Publications

Refereed Journal Publications
The order of authors in all papers is alphabetical, with the exception of the ones involving biologists.
It is customary in theoretical computer science that preliminary versions of papers (typically excluding proofs) appear in refereed conference proceedings, while the full versions of papers are published in refereed journals.
Lila Santean is the same person as Lila Kari .
  1. Simplifying the role of signals in self-assembly. L.Kari, A.Simjour. Accepted in Natural Computing. pdf .
  2. Smart tile self-assembly and replication. L.Kari, A.Simjour. Accepted in Fundamenta Informaticae. pdf
  3. ModMaps3D: An interactive webtool for the quantification and 3D visualization of interrelationships in a dataset of DNA sequences. R. Karamichalis, L.Kari. Accepted in Bioinformatics, DOI , pdf .
  4. Deciding whether a regular language is generated by a splicing system. L.Kari, S.Kopecki. JCSS (Journal of Computers and Systems Sciences), vol.84, 2017, 263-287 pdf
  5. Further remarks on DNA overlap assembly. S. Enaganti, O. Ibarra, L.Kari, S. Kopecki. Information and Computation, 253(1), 2017, 143-154. pdf .
  6. Additive methods for genomic signatures. R.Karamichalis, L.Kari, S.Konstantinidis, S.Kopecki, S.Solis-Reyes. BMC Bioinformatics, 17:313, 2016. pdf
  7. Binary pattern tile set synthesis is NP-hard. L. Kari, S. Kopecki, P.-E Meunier, M. Patitz, S. Seki. Algorithmica, 2016, pages 1-46. pdf
  8. On the overlap assembly of strings and languages. S. Enaganti, O.Ibarra, L.Kari, S.Kopecki. Natural Computing, 16(1) 2016, pages 175-185. pdf
  9. Disjunctivity and other properties of sets of pseudo-bordered words. L.Kari, M.Kulkarni. Acta Informatica, 2016, pages 1-20. pdf
  10. An investigation into inter- and intragenomic variations of graphic genomic signatures. R.Karamichalis, L.Kari, S.Konstantinidis, S.Kopecki. BMC Bioinformatics, 16:246 (2015). Note that the version from the journal's webpage has most figures either missing, or completely misplaced and with wrong captions. Please use the pdf version instead.
  11. Mapping the space of genomic signatures. L.Kari, K.Hill, A.Sayem, R.Karamichalis, N.Bryans, K.Davis, N.Dattani. PLoS ONE 10(5): e0119815. doi:10.1371/journal.pone.0119815, 2015, pdf
  12. A formal language model of DNA Polymerase enzymatic activity. S.Enaganti, L.Kari, S.Kopecki. Fundamenta Informaticae, 138, 2015, 179-192. pdf .
  13. 3-color bounded patterned self-assembly. L.Kari, S .Kopecki, S.Seki. Natural Computing, 14 (2015), 279-292, pdf .
  14. Hypergraph automata: A theoretical model for patterned self-assembly. L.Kari, S.Kopecki, A.Simjour. Intl. Journal of Foundations of Comp. Sci., IJFCS, vol.25, no.4, 2014, 419-439. pdf
  15. Generating the pseudo-powers of a word. L.Kari, M.Kulkarni. Journal of Automata, Languages and Combinatorics (JALC), 19(2014), 1-4, 157-171. pdf .
  16. On the maximality of languages with combined types of code properties. L.Kari, S.Konstantinidis, S. Kopecki. Theoretical Computer Science, 550 (2014), 79-89. pdf
  17. State complexity of star of union and square of union on k regular languages. Y. Gao, L.Kari. Theoretical Computer Science, 499, 2013, 38-50. pdf
  18. The power of nondeterminism in self-assembly. N.Bryans, E.Chiniforooshan, D.Doty, L.Kari, S.Seki. Theory of Computing, vol.9, 2013, 1-29. pdf
  19. Negative interactions in irreversible self-assembly.D.Doty, L.Kari, B.Masson. Algorithmica, vol. 66, issue 1, 2013, 153-172. pdf
  20. State complexity of combined operations with two basic operations. B.Cui, Y.Gao, L.Kari, S.Yu. Theoretical Computer Science, 437, 2012, 82-102. pdf
  21. State complexity of union and intersection of square and reversal on k regular languages. Y.Gao, L.Kari, S.Yu. Theoretical Computer Science, 454, 2012, 164-171. pdf
  22. State complexity of union and intersection of star on k regular languages. Y.Gao, L.Kari, S.Yu. Theoretical Computer Science, vol. 429, 2012, 98-107. pdf
  23. Relativized codes. M.Daley, H.Jurgensen, L.Kari, K.Mahalingam. Theoretical Computer Science, volume 429, 2012, 54-64. pdf
  24. One-reversal counter machines and multihead automata: Revisited. E.Chiniforooshan, M.Daley, O.Ibarra, L.Kari, S.Seki. Theoretical Computer Science, 454, 2012, 81-87. pdf
  25. De Bruijn Sequences Revisited. L.Kari, Z.Xu. International Journal of Foundations of Computer Science, IJFCS, vol.23, no.6, 2012, 1307-1321. pdf
  26. State complexity of two combined operations: catenation-union and catenation-intersection. B.Cui, Y.Gao, L.Kari, S.Yu. Intl. Journal of Foundations of Computer Science, IJFCS, vol.22, issue 8, 2011, 1797-1812. pdf.
  27. Pseudopower avoidance. E.Chiniforooshan, L.Kari, Z.Xu. Fundamenta Informaticae, 114 (2012), 1-18. pdf
  28. On the regularity of iterated hairpin completion of a single word. L.Kari, S.Kopecki, S.Seki. Fundamenta Informaticae, 110(1-4), 2011, 201-215. pdf
  29. Schema for parallel insertion and deletion: Revisited. L.Kari, S.Seki. International Journal of Foundations of Computer Science, IJFCS, vol.22, no. 7, 2011, 1655-1668. pdf
  30. State complexity of two combined operations: catenation-star and catenation-reversal. B.Cui, Y.Gao, L.Kari, S.Yu. Intl. Journal of Foundations of Computer Science, IJFCS, vol.23, no.1, 2012, 51-66. pdf.
