Refereed Journal Publications
The order of authors in all papers is alphabetical, with the exception of the ones involving biologists, where we follow the author-order conventions in the field.
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. Z. Gharaee, S. Lowe, Z. Gong, P. Millan Arias, N. Pellegrino, A. Wang, J. Bruslum Haurum, I. Zarubiieva, L. Kari, D. Steinke, G. Taylor, P. Fieguth, A. Chang. BIOSCAN-5M: A Multimodal Dataset for Insect Biodiversity. pdf
  2. F.Alipour, K.Hill, L.Kari. CGRclust: Chaos Game Representation for twin contrastive clustering of unlabelled DNA sequences. BMC Genomics, 25:1214 (2024). pdf
  3. F.Alipour, C.Holmes, Y.Y. Lu, K.Hill, L.Kari. Leveraging machine learning for taxonomic classification of emerging astroviruses. Frontiers in Molecular Biosciences, published January 2024 (vol.10, 2023). pdf .
  4. P. Millan Arias, J.Butler, G.Randhawa, M. Soltysiak, K.Hill, L.Kari. Environment and taxonomy shape the genomic signature of prokaryotic extremophiles. Nature Scientific Reports, issue 13, no. 16105, 2023. pdf .
  5. P. Millan Arias, K. Hill, L.Kari. iDeLUCS: A deep learning tool interactive tool for alignment-free clustering of DNA sequences. Bioinformatics, 39(9), 2023, btad508. pdf .
  6. W.Li, L.Kari, Y.Yu, L. Hug. MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenome-assembled genomes. PLOS ONE, 18(8), 2023, e0283536 pdf .
  7. D.Chen, G.Randhawa, M.Soltysiak, C. de Souza, L.Kari, S.Singh, K.Hill. Mutational patterns observed in SARS-CoV-2 genomes sampled from successive epochs delimited by major public health events in Ontario, Canada: Genomic surveillance study. JMIR Bioinformatics and Biotechnology, 3 (1), 2022, e42243. pdf .
  8. D.Chen, G.Randhawa, M.Soltysiak, C. de Souza, L.Kari, S.Singh, K.Hill. SomaticSimu: A mutational signature simulator. Bioinformatics, 38(9), 2022, 2619-2620. pdf
  9. P. Millan Arias, F.Alipour, K.Hill, L.Kari. DeLUCS - Deep learning for unsupervised clustering of DNA sequences. PLoS ONE, 17(1): e0261531, 2022 pdf .
  10. L.Kari, K.Mahalingam, P.Pandok, Z. Wang. Primitivity of atom Watson-Crick Fibonacci words. Journal of Automata, Languages and Combinatorics (JALC), 27(1-3), 2022, 151-178. pdf
  11. A. Sudalaiyadum Perumal, Z. Wang, G. Ippoliti, F. van Delft, L. Kari, D. Nicolau. As good as it gets: A scaling comparison of DNA computing, network biocomputing, and electronic computing approaches to an NP-complete problem. New Journal of Physics, vol.23, 2021 pdf
  12. L.Kari, M.Kulkarni, K.Mahalingam, Z.Wang. Involutive Fibonacci words. JALC (Journal of Automata, Languages, and Combinatorics), nr. 26 (2021), vol 3-4, pages 255-280. pdf
  13. F.Bellamoli, G.Franco, L.Kari, S.Lampis, T.Ng, Z.Wang. Conjugate word blending – Formal model and experimental implementation by XPCR . Natural Computing, 20(2021), 647-658. pdf
  14. L.Kari. T.Ng. Descriptional complexity of semi-simple splicing systems. International Journal of Foundations of Computer Science (IJFCS), vol.32, issue 06 (2021), pp. 685-711. pdf .
  15. J.Brzozowski, L.Kari, B.Li, M.Szykula. State complexity of overlap assembly. International Journal of Foundations of Computer Science (IJFCS), vol.31, issue 8 (2020), 1113-1132. pdf
  16. G.Randhawa, M.Soltysiak, H. El Roz, C. de Souza, K.Hill, L.Kari. Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study. PLOS ONE 16(1): e0246465, 2020 pdf
  17. S.Enaganti, L.Kari, T.Ng, Z.Wang. Word blending in formal languages. Fundamenta Informaticae, 171(1-4), 2020, pages 151-173. pdf
  18. G.Randhawa, K.Hill, L.Kari. MLDSP-GUI: An alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis. Bioinformatics, vol. 36, issue 7, 2020, pp. 2258–2259. pdf.
