Compressed representations of sequences and full-text indexes. Zbl 1321.68263
Ferragina, Paolo; Manzini, Giovanni; Mäkinen, Veli; Navarro, Gonzalo |
|
2007
|
Rank and select revisited and extended. Zbl 1144.68023
Mäkinen, Veli; Navarro, Gonzalo |
|
2007
|
Succinct suffix arrays based on run-length encoding. Zbl 1085.68031
Mäkinen, Veli; Navarro, Gonzalo |
|
2005
|
Faster entropy-bounded compressed suffix trees. Zbl 1187.68171
Fischer, Johannes; Mäkinen, Veli; Navarro, Gonzalo |
|
2009
|
Run-length compressed indexes are superior for highly repetitive sequence collections. Zbl 1345.68124
Sirén, Jouni; Välimäki, Niko; Mäkinen, Veli; Navarro, Gonzalo |
|
2008
|
Position-restricted substring searching. Zbl 1145.68392
Mäkinen, Veli; Navarro, Gonzalo |
|
2006
|
Versatile succinct representations of the bidirectional Burrows-Wheeler transform. Zbl 1394.68449
Belazzougui, Djamal; Cunial, Fabio; Kärkkäinen, Juha; Mäkinen, Veli |
|
2013
|
On the complexity of string matching for graphs. Zbl 07561548
Equi, Massimo; Grossi, Roberto; Mäkinen, Veli; Tomescu, Alexandru I. |
|
2019
|
Dynamic entropy-compressed sequences and full-text indexes. Zbl 1446.68043
Mäkinen, Veli; Navarro, Gonzalo |
|
2008
|
Space-efficient algorithms for document retrieval. Zbl 1138.68401
Välimäki, Niko; Mäkinen, Veli |
|
2007
|
Compact suffix array – a space-efficient full-text index. Zbl 1031.68053
Mäkinen, Veli |
|
2003
|
Succinct suffix arrays based on run-length encoding. Zbl 1131.68431
Mäkinen, Veli; Navarro, Gonzalo |
|
2005
|
Graphs cannot be indexed in polynomial time for sub-quadratic time string matching, unless SETH fails. Zbl 1490.68151
Equi, Massimo; Mäkinen, Veli; Tomescu, Alexandru I. |
|
2021
|
Forbidden patterns. Zbl 1353.68066
Fischer, Johannes; Gagie, Travis; Kopelowitz, Tsvi; Lewenstein, Moshe; Mäkinen, Veli; Salmela, Leena; Välimäki, Niko |
|
2012
|
Approximate matching of run-length compressed strings. Zbl 1045.68059
Mäkinen, Veli; Ukkonen, Esko; Navarro, Gonzalo |
|
2003
|
Transposition invariant string matching. Zbl 1083.68030
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko |
|
2005
|
Linear-time string indexing and analysis in small space. Zbl 1485.68079
Belazzougui, Djamal; Cunial, Fabio; Kärkkäinen, Juha; Mäkinen, Veli |
|
2020
|
The cycle switching graph of the Steiner triple systems of order 19 is connected. Zbl 1233.05050
Kaski, Petteri; Mäkinen, Veli; Östergård, Patric R. J. |
|
2011
|
An alphabet-friendly FM-index. Zbl 1111.68429
Ferragina, Paolo; Manzini, Giovanni; Mäkinen, Veli; Navarro, Gonzalo |
|
2004
|
Succinct suffix arrays based on run-length encoding. Zbl 1161.68402
Mäkinen, Veli; Navarro, Gonzalo |
|
2005
|
Dynamic entropy-compressed sequences and full-text indexes. Zbl 1196.68064
Mäkinen, Veli; Navarro, Gonzalo |
|
2006
|
Compact suffix array. Zbl 0964.68511
Mäkinen, Veli |
|
2000
|
Engineering a compressed suffix tree implementation. Zbl 1284.68710
Välimäki, N.; Mäkinen, V.; Gerlach, W.; Dixit, K. |
|
2009
|
An(other) entropy-bounded compressed suffix tree. Zbl 1143.68382
Fischer, Johannes; Mäkinen, Veli; Navarro, Gonzalo |
|
2008
|
Linear time construction of indexable founder block graphs. Zbl 1515.92048
Mäkinen, Veli; Cazaux, Bastien; Equi, Massimo; Norri, Tuukka; Tomescu, Alexandru I. |
|
2020
|