  31. Polyominoes simulating arbitrary-neighbourhood zippers and tilings. B.Masson, L.Kari. Theoretical Computer Science, 412(43), 2011, 6083-6100. pdf
  32. K-comma codes and their generalizations. B.Cui, L.Kari, S.Seki. Fundamenta Informaticae, 107, 2011, 1-18. pdf
  33. Properties of pseudo-primitive words and their applications. L.Kari, B.Masson, S.Seki. IJCFS, 22(2), 2011, 447-471. pdf
  34. Block insertion and deletion on trajectories. B.Cui, L.Kari, S.Seki. Theoretical Computer Science, 412(2011), 714-728 pdf
  35. Orthogonal shuffle on trajectories. M.Daley, L.Kari, S.Seki, P.Sosik. IJFCS, 22 (1), 2011, 213-222. pdf
  36. An extension of the Lyndon-Schutzenberger result to pseudoperiodic words. El.Czeizler, Eu.Czeizler, L.Kari, S.Seki. Information and Computation, 209, 2011, 717-730. pdf
  37. An improved bound for an extension of Fine and Wilf's theorem, and its optimality. L.Kari, S.Seki. Fundamenta Informaticae, 101 (3), 2010, 215-236. pdf
  38. Towards a neighborhood simplification of tile systems: From Moore to quasi-linear dependencies, Eu.Czeizler, L.Kari. Natural Computing, 10(2011), 103-117. pdf
  39. Geometrical tile design for complex neighborhoods. Eu.Czeizler, L.Kari. Frontiers in Computational Neuroscience, H.Siegelmann, Ed., 3:20, 2009, doi:10.3389/neuro.10.020.2009. pdf
  40. On a special class of primitive words. El.Czeizler, L.Kari, S.Seki. Theoretical Computer Science, Vol. 411, Issue 3, 2010, 617-630. pdf
  41. Watson-Crick palindromes in DNA computing. L.Kari, K.Mahalingam. Natural Computing, vol.9, nr.2, 2010, 297-316. pdf
  42. The Undecidability of the Infinite Ribbon Problem: Implications for Computing by Self-Assembly. L.Adleman, J.Kari, L.Kari, D.Reishus, P.Sosik. SIAM Journal on Computing, Volume 38, Issue 6, 2009, 2356-2381. pdf
  43. On the descriptional complexity of Watson-Crick automata. El. Czeizler, Eu.Czeizler, L.Kari, K.Salomaa. Theoretical Computer Science, 410(2009) 3250-3260. pdf
  44. Watson-Crick bordered words and their syntactic monoid. L.Kari, K.Mahalingam. International Journal of Foundations of Computer Science, vol.19, nr.5, 2008, 1163-1179. pdf
  45. On pseudoknot-bordered words and their properties. L.Kari, S.Seki. Journal of Computer and System Sciences, 75 (2009) 113-121. pdf
  46. Twin-roots of words and their properties. L.Kari, K.Mahalingam, S.Seki. Theoretical Computer Science, vol. 410, nr.24-25 (2009), 2393-2400. pdf
  47. Involution, solid and join codes. N.Jonoska, L.Kari and K.Mahalingam, Fundamenta Informaticae, 86(2008), 127-142. pdf
  48. On the weight of universal insertion grammars. L.Kari, P.Sosik. Theoretical Computer Science, 396(2008), 264-270. pdf
  49. Involutively bordered words. L.Kari, K.Mahalingam. Int. J. Found. Comput. Sci. 18(5) 2007, 1089-1106. pdf
  50. The syntactic monoid of hairpin languages. L.Kari, K.Mahalingam, G.Thierrin. Acta Informatica, 44(3-4) 2007, 153-166. pdf
  51. K-involution codes and related sets. L.Kari, K.Mahalingam. Journal of Discrete Mathematical Sciences and Cryptograpy, vol.10(2007), no.4, 485-503. pdf
  52. A formal language analysis of hairpin structures. L.Kari, S.Konstantinidis, E.Losseva, P.Sosik, G.Thierrin. Fundamenta Informaticae, vol. 71 , issue 4, 2006, 453 - 475. pdf
  53. Block substitutions and their properties. L.Kari, E.Losseva. Fundamenta Informaticae, 73(2006), 165-178. pdf
  54. Operations on trajectories with applications to coding and bioinformatics. L.Kari, S.Konstantinidis, P.Sosik. International Journal of Foundations of Computer Science, vol. 16, nr.3 (2005), 531-546. pdf
  55. On properties of bond-free DNA languages L.Kari, S.Konstantinidis, P.Sosik. Theoretical Computer Science, vol. 334, no. 1-3 (2005), 131-159. pdf
  56. The spectrum of genomic signatures: From dinucleotides to Chaos Game Representation Y.Wang, K.Hill, S.Singh, L.Kari. GENE, 346 (2005), 173-185. pdf
  57. Results on transforming NFA into DFCA. C.Campeanu, L.Kari, A.Paun. Fundamenta Informaticae, vol. 64 (2005), 53-63. pdf
  58. Bond-free languages: formalizations, maximality and construction methods. L.Kari, S.Konstantinidis, P.Sosik. Int. J. of Foundations of Computer Science, vol. 16 (5), 2005, 1039 - 1070. pdf
  59. Aspects of shuffle and deletion on trajectories L.Kari, P.Sosik. Theoretical Computer Science, vol. 332, no. 1-3 (2005), 47-61. pdf
  60. Language equations, maximality and error-detection L.Kari, S.Konstantinidis. Journal of Computer and System Sciences, 70 (2005), 157-178. pdf
  61. Computationally universal P systems without priorities: two catalysts are sufficient. R.Freund, L.Kari, M.Oswald, P.Sosik. Theoretical Computer Science, vol. 330 (2), 2005, 251-266. pdf
  62. Descriptional complexity of error/edit systems. L.Kari, S.Konstantinidis. Journal of Automata, Languages and Combinatorics, 9 (2004), 2/3, 293-309. pdf
  63. Families of languages defined by ciliate bio-operations M.Daley, L.Kari, I.McQuillan. Theoretical Computer Science, 320 (2004), 51-69. pdf
  64. The ld and dlad bio-operations on formal languages M.Daley, O.Ibarra, L.Kari, I.McQuillan, K.Nakano. Journal of Automata, Languages and Combinatorics, 8 (2003) 3, 477-498. pdf
  65. Closure properties and decision questions of some language classes under ciliate bio-operations. M.Daley, O.Ibarra, L.Kari. Theoretical Computer Science, 306 (1), 2003, 19-38. pdf.
