Publications by Michael Domaratzki

• S. Ravichandran, R. Ragupathy, T. Edwards, M. Domaratzki, S. Cloutier MicroRNA-guided regulation of heat stress response in wheat, BMC Genomics, 2019.
• A. Hogan and 16 others, Competitive Fitness of Essential Gene Knockdowns Reveals a Broad-Spectrum Antibacterial Inhibitor of the Cell Division Protein FtsZ, Antimicrobial Agents and Chemotherapy, 2018.
• A. Gislason, K. Turner, M. Domaratzki, S. Cardona, Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia Microbial Genomics, 2017.
• E. Marinier, R. Zaheer, C. Berry, K. Weedmark, M. Domaratzki, P. Mabon, N. Knox, A. Reimer, M. Graham, L. Chui, L. Patterson-Fortin, J. Zhang, F. Pagotto, J. Farber, J. Mahony, K. Seyer, S. Bekal, C. Tremblay, J. Isaac-Renton, N. Prystajecky, J. Chen, P. Slade, G. Van Domselaar, Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations Nucleic Acids Research, 2017.
• R. Ragupathy, S. Ravichandran, Md. Mahdi, D. Huang, E. Reimer, M. Domaratzki and S. Cloutier, Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV, Scientific Reports, 2016.
• M. Ayat and M. Domaratzki, Prediction of Insertion-Site Preferences of Transposons Using Support Vector Machines and Artificial Neural Networks, ANNPR 2014.
• A. Roche-Lima, M. Domaratzki and B. Fristensky, Metabolic Network Prediction Through Pairwise Rational Kernels, BMC Bioinformatics, 2014.
• A. Roche-Lima, M. Domaratzki and B. Fristensky, Pairwise Rational Kernels Obtained by Automaton Operations, CIAA 2014.
• M. Domaratzki and N. Rampersad, Abelian Primitive Words (LNCS version). DLT 2011, LNCS 6795.
• E. Charlier, M. Domaratzki, T. Haru and J. Shallit, Finite Orbits of Language Operations Intl. J. Comput. Math., 2013. (LNCS version: LATA 2011, LNCS 6638.)
• M. Domaratzki, Minimality in template-guided recombination. Information and Computation, vol 207 (2009), pp. 1209-1220
• M. Domaratzki and A. Okhotin, State Complexity of Power. Theoretical Computer Science, vol 410, n 24-25 (2009) 2377-2392.
• M. Domaratzki and K. Salomaa, Lower Bounds for the Transition Complexity of NFAs. JCSS, vol 74, n. 7 (2008) 1116-1130.
• M. Domaratzki, Equivalence in Template-Guided Recombination. (journal version) Natural Computing, vol 7, n. 3 (2008) 439-449.
• (with M. Daley and A. Morris) Intra-molecular Template-Guided Recombination (journal version) International Journal of Foundations of Computer Science, vol. 18, n. 6 (2007) 1177-1186.
• (with K. Salomaa) Transition Complexity of Language Operations. Theoretical Computer Science, vol 387, n. 2 (2007) 147-154.
• Hairpin Structures Defined by DNA Trajectories. (journal version) Theory of Computing Systems, vol 44, n. 3 (2009) 432-454.
• (with M. Daley) On Codes Defined by Bio-operations (journal version). Theoretical Computer Science, vol. 378, n. 1 (2007) pp. 3-16.
• (with P. Sosik and A. Rodriguez-Paton) Algebraic Properties of Substitution on Trajectories (journal version). Theoretical Computer Science, vol. 369, n. 1-3 (2006) pp. 183-196.
• Enumeration of Formal Languages. Bull. EATCS, vol. 89 (June 2006), 113-133.
• (with K. Salomaa) Lower Bounds for the Transition Complexity of NFAs (technical report version) MFCS 2006, LNCS 4162, pp. 315--326.
• (with K. Salomaa) Transition Complexity of Language Operations. Proceedings of DCFS 2006, Las Cruces, NM, 2006, pp. 141-152.
• Hairpin Structures Defined by DNA Trajectories. (technical report version) Proceedings of DNA 12, LNCS 4287, pp. 182--194.
• Characterizing DNA Bond Shapes Using Trajectories (proceedings version). DLT 2006, Santa Barbara, California. LNCS 4036, pp. 180-191.
• (with G. Rozenberg and K. Salomaa) Interpreted Trajectories. (journal version) Fundamenta Informaticae, vol. 73, n. 1-2 (2006), pp. 81--97.
• Bond-free DNA Language Classes. (technical report version) Natural Computing, vol 6, n 4 (2007) 371-402.
• (with K. Salomaa) Codes defined by Multiple Sets of Trajectories. (journal version) TCS, vol 366, n. 3 (2006) 182-193.
• (with K. Salomaa) Restricted sets of trajectories and decidability of shuffle decompositions (journal version). IJFCS, vol 16, n. 5 (2005) 897-912.
• (with K. Ellul, J. Shallit and M.-W. Wang) Non-Uniqueness and Radius of Cyclic Unary NFAs. (journal version). IJFCS, vol 16, n. 5 (2005) 883-896.
