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Volumn 13, Issue 4-5, 2013, Pages 675-690

Minimal intervention strategies in logical signaling networks with ASP

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACT REPRESENTATION; ANSWER SET PROGRAMMING; BIOLOGICAL SIGNALING; BIOLOGY AND MEDICINE; FIX-POINT SEMANTICS; INTERVENTION STRATEGY; LARGE-SCALE NETWORK; QUALITATIVE APPROACH;

EID: 84884749905     PISSN: 14710684     EISSN: 14753081     Source Type: Journal    
DOI: 10.1017/S1471068413000422     Document Type: Conference Paper
Times cited : (24)

References (48)
  • 1
    • 58149261709 scopus 로고    scopus 로고
    • Fault diagnosis engineering of digital circuits can identify vulnerable molecules in complex cellular pathways
    • Abdi, A., Tahoori, M. B. and Emamian, E. S. 2008. Fault diagnosis engineering of digital circuits can identify vulnerable molecules in complex cellular pathways. Science Signaling 1, 42, ra10.
    • (2008) Science Signaling , vol.1 , pp. 42
    • Abdi, A.1    Tahoori, M.B.2    Emamian, E.S.3
  • 2
    • 84867283013 scopus 로고    scopus 로고
    • Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks
    • September
    • Acuna, V. V.,Milreu, P. V. P., Cottret, L. L., Marchetti-Spaccamela, A. A., Stougie, L. L. and Sagot, M.-F. M. 2012. Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks. Bioinformatics 28, 19 (September), 2474-2483.
    • (2012) Bioinformatics , vol.28 , Issue.19 , pp. 2474-2483
    • Acuna, V.V.1    Milreu, P.V.P.2    Cottret, L.L.3    Marchetti-Spaccamela, A.A.4    Stougie, L.L.5    Sagot, M.-F.M.6
  • 5
    • 41149105962 scopus 로고    scopus 로고
    • Symbolic reachability analysis of genetic regulatory networks using discrete abstractions
    • March
    • Batt, G., de Jong, H., Page, M. and Geiselmann, J. 2008. Symbolic reachability analysis of genetic regulatory networks using discrete abstractions. Automatica 44, 4 (March), 982-989.
    • (2008) Automatica , vol.44 , Issue.4 , pp. 982-989
    • Batt, G.1    De Jong, H.2    Page, M.3    Geiselmann, J.4
  • 6
    • 85032751037 scopus 로고    scopus 로고
    • Methods for optimal intervention in gene regulatory networks. Signal Processing Magazine
    • December
    • Bouaynaya, N. N., Shterenberg, R. and Schonfeld, D. 2011. Methods for optimal intervention in gene regulatory networks. Signal Processing Magazine, IEEE 29, 1 (December), 158-163.
    • (2011) IEEE 29 , Issue.1 , pp. 158-163
    • Bouaynaya, N.N.1    Shterenberg, R.2    Schonfeld, D.3
  • 9
    • 77956769789 scopus 로고    scopus 로고
    • Solving satisfiability problems with preferences
    • Di Rosa, E., Giunchiglia, E. and Maratea, M. 2010. Solving satisfiability problems with preferences. Constraints 15, 4, 485-515.
    • (2010) Constraints , vol.15 , Issue.4 , pp. 485-515
    • Di Rosa, E.1    Giunchiglia, E.2    Maratea, M.3
  • 12
    • 0022180593 scopus 로고
    • A Kripke-Kleene semantics for logic programs
    • Fitting, M. 1985. A Kripke-Kleene semantics for logic programs. Journal of Logic Programming 2, 4, 295-312.
    • (1985) Journal of Logic Programming , vol.2 , Issue.4 , pp. 295-312
    • Fitting, M.1
  • 15
    • 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
  • 22
    • 84864247744 scopus 로고    scopus 로고
    • Correct Reasoning, E. Erdem, J. Lee, Y. Lierler and D. Pearce, Eds. Lecture Notes in Computer Science Springer
    • Inoue, K. and Sakama, C. 2012. Oscillating behavior of logic programs. In Correct Reasoning, E. Erdem, J. Lee, Y. Lierler and D. Pearce, Eds. Lecture Notes in Computer Science, vol. 7265. Springer, 345-362.