  66. Sticky-free and overhang-free DNA languages L.Kari, S.Konstantinidis, E.Losseva, G.Wozniak. Acta Informatica, 40 (2003), 119-157. pdf
  67. Coding properties of DNA languages. S.Hussini, L.Kari, S.Konstantinidis. Theoretical Computer Science, vol. 290/3, 2003, 1557-1579. pdf
  68. Morphisms preserving densities. H.Jurgensen, L.Kari, G.Thierrin. International Journal of Computer Mathematics, vol. 78 (2), 2001, 165-189. pdf
  69. Shuffle and scattered deletion closure of languages. M.Ito, L.Kari, G.Thierrin. Theoretical Computer Science, vol. 245, issue 1, 2000, 115-133. pdf
  70. Using DNA to solve the Bounded Post Correspondence Problem L.Kari, G.Gloor, S.Yu. Theoretical Computer Science, 231 (2000), 193-203. pdf
  71. Towards a DNA solution to the Shortest Common Superstring Problem. G.Gloor, L. Kari, M.Gaasenbeek, and S.Yu. International Journal of Artificial Intelligence Tools, vol. 8, Nr. 4, 1999. World Scientific Publishers, 385-400. pdf
  72. DNA computing based on splicing: the existence of universal computers. R.Freund, L.Kari, G.Paun. Theory of Computing Systems, vol. 32, 1999, 69-112. pdf
  73. Word insertions and primitivity. L.Kari, G.Thierrin. Utilitas Mathematica, vol. 53, 1998, 49--61. pdf
  74. DNA computing, sticker systems and universality L.Kari, G.Paun, G.Rozenberg, A.Salomaa, S.Yu. Acta Informatica, 35 (1998), 401--420. pdf
  75. Insertion and deletion closure of languages. M.Ito, L.Kari, G.Thierrin. Theoretical Computer Science, 183 (1997) 3--19. pdf
  76. Maximal and minimal solutions to language equations. L.Kari, G.Thierrin. Journal of Computer and System Sciences, vol. 53, no.3 (1996), 487-496. pdf.
  77. Contextual insertions/ deletions and computability. L.Kari, G.Thierrin. Information and Computation, vol. 131, 1 (1996), 47-61. pdf.
  78. The power of restricted splicing with rules from a regular set. L.Kari, G.Paun, A.Salomaa. Journal of Universal Computer Science, 2, 4 (1996). pdf
  79. Omega-syntactic congruences L.Kari, G.Thierrin. Journal of Automata, Languages and Combinatorics, 1 (1996) 1, 13-26. pdf
  80. Test tube distributed systems based on splicing E.Csuhaj-Varju, L.Kari, G.Paun. Computers and Artificial Intelligence, vol. 15, 1996, no. 2--3, 211-232. pdf
  81. Teams in cooperating grammar systems L.Kari, A.Mateescu, Gh.Paun, A.Salomaa. Journal of Experimental and Theoretical Artificial Intelligence, 7 (1995), 347-359. pdf
  82. K-insertion and k-deletion closure of languages L.Kari, G.Thierrin. Soochow Journal of Mathematics, vol. 21, no.4, 1995, 479-495. pdf
  83. Multi-pattern languages L.Kari, Al. Mateescu, Gh.Paun, A.Salomaa. Theoretical Computer Science, 141 (1995), 253-268. pdf
  84. Generalized DOL trees L.Kari, G.Rozenberg, A.Salomaa. Acta Cybernetica, vol. 12 (1995), No.1, 1-9. pdf
  85. K-catenation and applications: k-prefix codes L.Kari, G.Thierrin. Journal of Information and Optimization Sciences, vol. 16 (1995), No.2, 263-276. pdf
  86. Languages and monoids with disjunctive identity L.Kari, G.Thierrin. Collectanea Mathematica, 46, 1-2 (1995), 97-107. pdf
  87. On parallel deletions applied to a word L.Kari, A.Mateescu, Gh.Paun, A.Salomaa. RAIRO-- Theoretical Informatics and Applications, vol. 29 -- 2 (1995), 129-144. pdf
  88. On language equations with invertible operations. L.Kari. Theoretical Computer Science, 132 (1994), 129-150. pdf
  89. Deletion operations: closure properties L.Kari. International Journal of Computer Mathematics, 52 (1994), 23-42. pdf
  90. Some hierarchies for the communication complexity measures of cooperating grammar systems J.Hromkovic, L.Kari, J.Kari. Theoretical Computer Science 127 (1994), 123-147. pdf
  91. Generalized derivatives L.Kari. Fundamenta Informaticae, vol. 18, nr.1, 1993, 27-40. pdf
  92. Deletion sets L.Kari, A.Mateescu, Gh.Paun, A.Salomaa. Fundamenta Informaticae, vol. 19, 1993, 355-370. pdf
  93. Grammars with oracles. L.Kari, A. Mateescu, A.Salomaa, Gh. Paun. Analele Stiintifice ale Universitatii A.I.Cuza din Iasi, Tome II, Informatica, 1993, 1-12. pdf
  94. Semi-commutativity sets of morphisms over finitely generated free monoids L.Kari, Gh.Paun, A.Salomaa. Bulletin Mathematique de la Societe des Sciences Mathematiques de la Roumanie, Tome 36 (84), nr.3-4, 1992, 293-307. pdf
  95. The impact of the number of cooperating grammars on the generative power L.Santean, J.Kari. Theoretical Computer Science, nr.98, 1992, 249-262. pdf
  96. Secret ballot elections in computer networks H.Nurmi, A.Salomaa, L.Santean. Computers and Security, nr.10, 1991, 553-560. pdf
  97. Further remarks on parallel communicating grammar systems G.Paun, L.Santean. International Journal of Computer Mathematics, vol. 34, 1990, 187--203. pdf
  98. On a theorem of Gunter Asser. C.Calude, L.Santean. Zeitschrift fur mathematische Logik und Grundlagen der Mathematik, vol. 36, 1990, 143-147. pdf
