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Author ID: makinen.veli Recent zbMATH articles by "Mäkinen, Veli"
Published as: Mäkinen, Veli; Mäkinen, V.
External Links: MGP · ORCID

Publications by Year

Citations contained in zbMATH Open

60 Publications have been cited 644 times in 348 Documents Cited by Year
Compressed representations of sequences and full-text indexes. Zbl 1321.68263
Ferragina, Paolo; Manzini, Giovanni; Mäkinen, Veli; Navarro, Gonzalo
189
2007
Rank and select revisited and extended. Zbl 1144.68023
Mäkinen, Veli; Navarro, Gonzalo
46
2007
Succinct suffix arrays based on run-length encoding. Zbl 1085.68031
Mäkinen, Veli; Navarro, Gonzalo
28
2005
Faster entropy-bounded compressed suffix trees. Zbl 1187.68171
Fischer, Johannes; Mäkinen, Veli; Navarro, Gonzalo
27
2009
Run-length compressed indexes are superior for highly repetitive sequence collections. Zbl 1345.68124
Sirén, Jouni; Välimäki, Niko; Mäkinen, Veli; Navarro, Gonzalo
24
2008
Position-restricted substring searching. Zbl 1145.68392
Mäkinen, Veli; Navarro, Gonzalo
24
2006
Versatile succinct representations of the bidirectional Burrows-Wheeler transform. Zbl 1394.68449
Belazzougui, Djamal; Cunial, Fabio; Kärkkäinen, Juha; Mäkinen, Veli
21
2013
On the complexity of string matching for graphs. Zbl 07561548
Equi, Massimo; Grossi, Roberto; Mäkinen, Veli; Tomescu, Alexandru I.
20
2019
Dynamic entropy-compressed sequences and full-text indexes. Zbl 1446.68043
Mäkinen, Veli; Navarro, Gonzalo
18
2008
Space-efficient algorithms for document retrieval. Zbl 1138.68401
Välimäki, Niko; Mäkinen, Veli
16
2007
Compact suffix array – a space-efficient full-text index. Zbl 1031.68053
Mäkinen, Veli
12
2003
Succinct suffix arrays based on run-length encoding. Zbl 1131.68431
Mäkinen, Veli; Navarro, Gonzalo
12
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.
10
2021
Forbidden patterns. Zbl 1353.68066
Fischer, Johannes; Gagie, Travis; Kopelowitz, Tsvi; Lewenstein, Moshe; Mäkinen, Veli; Salmela, Leena; Välimäki, Niko
10
2012
Approximate matching of run-length compressed strings. Zbl 1045.68059
Mäkinen, Veli; Ukkonen, Esko; Navarro, Gonzalo
10
2003
Transposition invariant string matching. Zbl 1083.68030
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko
10
2005
Linear-time string indexing and analysis in small space. Zbl 1485.68079
Belazzougui, Djamal; Cunial, Fabio; Kärkkäinen, Juha; Mäkinen, Veli
9
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.
9
2011
An alphabet-friendly FM-index. Zbl 1111.68429
Ferragina, Paolo; Manzini, Giovanni; Mäkinen, Veli; Navarro, Gonzalo
9
2004
Succinct suffix arrays based on run-length encoding. Zbl 1161.68402
Mäkinen, Veli; Navarro, Gonzalo
9
2005
Dynamic entropy-compressed sequences and full-text indexes. Zbl 1196.68064
Mäkinen, Veli; Navarro, Gonzalo
8
2006
Compact suffix array. Zbl 0964.68511
Mäkinen, Veli
8
2000
Engineering a compressed suffix tree implementation. Zbl 1284.68710
Välimäki, N.; Mäkinen, V.; Gerlach, W.; Dixit, K.
7
2009
An(other) entropy-bounded compressed suffix tree. Zbl 1143.68382
Fischer, Johannes; Mäkinen, Veli; Navarro, Gonzalo
7
2008
Linear time construction of indexable founder block graphs. Zbl 1515.92048
Mäkinen, Veli; Cazaux, Bastien; Equi, Massimo; Norri, Tuukka; Tomescu, Alexandru I.