    • (2012) Oscillating Behavior of Logic Programs , vol.7265 , pp. 345-362
    • Inoue, K.1    Sakama, C.2
  • 23
    • 77951894568 scopus 로고    scopus 로고
    • Minimally perturbing a gene regulatory network to avoid a disease phenotype: The glioma network as a test case
    • Karlebach, G. G. and Shamir, R. R. 2009. Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case. BMC Systems Biology 4, 15-15.
    • (2009) BMC Systems Biology , vol.4 , pp. 15-15
    • Karlebach, G.G.1    Shamir, R.R.2
  • 24
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • (February)
    • Kauffman, S. 1969. Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology 22, 3 (February), 437-467.
    • (1969) Journal of Theoretical Biology , vol.22 , Issue.3 , pp. 437-467
    • Kauffman, S.1
  • 26
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • Kitano, H. 2002. Systems biology: a brief overview. Science 295, 5560, 1662-1664.
    • (2002) Science , vol.295 , Issue.5560 , pp. 1662-1664
    • Kitano, H.1
  • 27
    • 32144453095 scopus 로고    scopus 로고
    • Generalized concept of minimal cut sets in biochemical networks
    • January
    • Klamt, S. S. 2006. Generalized concept of minimal cut sets in biochemical networks. Biosystems 83, 2-3 (January), 233-247.
    • (2006) Biosystems , vol.83 , Issue.2-3 , pp. 233-247
    • Klamt, S.S.1
  • 30
    • 58849137994 scopus 로고    scopus 로고
    • Systems biology: Experimental design
    • (January)
    • Kreutz, C. and Timmer, J. 2009. Systems biology: experimental design. FEBS Journal 276, 4 (January), 923-942.
    • (2009) FEBS Journal , vol.276 , Issue.4 , pp. 923-942
    • Kreutz, C.1    Timmer, J.2
  • 31
    • 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 Computational Biology 5, 12, e1000591.
    • (2009) PLoS Computational Biology , vol.5 , Issue.12
    • Mitsos, A.1    Melas, I.2    Siminelakis, P.3    Chairakaki, A.4    Saez-Rodriguez, J.5    Alexopoulos, L.G.6
  • 32
    • 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, 15, 3216-3224.
    • (2010) Biochemistry , vol.49 , Issue.15 , pp. 3216-3224
    • Morris, M.1    Saez-Rodriguez, J.2    Sorger, P.3    Lauffenburger, D.A.4
  • 33
    • 78049424847 scopus 로고    scopus 로고
    • Diversity and plasticity of th cell types predicted from regulatory network modelling
    • December
    • Naldi, A., Carneiro, J., Chaouiya, C. and Thieffry, D. 2009. Diversity and plasticity of th cell types predicted from regulatory network modelling. PLoS Computational Biology 6, 9 (December), e1000912.
    • (2009) PLoS Computational Biology , vol.6 , Issue.9
    • Naldi, A.1    Carneiro, J.2    Chaouiya, C.3    Thieffry, D.4
  • 36
    • 80051692878 scopus 로고    scopus 로고
    • Comparing signaling networks between normal and transformed hepatocytes using discrete logical models
    • Saez-Rodriguez, J., Alexopoulos, L. G., Zhang, M., Morris, M., Lauffenburger, D. A. and Sorger, P. 2011. Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. Cancer Research 71, 16, 5400.