  99. Number-theoretic mappings computed by G.S.M.s. G.Paun, L.Santean. Bulletin Mathematique de la Societe des Sciences Mathematiques de la Roumanie, Tome 33 (81), nr.1, 1989, 71-82. pdf
  100. Parallel communicating grammar systems-- the regular case. G.Paun, L.Santean. Analele Universitatii din Bucuresti, Seria matematica-informatica,nr.2, 1989, 55-63. pdf
  101. Six arithmetic-like operations on languages. L.Santean. Revue Roumaine de Linguistique, Tome XXXIII, 1988, Cahiers de linguistique theorique et appliquee, Tome XXV, 1988, No.1, Janvier-Juin, 65-73. Appeared also in Proceedings of International Meeting of Young Computer Scientists (IMYCS 1988), Smolenice Castle, Slovakia, Nov. 1988. pdf
    Refereed Conference Proceedings Publications
  102. Transducer descriptions of DNA code properties and undecidability of antimorphic problems. L.Kari, S.Konstantinidis, S.Kopecki. Proceedings of DCFS 2015, LNCS, vol. 9118, 2015, J.Shallit, A.Okhotin, Eds., 141-152. pdf
  103. Binary pattern tile set synthesis is NP-hard. L.Kari, S.Kopecki, P-E. Meunier, M.Patitz, S.Seki. Proceedings of ICALP 2015. In LNCS, vol. 9134, 2015, M. Halldorsson, K. Iwama, N. Kobayashi, B. Speckmann, Eds., pages 1022-1034. pdf
  104. Hypergraph Automata: A theoretical model for patterned self-assembly. L.Kari, S.Kopecki, A.Simjour. Proceedings of "Unconventional Computation and Natural Computation", UCNC'13. In G.Mauri, A.Dennunzio, L.Manzoni, A.Porreca, Eds., LNCS 7956, 2013, 125-137. pdf
  105. 3-Color bounded patterned self-assembly. L.Kari, S.Kopecki, S.Seki. Proceedings of "DNA Computing and Molecular Programming", DNA19. In D.Soloveichik, B.Yurke, Eds., LNCS 8141, 2013, 105-117. pdf
  106. Deciding whether a regular language is generated by a splicing system. L.Kari, S.Kopecki. In Proceedings of "DNA Computing and Molecular Programming", DNA18. In D.Stefanovic, A.Turberfield Eds., LNCS, vol.7433, 2012, 98-109. pdf
  107. State complexity of star and square of union of k regular languages. Y.Gao, L.Kari. Proceedings of "Descriptional Complexity of Formal Systems", DCFS 2012. In M.Kutrib, N.Moreira, R. Reis, Eds., LNCS, vol. 7386, 2012, 155-168. pdf
  108. Triangular and hexagonal tile self-assembly systems. L.Kari, S.Seki, Z.Xu. Proceedings of Workshop in Theoretical Computer Science, WTCS 2012, M.J.Dineen et al Eds., LNCS 7160 (2012), 357-375. pdf
  109. Iterated hairpin completion of non-crossing words. L.Kari, S.Kopecki, S.Seki. Proc. of SOFSEM 2012: Theory and Practice of Computer Science - 38th Conference on Current Trends in Theory and Practice of Computer Science, Czech Republic. In M.Bielikova, G.Friedrich, G.Gottlob, S.Katzenbeisser, G.Turan (Eds.), LNCS, 7147 (2012), 337-348. pdf
  110. De Bruijn sequences revisited. L.Kari, Z.Xu. Proc. of Automata and Formal Languages. AFL 2011, Debrecen, Hungary, August 17-22, 2011, P. Dömösi, Sz. Iván (Eds.), 241-254. pdf
  111. Scalable, time-responsive, digital, energy-efficient molecular circuits using DNA strand displacement. E.Chiniforooshan, D.Doty, L.Kari, S.Seki. Proc. of International Conference on DNA Computing and Molecular programming, DNA16, Hong Kong, 2010. In Lecture Notes in Computer Science, LNCS, 6518, 2011, Y.Sakakibara, Y.MI, Eds., 25-36. pdf
  112. Negative interactions in irreversible self-assembly. D.Doty, L.Kari, B.Masson. Proc. of International Conference on DNA Computing and Molecular programming, DNA16, Hong Kong, 2010. In Lecture Notes in Computer Science, LNCS, 6518, 2011, Y.Sakakibara, Y.Mi, Eds., 37-48. pdf
  113. Triangular self-assembly. L.Kari, S.Seki, Z.Xu. Proc. of International Conference on DNA Computing and Molecular programming, DNA 16, Hong Kong, 2010. In Lecture Notes in Computer Science, LNCS, vol.6518, 2011, Y.Sakakibara, Y.Mi, Eds., 89-99. pdf
  114. The power of nondeterminism in self-assembly. N.Bryans, E.Chiniforooshan, D.Doty, L.Kari, S.Seki. Proc. of ACM-SIAM Symposium on Discrete Algorithms, SODA 2011, San Francisco, California, USA, January 23-25, 2011, 590-602. pdf
  115. One-reversal counter machines and multihead automata: Revisited. E.Chiniforooshan, M.Daley, O.Ibarra, L.Kari. Proc. of International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2011, Novy Smokovec, Slovakia, Jan. 22-28, 2011. In Lecture Notes in Computer Science, LNCS, 6543, 2011, I.Cerna, T.Gyimothy, J.Hromkovic, K.Jeffery, R.Kralovic, M.Vukolic, S.Wolf, Eds., 166-177. pdf
  116. State complexity of catenation combined with union and intersection. B. Cui, Y. Gao, L. Kari and S. Yu: Proc. of International Conference on Implementation and Application of Automata, CIAA 2010, Winnipeg, Canada. In Lecture Notes in Computer Science, LNCS, 6482, 2011, M.Domaratzki, K.Salomaa, Eds., 95-104. Full version to appear in IJFCS, above.
