objective optimization methods for engineering. Struct. Multidiscipl. Optim. 26, 369-395. doi:10.1007/s00158-003-0368-6
    • (2004) Struct. Multidiscipl. Optim , vol.26 , pp. 369-395
    • Marler, R.T.1    Arora, J.S.2
  • 13
    • 84881110269 scopus 로고    scopus 로고
    • Logical modelling of Drosophila signalling pathways
    • Mbodj, A., Junion, G., Brun, C., Furlong, E. E., and Thieffry, D. (2013). Logical modelling of Drosophila signalling pathways. Mol. Biosyst. 9, 2248-2258. doi:10.1039/c3mb70187e
    • (2013) Mol. Biosyst , vol.9 , pp. 2248-2258
    • Mbodj, A.1    Junion, G.2    Brun, C.3    Furlong, E.E.4    Thieffry, D.5
  • 14
    • 84859880192 scopus 로고    scopus 로고
    • Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data
    • Melas, I. N., Mitsos, A., Messinis, D. E., Weiss, T. S., Saez Rodriguez, J., and Alexopoulos, L. G. (2012). Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data. Mol. Biosyst. 8, 1571-1584. doi:10.1039/c2mb05482e
    • (2012) Mol. Biosyst , vol.8 , pp. 1571-1584
    • Melas, I.N.1    Mitsos, A.2    Messinis, D.E.3    Weiss, T.S.4    Saez Rodriguez, J.5    Alexopoulos, L.G.6
  • 15
    • 77950535005 scopus 로고    scopus 로고
    • Discriminating between rival biochemical network models: three approaches to optimal experiment design
    • Mélykúti, B., August, E., Papachristodoulou, A., and El-Samad, H. (2010). Discriminating between rival biochemical network models: three approaches to optimal experiment design. BMC Syst. Biol. 4:38. doi:10.1186/1752-0509-4-38
    • (2010) BMC Syst. Biol , vol.4 , pp. 38
    • Mélykúti, B.1    August, E.2    Papachristodoulou, A.3    El-Samad, H.4
  • 16
    • 84893710009 scopus 로고    scopus 로고
    • Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach
    • Meyer, P., Cokelaer, T., Chandran, D., Kim, K. H., Loh, P.-R., Tucker, G., et al. (2014). Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Syst. Biol. 8:13. doi:10.1186/1752-0509-8-13
    • (2014) BMC Syst. Biol , vol.8 , pp. 13
    • Meyer, P.1    Cokelaer, T.2    Chandran, D.3    Kim, K.H.4    Loh, P.-R.5    Tucker, G.6
  • 17
    • 74549168922 scopus 로고    scopus 로고
    • Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data
    • Mitsos, A., Melas, I., Siminelakis, P., Chairakaki, A., Saez-Rodriguez, J., and Alexopoulos, L. G. (2009). Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data. PLoS Comput. Biol. 5:e1000591. doi:10.1371/journal.pcbi.1000591
    • (2009) PLoS Comput. Biol , vol.5
    • Mitsos, A.1    Melas, I.2    Siminelakis, P.3    Chairakaki, A.4    Saez-Rodriguez, J.5    Alexopoulos, L.G.6
  • 18
    • 77950943011 scopus 로고    scopus 로고
    • Logic-based models for the analysis of cell signaling networks
    • Morris, M., Saez-Rodriguez, J., Sorger, P., and Lauffenburger, D. A. (2010). Logic-based models for the analysis of cell signaling networks. Biochemistry 49, 3216-3224. doi:10.1021/bi902202q
    • (2010) Biochemistry , vol.49 , pp. 3216-3224
    • Morris, M.1    Saez-Rodriguez, J.2    Sorger, P.3    Lauffenburger, D.A.4
  • 19
    • 49549085003 scopus 로고    scopus 로고
    • Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework
    • Remy, E., Ruet, P., and Thieffry, D. (2008). Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework. Adv. Appl. Math. 41, 335-350. doi:10.1016/j.aam.2007.11.003
    • (2008) Adv. Appl. Math , vol.41 , pp. 335-350
    • Remy, E.1    Ruet, P.2    Thieffry, D.3
  • 20