  19. ML-DSP: Machine learning with Digital Signal Processing for ultrafast, accurate and scalable DNA sequence classification at all taxonomic levels. G.Randhawa, K.Hill, L.Kari. BMC Genomics, 2019, 20:267. pdf .
  20. Simplifying the role of signals in self-assembly. L.Kari, A.Simjour. Natural Computing, vol. 18, issue 2, 2019, pages 383-401. pdf .
  21. Efficient algorithms for computing the inner edit distance of a regular language via transducers. L.Kari, S.Konstantinidis, S.Kopecki. Algorithms 2018, 11(11), 165; https://doi.org/10.3390/a11110165. pdf.
  22. An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-I genomes S. Solis-Reyes, M.Avino, A. Poon, L.Kari. PLOS ONE 13(11): e0206409, 2018. https://doi.org/10.1371/journal.pone.0206409. pdf
  23. Relative Watson-Crick primitivity of words. L.Kari, M.Kulkarni, K.Mahalingam. Journal of Automata, Languages, and Combinatorics (JALC), 23 (1-3), 2018, 201-217. pdf .
  24. Transducer descriptions of DNA code properties and undecidability of antimorphic problems. L.Kari, S.Konstantinidis, S.Kopecki. Information and Computation, 2017. pdf
  25. Smart tile self-assembly and replication. L.Kari, A.Simjour.Fundamenta Informaticae, 154 (1-4) 2017, 239-260. pdf
  26. ModMaps3D: An interactive webtool for the quantification and 3D visualization of interrelationships in a dataset of DNA sequences. R. Karamichalis, L.Kari. Bioinformatics, 33(19), 2017, pages 3091-3093. DOI , pdf .
  27. 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
  28. Further remarks on DNA overlap assembly. S. Enaganti, O. Ibarra, L.Kari, S. Kopecki. Information and Computation, 253(1), 2017, 143-154. pdf .
  29. Binary pattern tile set synthesis is NP-hard. L. Kari, S. Kopecki, P.-E Meunier, M. Patitz, S. Seki. Algorithmica, 78 (2017), 1-46. pdf
  30. On the overlap assembly of strings and languages. S. Enaganti, O.Ibarra, L.Kari, S.Kopecki. Natural Computing, 16 (2017), pages 175-185. pdf
  31. Disjunctivity and other properties of sets of pseudo-bordered words. L.Kari, M.Kulkarni. Acta Informatica, 54 (2017), pages 379-398. pdf
  32. Additive methods for genomic signatures. R.Karamichalis, L.Kari, S.Konstantinidis, S.Kopecki, S.Solis-Reyes. BMC Bioinformatics, 17:313, 2016. pdf
  33. 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.
  34. 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
  35. A formal language model of DNA Polymerase enzymatic activity. S.Enaganti, L.Kari, S.Kopecki. Fundamenta Informaticae, 138, 2015, 179-192. pdf .
  36. 3-color bounded patterned self-assembly. L.Kari, S .Kopecki, S.Seki. Natural Computing, 14 (2015), 279-292, pdf .
  37. 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
  38. 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 .
  39. 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
  40. 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
  41. 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
  42. Negative interactions in irreversible self-assembly.D.Doty, L.Kari, B.Masson. Algorithmica, vol. 66, issue 1, 2013, 153-172. pdf
  43. 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
  44. 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
  45. 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
  46. Relativized codes. M.Daley, H.Jurgensen, L.Kari, K.Mahalingam. Theoretical Computer Science, volume 429, 2012, 54-64. pdf
  47. 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
  48. De Bruijn Sequences Revisited. L.Kari, Z.Xu. International Journal of Foundations of Computer Science, IJFCS, vol.23, no.6, 2012, 1307-1321. pdf
  49. 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.
  50. Pseudopower avoidance. E.Chiniforooshan, L.Kari, Z.Xu. Fundamenta Informaticae, 114 (2012), 1-18. pdf
  51. 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
  52. 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
  53. 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.