7
2020
Storage and retrieval of individual genomes. Zbl 1345.68122
Mäkinen, Veli; Navarro, Gonzalo; Sirén, Jouni; Välimäki, Niko
6
2009
Approximate all-pairs suffix/prefix overlaps. Zbl 1286.68535
Välimäki, Niko; Ladra, Susana; Mäkinen, Veli
6
2010
Bidirectional variable-order de Bruijn graphs. Zbl 1415.68063
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J.
6
2016
Rotation and lighting invariant template matching. Zbl 1196.68216
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo
5
2004
Compressed compact suffix arrays. Zbl 1103.68481
Mäkinen, Veli; Navarro, Gonzalo
5
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
4
2019
Algorithms for transposition invariant string matching. Zbl 1035.68507
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko
4
2003
Linear time maximum segmentation problems in column stream model. Zbl 1539.68105
Cazaux, Bastien; Kosolobov, Dmitry; Mäkinen, Veli; Norri, Tuukka
4
2019
Fully dynamic de Bruijn graphs. Zbl 1397.68029
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco
3
2016
Unified view of backward backtracking in short read mapping. Zbl 1284.92075
Mäkinen, Veli; Välimäki, Niko; Laaksonen, Antti; Katainen, Riku
3
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
3
2018
Minimum segmentation for pan-genomic founder reconstruction in linear time. Zbl 1494.92072
Norri, Tuukka; Cazaux, Bastien; Kosolobov, Dmitry; Mäkinen, Veli
3
2018
Bidirectional variable-order de Bruijn graphs. Zbl 1415.68064
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J.
3
2018
Approximate matching of run-length compressed strings. Zbl 0990.68526
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko
3
2001
Sweepline the music! Zbl 1023.68687
Ukkonen, Esko; Lemström, Kjell; Mäkinen, Veli
3
2003
Flexible music retrieval in sublinear time. Zbl 1169.68390
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo
3
2006
Rotation and lighting invariant template matching. Zbl 1122.68105
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo
3
2007
Linear time construction of indexable elastic founder graphs. Zbl 07577720
Rizzo, Nicola; Mäkinen, Veli
3
2022
Approximate all-pairs suffix/prefix overlaps. Zbl 1254.68361
Välimäki, Niko; Ladra, Susana; Mäkinen, Veli
2
2012
Applying the positional Burrows-Wheeler transform to all-pairs Hamming distance. Zbl 1483.68506
Mäkinen, Veli; Norri, Tuukka
2
2019
Indexed multi-pattern matching. Zbl 1353.68067
Gagie, Travis; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Salmela, Leena; Tarhio, Jorma
2
2012
Local similarity based point-pattern matching. Zbl 1077.68805
Mäkinen, Veli; Ukkonen, Esko
2
2002
Algorithms and complexity on indexing elastic founder graphs. Zbl 07788593
Equi, Massimo; Norri, Tuukka; Alanko, Jarno; Cazaux, Bastien; Tomescu, Alexandru I.; Mäkinen, Veli
2
2021
Indexable elastic founder graphs of minimum height. Zbl 07842480
Rizzo, Nicola; Mäkinen, Veli
2
2022
Algorithms and complexity on indexing founder graphs. Zbl 07691814
Equi, Massimo; Norri, Tuukka; Alanko, Jarno; Cazaux, Bastien; Tomescu, Alexandru I.; Mäkinen, Veli
2
2023
Multi-pattern matching with bidirectional indexes. Zbl 1334.68318
Gog, Simon; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Välimäki, Niko
1
2014
Multi-pattern matching with bidirectional indexes. Zbl 1334.68317
Gog, Simon; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Välimäki, Niko
1
2012
On minimizing pattern splitting in multi-track string matching. Zbl 1279.68370
Lemström, Kjell; Mäkinen, Veli
1
2003
Interval scheduling maximizing minimum coverage. Zbl 1370.68040
Mäkinen, Veli; Staneva, Valeria; Tomescu, Alexandru I.; Valenzuela, Daniel; Wilzbach, Sebastian
1
2017
Tailoring \(r\)-index for document listing towards metagenomics applications. Zbl 1511.68099
Cobas, Dustin; Mäkinen, Veli; Rossi, Massimiliano
1
2020
Chaining with overlaps revisited. Zbl 07651116
Mäkinen, Veli; Sahlin, Kristoffer
1
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.