    • 71449120701 scopus 로고    scopus 로고
    • Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction
    • Saez-Rodriguez, J., Alexopoulos, L. G., Epperlein, J., Samaga, R., Lauffenburger, D. A., Klamt, S., et al. (2009). Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol. Syst. Biol. 5, 331. doi:10.1038/msb.2009.87
    • (2009) Mol. Syst. Biol , vol.5 , pp. 331
    • Saez-Rodriguez, J.1    Alexopoulos, L.G.2    Epperlein, J.3    Samaga, R.4    Lauffenburger, D.A.5    Klamt, S.6
  • 21
    • 84940644968 scopus 로고
    • A mathematical theory of communication
    • Shannon, C. E. (1948). A mathematical theory of communication. Bell Syst. Tech. J. 27, 379-423. doi:10.1002/j.1538-7305.1948.tb00917.x
    • (1948) Bell Syst. Tech. J , vol.27 , pp. 379-423
    • Shannon, C.E.1
  • 22
    • 84874675754 scopus 로고    scopus 로고
    • Reconstructing Boolean models of signaling
    • Sharan, R., and Karp, R. M. (2013). Reconstructing Boolean models of signaling. J. Comput. Biol. 20, 249-257. doi:10.1089/cmb.2012.0241
    • (2013) J. Comput. Biol , vol.20 , pp. 249-257
    • Sharan, R.1    Karp, R.M.2
  • 23
    • 77956355606 scopus 로고    scopus 로고
    • Towards robot scientists for autonomous scientific discovery
    • Sparkes, A., Aubrey, W., Byrne, E., Clare, A., Khan, M. N., Liakata, M., et al. (2010). Towards robot scientists for autonomous scientific discovery. Autom. Exp. 2, 1. doi:10.1186/1759-4499-2-1
    • (2010) Autom. Exp , vol.2 , pp. 1
    • Sparkes, A.1    Aubrey, W.2    Byrne, E.3    Clare, A.4    Khan, M.N.5    Liakata, M.6
  • 24
    • 84873487641 scopus 로고    scopus 로고
    • Robust optimal design of experiments for model discrimination using an interactive software tool
    • Stegmaier, J., Skanda, D., and Lebiedz, D. (2013). Robust optimal design of experiments for model discrimination using an interactive software tool. PLoS ONE 8:e55723. doi:10.1371/journal.pone.0055723
    • (2013) PLoS ONE , vol.8
    • Stegmaier, J.1    Skanda, D.2    Lebiedz, D.3
  • 25
    • 68149168970 scopus 로고    scopus 로고
    • Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments
    • Szczurek, E., Gat-Viks, I., Tiuryn, J., and Vingron, M. (2008). Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments. Mol. Syst. Biol. 5, 287-287. doi:10.1038/msb.2009.45
    • (2008) Mol. Syst. Biol , vol.5 , pp. 287-287
    • Szczurek, E.1    Gat-Viks, I.2    Tiuryn, J.3    Vingron, M.4
  • 26
    • 32944459689 scopus 로고    scopus 로고
    • Experiment selection for the discrimination of semi-quantitative models of dynamical systems
    • Vatcheva, I., de Jong, H., Bernard, O., and Mars, N. J. I. (2005). Experiment selection for the discrimination of semi-quantitative models of dynamical systems. Artif. Intell. 170, 472-506. doi:10.1016/j.artint.2005.11.001
    • (2005) Artif. Intell , vol.170 , pp. 472-506
    • Vatcheva, I.1    de Jong, H.2    Bernard, O.3    Mars, N.J.I.4
  • 28
    • 27744521520 scopus 로고    scopus 로고
    • Validation and refinement of gene-regulatory pathways on a network of physical interactions
    • Yeang, C., Mak, H. C., McCuine, S., Workman, C., Jaakkola, T., and Ideker, T. E. (2005). Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol. 6, R62. doi:10.1186/gb-2005-6-7-r62
    • (2005) Genome Biol , vol.6
    • Yeang, C.1    Mak, H.C.2    McCuine, S.3    Workman, C.4    Jaakkola, T.5    Ideker, T.E.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.