  117. Ciliate Gene Unscrambling with Fewer Templates L.Kari, A.Rahman. Proc. of Descriptional Complexity of Formal Systems, DCFS 2010, Saskatoon, Canada, I.McQuillan, G.Pighizzini, Eds, 120-129. pdf
  118. State complexity of catenation combined with star and reversal. B.Cui, Y.Gao, L.Kari, S.Yu. Proc. of Descriptional Complexity of Formal Systems 12th Workshop (DCFS 2010), Saskatoon, Canada, 2010, I.McQuillan, G.Pighizzini, Eds, 58-67. pdf
  119. Schema for parallel insertion and deletion. L.Kari, S.Seki. Proc. of Developments in Language Theory, DLT 2010, London, Ontario, Canada. In Lecture Notes in Computer Science, LNCS, 6224, 2010, Y.Gao, H.Lu, S.Seki, S.Yu, Eds., 267-278. pdf
  120. On the reversibility of parallel insertion, and its relation to comma codes. B.Cui, L.Kari, S.Seki. Proc. of Conference on Algebraic Informatics, CAI 2009. In Lecture Notes in Computer Science, LNCS 5275, 2009, S.Bozapalidis, G.Rahonis, Eds., 204-219. pdf
  121. An extension of the Lyndon-Schutzenberger result to pseudoperiodic words. El.Czeizler, Eu.Czeizler, L.Kari, S.Seki. Proc. of Developments in Language Theory, DLT 2009. In Lecture Notes in Computer Science, LNCS, 5583, 2009, V.Diekert, D.Nowotka, Eds., 183-194. pdf.
  122. Towards the sequence design preventing pseudoknot formation, L. Kari, S. Seki. In Proceedings in Information and Communications Technology, PICT 2009, vol.1, Natural Computing, Y.Suzuki, M.Hagiya, H.Umeo, A.Adamatzky, Eds., Springer, 101-110. pdf
  123. On duplications in DNA sequences. M.Ito, L.Kari, Z.Kincaid, S.Seki. Proc. of Developments in Language Theory, DLT 2008. In Lecture Notes in Computer Science, LNCS, 5257, 2008, M.Ito, M.Toyama, Eds., 419-430. pdf
  124. On a special class of primitive words. El.Czeizler, L.Kari, S.Seki. Proc. of Mathematical Foundations of Computer Science, MFCS 2008. In Lecture Notes in Computer Science, LNCS, 5162, 2008, E.Ochmanski, J.Tyszkiewicz, Eds., 265-277. pdf
  125. Watson-Crick automata: determinism and state complexity. El.Czeizler, Eu.Czeizler, L.Kari, K.Salomaa. Proc. of Descriptional Complexity of Formal Systems, DCFS 2008, C.Campeanu, G.Pighizzini, Eds., 121-133. pdf
  126. Watson-Crick conjugate and commutative words. L.Kari, K.Mahalingam. Proc. of DNA Computing 13, DNA13. In Lecture Notes in Computer Science, LNCS, 4848, 2008, M.Garzon, H.Yan, Eds., 273-283. pdf
  127. Watson-Crick bordered words and their syntactic monoid. L.Kari, K.Mahalingam. Unconventional Computing, UC'07, Kingston, Canada, 2007, Proc. of Language Theory in Biocomputing Workshop, M.Domaratzki, K.Salomaa, Eds., 64-75. pdf
  128. Involution, solid and join codes. N.Jonoska, L.Kari and K.Mahalingam, Proc. of Developments in Language Theory, DLT 2006, Santa Barbara, California, June 2006. In Lecture Notes in Computer Science, LNCS, 4036, 2006,, O.Ibarra, Z.Dang, Eds., 192-202. pdf
  129. DNA codes and their properties. L.Kari, K.Mahalingam. Proc. of DNA Computing 12, DNA12, Korea, 2006. In Lecture Notes in Computer Science, LNCS, 4287, 2006, C. Mao, T. Yokomori, Eds., 127-142. pdf
  130. Hairpin structures in DNA words. L.Kari, S.Konstantinidis, E.Losseva, P.Sosik, G.Thierrin. Proc. of DNA Computing 11, DNA11, London, Canada, 2005. In Lecture Notes in Computer Science, LNCS, 3892, 2006, A.Carbone, N.Pierce, Eds., 158-170. pdf
  131. Who counts your votes? H. Kaminski, L.Kari, M. Perry. Proc. of IEEE International Conference on e-Technology, e-Commerce and e-Service, EEE05, IEEE Proceedings, Hong Kong, March 2005, 598-603.pdf
  132. Insertion and deletion for involution codes. L.Kari and K.Mahalingam, Proc. of Conference of Algebraic Informatics, CAI 2005, Thessaloniki, Greece, 2005, S.Bozapalidis, A.Kalampakas, G.Rahonis, Eds., 207-219. pdf
  133. On the weight of universal insertion grammars. L.Kari, P.Sosik. Proc. of Descriptional Complexity of Formal Systems, DCFS 2005, Milano, Italy, C.Mereghetti, B.Palano, G.Pighizzini, D.Wotschke, Eds., 206-214. pdf
  134. Bond-free languages, formalizations, maximality and construction methods. L.Kari, S.Konstantinidis, P.Sosik. Proc. of DNA Computing 10, DNA10, Milano, Italy, June 2004. In Lecture Notes in Computer Science, LNCS, 3384, 2005, C.Ferreti, G.Mauri, C.Zandron, Eds., 169-181. pdf
  135. Preventing undesirable bonds between DNA codewords. L.Kari, S.Konstantinidis, P.Sosik. Proc. of DNA Computing 10, DNA10, Milano, Italy, June 2004. In Lecture Notes in Computer Science, LNCS, 3384, 2005, C.Ferreti, G.Mauri, C.Zandron, Eds., 182-191. pdf
  136. On hairpin-free words and languages. L.Kari, S.Konstantinidis, P.Sosik, G.Thierrin. Proc. of Developments in Language Theory, DLT 2005. In Lecture Notes in Computer Science, LNCS, 3572, 2005, C.Di Felice, A.Restivo, Eds., 296-307. pdf
  137. Substitutions, trajectories and noisy channels. L.Kari, S.Konstantinidis, P.Sosik. Proc. of Conference on Implementation and Application of Automata, CIAA 2004, Kingston, Canada. In Lecture Notes in Computer Science, LNCS, 3317, 2005, M.Domaratzki, A.Okhotin, K.Salomaa, S.Yu, Eds., 202-212. pdf