1
2023
Advantages of backward searching – efficient secondary memory and distributed implementation of compressed suffix arrays. Zbl 1116.68408
Mäkinen, Veli; Navarro, Gonzalo; Sadakane, Kunihiko
1
2004
On the complexity of string matching for graphs. Zbl 07753172
Equi, Massimo; Mäkinen, Veli; Tomescu, Alexandru I.; Grossi, Roberto
1
2023
Gap filling as exact path length problem. Zbl 1355.92033
Salmela, Leena; Sahlin, Kristoffer; Mäkinen, Veli; Tomescu, Alexandru
1
2015
Algorithms and complexity on indexing founder graphs. Zbl 07691814
Equi, Massimo; Norri, Tuukka; Alanko, Jarno; Cazaux, Bastien; Tomescu, Alexandru I.; Mäkinen, Veli
2
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.
1
2023
On the complexity of string matching for graphs. Zbl 07753172
Equi, Massimo; Mäkinen, Veli; Tomescu, Alexandru I.; Grossi, Roberto
1
2023
Linear time construction of indexable elastic founder graphs. Zbl 07577720
Rizzo, Nicola; Mäkinen, Veli
3
2022
Indexable elastic founder graphs of minimum height. Zbl 07842480
Rizzo, Nicola; Mäkinen, Veli
2
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.
10
2021
Algorithms and complexity on indexing elastic founder graphs. Zbl 07788593
Equi, Massimo; Norri, Tuukka; Alanko, Jarno; Cazaux, Bastien; Tomescu, Alexandru I.; Mäkinen, Veli
2
2021
Linear-time string indexing and analysis in small space. Zbl 1485.68079
Belazzougui, Djamal; Cunial, Fabio; Kärkkäinen, Juha; Mäkinen, Veli
9
2020
Linear time construction of indexable founder block graphs. Zbl 1515.92048
Mäkinen, Veli; Cazaux, Bastien; Equi, Massimo; Norri, Tuukka; Tomescu, Alexandru I.
7
2020
Tailoring \(r\)-index for document listing towards metagenomics applications. Zbl 1511.68099
Cobas, Dustin; Mäkinen, Veli; Rossi, Massimiliano
1
2020
Chaining with overlaps revisited. Zbl 07651116
Mäkinen, Veli; Sahlin, Kristoffer
1
2020
On the complexity of string matching for graphs. Zbl 07561548
Equi, Massimo; Grossi, Roberto; Mäkinen, Veli; Tomescu, Alexandru I.
20
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
4
2019
Linear time maximum segmentation problems in column stream model. Zbl 1539.68105
Cazaux, Bastien; Kosolobov, Dmitry; Mäkinen, Veli; Norri, Tuukka
4
2019
Applying the positional Burrows-Wheeler transform to all-pairs Hamming distance. Zbl 1483.68506
Mäkinen, Veli; Norri, Tuukka
2
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
3
2018
Minimum segmentation for pan-genomic founder reconstruction in linear time. Zbl 1494.92072
Norri, Tuukka; Cazaux, Bastien; Kosolobov, Dmitry; Mäkinen, Veli
3
2018
Bidirectional variable-order de Bruijn graphs. Zbl 1415.68064
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J.
3
2018
Interval scheduling maximizing minimum coverage. Zbl 1370.68040
Mäkinen, Veli; Staneva, Valeria; Tomescu, Alexandru I.; Valenzuela, Daniel; Wilzbach, Sebastian
1
2017
Bidirectional variable-order de Bruijn graphs. Zbl 1415.68063
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J.