Storage and retrieval of individual genomes. Zbl 1345.68122
Mäkinen, Veli; Navarro, Gonzalo; Sirén, Jouni; Välimäki, Niko |
|
2009
|
Approximate all-pairs suffix/prefix overlaps. Zbl 1286.68535
Välimäki, Niko; Ladra, Susana; Mäkinen, Veli |
|
2010
|
Bidirectional variable-order de Bruijn graphs. Zbl 1415.68063
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J. |
|
2016
|
Rotation and lighting invariant template matching. Zbl 1196.68216
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo |
|
2004
|
Compressed compact suffix arrays. Zbl 1103.68481
Mäkinen, Veli; Navarro, Gonzalo |
|
2004
|
Sparse dynamic programming on DAGs with small width. Zbl 1454.68112
Mäkinen, Veli; Tomescu, Alexandru I.; Kuosmanen, Anna; Paavilainen, Topi; Gagie, Travis; Chikhi, Rayan |
|
2019
|
Algorithms for transposition invariant string matching. Zbl 1035.68507
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko |
|
2003
|
Linear time maximum segmentation problems in column stream model. Zbl 1539.68105
Cazaux, Bastien; Kosolobov, Dmitry; Mäkinen, Veli; Norri, Tuukka |
|
2019
|
Fully dynamic de Bruijn graphs. Zbl 1397.68029
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco |
|
2016
|
Unified view of backward backtracking in short read mapping. Zbl 1284.92075
Mäkinen, Veli; Välimäki, Niko; Laaksonen, Antti; Katainen, Riku |
|
2010
|
Using minimum path cover to boost dynamic programming on DAGs: co-linear chaining extended. Zbl 1510.92142
Kuosmanen, Anna; Paavilainen, Topi; Gagie, Travis; Chikhi, Rayan; Tomescu, Alexandru; Mäkinen, Veli |
|
2018
|
Minimum segmentation for pan-genomic founder reconstruction in linear time. Zbl 1494.92072
Norri, Tuukka; Cazaux, Bastien; Kosolobov, Dmitry; Mäkinen, Veli |
|
2018
|
Bidirectional variable-order de Bruijn graphs. Zbl 1415.68064
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J. |
|
2018
|
Approximate matching of run-length compressed strings. Zbl 0990.68526
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko |
|
2001
|
Sweepline the music! Zbl 1023.68687
Ukkonen, Esko; Lemström, Kjell; Mäkinen, Veli |
|
2003
|
Flexible music retrieval in sublinear time. Zbl 1169.68390
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo |
|
2006
|
Rotation and lighting invariant template matching. Zbl 1122.68105
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo |
|
2007
|
Linear time construction of indexable elastic founder graphs. Zbl 07577720
Rizzo, Nicola; Mäkinen, Veli |
|
2022
|
Approximate all-pairs suffix/prefix overlaps. Zbl 1254.68361
Välimäki, Niko; Ladra, Susana; Mäkinen, Veli |
|
2012
|
Applying the positional Burrows-Wheeler transform to all-pairs Hamming distance. Zbl 1483.68506
Mäkinen, Veli; Norri, Tuukka |
|
2019
|
Indexed multi-pattern matching. Zbl 1353.68067
Gagie, Travis; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Salmela, Leena; Tarhio, Jorma |
|
2012
|
Local similarity based point-pattern matching. Zbl 1077.68805
Mäkinen, Veli; Ukkonen, Esko |
|
2002
|
Algorithms and complexity on indexing elastic founder graphs. Zbl 07788593
Equi, Massimo; Norri, Tuukka; Alanko, Jarno; Cazaux, Bastien; Tomescu, Alexandru I.; Mäkinen, Veli |
|
2021
|
Indexable elastic founder graphs of minimum height. Zbl 07842480
Rizzo, Nicola; Mäkinen, Veli |
|
2022
|
Algorithms and complexity on indexing founder graphs. Zbl 07691814
