References
Our publications
- Collet, G., Eveillard, D., Gebser, M., Prigent, S., Schaub, T., Siegel, A. and Thiele, S. (2013). Extending the Metabolic Network of Ectocarpus Siliculosus using Answer Set Programming. Proceedings of the 12th Conference on Logic Programming and Nonmonotonic Reasoning 2013. doi
- Bordron P., Eveillard, D., Maass, A., Siegel, A. and Thiele, S. (2013). An ASP application in integrative biology: identification of functional gene units. Proceedings of the 12th Conference on Logic Programming and Nonmonotonic Reasoning 2013. doi
- Kaminski, R., Schaub, T., Siegel, A. & Videla, S. (2013). Minimal intervention strategies in logical signaling networks with Answer Set Programming. Theory and Practice of Logic Programming 13 (4-5), 675-690 doi
- Guziolowski, C., Videla, S., Eduati, F., Thiele, S., Cokelaer, T., Siegel, A., & Saez-Rodriguez, J. (2013). Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics, 29(18), 2320–2326. doi
- Videla, S., Guziolowski, C., Eduati, F., Thiele, S., Grabe, N., Saez-Rodriguez, J., & Siegel, A. (2012). Revisiting the Training of Logic Models of Protein Signaling Networks with ASP. Proceedings of the 10th Conference on Computational Methods in Systems Biology 2012. doi
- Gebser, M., Schaub, T., Thiele, S., & Veber, P. (2011). Detecting inconsistencies in large biological networks with answer set programming. Theory and Practice of Logic Programming, 11, 323–360. doi
- Durzinsky, M., Marwan, W., Ostrowski, M., Schaub, T., & Wagler, A. (2011). Automatic network reconstruction using ASP. Theory and Practice of Logic Programming, 11, 749–766. doi
- Gebser, M., Guziolowski, C., & Ivanchev, M. (2010). Repair and prediction (under inconsistency) in large biological networks with answer set programming. Proceedings of the 12th International Conference on Principles of Knowledge Representation and Reasoning. ee
- Schaub, T., & Thiele, S. (2009). Metabolic network expansion with answer set programming. 25th International Conference on Logic Programming, ICLP 2009. doi
Related work
- Papatheodorou, I., Ziehm, M., Wieser, D., Alic, N., Partridge, L., & Thornton, J. M. (2012). Using Answer Set Programming to Integrate RNA Expression with Signalling Pathway Information to Infer How Mutations Affect Ageing. (Y. Suh, Ed.)PLoS ONE, 7(12), e50881. doi:10.1371/journal.pone.0050881.t002
- Ray, O., & Soh, T. (2012). Analyzing Pathways Using ASP-Based Approaches. Algebraic and Numeric Biology.
- Inoue, K. (2011). Logic programming for Boolean networks. Proceedings of the Twenty-Second international joint conference on Artificial Intelligence (pp. 924–930). AAAI Press. doi:10.5591/978-1-57735-516-8/IJCAI11-160
- Fayruzov, T., Janssen, J., Vermeir, D., Cornelis, C., & De Cock, M. (2011). Modelling gene and protein regulatory networks with Answer Set Programming. IJDMB, 5(2), 209–229.
- Ray, O., Whelan, K., & King, R. (2010). Logic-Based Steady-State Analysis and Revision of Metabolic Networks with Inhibition. Proceedings of the 2010 International Conference on Complex, Intelligent and Software Intensive Systems (CISIS '10), 0, 661–666. doi:10.1109/CISIS.2010.184
- Fayruzov, T., De Cock, M., Cornelis, C., & Vermeir, D. (2009). Modeling Protein Interaction Networks with Answer Set Programming (pp. 99–104). Presented at the Bioinformatics and Biomedicine, 2009. BIBM '09. IEEE International Conference on. doi:10.1109/BIBM.2009.9
- Baral, C., Chancellor, K., Tran, N., Tran, N., Joy, A., & Berens, M. (2004). A knowledge based approach for representing and reasoning about signaling networks. Bioinformatics, 20 Suppl 1.
Books on Answer Set Programming
- Knowledge Representation, Reasoning and Declarative Problem Solving. Chitta Baral. Cambridge University Press (2003). isbn
- Answer Set Solving in Practice. Martin Gebser, Roland Kaminski, Benjamin Kaufmann and Torsten Schaub. Volume 19 of Synthesis Lectures on Artificial Intelligence and Machine Learning. Morgan and Claypool Publishers (2013). doi