  138. DNA involutions and hairpin structures. L.Kari, E.Losseva, S.Konstantinidis, P.Sosik, G.Thierrin. In Proc. of Grammar Systems Week 2004, Budapest, Hungary, E.Csuhaj-Varju, G.Vaszil, Eds., MTA Sztaki, 188-200. pdf
  139. Computing the Hamming distance of a regular language in quadratic time. L. Kari, S. Konstantinidis, S. Perron, G. Wozniak, J. Xu. In Proc. of WSEAS International Conference on Computers, Vouliagmeni, Greece, July 12-15, 2004. In WSEAS Transactions on Information Science & Applications, Issue 1, vol.1, 2004, 445-449. pdf
  140. Static and dynamic properties of DNA languages. L.Kari, S.Konstantinidis. Proc. of Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Cancun,Mexico, 2003, 3846-3849. pdf
  141. Some properties of ciliate bio-operations. M.Daley, L.Kari. Proce. of International Conference on Developments in Language Theory, DLT 2002, Kyoto, Japan. In Lecture Notes in Computer Science, LNCS, 2450, 2003, M.Ito, M.Toyama, Eds., 117-127. pdf
  142. On the decidability of self-assembly of infinite ribbons. L.Adleman, J.Kari, L.Kari, D.Reishus. Proc. of IEEE Symposium on Foundations of Computer Science, FOCS 2002, IEEE Computer Society Press, Washington, 530-537. pdf
  143. Descriptional complexity of error/edit systems. L.Kari, S.Konstantinidis. Proc. of Descriptional Complexity of Formal Systems, DCFS 2002, London, Canada, J.Dassow, H.Jurgensen, D.Wotschke Eds., 133-147. (Preliminary version of a paper in JALC, 2004, above)
  144. Coding properties of DNA languages. S.Hussini, L.Kari, S.Konstantinidis. Proc. of DNA Based Computers 7, DNA7, Tampa, Florida. In Lecture Notes in Computer Science, LNCS, 2340, 2002, N.Jonoska, N.Seeman, Eds., 57-69. pdf
  145. Computational power of gene rearrangement. L.Kari, L.F.Landweber. Proc. of DNA Based Computers V, DNA5, MIT, Boston, June 1999. In DIMACS Series, vol.54, 2000, E.Winfree, D.Gifford, Eds., AMS Press, 207-216. pdf
  146. The evolution of cellular computing: Nature's solution to a computational problem. L.F.Landweber, L.Kari. Proc. of DNA Based Computers IV, DNA4. In In Biosystems, vol.52, no.1-3, 1999, L.Kari, H.Rubin, D.Wood, Eds., Elsevier, 3-13. pdf.
  147. At the crossroads of DNA computing and formal languages: Characterizing recursively enumerable languages by insertion-deletion systems. L.Kari, G.Paun, G.Thierrin, S.Yu. Proc. of DNA Based Computers III (DNA3). In DIMACS Series, vol.48, 1999, H.Rubin, D.Wood, Eds., AMS Press, 329-347. pdf
  148. DNA computing based on splicing: universality results. E.Csuhaj-Varju, R.Freund, L.Kari, G.Paun. Proc. of Annual Pacific Symposium on Biocomputing, Hawaii 1996, L.Hunter, T.Klein, eds., World Scientific Publ., 1996, 179-190. pdf
  149. Morphisms and associated congruences. L.Kari, G.Thierrin. Proc. of Developments in Language Theory, DLT II. In At the crossroads of mathematics, computer science and biology, 1996, J.Dassow, G.Rozenberg, A.Salomaa, Eds., World Scientific, 119-128. pdf
  150. Subapical bracketed L-systems. P.Prusinkiewicz, L.Kari. Proc. of International Workshop on Graph Grammars and their Applications to Computer Science. In Lecture Notes in Computer Science, LNCS, 1073, 1996, 550-564. Early version ''Subapical L-systems`` appeared in the Proc. of the workshop Artificial Life: Grammatical Models, Black Sea University Press, Bucharest, Romania, 1995, 116-121. pdf
  151. Two lower bounds on distributive generation of languages. J.Hromkovic, J.Kari, L.Kari, D.Pardubska. Proc. of Mathematical Foundations of Computer Science, MFCS 1994. In Lecture Notes in Computer Science, LNCS, 841, 1994, I.Privara, B.Rovan, P.Rudzicka, Eds., 423-433. pdf
  152. Some hierarchies for the communication complexity measures of cooperating grammar systems. J.Hromkovic, L.Kari, J.Kari. Proc. of Mathematical Foundations of Computer Science, MFCS 1993. In Lecture Notes in Computer Science, LNCS, 711, 1993, A.Borzyszkowski, S.Sokolowski, Eds. 495-505. pdf
  153. Insertion and deletion of words: determinism and reversibility. L.Kari. Proc. of Mathematical Foundations of Computer Science, MFCS 1992. In Lecture Notes in Computer Science, LNCS, 629, 1992, I.Havel, V.Koubek, Eds., 315-327. pdf
  154. A hierarchy of unary primitive recursive string-functions. L.Santean. Proc. of International Meeting of Young Computer Scientists, IMYCS 1990. In Lecture Notes in Computer Science, LNCS, 464, 1990, J.Dassow, J.Kelemen, Eds., 225-233. Appeared also in Analele Stiintifice ale Universitatii Al.I.Cuza din Iasi, Seria informatica, nr.35, 1989, 323-327. pdf
    Refereed Invited Papers
  155. Methods for relativizing properties of codes. H.Jurgensen, L.Kari, S.Kopecki. Acta Cybernetica, 22(2), 2015, pp.259-292. pdf
  156. Pseudo-identities and bordered words. L.Kari, M.Kulkarni. In "Discrete Mathematics and Computer Science", G.Paun, G.Rozenberg, A.Salomaa, Eds., Editura Academiei Romane, 2014, 207-222. pdf .
