| 2025 | UC | Bridging Chaos Game Representations and k-mer Frequencies of DNA Sequences. | Haoze He, Lila Kari, Pablo Millan Arias |
| 2020 | DLT | Descriptional Complexity of Semi-simple Splicing Systems. | Lila Kari, Timothy Ng |
| 2019 | LATA | State Complexity of Pseudocatenation. | Lila Kari, Timothy Ng |
| 2018 | UC | Word Blending in Formal Languages: The Brangelina Effect. | Srujan Kumar Enaganti, Lila Kari, Timothy Ng, Zihao Wang |
| 2015 | ICALP | Binary Pattern Tile Set Synthesis Is NP-hard. | Lila Kari, Steffen Kopecki, Pierre-tienne Meunier, Matthew J. Patitz, Shinnosuke Seki |
| 2013 | CiE | Negative Glues and Non-determinism in Nanocomputations by Self-assembly. | Lila Kari |
| 2013 | DNA | 3-Color Bounded Patterned Self-assembly - (Extended Abstract). | Lila Kari, Steffen Kopecki, Shinnosuke Seki |
| 2013 | UC | Hypergraph Automata: A Theoretical Model for Patterned Self-assembly. | Lila Kari, Steffen Kopecki, Amirhossein Simjour |
| 2012 | DNA | Deciding Whether a Regular Language Is Generated by a Splicing System. | Lila Kari, Steffen Kopecki |
| 2012 | SOFSEM | Iterated Hairpin Completions of Non-crossing Words. | Lila Kari, Steffen Kopecki, Shinnosuke Seki |
| 2011 | SODA | The Power of Nondeterminism in Self-Assembly. | Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki |
| 2011 | SOFSEM | One-Reversal Counter Machines and Multihead Automata: Revisited. | Ehsan Chiniforooshan, Mark Daley, Oscar H. Ibarra, Lila Kari, Shinnosuke Seki |
| 2010 | DLT | Pseudo-power Avoidance. | Ehsan Chiniforooshan, Lila Kari, Zhi Xu |
| 2010 | DLT | DNA Computing and Its Implications for Theoretical Computer Science. | Lila Kari |
| 2010 | DLT | Schema for Parallel Insertion and Deletion. | Lila Kari, Shinnosuke Seki |
| 2010 | DNA | Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement. | Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki |
| 2010 | DNA | Negative Interactions in Irreversible Self-assembly. | David Doty, Lila Kari, Benot Masson |
| 2010 | DNA | Triangular Tile Self-assembly Systems. | Lila Kari, Shinnosuke Seki, Zhi Xu |
| 2009 | DLT | An Extension of the Lyndon Schtzenberger Result to Pseudoperiodic Words. | Elena Czeizler, Eugen Czeizler, Lila Kari, Shinnosuke Seki |
| 2008 | DLT | Duplication in DNA Sequences. | Masami Ito, Lila Kari, Zachary Kincaid, Shinnosuke Seki |
| 2008 | MFCS | On a Special Class of Primitive Words. | Elena Czeizler, Lila Kari, Shinnosuke Seki |
| 2007 | DNA | Watson-Crick Conjugate and Commutative Words. | Lila Kari, Kalpana Mahalingam |
| 2007 | UC | Nanocomputing by Self-assembly. | Lila Kari |
| 2006 | DLT | Involution Solid and Join Codes. | Natasa Jonoska, Lila Kari, Kalpana Mahalingam |
| 2006 | DNA | DNA Codes and Their Properties. | Lila Kari, Kalpana Mahalingam |
| 2005 | DLT | On Hairpin-Free Words and Languages. | Lila Kari, Stavros Konstantinidis, Petr Sosk, Gabriel Thierrin |
| 2005 | DNA | Hairpin Structures in DNA Words. | Lila Kari, Stavros Konstantinidis, Elena Losseva, Petr Sosk, Gabriel Thierrin |
| 2004 | DNA | Bond-Free Languages: Formalizations, Maximality and Construction Methods. | Lila Kari, Stavros Konstantinidis, Petr Sosk |
| 2004 | DNA | Preventing Undesirable Bonds Between DNA Codewords. | Lila Kari, Stavros Konstantinidis, Petr Sosk |
| 2002 | DLT | Some Properties of Ciliate Bio-operations. | Mark Daley, Lila Kari |
| 2002 | FOCS | On the Decidability of Self-Assembly of Infinite Ribbons. | Leonard M. Adleman, Jarkko Kari, Lila Kari, Dustin Reishus |
| 2001 | DNA | Coding Properties of DNA Languages. | Salah Hussini, Lila Kari, Stavros Konstantinidis |
| 1999 | SPIRE | Circular Contextual Insertions/Deletions with Applications to Biomolecular Computation. | Mark Daley, Lila Kari, Greg Gloor, Rani Siromoney |
| 1998 | MCU | Using DNA to solve the Bounded Post Correspondence Problem. | Lila Kari, Greg Gloor, Sheng Yu |
| 1995 | DLT | Morphisms and Associated Congruences. | Lila Kari, Gabriel Thierrin |
| 1994 | MFCS | Two Lower Bounds on Distributive Generation of Languages. | Juraj Hromkovic, Jarkko Kari, Lila Kari, Dana Pardubsk |
| 1993 | MFCS | Some Hierarchies for the Communication Complexity Measures of Cooperating Grammar Systems. | Juraj Hromkovic, Jarkko Kari, Lila Kari |
| 1992 | MFCS | Insertion and Deletion of Words: Determinism and Reversibility. | Lila Kari |