| 2017 | WABI | Seed-driven Learning of Position Probability Matrices from Large Sequence Sets. | Jarkko Toivonen, Jussi Taipale, Esko Ukkonen |
| 2013 | IWOCA | Motif Matching Using Gapped Patterns. | Emanuele Giaquinta, Kimmo Fredriksson, Szymon Grabowski, Esko Ukkonen |
| 2012 | MFCS | How to Reconstruct a Genome. | Esko Ukkonen |
| 2011 | ALT | Editors' Introduction. | Jyrki Kivinen, Csaba Szepesvri, Esko Ukkonen, Thomas Zeugmann |
| 2007 | MFCS | Structural Analysis of Gapped Motifs of a String. | Esko Ukkonen |
| 2007 | WABI | Haplotype Inference Via Hierarchical Genotype Parsing. | Pasi Rastas, Esko Ukkonen |
| 2005 | WABI | A Hidden Markov Technique for Haplotype Reconstruction. | Pasi Rastas, Mikko Koivisto, Heikki Mannila, Esko Ukkonen |
| 2004 | ALT | Hidden Markov Modelling Techniques for Haplotype Analysis. | Mikko Koivisto, Teemu Kivioja, Heikki Mannila, Pasi Rastas, Esko Ukkonen |
| 2004 | ICCS | The Computational Complexity of Orientation Search in Cryo-Electron Microscopy. | Taneli Mielikinen, Janne Ravantti, Esko Ukkonen |
| 2003 | PSB | An MDL Method for Finding Haplotype Blocks and for Estimating the Strength of Haplotype Block Boundaries. | Mikko Koivisto, Markus Perola, T. Varilo, W. Hennah, J. Ekelund, Margus Lukk, L. Peltonen, Esko Ukkonen, Heikki Mannila |
| 2003 | STACS | Algorithms for Transposition Invariant String Matching. | Veli Mkinen, Gonzalo Navarro, Esko Ukkonen |
| 2002 | CPM | Optimal Exact and Fast Approximate Two Dimensional Pattern Matching Allowing Rotations. | Kimmo Fredriksson, Gonzalo Navarro, Esko Ukkonen |
| 2002 | CPM | Local Similarity Based Point-Pattern Matching. | Veli Mkinen, Esko Ukkonen |
| 2002 | ECCB | Correlating gene promoters and expression in gene disruption experiments. | Kimmo Palin, Esko Ukkonen, Alvis Brazma, Jaak Vilo |
| 2002 | ISMB | Assigning probes into a small number of pools separable by electrophoresis. | Teemu Kivioja, Mikko Arvas, Kari Kataja, Merja Penttil, Hans Sderlund, Esko Ukkonen |
| 2002 | WABI | Finding Founder Sequences from a Set of Recombinants. | Esko Ukkonen |
| 2001 | CPM | Approximate Matching of Run-Length Compressed Strings. | Veli Mkinen, Gonzalo Navarro, Esko Ukkonen |
| 2001 | FCT | The Complexity of Maximum Matroid-Greedoid Intersection. | Taneli Mielikinen, Esko Ukkonen |
| 2001 | ICIP | Faster template matching without FFT. | Kimmo Fredriksson, Esko Ukkonen |
| 2000 | CPM | Approximate String Matching over Ziv-Lempel Compressed Text. | Juha Krkkinen, Gonzalo Navarro, Esko Ukkonen |
| 2000 | ISMB | Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data. | Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan J. Robinson, Esko Ukkonen |
| 2000 | SPIRE | Combinatorial Methods for Approximate Pattern Matching under Rotations and Translations in 3D Arrays. | Kimmo Fredriksson, Esko Ukkonen |
| 1999 | PADL | Implementing a Declarative String Query Language with String Restructuring. | Raul Hakli, Matti Nyknen, Hellis Tamm, Esko Ukkonen |
| 1999 | STACS | Finding Paths with the Right Cost. | Matti Nyknen, Esko Ukkonen |
| 1998 | ADBIS | Term Weighting in Query-Based Document Clustering (Extended Abstract). | Kai Korpimies, Esko Ukkonen |
| 1998 | CPM | A Rotation Invariant Filter for Two-Dimensional String Matching. | Kimmo Fredriksson, Esko Ukkonen |
| 1998 | FQAS | Searching for General Documents. | Kai Korpimies, Esko Ukkonen |
| 1997 | ICONIP | Using Trainable Computing Networks in the Optimization of Lake Regulation. | Markus Huttunen, Esko Ukkonen, Bertel Vehvilinen |
| 1997 | ISMB | Data Mining for Regulatory Elements in Yeast Genome. | Alvis Brazma, Jaak Vilo, Esko Ukkonen, Kimmo Valtonen |
| 1996 | COCOON | Sparse Suffix Trees. | Juha Krkkinen, Esko Ukkonen |
| 1996 | ISAAC | Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract). | Alvis Brazma, Esko Ukkonen, Jaak Vilo |
| 1996 | ISMB | Discovering Patterns and Subfamilies in Biosequences. | Alvis Brazma, Inge Jonassen, Esko Ukkonen, Jaak Vilo |
| 1996 | MFCS | On the Equivalence Problem for E-Pattern Languages. | Enno Ohlebusch, Esko Ukkonen |
| 1994 | PODS | Reasoning about Strings in Databases. | Gsta Grahne, Matti Nyknen, Esko Ukkonen |
| 1994 | SODA | Two and Higher Dimensional Pattern Matching in Optimal Expected Time. | Juha Krkkinen, Esko Ukkonen |
| 1993 | CPM | Approximate String-Matching over Suffix Trees. | Esko Ukkonen |
| 1992 | COLT | Learning Hierarchical Rule Sets. | Jyrki Kivinen, Heikki Mannila, Esko Ukkonen |
| 1991 | MFCS | Two Algorithms for Approximate String Matching in Static Texts. | Petteri Jokinen, Esko Ukkonen |
| 1986 | ICALP | The Set Union Problem with Backtracking. | Heikki Mannila, Esko Ukkonen |
| 1986 | ICLP | On the Complexity of Unification Sequences. | Heikki Mannila, Esko Ukkonen |
| 1986 | MFCS | A Greedy Algorithm for Constructing Shortest Common Superstrings. | Jorma Tarhio, Esko Ukkonen |
| 1983 | FCT | On Approximate String Matching. | Esko Ukkonen |
| 1981 | ICALP | On Size Bounds for Deterministic Parsers. | Esko Ukkonen |
| 1981 | STOC | LALR(k) Testing is PSPACE-Complete | Esko Ukkonen, Eljas Soisalon-Soininen |
| 1980 | ICALP | On the Optimal Assignment of Attributes to Passes in Multi-Pass Attribute Evaluators. | Kari-Jouko Rih, Esko Ukkonen |
| 1980 | STOC | A Decision Method for the Equivalence of some Non-Real-Time Deterministic Pushdown Automata | Esko Ukkonen |
| 1979 | ICALP | A Modification of the LR(k) Method for Constructing Compact Bottom-Up Parsers. | Esko Ukkonen |
| 1978 | MFCS | Tranformations to Produce Certain Covering Grammars. | Esko Ukkonen |
| 1976 | ICALP | A Characterization of LL(k) Languages. | Eljas Soisalon-Soininen, Esko Ukkonen |