  54. Polyominoes simulating arbitrary-neighbourhood zippers and tilings. B.Masson, L.Kari. Theoretical Computer Science, 412(43), 2011, 6083-6100. pdf
  55. K-comma codes and their generalizations. B.Cui, L.Kari, S.Seki. Fundamenta Informaticae, 107, 2011, 1-18. pdf
  56. Properties of pseudo-primitive words and their applications. L.Kari, B.Masson, S.Seki. IJCFS, 22(2), 2011, 447-471. pdf
  57. Block insertion and deletion on trajectories. B.Cui, L.Kari, S.Seki. Theoretical Computer Science, 412(2011), 714-728 pdf
  58. Orthogonal shuffle on trajectories. M.Daley, L.Kari, S.Seki, P.Sosik. IJFCS, 22 (1), 2011, 213-222. pdf
  59. 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
  60. 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
  61. Towards a neighborhood simplification of tile systems: From Moore to quasi-linear dependencies, Eu.Czeizler, L.Kari. Natural Computing, 10(2011), 103-117. pdf
  62. 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
  63. On a special class of primitive words. El.Czeizler, L.Kari, S.Seki. Theoretical Computer Science, Vol. 411, Issue 3, 2010, 617-630. pdf
  64. Watson-Crick palindromes in DNA computing. L.Kari, K.Mahalingam. Natural Computing, vol.9, nr.2, 2010, 297-316. pdf
  65. 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
  66. On the descriptional complexity of Watson-Crick automata. El. Czeizler, Eu.Czeizler, L.Kari, K.Salomaa. Theoretical Computer Science, 410(2009) 3250-3260. pdf
  67. 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
  68. On pseudoknot-bordered words and their properties. L.Kari, S.Seki. Journal of Computer and System Sciences, 75 (2009) 113-121. pdf
  69. 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
  70. Involution, solid and join codes. N.Jonoska, L.Kari and K.Mahalingam, Fundamenta Informaticae, 86(2008), 127-142. pdf
  71. On the weight of universal insertion grammars. L.Kari, P.Sosik. Theoretical Computer Science, 396(2008), 264-270. pdf
  72. Involutively bordered words. L.Kari, K.Mahalingam. Int. J. Found. Comput. Sci. 18(5) 2007, 1089-1106. pdf
  73. The syntactic monoid of hairpin languages. L.Kari, K.Mahalingam, G.Thierrin. Acta Informatica, 44(3-4) 2007, 153-166. pdf
  74. 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
  75. 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
  76. Block substitutions and their properties. L.Kari, E.Losseva. Fundamenta Informaticae, 73(2006), 165-178. pdf
  77. 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
  78. 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
  79. 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
  80. Results on transforming NFA into DFCA. C.Campeanu, L.Kari, A.Paun. Fundamenta Informaticae, vol. 64 (2005), 53-63. pdf
  81. 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
  82. Aspects of shuffle and deletion on trajectories L.Kari, P.Sosik. Theoretical Computer Science, vol. 332, no. 1-3 (2005), 47-61. pdf
  83. Language equations, maximality and error-detection L.Kari, S.Konstantinidis. Journal of Computer and System Sciences, 70 (2005), 157-178. pdf
  84. 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
  85. Descriptional complexity of error/edit systems. L.Kari, S.Konstantinidis. Journal of Automata, Languages and Combinatorics, 9 (2004), 2/3, 293-309. pdf
  86. Families of languages defined by ciliate bio-operations M.Daley, L.Kari, I.McQuillan. Theoretical Computer Science, 320 (2004), 51-69. pdf
  87. 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
  88. 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.
  89. Sticky-free and overhang-free DNA languages L.Kari, S.Konstantinidis, E.Losseva, G.Wozniak. Acta Informatica, 40 (2003), 119-157. pdf
  90. Coding properties of DNA languages. S.Hussini, L.Kari, S.Konstantinidis. Theoretical Computer Science, vol. 290/3, 2003, 1557-1579. pdf
  91. Morphisms preserving densities. H.Jurgensen, L.Kari, G.Thierrin. International Journal of Computer Mathematics, vol. 78 (2), 2001, 165-189. pdf
  92. Shuffle and scattered deletion closure of languages. M.Ito, L.Kari, G.Thierrin. Theoretical Computer Science, vol. 245, issue 1, 2000, 115-133. pdf
  93. Using DNA to solve the Bounded Post Correspondence Problem L.Kari, G.Gloor, S.Yu. Theoretical Computer Science, 231 (2000), 193-203. pdf
  94. 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
  95. 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
  96. Word insertions and primitivity. L.Kari, G.Thierrin. Utilitas Mathematica, vol. 53, 1998, 49--61. pdf
  97. DNA computing, sticker systems and universality L.Kari, G.Paun, G.Rozenberg, A.Salomaa, S.Yu. Acta Informatica, 35 (1998), 401--420. pdf
  98. Insertion and deletion closure of languages. M.Ito, L.Kari, G.Thierrin. Theoretical Computer Science, 183 (1997) 3--19. pdf
  99. 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.
