| 2021 | DLT | Integer Weighted Automata on Infinite Words. | Vesa Halava, Tero Harju, Reino Niskanen, Igor Potapov |
| 2015 | CiE | Weighted Automata on Infinite Words in the Context of Attacker-Defender Games. | Vesa Halava, Tero Harju, Reino Niskanen, Igor Potapov |
| 2011 | LATA | Finite Orbits of Language Operations. | Emilie Charlier, Michael Domaratzki, Tero Harju, Jeffrey O. Shallit |
| 2010 | DLT | On the Periodicity of Morphic Words. | Vesa Halava, Tero Harju, Tomi Krki, Michel Rigo |
| 2009 | DLT | Post Correspondence Problem and Small Dimensional Matrices. | Tero Harju |
| 2005 | CiE | Combinatorial Models of Gene Assembly. | Tero Harju |
| 2005 | DNA | Simple Operations for Gene Assembly. | Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg |
| 2004 | DNA | Parallelism in Gene Assembly. | Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg |
| 2004 | DNA | Splicing Systems for Universal Turing Machines. | Tero Harju, Maurice Margenstern |
| 2004 | STACS | Periodicity and Unbordered Words: A Proof of Duval?s Conjecture. | Tero Harju, Dirk Nowotka |
| 2003 | DLT | About Duval's Conjecture. | Tero Harju, Dirk Nowotka |
| 2003 | FCT | Languages Defined by Generalized Equality Sets. | Vesa Halava, Tero Harju, Hendrik Jan Hoogeboom, Michel Latteux |
| 2002 | DLT | Computational Processes in Living Cells: Gene Assembly in Ciliates. | Tero Harju, Grzegorz Rozenberg |
| 2001 | DLT | An Undecidability Result Concerning Periodic Morphisms. | Vesa Halava, Tero Harju |
| 2001 | DLT | Decision Questions on Integer Matrices. | Tero Harju |
| 2001 | DNA | Patterns of Micronuclear Genes in ciliates. | Andrzej Ehrenfeucht, Tero Harju, Ion Petre, Grzegorz Rozenberg |
| 2001 | ICALP | Decision Questions Concerning Semilinearity, Morphisms, and Commutation of Languages. | Tero Harju, Oscar H. Ibarra, Juhani Karhumki, Arto Salomaa |
| 1999 | FCT | Generalized PCP Is Decidable for Marked Morphisms. | Vesa Halava, Tero Harju, Mika Hirvensalo |
| 1998 | MFCS | Shuffle on Trajectories: The Schtzenberger Product and Related Operations. | Tero Harju, Alexandru Mateescu, Arto Salomaa |
| 1996 | STACS | Remarks on Generalized Post Correspondence Problem. | Tero Harju, Juhani Karhumki, Daniel Krob |
| 1995 | ICALP | Theory of 2-Structures. | Andrzej Ehrenfeucht, Tero Harju, Grzegorz Rozenberg |
| 1995 | ICALP | Compactness of Systems of Equations in Semigroups. | Tero Harju, Juhani Karhumki, Wojciech Plandowski |
| 1990 | STOC | Decidability of the Multiplicity Equivalence of Multitape Finite Automata | Tero Harju, Juhani Karhumki |
| 1989 | ICALP | Dominoes and the Regularity of DNS Splicing Languages. | Karel Culk II, Tero Harju |
| 1981 | STOC | The omega-Sequence Equivalence Problem for DOL Systems Is Decidable | Karel Culk II, Tero Harju |