-
1
-
-
58149261709
-
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
-
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
-
4
-
-
24744445173
-
A knowledge based approach for representing and reasoning about signaling networks
-
Baral, C., Chancellor, K., Tran, N., Tran, N., Joy, A. and Berens, M. 2004. A knowledge based approach for representing and reasoning about signaling networks. In Proceedings of the Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology (ISMB04/ECCB04), 15-22.
-
(2004)
Proceedings of the Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology (ISMB04/ECCB04)
, pp. 15-22
-
-
Baral, C.1
Chancellor, K.2
Tran, N.3
Tran, N.4
Joy, A.5
Berens, M.6
-
5
-
-
41149105962
-
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
-
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
-
7
-
-
77950825394
-
Mathematical modelling of cell-fate decision in response to death receptor engagement
-
February
-
Calzone, L. L., Tournier, L. L., Fourquet, S. S., Thieffry, D. D., Zhivotovsky, B. B., Barillot, E. E. and Zinovyev, A. A. 2010. Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS Computational Biology 6, 3 (February), e1000702-e1000702.
-
(2010)
PLoS Computational Biology
, vol.6
, Issue.3
-
-
Calzone, L.L.1
Tournier, L.L.2
Fourquet, S.S.3
Thieffry, D.D.4
Zhivotovsky, B.B.5
Barillot, E.E.6
Zinovyev, A.A.7
-
8
-
-
0003379809
-
Using the Davis and Putnam procedure for an efficient computation of preferred models
-
W. Wahlster, Ed. John Wiley & sons
-
Castell, T., Cayrol, C., Cayrol, M. and Le Berre, D. 1996. Using the Davis and Putnam procedure for an efficient computation of preferred models. In Proceedings of the Twelfth European Conference on Artificial Intelligence (ECAI96), W. Wahlster, Ed. John Wiley & sons, 350-354.
-
(1996)
Proceedings of the Twelfth European Conference on Artificial Intelligence (ECAI96)
, pp. 350-354
-
-
Castell, T.1
Cayrol, C.2
Cayrol, M.3
Le Berre, D.4
-
9
-
-
77956769789
-
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
-
11
-
-
45749138411
-
Optimal constrained stationary intervention in gene regulatory networks
-
Faryabi, B., Vahedi, G., Chamberland, J.-F., Datta, A. and Dougherty, E. R. 2008. Optimal constrained stationary intervention in gene regulatory networks. EURASIP Journal of Bioinformatics and Systems Biology 2008.
-
(2008)
EURASIP Journal of Bioinformatics and Systems Biology
, vol.2008
-
-
Faryabi, B.1
Vahedi, G.2
Chamberland, J.-F.3
Datta, A.4
Dougherty, E.R.5
-
12
-
-
0022180593
-
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
-
13
-
-
79952021547
-
Repair and prediction (under inconsistency) in large biological networks with answer set programming
-
Gebser, M., Guziolowski, C., Ivanchev, M., Schaub, T., Siegel, A., Thiele, S. and Veber, P. 2010. Repair and prediction (under inconsistency) in large biological networks with answer set programming. In Proceedings of the Twelfth International Conference on Principles of Knowledge Representation and Reasoning (KR10), F. Lin and U. Sattler, Eds. AAAI Press, 497-507.
-
(2010)
Proceedings of the Twelfth International Conference on Principles of Knowledge Representation and Reasoning (KR10), F. Lin and U. Sattler, Eds. AAAI Press
, pp. 497-507
-
-
Gebser, M.1
Guziolowski, C.2
Ivanchev, M.3
Schaub, T.4
Siegel, A.5
Thiele, S.6
Veber, P.7
-
14
-
-
70349882317
-
-
Clasp, clingo, and iclingo
-
Gebser, M., Kaminski, R., Kaufmann, B., Ostrowski, M., Schaub, T. and Thiele, S. A users guide to gringo, clasp, clingo, and iclingo.
-
A Users Guide to Gringo
-
-
Gebser, M.1
Kaminski, R.2
Kaufmann, B.3
Ostrowski, M.4
Schaub, T.5
Thiele, S.6
-
15
-
-
84872075045
-
-
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
-
16
-
-
80054965162
-
Complex optimization in answer set programming
-
Gebser, M., Kaminski, R. and Schaub, T. 2011. Complex optimization in answer set programming. Theory and Practice of Logic Programming 11, 4-5, 821-839.