  100. Contextual insertions/ deletions and computability. L.Kari, G.Thierrin. Information and Computation, vol. 131, 1 (1996), 47-61. pdf.
  101. 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
  102. Omega-syntactic congruences L.Kari, G.Thierrin. Journal of Automata, Languages and Combinatorics, 1 (1996) 1, 13-26. pdf
  103. 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
  104. 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
  105. K-insertion and k-deletion closure of languages L.Kari, G.Thierrin. Soochow Journal of Mathematics, vol. 21, no.4, 1995, 479-495. pdf
  106. Multi-pattern languages L.Kari, Al. Mateescu, Gh.Paun, A.Salomaa. Theoretical Computer Science, 141 (1995), 253-268. pdf
  107. Generalized DOL trees L.Kari, G.Rozenberg, A.Salomaa. Acta Cybernetica, vol. 12 (1995), No.1, 1-9. pdf
  108. 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
  109. Languages and monoids with disjunctive identity L.Kari, G.Thierrin. Collectanea Mathematica, 46, 1-2 (1995), 97-107. pdf
  110. 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
  111. On language equations with invertible operations. L.Kari. Theoretical Computer Science, 132 (1994), 129-150. pdf
  112. Deletion operations: closure properties L.Kari. International Journal of Computer Mathematics, 52 (1994), 23-42. pdf
  113. 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
  114. Generalized derivatives L.Kari. Fundamenta Informaticae, vol. 18, nr.1, 1993, 27-40. pdf
  115. Deletion sets L.Kari, A.Mateescu, Gh.Paun, A.Salomaa. Fundamenta Informaticae, vol. 19, 1993, 355-370. pdf
  116. 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
  117. 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
  118. 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
  119. Secret ballot elections in computer networks H.Nurmi, A.Salomaa, L.Santean. Computers and Security, nr.10, 1991, 553-560. pdf
  120. Further remarks on parallel communicating grammar systems G.Paun, L.Santean. International Journal of Computer Mathematics, vol. 34, 1990, 187--203. pdf
  121. On a theorem of Gunter Asser. C.Calude, L.Santean. Zeitschrift fur mathematische Logik und Grundlagen der Mathematik, vol. 36, 1990, 143-147. pdf
  122. 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
  123. Parallel communicating grammar systems-- the regular case. G.Paun, L.Santean. Analele Universitatii din Bucuresti, Seria matematica-informatica,nr.2, 1989, 55-63. pdf
  124. 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
  125. P. Millan Arias, N.Sadjadi, M.Safari, Z.Gong, A.Wang, S.Lowe, J.Haurum, I.Zarubiieva, D.Steinke, L.Kari, A.Chang, G.Taylor. BarcodeBERT: Transformers for biodiversity analysis. In 4th Workshop on Self-Supervised Learning: Theory and Practice (NeurIPS 2023). pdf
  126. L.Kari, K.Mahalingam. Watson-Crick powers of a word. Proceedings of the "9th International Conference on Algebraic Informatics", CAI 2022. In "Lecture Notes in Computer Science" (LNCS), vol. 13706 (2022), 136-148. pdf .
  127. L.Kari, T.Ng. Descriptional complexity of semi-simple splicing systems. Proceedings of DLT 2020 (Developments in Language Theory). In LNCS, vol. 12086, 2020, N.Jonoska, D. Savchuk, Eds., pp. 150-163. pdf
  128. State complexity of simple splicing. L.Kari, T.Ng. Proceedings of DCFS 2019 (Descriptional Complexity of Formal Systems). In LNCS, vol. 11612 (2019), M. Hospodar, G. Jiraskova, S. Konstantinidis Eds., 197-209. pdf
  129. State complexity of pseudocatenation. L.Kari, T.Ng. Proceedings of LATA 2019 (Language and Automata Theory and Applications). In LNCS, vol.11417, 2019, C.Martin-Vide, A.Okhotin, D.Shapira, Eds, 203-214. pdf
  130. Word blending in formal languages: The Brangelina effect. S.Enaganti, L.Kari, T.Ng, Z.Wang. Proceedings of UCNC 2018. In LNCS, vol.10867, 2018, S. Stepney, S.Verlan Eds., 72-85. pdf .