  157. The many facets of natural computing L.Kari, G.Rozenberg. Communications of the ACM, vol.51, no.10, 2008 (cover page) 72-83. pdf
  158. Involution solid codes. L.Kari and K.Mahalingam, In Nanotechnology: Science and Computation. J.Chen, N.Jonoska, G.Rozenberg, Eds., in Natural Computing Series, Springer Verlag, Berlin, 2006, 137-146. pdf
  159. On the universality of P systems with minimal symport/antiport rules. L.Kari, C.Martin-Vide, A.Paun. In Lecture Notes in Computer Science, LNCS, 2950, 2004, Jonoska, Gh. Paun and G. Rozenberg, Eds., 254-266. pdf
  160. Substitutions on trajectories. L.Kari, S.Konstantinidis, P.Sosik.In Lecture Notes in Computer Science, LNCS, 3113, 2004, J.Karhumaki, G.Maurer, G.Paun, G.Rozenberg, Eds., 145-159. pdf
  161. Codes, involutions and DNA encodings. L.Kari, R.Kitto, G.Thierrin. In Lecture Notes in Computer Science, LNCS, 2300, 2002, W.Brauer, H.Ehrig, J.Karhumaki, A.Salomaa, Eds., 376-393. pdf
  162. Universal molecular computation in ciliates. L.F.Landweber, L.Kari. In Proc. of Evolution as Computation. In Natural Computing Series, Springer Verlag, L.F.Landweber, E.Winfree, Eds., 2002, 257-274. pdf
  163. Context-free recombinations. J. Kari, L.Kari. In Where mathematics, computer science, linguistics and biology meet,C.Martin-Vide, V.Mitrana, Eds., Kluwer, 2001, 361-375. pdf
  164. String operations suggested by DNA biochemistry: the balanced cut operation. L.Kari, A.Paun. In Words, Semigroups and Transductions, M.Ito, G.Paun, S.Yu, eds., World Scientific Series in Computer Science, World Scientific, Singapore, 2001, 275-289. pdf
  165. Reversible molecular computation in ciliates. L.Kari, J.Kari, L.F.Landweber. In Jewels are Forever, Karhumaki, J.,Maurer, H., Paun, G., Rozenberg, G., Eds., Springer-Verlag 1999, 353-363. pdf
  166. Circular contextual insertions/ deletions with applications to biomolecular computation. M.Daley, L.Kari, G.Gloor, R.Siromoney. Proc. of International Symposium on String Processing and Information Retrieval, SPIRE 1999, Cancun, Mexico,IEEE Computer Society Press, Los Alamitos, California, 1999, 47-54. pdf
  167. Bringing PC Grammar Systems closer to Hoare's CSP. L.Kari, H.Lutfiyya, G.Paun. C.Martin-Vide. Grammatical Models of Multi-Agent Systems. In Topics in Computer Mathematics Series, vol. 8, Gh.Paun, A.Salomaa, Eds., Gordon and Breach, 1999, 64-86. pdf
  168. Towards a DNA solution to the Shortest Common Superstring Problem. Proc. of IEEE International Joint Symposia on Intelligence and Systems, Rockville, MD, 1998, 140-145. pdf
  169. Languages and compatible relations on monoids. L.Kari, G.Thierrin. Mathematical Linguistics and Related Topics, edited by Gh.Paun, Ed. Academiei Romane, Bucuresti 1995, 212-220. pdf
  170. Aperiodic languages and generalizations. L.Kari, G.Thierrin. In Mathematical Aspects of Natural and Formal Languages, World Scientific Series in Computer Science, vol. 43, 1994, Gh.Paun, Ed., 233-243. pdf
    Invited Book Chapters
  171. DNA Computing: Foundations and Implications. L.Kari, S.Seki, P.Sosik. In Handbook for Natural Computing, G.Rozenberg, T.Back, J.Kok, Eds., Springer Verlag, vol.3, 2012, 1073-1127. pdf
  172. DNA Computing: A Research Snapshot. L.Kari, K.Mahalingam. In Algorithms and Theory of Computation Handbook, M. Atallah and M. Blanton, Eds., Second Edition (two volume set), Vol. "Special Topics and Techniques", CRC Press 2010, 31-1 -- 31-24. pdf
  173. DNA Computing and errors: a computer science perspective. L.Kari, E.Losseva, P.Sosik. In Molecular Computational Models: Unconventional Approaches, Marian Gheorghe, Ed., Idea Group Publishing, Hershey, 2005, 56-77. pdf
  174. Biocomputation in ciliates. L.Kari, L.F.Landweber. In Cellular Computing, M.Amos, Ed., Oxford University Press, 2004, 202-216. pdf
  175. Computing with DNA. L.Kari, L.F.Landweber. In Bioinformatics: Methods and Protocols, S.Misener, S.Krawetz, Eds. In Methods in Molecular Biology series, vol. 132, Humana Press, New Jersey, 2000, 413-431. pdf
  176. L-systems. L.Kari, G.Rozenberg, A.Salomaa. In volume 1 of Handbook of Formal Languages, Springer-Verlag, 1997, 253-328. pdf
  177. Power of controlled insertion and deletion. L.Kari. Proc. of Results and Trends in Theoretical Computer Science, Graz, Austria, In Lecture Notes in Computer Science, 812, 1994, J. Karhumaki, H.Maurer, G.Rozenberg, Eds., 197-212. pdf
    Invited Survey Papers
  178. DNA computing: Models and implementations. M.Daley, L.Kari. Comments on Theoretical Biology, vol. 7, No.3, 2002, 177-198. pdf
  179. A computer scientist's guide to molecular biology L.Kari, R.Kitto, G.Gloor. In Soft Computing, Springer Verlag, vol.5, nr.2, 2001, G.Paun,T.Yokomori, Eds., 95-101. pdf
  180. Biocomputing: an application for micro-arrays? L.Kari. In SIGBIO Newsletter, Special Interest Group on BioMedical Computing of the Association for Computing Machinery, vol. 21, Nr.1, 2001, ACMPress, 10-15. pdf
  181. DNA computing in vitro and in vivo. L.Kari. Proc. of Theory and Mathematics in Biology and Medicine, Amsterdam, June 29-July 3, 1999. In Future Generation Computer Systems, vol.17, nr.7, 2001, 823-834. pdf
  182. L'ordinateur biologique, pour demain? L.Kari, L.F.Landweber. In Cahiers de Sciences \& Vie, No.53, 1999, 88-93. (In French.) pdf
  183. How to compute with DNA. L.Kari, M.Daley, G.Gloor, R.Siromoney, L.F.Landweber. Proc. of Foundations of Software Technology and Theoretical Computer Science, December 1999, Chennai, India. In Lecture Notes in Computer Science, 1738, 1999,C.Pandu Rangan, R.Ramanujam, Eds., 269-282. pdf
  184. The evolution of DNA Computing: Nature's solution to a combinatorial problem. L.F.Landweber, and L. Kari. Proc. of Genetic Programming 1998, July 22-25, 1998, J.Koza, W.Banzhaf, K.Chellapilla, K.Deb, M.Dorigo, D.Fogel, M.Garzon, D.Goldberg, H.Iba, R.Riolo, Eds., Morgan Kaufmann Publishers, San Francisco, 700-708.