-
(2011)
Theory and Practice of Logic Programming
, vol.11
, Issue.4-5
, pp. 821-839
-
-
Gebser, M.1
Kaminski, R.2
Schaub, T.3
-
17
-
-
38049060388
-
Clasp: A conflictdriven answer set solver
-
C. Baral, G. Brewka, and J. Schlipf, Eds. Lecture Notes in Artificial Intelligence, Springer-Verlag
-
Gebser, M., Kaufmann, B., Neumann, A. and Schaub, T. 2007. clasp: A conflictdriven answer set solver. In Proceedings of the Ninth International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR07), C. Baral, G. Brewka, and J. Schlipf, Eds. Lecture Notes in Artificial Intelligence, vol. 4483, Springer-Verlag, 260-265.
-
(2007)
Proceedings of the Ninth International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR07)
, vol.4483
, pp. 260-265
-
-
Gebser, M.1
Kaufmann, B.2
Neumann, A.3
Schaub, T.4
-
18
-
-
84893348717
-
Domainspecific heuristics in answer set programming
-
M. desJardins and M. Littman, Eds. AAAI Press. To appear
-
Gebser, M., Kaufmann, B., Otero, R., Romero, J., Schaub, T. and Wanko, P. 2013. Domainspecific heuristics in answer set programming. In Proceedings of the Twenty-Seventh National Conference on Artificial Intelligence (AAAI13), M. desJardins and M. Littman, Eds. AAAI Press. To appear.
-
(2013)
Proceedings of the Twenty-Seventh National Conference on Artificial Intelligence (AAAI13)
-
-
Gebser, M.1
Kaufmann, B.2
Otero, R.3
Romero, J.4
Schaub, T.5
Wanko, P.6
-
19
-
-
84896063922
-
Advanced conflict-driven disjunctive answer set solving
-
F. Rossi, Ed. IJCAI/AAAI. To appear
-
Gebser, M., Kaufmann, B. and Schaub, T. 2013. Advanced conflict-driven disjunctive answer set solving. In Proceedings of the Twenty-third International Joint Conference on Artificial Intelligence (IJCAI13), F. Rossi, Ed. IJCAI/AAAI. To appear.
-
(2013)
Proceedings of the Twenty-third International Joint Conference on Artificial Intelligence (IJCAI13)
-
-
Gebser, M.1
Kaufmann, B.2
Schaub, T.3
-
20
-
-
79960351364
-
-
Gebser, M., Schaub, T., Thiele, S. and Veber, P. 2011. Detecting inconsistencies in large biological networks with answer set programming. Theory and Practice of Logic Programming 11, 2-3, 323-360.
-
(2011)
Detecting inconsistencies in large biological networks with answer set programming. Theory and Practice of Logic Programming
, vol.11
, Issue.2-3
, pp. 323-360
-
-
Gebser, M.1
Schaub, T.2
Thiele, S.3
Veber, P.4
-
22
-
-
84864247744
-
-
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
-
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
-
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
-
25
-
-
0142122303
-
Advances in flux balance analysis
-
(October)
-
Kauffman, K. J., Prakash, P. and Edwards, J. S. 2003. Advances in flux balance analysis. Current opinion in biotechnology 14, 5 (October), 491-496.
-
(2003)
Current Opinion in Biotechnology
, vol.14
, Issue.5
, pp. 491-496
-
-
Kauffman, K.J.1
Prakash, P.2
Edwards, J.S.3
-
26
-
-
0036500993
-
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
-
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
-
28
-
-
67049098922
-
Hypergraphs and cellular networks
-
(May)
-
Klamt, S., Haus, U.-U. and Theis, F. J. 2009. Hypergraphs and cellular networks. PLoS Computational Biology 5, 5 (May), e1000385.