  131. State complexity of overlap assembly. J.Brzozowski, L.Kari, B.Li, M.Szykula. Proceedings of CIAA 2018. ``Sheng Yu'' Best Paper Award . In LNCS, vol.10977, 2018, C.Campeanu Ed., 109--120. pdf .
  132. 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
  133. 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
  134. 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
  135. 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
  136. 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
  137. 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
  138. 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
  139. 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
  140. De Bruijn sequences revisited. L.Kari, Z.Xu. Proc. of Automata and Formal Languages. AFL 2011, Debrecen, Hungary, August 17-22, 2011, P. Domosi, Sz. Ivan (Eds.), 241-254. pdf
  141. 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
  142. 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
  143. 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
  144. 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
  145. 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
  146. 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.
  147. 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
  148. 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
  149. 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
  150. 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
  151. 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.
  152. 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
  153. 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
  154. 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
  155. 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
  156. 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
  157. 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
  158. 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
  159. 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
  160. 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
  161. 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
  162. 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
  163. 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
  164. 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
  165. 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
  166. 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
  167. 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
  168. 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
  169. 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
  170. 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
  171. 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
  172. 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
  173. 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)
  174. 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
  175. 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
  176. 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.
  177. 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
  178. 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
  179. 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
  180. 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
  181. 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
  182. 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
  183. 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
  184. 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
  185. Methods for relativizing properties of codes. H.Jurgensen, L.Kari, S.Kopecki. Acta Cybernetica, 22(2), 2015, pp.259-292. pdf
  186. 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 .
  187. The many facets of natural computing L.Kari, G.Rozenberg. Communications of the ACM, vol.51, no.10, 2008 (cover page) 72-83. pdf
  188. 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
  189. 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
  190. 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
  191. 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
  192. 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
  193. 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
  194. 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
  195. 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
  196. 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
  197. 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
  198. 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
  199. 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
  200. 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
  201. 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
  202. 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
  203. 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
  204. Biocomputation in ciliates. L.Kari, L.F.Landweber. In Cellular Computing, M.Amos, Ed., Oxford University Press, 2004, 202-216. pdf
  205. 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
  206. L-systems. L.Kari, G.Rozenberg, A.Salomaa. In volume 1 of Handbook of Formal Languages, Springer-Verlag, 1997, 253-328. pdf
  207. 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
  208. DNA computing: Models and implementations. M.Daley, L.Kari. Comments on Theoretical Biology, vol. 7, No.3, 2002, 177-198. pdf
  209. 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
  210. 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
  211. 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
  212. L'ordinateur biologique, pour demain? L.Kari, L.F.Landweber. In Cahiers de Sciences \& Vie, No.53, 1999, 88-93. (In French.) pdf
  213. 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
  214. 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.
  215. 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
  216. 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
  217. DNA computing -- The arrival of biological mathematics. L.Kari. The Mathematical Intelligencer, vol.19, 2, 1997, 9-22. pdf
  218. 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
  219. DNA computers: tomorrow's reality. L.Kari. In European Association of Theoretical Computer Science, EATCS, Bulletin, no.59, 1996, 256-266. pdf
  220. 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
  221. Insertion operations: closure properties L.Kari. European Association of Theoretical Computer Science (EATCS) Bulletin, nr.51, 1993, 181-191. pdf
  222. 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
  223. 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
  224. 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
  225. Special Issue of Theoretical Computer Science in memory of Maurice Nivat, G.Ausiello, P.L. Curien, L.Kari, D.Sannella, P.Spirakis, G.Rozenberg, Eds., Part II, TCS, vol. 807, 2020, 340 pages.
  226. Special Issue of Theoretical Computer Science in memory of Maurice Nivat, G.Ausiello, P.L. Curien, L.Kari, D.Sannella, P.Spirakis, G.Rozenberg, Eds., Part I, TCS, vol. 777, 2019, 490 pages.
  227. 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.
  228. 40th Anniversary of Theoretical Computer Science, Virtual Special Issue of "Theoretical Computer Science", G.Ausiello, L.Kari, D. Sannella, Eds., 2015.
