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Nadja Betzler, René van Bevern, Michael R. Fellows, Christian Komusiewicz, Rolf Niedermeier, "Parameterized Algorithmics for Finding Connected Motifs in Biological Networks," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 5, pp. 12961308, September/October, 2011.  
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@article{ 10.1109/TCBB.2011.19, author = {Nadja Betzler and René van Bevern and Michael R. Fellows and Christian Komusiewicz and Rolf Niedermeier}, title = {Parameterized Algorithmics for Finding Connected Motifs in Biological Networks}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {8}, number = {5}, issn = {15455963}, year = {2011}, pages = {12961308}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.19}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
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TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  Parameterized Algorithmics for Finding Connected Motifs in Biological Networks IS  5 SN  15455963 SP1296 EP1308 EPD  12961308 A1  Nadja Betzler, A1  René van Bevern, A1  Michael R. Fellows, A1  Christian Komusiewicz, A1  Rolf Niedermeier, PY  2011 KW  Parameterized complexity KW  colorcoding KW  listcolored graphs KW  pattern matching in graphs KW  proteininteraction networks. VL  8 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] E. Alm and A.P. Arkin, “Biological Networks,” Current Opinion in Structural Biology, vol. 13, no. 2, pp. 193202, 2003.
[2] N. Alon, R. Yuster, and U. Zwick, “Colorcoding,” J. ACM, vol. 42, no. 4, pp. 844856, 1995.
[3] D. Barrell, E. Dimmer, R.P. Huntley, D. Binns, C. O'Donovan, and R. Apweiler, “The GOA Database in 2009—An Integrated Gene Ontology Annotation Resource,” Nucleic Acids Research, vol. 37, pp. 396403, 2009/2010.
[4] N. Betzler, M.R. Fellows, C. Komusiewicz, and R. Niedermeier, “Parameterized Algorithms and Hardness Results for Some Graph Motif Problems,” Proc. 19th Ann. Symp. Combinatorial Pattern Matching (CPM '08), LNCS, vol. 5029, pp. 3143, 2008.
[5] A. Björklund, T. Husfeldt, P. Kaski, and M. Koivisto, “Fourier Meets Möbius: Fast Subset Convolution,” Proc. 39th Ann. ACM Symp. Theory of Computing (STOC '07), pp. 6774, 2007.
[6] G. Blin, F. Sikora, and S. Vialette, “GraMoFoNe: A Cytoscape Plugin for Querying Motifs without Topology in ProteinProtein Interactions networks,” Proc. Second Int'l Conf. Bioinformatics and Computational Biology (BICoB '10), pp. 3843, 2010.
[7] E.I. Boyle, S. Weng, J. Gollub, H. Jin, D. Botstein, J.M. Cherry, and G. Sherlock, “GO::TermFinderOpen Source Software for Accessing Gene Ontology Information and Finding Significantly Enriched Gene Ontology Terms Associated with a List of Genes,” Bioinformatics, vol. 20, no. 18, pp. 37103715, 2004.
[8] S. Bruckner, F. Hüffner, R.M. Karp, R. Shamir, and R. Sharan, “Torque: TopologyFree Querying of Protein Interaction Networks,” Nucleic Acids Research, vol. 37, pp. W106W108, 2009.
[9] S. Bruckner, F. Hüffner, R.M. Karp, R. Shamir, and R. Sharan, “TopologyFree Querying of Protein Interaction Networks,” J. Computational Biology, vol. 17, no. 3, pp. 237252, 2010.
[10] M. Cesati, “Perfect Code is W[1]Complete,” Information Processing Letters, vol. 81, pp. 163168, 2002.
[11] J. Chen and J. Meng, “On Parameterized Intractability: Hardness and Completeness,” The Computer J., vol. 51, no. 1, pp. 3959, 2008.
[12] Y. Chen, J. Flum, and M. Grohe, “MachineBased Methods in Parameterized Complexity Theory,” Theoretical Computer Science, vol. 339, nos. 2/3, pp. 167199, 2005.