    • (2011) Cancer Research , vol.71 , Issue.16 , pp. 5400
    • Saez-Rodriguez, J.1    Alexopoulos, L.G.2    Zhang, M.3    Morris, M.4    Lauffenburger, D.A.5    Sorger, P.6
  • 38
    • 70049105859 scopus 로고    scopus 로고
    • The logic of EGFR/ErbB signaling: Theoretical properties and analysis of high-throughput data
    • August
    • Samaga, R., Saez-Rodriguez, J., Alexopoulos, L. G., Sorger, P. and Klamt, S. 2009. The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Computational Biology 5, 8 (August), e1000438.
    • (2009) PLoS Computational Biology , vol.5 , Issue.8
    • Samaga, R.1    Saez-Rodriguez, J.2    Alexopoulos, L.G.3    Sorger, P.4    Klamt, S.5
  • 39
    • 77149160061 scopus 로고    scopus 로고
    • Computing combinatorial intervention strategies and failure modes in signaling networks
    • Jan
    • Samaga, R., Von Kamp, A. and Klamt, S. 2010. Computing combinatorial intervention strategies and failure modes in signaling networks. Journal of Computational Biology 17, 1 (Jan.), 39-53.
    • (2010) Journal of Computational Biology , vol.17 , Issue.1 , pp. 39-53
    • Samaga, R.1    Von Kamp, A.2    Klamt, S.3
  • 40
    • 84860823769 scopus 로고    scopus 로고
    • Reconstructing boolean models of signaling
    • Springer Berlin Heidelberg, Berlin, Heidelberg
    • Sharan, R. and Karp, R.M. 2012. Reconstructing boolean models of signaling. In Research in Computational Molecular Biology. Springer Berlin Heidelberg, Berlin, Heidelberg, 261-271.
    • (2012) Research in Computational Molecular Biology , pp. 261-271
    • Sharan, R.1    Karp, R.M.2
  • 42
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • November
    • Stelling, J. J., Klamt, S. S., Bettenbrock, K. K., Schuster, S. S. and Gilles, E. D. E. 2002. Metabolic network structure determines key aspects of functionality and regulation. Nature 420, 6912 (November), 190-193.
    • (2002) Nature , vol.420 , Issue.6912 , pp. 190-193
    • Stelling, J.J.1    Klamt, S.S.2    Bettenbrock, K.K.3    Schuster, S.S.4    Gilles, E.D.E.5
  • 44
    • 0015823097 scopus 로고
    • Boolean formalization of genetic control circuits
    • November
    • Thomas, R. R. 1973. Boolean formalization of genetic control circuits. Journal of Theoretical Biology 42, 3 (November), 563-585.
    • (1973) Journal of Theoretical Biology , vol.42 , Issue.3 , pp. 563-585
    • Thomas, R.R.1
  • 46
    • 79953109968 scopus 로고    scopus 로고
    • Elementary signaling modes predict the essentiality of signal transduction network components
    • Wang, R.-S. and Albert, R. 2011. Elementary signaling modes predict the essentiality of signal transduction network components. BMC Systems Biology 5, 44.
    • (2011) BMC Systems Biology , vol.5 , pp. 44
    • Wang, R.-S.1    Albert, R.2
  • 47
    • 84864301081 scopus 로고    scopus 로고
    • Customizing cell signaling using engineered genetic logic circuits
    • August
    • Wang, B. and Buck, M. 2012. Customizing cell signaling using engineered genetic logic circuits. Trends in Microbiology 20, 8 (August), 376-384.
    • (2012) Trends in Microbiology , vol.20 , Issue.8 , pp. 376-384
    • Wang, B.1    Buck, M.2
  • 48
    • 84867272347 scopus 로고    scopus 로고
    • Boolean modeling in systems biology: An overview of methodology and applications
    • September
    • Wang, R.-S. R., Saadatpour, A. A. and Albert, R. R. 2012. Boolean modeling in systems biology: an overview of methodology and applications. Physical biology 9, 5 (September), 055001-055001.
    • (2012) Physical Biology , vol.9 , Issue.5 , pp. 055001-055001
    • Wang, R.-S.R.1    Saadatpour, A.A.2    Albert, R.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.