Equi, Massimo; Norri, Tuukka; Alanko, Jarno; Cazaux, Bastien; Tomescu, Alexandru I.; Mäkinen, Veli |
|
2023
|
Multi-pattern matching with bidirectional indexes. Zbl 1334.68318
Gog, Simon; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Välimäki, Niko |
|
2014
|
Multi-pattern matching with bidirectional indexes. Zbl 1334.68317
Gog, Simon; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Välimäki, Niko |
|
2012
|
On minimizing pattern splitting in multi-track string matching. Zbl 1279.68370
Lemström, Kjell; Mäkinen, Veli |
|
2003
|
Interval scheduling maximizing minimum coverage. Zbl 1370.68040
Mäkinen, Veli; Staneva, Valeria; Tomescu, Alexandru I.; Valenzuela, Daniel; Wilzbach, Sebastian |
|
2017
|
Tailoring \(r\)-index for document listing towards metagenomics applications. Zbl 1511.68099
Cobas, Dustin; Mäkinen, Veli; Rossi, Massimiliano |
|
2020
|
Chaining with overlaps revisited. Zbl 07651116
Mäkinen, Veli; Sahlin, Kristoffer |
|
2020
|
Genome-scale algorithm design. Bioinformatics in the era of high-throughput sequencing.
2nd edition. Zbl 1523.92002
Mäkinen, Veli; Belazzougui, Djamal; Cunial, Fabio; Tomescu, Alexandru I. |
|
2023
|
Advantages of backward searching – efficient secondary memory and distributed implementation of compressed suffix arrays. Zbl 1116.68408
Mäkinen, Veli; Navarro, Gonzalo; Sadakane, Kunihiko |
|
2004
|
On the complexity of string matching for graphs. Zbl 07753172
Equi, Massimo; Mäkinen, Veli; Tomescu, Alexandru I.; Grossi, Roberto |
|
2023
|
Gap filling as exact path length problem. Zbl 1355.92033
Salmela, Leena; Sahlin, Kristoffer; Mäkinen, Veli; Tomescu, Alexandru |
|
2015
|
Algorithms and complexity on indexing founder graphs. Zbl 07691814
Equi, Massimo; Norri, Tuukka; Alanko, Jarno; Cazaux, Bastien; Tomescu, Alexandru I.; Mäkinen, Veli |
|
2023
|
Genome-scale algorithm design. Bioinformatics in the era of high-throughput sequencing.
2nd edition. Zbl 1523.92002
Mäkinen, Veli; Belazzougui, Djamal; Cunial, Fabio; Tomescu, Alexandru I. |
|
2023
|
On the complexity of string matching for graphs. Zbl 07753172
Equi, Massimo; Mäkinen, Veli; Tomescu, Alexandru I.; Grossi, Roberto |
|
2023
|
Linear time construction of indexable elastic founder graphs. Zbl 07577720
Rizzo, Nicola; Mäkinen, Veli |
|
2022
|
Indexable elastic founder graphs of minimum height. Zbl 07842480
Rizzo, Nicola; Mäkinen, Veli |
|
2022
|
Graphs cannot be indexed in polynomial time for sub-quadratic time string matching, unless SETH fails. Zbl 1490.68151
Equi, Massimo; Mäkinen, Veli; Tomescu, Alexandru I. |
|
2021
|
Algorithms and complexity on indexing elastic founder graphs. Zbl 07788593
Equi, Massimo; Norri, Tuukka; Alanko, Jarno; Cazaux, Bastien; Tomescu, Alexandru I.; Mäkinen, Veli |
|
2021
|
Linear-time string indexing and analysis in small space. Zbl 1485.68079
Belazzougui, Djamal; Cunial, Fabio; Kärkkäinen, Juha; Mäkinen, Veli |
|
2020
|
Linear time construction of indexable founder block graphs. Zbl 1515.92048
Mäkinen, Veli; Cazaux, Bastien; Equi, Massimo; Norri, Tuukka; Tomescu, Alexandru I. |
|
2020
|
Tailoring \(r\)-index for document listing towards metagenomics applications. Zbl 1511.68099
Cobas, Dustin; Mäkinen, Veli; Rossi, Massimiliano |
|
2020
|
Chaining with overlaps revisited. Zbl 07651116
Mäkinen, Veli; Sahlin, Kristoffer |