[13] R. Dondi, G. Fertin, and S. Vialette, “Weak Pattern Matching in Colored Graphs: Minimizing the Number of Connected Components,” Proc. 10th Italian Conf. Theoretical Computer Science (ICTCS '07), vol. 4596, pp. 2738, 2007.
[14] R. Dondi, G. Fertin, and S. Vialette, “Maximum Motif Problem in VertexColored Graphs,” Proc. 20th Ann. Symp. Combinatorial Pattern Matching (CPM '09), LNCS, vol. 5577, pp. 221235, 2009.
[15] B. Dost, T. Shlomi, N. Gupta, E. Ruppin, V. Bafna, and R. Sharan, “Qnet: A Tool for Querying Protein Interaction Networks,” J. Computational Biology, vol. 15, no. 7, pp. 913925, 2008.
[16] R.G. Downey and M.R. Fellows, Parameterized Complexity. Springer, 1999.
[17] M.R. Fellows, “Towards Fully Multivariate Algorithmics: Some New Results and Directions in Parameter Ecology,” Proc. 20th Int'l Workshop Combinatorial Algorithms (IWOCA '09), LNCS, vol. 5874, pp. 210, 2009.
[18] M.R. Fellows, G. Fertin, D. Hermelin, and S. Vialette, “Upper and Lower Bounds for Finding Connected Motifs in VertexColored Graphs,” J. Computer and System Sciences, vol. 77, no. 4, pp. 799811, 2011.
[19] J. Flum and M. Grohe, Parameterized Complexity Theory. Springer, 2006.
[20] S. Guillemot and F. Sikora, “Finding and Counting VertexColored Subtrees,” Proc. 35th Int'l Symp. Math. Foundations of Computer Science (MFCS '10), LNCS, vol. 6281, pp. 405416, 2010.
[21] J. Guo, R. Niedermeier, and S. Wernicke, “Parameterized Complexity of Vertex Cover Variants,” Theory of Computing Systems, vol. 41, no. 3, pp. 501520, 2007.
[22] F. Hüffner, S. Wernicke, and T. Zichner, “FASPAD: Fast Signaling Pathway Detection,” Bioinformatics, vol. 23, no. 13, pp. 17081709, 2007.
[23] F. Hüffner, S. Wernicke, and T. Zichner, “Algorithm Engineering for ColorCoding with Applications to Signaling Pathway Detection,” Algorithmica, vol. 52, no. 2, pp. 114132, 2008.
[24] V. Lacroix, C.G. Fernandes, and M.F. Sagot, “Motif Search in Graphs: Application to Metabolic Networks,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 4, pp. 360368, Oct.Dec. 2006.
[25] R. Niedermeier, Invitation to FixedParameter Algorithms. Oxford Univ. Press, 2006.
[26] R. Niedermeier, “Reflections on Multivariate Algorithmics and Problem Parameterization,” Proc. 27th Int'l Symp. Theoretical Aspects of Computer Science (STACS '10), pp. 1732, 2010.
[27] J. Scott, T. Ideker, R.M. Karp, and R. Sharan, “Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks,” J. Computational Biology, vol. 13, no. 2, pp. 133144, 2006.
[28] SGD project, Saccharomyces genome database, http:/ downloads.yeastgenome.org/. 2010.
[29] R. Sharan and T. Ideker, “Modeling Cellular Machinery through Biological Network Comparison,” Nature Biotechnology, vol. 24, pp. 427433, Apr. 2006.
[30] S. ShenOrr, R. Milo, S. Mangan, and U. Alon, “Network Motifs in the Transcriptional Regulation Network of Escherichia Coli,” Nature Genetics, vol. 31, no. 1, pp. 6468, 2002.
[31] S. Tweedie, M. Ashburner, K. Falls, P. Leyland, P. McQuilton, S. Marygold, G.H. Millburn, D. OsumiSutherland, A. Schroeder, R. Seal, and H. Zhang, “Flybase: Enhancing Drosophila Gene Ontology annotations,” Nucleic Acids Research, vol. 37, pp. 555559, 2009/2010.
[32] S. Wernicke, “Efficient Detection of Network Motifs,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 4, pp. 347359, Oct.Dec. 2006.