  185. From Microsoft to Biosoft: Computing with DNA. L.Kari. Proc. of Bio-Computing and Emergent Computation, BCEC 1997, Skovde, Sweden, D.Lundh, B.Olsson, A.Narayanan, Eds., World Scientific, 146--164. pdf
  186. DNA computers. L.Kari, Y.Sakakibara. Journal of the Institute of Electronics, Information and Communication Engineers, vol.80, no.9, 1997, 935-939 (in Japanese) . pdf
  187. DNA computing -- The arrival of biological mathematics. L.Kari. The Mathematical Intelligencer, vol.19, 2, 1997, 9-22. pdf
  188. DNA computing based on insertions and deletions. L.Kari. Proc. of Conceptual tools for understanding dynamics in biological systems, London, 1996. In COENOSES, C.E.T.A. Gorizia, Italy, N. Kenkel, Ed., vol.12, 2-3, 1997, 89-95. pdf
  189. DNA computers: tomorrow's reality. L.Kari. In European Association of Theoretical Computer Science, EATCS, Bulletin, no.59, 1996, 256-266. pdf
  190. Invertible insertion and deletion operations. L.Kari. Proc. of International Meeting of Young Computer Scientists, IMYCS 1992. In Topics in Computer Mathematics, Gordon and Breach Science Publishers, vol. 6, 1994, 45-59. pdf
  191. Insertion operations: closure properties L.Kari. European Association of Theoretical Computer Science (EATCS) Bulletin, nr.51, 1993, 181-191. pdf
  192. In the prehistory of formal language theory: Gauss languages. L.Kari, S.Marcus, Gh.Paun, A.Salomaa. In World Scientific Series in Computer Science -- Essays and Tutorials, vol. 40, 1993, 551-562. Preliminary version appeared in European Association of Theoretical Computer Science (EATCS) Bulletin, nr.46, 1991, 124-139. pdf
  193. Parallel communicating grammar systems. L.Santean. In World Scientific Series in Computer Science -- Essays and Tutorials, vol. 40, 1993, 603-615. Preliminary version appeared in European Association of Theoretical Computer Science (EATCS) Bulletin, nr.42, 1990, 160-171. pdf
  194. Secret selling of secrets with several buyers. A.Salomaa, L.Santean. European Association of Theoretical Computer Science (EATCS) Bulletin, nr.42, 1990, 178--186. pdf
    Books and Edited Works
  195. Special Issue on Unconventional Computation and Natural Computation, with selected papers from UCNC 2014, O.Ibarra, L.Kari, S.Kopecki, Eds., Natural Computing, vol.15, issue 1, 2016, 194 pages.
  196. 40th Anniversary of Theoretical Computer Science, Virtual Special Issue of "Theoretical Computer Science", G.Ausiello, L.Kari, D. Sannella, Eds., 2015.
  197. Unconventional Computation and Natural Computation, 13th International Conference, UCNC 2014, London, ON, Canada, July 14-18, 2014, Proceedings, Lecture Notes in Computer Science, LNCS, 8553(2014), Springer Verlag, O.Ibarra, L.Kari, S.Kopecki, Eds., 394 pages.
  198. Handbook for Natural Computing, Eds., Springer Verlag, 2012. G.Rozenberg, T.Back, J.Kok, Eds.; L. Kari -- Area Editor for Molecular Computing, 2,100 pages.
  199. Pre-Proceedings of The 11th International Meeting on DNA Computing (DNA11). A.Carbone, M.Daley, L.Kari, I.McQuillan, N.Pierce, June 2005, 415 pages.
  200. Proceedings of The 4th International Meeting on DNA-Based Computers (DNA4). L.Kari, H.Rubin, D.Wood, eds., Special issue of Biosystems, vol. 52, nr. 1-3, 1999, Elsevier, pages 1-246.
  201. On Insertion and Deletion in Formal Languages. L.Kari. Ph.D. Thesis, University of Turku, 1991. Cover page , Title page , ISBN , Acknowledgements , Part I , Part II .
    Other Research Publications
  202. On language equations with deletion. L.Kari, P.Sosik. European Association of Theoretical Computer Science (EATCS) Bulletin, nr.83, 2004, 173-180.
  203. On the construction and properties of bond-free DNA languages. L.Kari, S.Konstantinidis, P.Sosik, Abstracts of Papers Presented to the American Math. Society, 24 (4), 2003.
  204. Language deletion on trajectories. L.Kari, P.Sosik. Dept. of Computer Science Technical Report 606, Univ. of Western Ontario, 2003.
  205. Finite-state error-edit systems and difference measures for languages and words. L.Kari, S.Konstantinidis, S.Peron, G.Wozniak, J.Xu. Technical Report 2003-01, Dept.Math. and Computing Sci., Saint Mary's Univ., April 2003, 10 pages.
  206. Criptografie cu Chei Publice. A. Salomaa Editura militara, Bucuresti, 1993, 253 pages. translated by L.Kari, M.Andrasiu from Public Key Cryptography.
  207. Tagged symbols for parallel unification. L.Santean. Studies and Researches in Computers and Informatics, I.T.C.I., Bucharest, vol. 1, 1989, 121-123.
  208. Parallel communicating grammar systems: a grammatical approach to parallel processing. I.Georgescu, G.Paun, L.Santean. Research report PKPS-14-89, Institute for Computers and Informatics, Bucharest, 1989, 1-37.
  209. On some classes of hypercubes. I.Georgescu, L.Santean. Buletinul Roman de Informatica si Tehnica de Calcul, I.T.C.I., vol. 9,nr.3, 1988, 37-48 (in Romanian).
  210. Twisted hypercubes for multiprocessor architectures. L.Santean. Proc. of Conference on Informatics and Technology (INFOTEC 1988), Bucharest, Lucrarea 3, 9-19, 1988, 728-733 (in Romanian).
    Articles Submitted to Refereed Journals or Conferences
  211. An efficient algorithm for computing the edit distance of a regular language via input-altering transducers. L.Kari, S.Konstantinidis, S.Kopecki, M. Yang. pdf .
  212. Relative Watson-Crick primitivity of words. L.Kari, M.Kulkarni, K.Mahalingam. pdf .
  213. Transducer descriptions of DNA code properties and undecidability of antimorphic problems. L.Kari, S.Konstantinidis, S.Kopecki. pdf .