  229. 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.
  230. 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.
  231. 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.
  232. 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.
  233. 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
  234. On language equations with deletion. L.Kari, P.Sosik. European Association of Theoretical Computer Science (EATCS) Bulletin, nr.83, 2004, 173-180.
  235. 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.
  236. Language deletion on trajectories. L.Kari, P.Sosik. Dept. of Computer Science Technical Report 606, Univ. of Western Ontario, 2003.
  237. 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.
  238. Criptografie cu Chei Publice. A. Salomaa Editura militara, Bucuresti, 1993, 253 pages. translated by L.Kari, M.Andrasiu from Public Key Cryptography.
  239. Tagged symbols for parallel unification. L.Santean. Studies and Researches in Computers and Informatics, I.T.C.I., Bucharest, vol. 1, 1989, 121-123.
  240. 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.
  241. 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).
  242. 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).
    Conference Posters
  243. F. Alipour, C.Holmes, J.Butler, Y.Y.Lu, K.Hill, L.Kari. (2024). ``A novel three-pronged alignment-free machine learning approach for taxonomic classification: A case study of human astroviruses.'' 31st Conference on International Dynamics and Evolution of Human Viruses, Squamish, BC.
  244. J.Butler, F. Alipour, C.Holmes, Y.Y. Lu, L. Kari, K. Hill, (2024). ``A combined supervised and unsupervised machine learning approach with intraspecific classification of human astroviruses,'' 31st Conference on International Dynamics and Evolution of Human Viruses, Squamish, BC.
  245. R.Pandey, G.Randhawa, K.Hill, L.Kari, “Enhancing Efficiency and Accuracy of DNA Sequence Classification through Dimensionality Reduction of Chaos Game Representation Features using Principal Component Analysis”. In: the 54th annual meeting of the Environmental Mutagenesis & Genomics Society; 2023 Sept 9-13; Chicago, IL, USA; Poster nr P71; Environment and Molecular Mutagenesis. 2023; 64(S1): 101.
  246. P.Millan Arias, J.Butler, G.Randhawa, M.Soltysiak, K.Hill, L.Kari, “Alignment-Free Genomic Analysis of Microbial Organisms in Extreme Environments: Uncovering Convergent Evolution through Deep Learning”. In: the 54th annual meeting of the Environmental Mutagenesis & Genomics Society; 2023 Sept 9-13; Chicago, IL, USA; Poster nr P73; Environment and Molecular Mutagenesis. 2023; 64(S1): 102-103.
  247. J.Butler, P. Millan Arias, G. Randhawa, M. Soltysiak, L. Kari, K. Hill,“Extreme Environments and their Impact on Microbial Genomic Signature Composition”. In: the 54th annual meeting of the Environmental Mutagenesis & Genomics Society; 2023 Sept 9-13; Chicago, IL, USA; Poster nr P74; Environment and Molecular Mutagenesis. 2023; 64(S1): 103-104.
  248. J.Butler, P. Millan Arias, G. Randhawa, M. Soltysiak, L. Kari, K. Hill, “Evidence for markers of adaptation to extreme environments in microbial genome sequence composition”. In: the Ontario Ecology Ethology and Evolution; University of Western Ontario, London, Canada; 2023.
  249. M. Soltysiak, G. Randhawa, A. Osman, C. de Souza, K. Hill, L. Kari. Investigating genomic and mutational signatures of organisms living in extreme environments. 51st annual meeting of the Environmental Mutagenesis & Genomics Society (EMGS), 2020, Sept 12-16 (virtual).
  250. G. Randhawa, M. Soltysiak, H. El Roz, C. de Souza, K. Hill, L. Kari. Rapid and accurate classification of SARS-CoV-2 using genomic signature analysis with machine learning. The 28th conference on Intelligent Systems for Molecular Biology (ISMB 2020); International Society for Computational Biology; 2020 July 13-16; 2020, Abstract nr. C48.
  251. K. Hill, G. Randhawa, N. Boehler, H. Pavanel, A. Coyle, P. Wan, L. Kari. Machine Learning with Digital Signal Processing for classification of mouse genotypes. The Allied Genetics Conference (TAGC 2020)}; Genetics Society of America; 2020 April 22-25; 2020, Abstract nr. 1200C.