-
(2009)
PLoS Computational Biology
, vol.5
, Issue.5
-
-
Klamt, S.1
Haus, U.-U.2
Theis, F.J.3
-
30
-
-
58849137994
-
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
-
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
-
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
-
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
-
34
-
-
77952690947
-
Logic-based steady-state analysis and revision of metabolic networks with inhibition
-
CISIS 10
-
Ray, O., Whelan, K. and King, R. 2010. Logic-based steady-state analysis and revision of metabolic networks with inhibition. In Proceedings of the 2010 International Conference onComplex, Intelligent and Software Intensive Systems (CISIS 10) 0, 661-666.
-
(2010)
Proceedings of the 2010 International Conference OnComplex, Intelligent and Software Intensive Systems
, pp. 661-666
-
-
Ray, O.1
Whelan, K.2
King, R.3
-
35
-
-
71449120701
-
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. and Sorger, P. 2009. Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology 5, 331.
-
(2009)
Molecular Systems Biology
, vol.5
, pp. 331
-
-
Saez-Rodriguez, J.1
Alexopoulos, L.G.2
Epperlein, J.3
Samaga, R.4
Lauffenburger, A.5
Klamt, D.S.6
Sorger, P.7
-
36
-
-
80051692878
-
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
-
37
-
-
34548431024
-
A logical model provides insights into T cell receptor signaling
-
August
-
Saez-Rodriguez, J., Simeoni, L., Lindquist, J., Hemenway, R., Bommhardt, U., Arndt, B., Haus, U.-U., Weismantel, R., Gilles, E., Klamt, S. and Schraven, B. 2007. A logical model provides insights into T cell receptor signaling. PLOS Computational Biology 3, 8 (August), e163.
-
(2007)
PLOS Computational Biology
, vol.3
, Issue.8
-
-
Saez-Rodriguez, J.1
Simeoni, L.2
Lindquist, J.3
Hemenway, R.4
Bommhardt, U.5
Arndt, B.6
Haus, U.-U.7
Weismantel, R.8
Gilles, E.9
Klamt, S.10
Schraven, B.11
-
38
-
-
70049105859
-
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
-
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
-
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
-
41
-
-
77956355606
-
Towards robot scientists for autonomous scientific discovery
-
Sparkes, A., Aubrey, W., Byrne, E., Clare, A., Khan, M. N., Liakata, M., Markham, M., Rowland, J., Soldatova, L. N.,Whelan, K. E., Young, M. and King, R. D. 2010. Towards robot scientists for autonomous scientific discovery. Automated Experimentation 2, 1-1.
-
(2010)
Automated Experimentation
, vol.2
, pp. 1-1
-
-
Sparkes, A.1
Aubrey, W.2
Byrne, E.3
Clare, A.4
Khan, M.N.5
Liakata, M.6
Markham, M.7
Rowland, J.8
Soldatova, N.9
Whelan, L.K.E.10
Young, M.11
King, R.D.12
-
42
-
-
0037079050
-
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
-
43
-
-
4544346660
-
Robustness of Cellular Functions
-
Stelling, J., Sauer, U., Szallasi, Z., Doyle, F. and Doyle, J. 2004. Robustness of Cellular Functions. Cell 118, 6, 675-685.
-
(2004)
Cell
, vol.118
, Issue.6
, pp. 675-685
-
-
Stelling, J.1
Sauer, U.2
Szallasi, Z.3
Doyle, F.4
Doyle, J.5
-
44
-
-
0015823097
-
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
-
45
-
-
84867851090
-
Revisiting the training of logic models of protein signaling networks with ASP
-
D. Gilbert and M. Heiner, Eds Springer Berlin / Heidelberg
-
Videla, S., Guziolowski, C., Eduati, F., Thiele, S., Grabe, N., Saez-Rodriguez, J. and Siegel, A. 2012. Revisiting the training of logic models of protein signaling networks with ASP. In Computational Methods in Systems Biology 2012, D. Gilbert and M. Heiner, Eds. Springer Berlin / Heidelberg, 342-361.
-
(2012)
Computational Methods in Systems Biology 2012
, pp. 342-361
-
-
Videla, S.1
Guziolowski, C.2
Eduati, F.3
Thiele, S.4
Grabe, N.5
Saez-Rodriguez, J.6
Siegel, A.7
-
46
-
-
79953109968
-
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
-
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
-
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
|