|
2020
|
On the complexity of string matching for graphs. Zbl 07561548
Equi, Massimo; Grossi, Roberto; Mäkinen, Veli; Tomescu, Alexandru I. |
|
2019
|
Sparse dynamic programming on DAGs with small width. Zbl 1454.68112
Mäkinen, Veli; Tomescu, Alexandru I.; Kuosmanen, Anna; Paavilainen, Topi; Gagie, Travis; Chikhi, Rayan |
|
2019
|
Linear time maximum segmentation problems in column stream model. Zbl 1539.68105
Cazaux, Bastien; Kosolobov, Dmitry; Mäkinen, Veli; Norri, Tuukka |
|
2019
|
Applying the positional Burrows-Wheeler transform to all-pairs Hamming distance. Zbl 1483.68506
Mäkinen, Veli; Norri, Tuukka |
|
2019
|
Using minimum path cover to boost dynamic programming on DAGs: co-linear chaining extended. Zbl 1510.92142
Kuosmanen, Anna; Paavilainen, Topi; Gagie, Travis; Chikhi, Rayan; Tomescu, Alexandru; Mäkinen, Veli |
|
2018
|
Minimum segmentation for pan-genomic founder reconstruction in linear time. Zbl 1494.92072
Norri, Tuukka; Cazaux, Bastien; Kosolobov, Dmitry; Mäkinen, Veli |
|
2018
|
Bidirectional variable-order de Bruijn graphs. Zbl 1415.68064
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J. |
|
2018
|
Interval scheduling maximizing minimum coverage. Zbl 1370.68040
Mäkinen, Veli; Staneva, Valeria; Tomescu, Alexandru I.; Valenzuela, Daniel; Wilzbach, Sebastian |
|
2017
|
Bidirectional variable-order de Bruijn graphs. Zbl 1415.68063
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J. |
|
2016
|
Fully dynamic de Bruijn graphs. Zbl 1397.68029
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco |
|
2016
|
Gap filling as exact path length problem. Zbl 1355.92033
Salmela, Leena; Sahlin, Kristoffer; Mäkinen, Veli; Tomescu, Alexandru |
|
2015
|
Multi-pattern matching with bidirectional indexes. Zbl 1334.68318
Gog, Simon; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Välimäki, Niko |
|
2014
|
Versatile succinct representations of the bidirectional Burrows-Wheeler transform. Zbl 1394.68449
Belazzougui, Djamal; Cunial, Fabio; Kärkkäinen, Juha; Mäkinen, Veli |
|
2013
|
Forbidden patterns. Zbl 1353.68066
Fischer, Johannes; Gagie, Travis; Kopelowitz, Tsvi; Lewenstein, Moshe; Mäkinen, Veli; Salmela, Leena; Välimäki, Niko |
|
2012
|
Approximate all-pairs suffix/prefix overlaps. Zbl 1254.68361
Välimäki, Niko; Ladra, Susana; Mäkinen, Veli |
|
2012
|
Indexed multi-pattern matching. Zbl 1353.68067
Gagie, Travis; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Salmela, Leena; Tarhio, Jorma |
|
2012
|
Multi-pattern matching with bidirectional indexes. Zbl 1334.68317
Gog, Simon; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Välimäki, Niko |
|
2012
|
The cycle switching graph of the Steiner triple systems of order 19 is connected. Zbl 1233.05050
Kaski, Petteri; Mäkinen, Veli; Östergård, Patric R. J. |
|
2011
|
Approximate all-pairs suffix/prefix overlaps. Zbl 1286.68535
Välimäki, Niko; Ladra, Susana; Mäkinen, Veli |
|
2010
|
Unified view of backward backtracking in short read mapping. Zbl 1284.92075
Mäkinen, Veli; Välimäki, Niko; Laaksonen, Antti; Katainen, Riku |
|
2010
|
Faster entropy-bounded compressed suffix trees. Zbl 1187.68171
Fischer, Johannes; Mäkinen, Veli; Navarro, Gonzalo |
|
2009
|
Engineering a compressed suffix tree implementation. Zbl 1284.68710
Välimäki, N.; Mäkinen, V.; Gerlach, W.; Dixit, K. |
