| Compressed full-text indexes G Navarro, V Mäkinen ACM Computing Surveys (CSUR) 39 (1), 2, 2007 | 882 | 2007 |
| Compressed representations of sequences and full-text indexes P Ferragina, G Manzini, V Mäkinen, G Navarro ACM Transactions on Algorithms (TALG) 3 (2), 20, 2007 | 455 | 2007 |
| Computational pan-genomics: status, promises and challenges Briefings in bioinformatics 19 (1), 118-135, 2018 | 369 | 2018 |
| Indexing graphs for path queries with applications in genome research J Sirén, N Välimäki, V Mäkinen IEEE/ACM transactions on computational biology and bioinformatics 11 (2 …, 2014 | 317 | 2014 |
| Practical implementation of rank and select queries R González, S Grabowski, V Mäkinen, G Navarro Poster Proc. Volume of 4th Workshop on Efficient and Experimental Algorithms …, 2005 | 296 | 2005 |
| Succinct suffix arrays based on run-length encoding V Mäkinen, G Navarro Combinatorial Pattern Matching: 16th Annual Symposium, CPM 2005, Jeju Island …, 2005 | 274 | 2005 |
| Storage and retrieval of highly repetitive sequence collections V Mäkinen, G Navarro, J Sirén, N Välimäki Journal of Computational Biology 17 (3), 281-308, 2010 | 254 | 2010 |
| The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera V Ahola, R Lehtonen, P Somervuo, L Salmela, P Koskinen, P Rastas, ... Nature communications 5 (1), 4737, 2014 | 245 | 2014 |
| Rank and select revisited and extended V Mäkinen, G Navarro Theoretical Computer Science 387 (3), 332-347, 2007 | 193 | 2007 |
| Genome-scale algorithm design V Mäkinen, D Belazzougui, F Cunial, AI Tomescu Cambridge University Press, 2015 | 183 | 2015 |
| Dynamic entropy-compressed sequences and full-text indexes V Mäkinen, G Navarro ACM Transactions on Algorithms (TALG) 4 (3), 1-38, 2008 | 178 | 2008 |
| An alphabet-friendly FM-index P Ferragina, G Manzini, V Mäkinen, G Navarro International Symposium on String Processing and Information Retrieval, 150-160, 2004 | 166 | 2004 |
| Faster entropy-bounded compressed suffix trees J Fischer, V Mäkinen, G Navarro Theoretical Computer Science 410 (51), 5354-5364, 2009 | 115 | 2009 |
| Geometric algorithms for transposition invariant content-based music retrieval E Ukkonen, K Lemström, V Mäkinen Johns Hopkins University, 2003 | 110 | 2003 |
| A novel min-cost flow method for estimating transcript expression with RNA-Seq AI Tomescu, A Kuosmanen, R Rizzi, V Mäkinen BMC bioinformatics 14, 1-10, 2013 | 109 | 2013 |
| Fast scaffolding with small independent mixed integer programs L Salmela, V Mäkinen, N Välimäki, J Ylinen, E Ukkonen Bioinformatics 27 (23), 3259-3265, 2011 | 100 | 2011 |
| Space-efficient algorithms for document retrieval N Välimäki, V Mäkinen Annual Symposium on Combinatorial Pattern Matching, 205-215, 2007 | 94 | 2007 |
| Run-length compressed indexes are superior for highly repetitive sequence collections J Sirén, N Välimäki, V Mäkinen, G Navarro International Symposium on String Processing and Information Retrieval, 164-175, 2008 | 92 | 2008 |
| Position-restricted substring searching V Mäkinen, G Navarro LATIN 2006: Theoretical Informatics: 7th Latin American Symposium, Valdivia …, 2006 | 92 | 2006 |
| Implicit compression boosting with applications to self-indexing V Mäkinen, G Navarro String Processing and Information Retrieval: 14th International Symposium …, 2007 | 91 | 2007 |
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