  252. G. Randhawa, K. Hill, L. Kari. A stand-alone software tool with a graphical user interface employing Machine-Learning and Digital Signal Processing (ML-DSP) for accurate genome-wide classification of human mitochondrial diseases and cancer types. 50th Annual Meeting of the Environmental Mutagenesis & Genomics Society (EMGS), 2019 Sept 19-23, Washington, DC, USA.
  253. M. Soltysiak, G. Randhawa, L. Kari, K. Hill. Machine Learning – Digital Signal Processing and genomic signatures to elucidate the ancestral proteobacterial origin of mitochondria. 50th Annual Meeting of the Environmental Mutagenesis & Genomics Society (EMGS), 2019 Sept 19-23, Washington, DC, USA.
  254. G. Randhawa, K.Hill, L. Kari. Machine-Learning and Digital Signal Processing approach for accurate genome-wide classification of human haplogroups, extant and extinct hominids, mitochondrial diseases and cancer types. In the 8th Canadian Human and Statistical Genetics Meeting, 2019 June 16-19; Montebello, Québec, Canada: CHSGM; 2019. Abstract nr. 41.
  255. B. Valente, M. Soltysiak, G. Randhawa, C. De Souza, L. Kari, K. Hill. Classification of organisms based on genome sequence composition: Case studies in alignment-free approaches to virus-host pair classifications and viral subtyping. In the 8th Canadian Human and Statistical Genetics Meeting, 2019 June 16-19; Montebello, Québec, Canada: CHSGM; 2019. Abstract nr. 34.
  256. G. Randhawa, B. Valente, M. Soltysiak, K. Hill, L. Kari. Machine learning-based alignment-free method demonstrates the potential to analyze sequence instability of synthetized genomes. In the 4th Annual Synthetic Biology Symposium, 2019 May 26-28; Waterloo, Ontario, Canada: SynBio 4.0; 2019. Abstract nr. 30.
  257. G. Randhawa, K. Hill, L. Kari. Classification of cancer genomes using Machine Learning and Digital Signal Processing. In the Annual Terry Fox Research Institute Ontario Node Cancer Research Symposium, 2018 December 10; Toronto, Ontario, Canada: TFRI Symposium; 2018. Abstract nr. 83.
  258. G. Randhawa, K. Hill, L. Kari. Genomic Signatures: Machine Learning and Digital Signal Processing of genomic sequences provides ultrafast and accurate classification of cancer genomes. In the 4th International Cancer Research Conference, 2018 November 17; Windsor, Ontario, Canada: WCRG; 2018. Abstract nr. 07.
  259. G. Randhawa, K. Hill, L. Kari. Genomic Signatures: Machine Learning and Digital Signal Processing of genomic sequences provides ultrafast and accurate taxonomic classification. In the 49th Annual Meeting of the Environmental Mutagenesis & Genomics Society, 2018 Sept 22-26; San Antonio, Texas, USA: EMGS; 2018, p. 104. Abstract nr. 51.
  260. M. Soltysiak, G. Randhawa, N. Boehler, L. Kari, K. Hill. Tracking down contributors to genomic signatures: Cross-species comparisons of subsequence avoidance. In the 49th Annual Meeting of the Environmental Mutagenesis & Genomics Society, 2018 Sept 22-26; San Antonio, Texas, USA: EMGS; 2018, p. 104. Abstract nr. 52.
    Articles Submitted to Refereed Journals or Conferences
  261. P. Millan Arias, N. Sadjadi, M. Safari, Z. Gong, A. Wang, J. Bruslund Haurum, I. Zarubiieva, D. Steinke, Lila Kari, A. Chang, S. Lowe, G. Taylor. BarcodeBERT: Transformers for biodiversity analyses. pdf
  262. M. Safari, J. Butler, G. Randhawa, K. Hill, L. Kari. Maximally divergent microbes share similar genomic signatures linked to extreme environments.
  263. N. Sadjadi, J. Butler, C. de Souza, K. Hill, L. Kari. Evidence for the pervasive nature of a genomic signature in the human genome.
  264. H. He, L.Kari, P. Millan Arias. Mathematical properties of Chaos Game Representations (CGR) of DNA sequences.
  265. F.Bellamoli, G. Franco, L.Kari, K.Mahalingam. A variety of word blending bio-operations.
  266. L.Kari, K.Mahalingam. Strong-Θ-catenation and Watson-Crick powers of a word.