|
2009
|
Storage and retrieval of individual genomes. Zbl 1345.68122
Mäkinen, Veli; Navarro, Gonzalo; Sirén, Jouni; Välimäki, Niko |
|
2009
|
Run-length compressed indexes are superior for highly repetitive sequence collections. Zbl 1345.68124
Sirén, Jouni; Välimäki, Niko; Mäkinen, Veli; Navarro, Gonzalo |
|
2008
|
Dynamic entropy-compressed sequences and full-text indexes. Zbl 1446.68043
Mäkinen, Veli; Navarro, Gonzalo |
|
2008
|
An(other) entropy-bounded compressed suffix tree. Zbl 1143.68382
Fischer, Johannes; Mäkinen, Veli; Navarro, Gonzalo |
|
2008
|
Compressed representations of sequences and full-text indexes. Zbl 1321.68263
Ferragina, Paolo; Manzini, Giovanni; Mäkinen, Veli; Navarro, Gonzalo |
|
2007
|
Rank and select revisited and extended. Zbl 1144.68023
Mäkinen, Veli; Navarro, Gonzalo |
|
2007
|
Space-efficient algorithms for document retrieval. Zbl 1138.68401
Välimäki, Niko; Mäkinen, Veli |
|
2007
|
Rotation and lighting invariant template matching. Zbl 1122.68105
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo |
|
2007
|
Position-restricted substring searching. Zbl 1145.68392
Mäkinen, Veli; Navarro, Gonzalo |
|
2006
|
Dynamic entropy-compressed sequences and full-text indexes. Zbl 1196.68064
Mäkinen, Veli; Navarro, Gonzalo |
|
2006
|
Flexible music retrieval in sublinear time. Zbl 1169.68390
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo |
|
2006
|
Succinct suffix arrays based on run-length encoding. Zbl 1085.68031
Mäkinen, Veli; Navarro, Gonzalo |
|
2005
|
Succinct suffix arrays based on run-length encoding. Zbl 1131.68431
Mäkinen, Veli; Navarro, Gonzalo |
|
2005
|
Transposition invariant string matching. Zbl 1083.68030
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko |
|
2005
|
Succinct suffix arrays based on run-length encoding. Zbl 1161.68402
Mäkinen, Veli; Navarro, Gonzalo |
|
2005
|
An alphabet-friendly FM-index. Zbl 1111.68429
Ferragina, Paolo; Manzini, Giovanni; Mäkinen, Veli; Navarro, Gonzalo |
|
2004
|
Rotation and lighting invariant template matching. Zbl 1196.68216
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo |
|
2004
|
Compressed compact suffix arrays. Zbl 1103.68481
Mäkinen, Veli; Navarro, Gonzalo |
|
2004
|
Advantages of backward searching – efficient secondary memory and distributed implementation of compressed suffix arrays. Zbl 1116.68408
Mäkinen, Veli; Navarro, Gonzalo; Sadakane, Kunihiko |
|
2004
|
Compact suffix array – a space-efficient full-text index. Zbl 1031.68053
Mäkinen, Veli |
|
2003
|
Approximate matching of run-length compressed strings. Zbl 1045.68059
Mäkinen, Veli; Ukkonen, Esko; Navarro, Gonzalo |
|
2003
|
Algorithms for transposition invariant string matching. Zbl 1035.68507
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko |
|
2003
|
Sweepline the music! Zbl 1023.68687
Ukkonen, Esko; Lemström, Kjell; Mäkinen, Veli |
|
2003
|
On minimizing pattern splitting in multi-track string matching. Zbl 1279.68370
Lemström, Kjell; Mäkinen, Veli |
|
2003
|
Local similarity based point-pattern matching. Zbl 1077.68805
Mäkinen, Veli; Ukkonen, Esko |
|
2002
|
Approximate matching of run-length compressed strings. Zbl 0990.68526
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko |
|
2001
|
Compact suffix array. Zbl 0964.68511
Mäkinen, Veli |
|
2000
|