| 2023 | CPM | From Bit-Parallelism to Quantum String Matching for Labelled Graphs. | Massimo Equi, Arianne Meijer-van de Griend, Veli Mkinen |
| 2023 | SPIRE | Chaining of Maximal Exact Matches in Graphs. | Nicola Rizzo, Manuel Cceres, Veli Mkinen |
| 2023 | WABI | Finding Maximal Exact Matches in Graphs. | Nicola Rizzo, Manuel Cceres, Veli Mkinen |
| 2022 | CPM | Indexable Elastic Founder Graphs of Minimum Height. | Nicola Rizzo, Veli Mkinen |
| 2022 | IWOCA | Linear Time Construction of Indexable Elastic Founder Graphs. | Nicola Rizzo, Veli Mkinen |
| 2021 | ISAAC | Algorithms and Complexity on Indexing Elastic Founder Graphs. | Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mkinen |
| 2021 | SOFSEM | Graphs Cannot Be Indexed in Polynomial Time for Sub-quadratic Time String Matching, Unless SETH Fails. | Massimo Equi, Veli Mkinen, Alexandru I. Tomescu |
| 2020 | CPM | Chaining with Overlaps Revisited. | Veli Mkinen, Kristoffer Sahlin |
| 2020 | SPIRE | Tailoring r-index for Document Listing Towards Metagenomics Applications. | Dustin Cobas, Veli Mkinen, Massimiliano Rossi |
| 2020 | WABI | Linear Time Construction of Indexable Founder Block Graphs. | Veli Mkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri, Alexandru I. Tomescu |
| 2019 | ICALP | On the Complexity of String Matching for Graphs. | Massimo Equi, Roberto Grossi, Veli Mkinen, Alexandru I. Tomescu |
| 2019 | SPIRE | Linear Time Maximum Segmentation Problems in Column Stream Model. | Bastien Cazaux, Dmitry Kosolobov, Veli Mkinen, Tuukka Norri |
| 2018 | RECOMB | Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. | Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mkinen |
| 2018 | WABI | Minimum Segmentation for Pan-genomic Founder Reconstruction in Linear Time. | Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov, Veli Mkinen |
| 2016 | LATIN | Bidirectional Variable-Order de Bruijn Graphs. | Djamal Belazzougui, Travis Gagie, Veli Mkinen, Marco Previtali, Simon J. Puglisi |
| 2016 | RECOMB | MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows. | Ahmed Sobih, Alexandru I. Tomescu, Veli Mkinen |
| 2016 | SPIRE | Fully Dynamic de Bruijn Graphs. | Djamal Belazzougui, Travis Gagie, Veli Mkinen, Marco Previtali |
| 2015 | RECOMB | Gap Filling as Exact Path Length Problem. | Leena Salmela, Kristoffer Sahlin, Veli Mkinen, Alexandru I. Tomescu |
| 2013 | ESA | Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform. | Djamal Belazzougui, Fabio Cunial, Juha Krkkinen, Veli Mkinen |
| 2013 | WABI | A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. | Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mkinen |
| 2012 | COCOON | Multi-pattern Matching with Bidirectional Indexes. | Simon Gog, Kalle Karhu, Juha Krkkinen, Veli Mkinen, Niko Vlimki |
| 2012 | LATIN | Forbidden Patterns. | Johannes Fischer, Travis Gagie, Tsvi Kopelowitz, Moshe Lewenstein, Veli Mkinen, Leena Salmela, Niko Vlimki |
| 2012 | LATIN | Indexed Multi-pattern Matching. | Travis Gagie, Kalle Karhu, Juha Krkkinen, Veli Mkinen, Leena Salmela, Jorma Tarhio |
| 2011 | WABI | Indexing Finite Language Representation of Population Genotypes. | Jouni Sirn, Niko Vlimki, Veli Mkinen |
| 2010 | CPM | Approximate All-Pairs Suffix/Prefix Overlaps. | Niko Vlimki, Susana Ladra, Veli Mkinen |
| 2010 | ICDE | Fast in-memory XPath search using compressed indexes. | Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirn, Niko Vlimki |
| 2009 | RECOMB | Storage and Retrieval of Individual Genomes. | Veli Mkinen, Gonzalo Navarro, Jouni Sirn, Niko Vlimki |
| 2008 | CPM | An(other) Entropy-Bounded Compressed Suffix Tree. | Johannes Fischer, Veli Mkinen, Gonzalo Navarro |
| 2008 | DCC | On Self-Indexing Images - Image Compression with Added Value. | Veli Mkinen, Gonzalo Navarro |
| 2008 | ICDM | Space Efficient String Mining under Frequency Constraints. | Johannes Fischer, Veli Mkinen, Niko Vlimki |
| 2008 | SPIRE | Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections. | Jouni Sirn, Niko Vlimki, Veli Mkinen, Gonzalo Navarro |
| 2007 | CPM | Space-Efficient Algorithms for Document Retrieval. | Niko Vlimki, Veli Mkinen |
| 2007 | SPIRE | Implicit Compression Boosting with Applications to Self-indexing. | Veli Mkinen, Gonzalo Navarro |
| 2006 | CPM | Dynamic Entropy-Compressed Sequences and Full-Text Indexes. | Veli Mkinen, Gonzalo Navarro |
| 2006 | LATIN | Position-Restricted Substring Searching. | Veli Mkinen, Gonzalo Navarro |
| 2005 | CPM | Succinct Suffix Arrays Based on Run-Length Encoding. | Veli Mkinen, Gonzalo Navarro |
| 2004 | CPM | Compressed Compact Suffix Arrays. | Veli Mkinen, Gonzalo Navarro |
| 2004 | ISAAC | Advantages of Backward Searching - Efficient Secondary Memory and Distributed Implementation of Compressed Suffix Arrays. | Veli Mkinen, Gonzalo Navarro, Kunihiko Sadakane |
| 2004 | LATIN | Rotation and Lighting Invariant Template Matching. | Kimmo Fredriksson, Veli Mkinen, Gonzalo Navarro |
| 2004 | SPIRE | An Alphabet-Friendly FM-Index. | Paolo Ferragina, Giovanni Manzini, Veli Mkinen, Gonzalo Navarro |
| 2004 | SPIRE | First Huffman, Then Burrows-Wheeler: A Simple Alphabet-Independent FM-Index. | Szymon Grabowski, Veli Mkinen, Gonzalo Navarro |
| 2004 | WABI | Finding Missing Patterns. | Shunsuke Inenaga, Teemu Kivioja, Veli Mkinen |
| 2003 | CPM | On Minimizing Pattern Splitting in Multi-track String Matching. | Kjell Lemstrm, Veli Mkinen |
| 2003 | STACS | Algorithms for Transposition Invariant String Matching. | Veli Mkinen, Gonzalo Navarro, Esko Ukkonen |
| 2002 | CPM | Local Similarity Based Point-Pattern Matching. | Veli Mkinen, Esko Ukkonen |
| 2001 | ALENEX | Trade Off Between Compression and Search Times in Compact Suffix Array. | Veli Mkinen |
| 2001 | CPM | Approximate Matching of Run-Length Compressed Strings. | Veli Mkinen, Gonzalo Navarro, Esko Ukkonen |
| 2001 | SPIRE | Using Edit Distance in Point-Pattern Matching. | Veli Mkinen |
| 2000 | CPM | Compact Suffix Array. | Veli Mkinen |