• (with K. Salomaa) State Complexity of Shuffle on Trajectories. Journal of Automata, Languages and Combinatorics vol. 9, no. 2-3 (2004) pp. 217-232.
• (with K. Salomaa) Decidability of Trajectory-Based Equations, TCS, vol. 345, no. 2-3, 2005, pp. 304-330.
• (with A. Okhotin and J. Shallit) Enumeration of Context-Free Languages. Proceedings of DCFS 2005, pp. 85-96.
• More Words on Trajectories. Bull. EATCS, vol. 86 (June 2005), 107-145.
• (with K. Salomaa) Codes defined by Multiple Sets of Trajectories. AFL 2005, pp. 97-111.
• Combinatorial Interpretations of a Generalization of the Genocchi Numbers. Journal of Integer Sequences, 7 (2004) Article 04.3.6.
• (with M. Daley) On Codes Defined by Bio-operations. DLT 2004, LNCS 3340, pp. 127-138.
• Semantic Shuffle on and Deletion along Trajectories. DLT 2004, LNCS 3340, pp. 163-174.
• Trajectory-Based Operations. Ph.D Thesis, Queen's University, Kingston, ON, August 2004.
• (with K. Salomaa) Restricted sets of trajectories and decidability of shuffle decompositions. In L. Ilie and D. Wotschke (eds.), Descriptional Complexity of Formal Systems (DCFS), Pre-proceedings, 2004, pp. 37-51.
• (with K. Ellul, J. Shallit and M.-W. Wang) Non-Uniqueness and Radius of Cyclic Unary NFAs. In L. Ilie and D. Wotschke (eds.), Descriptional Complexity of Formal Systems (DCFS), Pre-proceedings, 2004, pp. 178-190.
• (with K. Salomaa) Decidability of Trajectory-Based Equations, In Mathematical Foundations of Computer Science 2004: 29th International Symposium, MFCS 2004. LNCS 3153, Springer, 2004. pp. 723-734.
• Trajectory-Based Embedding Relations (journal version). Fundamenta Informaticae, vol. 59, n. 4 (2004) 349-363.
• Deletion along Trajectories (journal version). Theoretical Computer Science, vol. 320, n. 2-3 (2004) 293-313.
• Trajectory-Based Codes (journal version). Acta Informatica, vol. 40, n. 6-7 (2004) 491-527.
• (with A. Okhotin) Representing Recursively Enumerable Languages by Iterated Deletion. (journal version) Theoretical Computer Science, vol. 314., n. 3 (2004) pp. 451-457.
• Improved Bounds on the Number of Automata Accepting Finite Languages (journal version) International Journal of Foundations of Computer Science, vol. 15, n. 1 (2004) pp. 143-161.
• (with A. Mateescu, K. Salomaa and S. Yu) Deletion on Trajectories and Commutative Closure. In Proceedings of WORDS'03: 4th International Conference on Combinatorics on Words (Turku, Finland). T. Harju and J. Karhumaki, eds. TUCS General Publication No. 27, Aug. 2003. pp. 309-319.
• On Iterated Scattered Deletion. Bull. EATCS, vol. 80 (June 2003), pp. 159-161. Revised Version (18 July 2003).
• On Enumeration of Müller Automata. In Developments in Language Theory (DLT 2003, Szeged, Hungary). Z. Esik and Z. Fulop, eds. LNCS 2710, Springer, 2003. pp. 254-265.
• (with J. Shallit and D. Kisman) On the Number of Distinct Languages Accepted by Finite Automata with n States, Journal of Automata, Languages and Combinatorics, vol. 7, n. 4 (2002) pp. 469-486.
• State Complexity and Proportional Removals. Journal of Automata, Languages and Combinatorics, vol. 7, n. 4 (2002) pp. 455-468. (conference version: DCAGRS 2001)
• (with A. Okhotin and K. Salomaa) One-Visit Caterpillar Tree Automata, Fundamenta Informaticae, vol. 52, n. 4 (2002), pp. 361-375.
• Improved Bounds on the Number of Automata Accepting Finite Languages. In Developments in Language Theory (DLT 2002, Kyoto, Japan). M. Ito and M. Toyama, eds. LNCS 2450, Springer, 2003. pp. 209-220.
• (with K. Salomaa) State Complexity of Shuffle on Trajectories. Pre-Proc. DCFS 2002 (London, ON), pp. 95-109.
• (with G. Pighizzini and J. Shallit) Simulating Finite Automata with Context-free Grammars. Information Processing Letters, vol. 84, no. 6 (2002), pp. 339-344.
• (with J. Shallit and D. Kisman) On the Number of Distinct Languages Accepted by Finite Automata with n States. Proceedings, Descriptional Complexity of Automata, Grammars and Related Structures (DCAGRS 2001), pp. 67-78.
• (with S. Yu and J. Shallit) Minimal Covers of Formal Languages. in W. Kuich, G. Rozenberg and A. Salomaa, eds., Developments in Language Theory (DLT 2001), LNCS 2295, Springer, 2001, pp. 319-329.
• Minimal Covers of Formal Languages M.Math Thesis, University of Waterloo, Waterloo, ON., 2001

mdomarat a@t cs d.ot umanitoba d.ot ca