6
2016
Fully dynamic de Bruijn graphs. Zbl 1397.68029
Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco
3
2016
Gap filling as exact path length problem. Zbl 1355.92033
Salmela, Leena; Sahlin, Kristoffer; Mäkinen, Veli; Tomescu, Alexandru
1
2015
Multi-pattern matching with bidirectional indexes. Zbl 1334.68318
Gog, Simon; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Välimäki, Niko
1
2014
Versatile succinct representations of the bidirectional Burrows-Wheeler transform. Zbl 1394.68449
Belazzougui, Djamal; Cunial, Fabio; Kärkkäinen, Juha; Mäkinen, Veli
21
2013
Forbidden patterns. Zbl 1353.68066
Fischer, Johannes; Gagie, Travis; Kopelowitz, Tsvi; Lewenstein, Moshe; Mäkinen, Veli; Salmela, Leena; Välimäki, Niko
10
2012
Approximate all-pairs suffix/prefix overlaps. Zbl 1254.68361
Välimäki, Niko; Ladra, Susana; Mäkinen, Veli
2
2012
Indexed multi-pattern matching. Zbl 1353.68067
Gagie, Travis; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Salmela, Leena; Tarhio, Jorma
2
2012
Multi-pattern matching with bidirectional indexes. Zbl 1334.68317
Gog, Simon; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Välimäki, Niko
1
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.
9
2011
Approximate all-pairs suffix/prefix overlaps. Zbl 1286.68535
Välimäki, Niko; Ladra, Susana; Mäkinen, Veli
6
2010
Unified view of backward backtracking in short read mapping. Zbl 1284.92075
Mäkinen, Veli; Välimäki, Niko; Laaksonen, Antti; Katainen, Riku
3
2010
Faster entropy-bounded compressed suffix trees. Zbl 1187.68171
Fischer, Johannes; Mäkinen, Veli; Navarro, Gonzalo
27
2009
Engineering a compressed suffix tree implementation. Zbl 1284.68710
Välimäki, N.; Mäkinen, V.; Gerlach, W.; Dixit, K.
7
2009
Storage and retrieval of individual genomes. Zbl 1345.68122
Mäkinen, Veli; Navarro, Gonzalo; Sirén, Jouni; Välimäki, Niko
6
2009
Run-length compressed indexes are superior for highly repetitive sequence collections. Zbl 1345.68124
Sirén, Jouni; Välimäki, Niko; Mäkinen, Veli; Navarro, Gonzalo
24
2008
Dynamic entropy-compressed sequences and full-text indexes. Zbl 1446.68043
Mäkinen, Veli; Navarro, Gonzalo
18
2008
An(other) entropy-bounded compressed suffix tree. Zbl 1143.68382
Fischer, Johannes; Mäkinen, Veli; Navarro, Gonzalo
7
2008
Compressed representations of sequences and full-text indexes. Zbl 1321.68263
Ferragina, Paolo; Manzini, Giovanni; Mäkinen, Veli; Navarro, Gonzalo
189
2007
Rank and select revisited and extended. Zbl 1144.68023
Mäkinen, Veli; Navarro, Gonzalo
46
2007
Space-efficient algorithms for document retrieval. Zbl 1138.68401
Välimäki, Niko; Mäkinen, Veli
16
2007
Rotation and lighting invariant template matching. Zbl 1122.68105
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo
3
2007
Position-restricted substring searching. Zbl 1145.68392
Mäkinen, Veli; Navarro, Gonzalo
24
2006
Dynamic entropy-compressed sequences and full-text indexes. Zbl 1196.68064
Mäkinen, Veli; Navarro, Gonzalo
8
2006
Flexible music retrieval in sublinear time. Zbl 1169.68390
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo
3
2006
Succinct suffix arrays based on run-length encoding. Zbl 1085.68031
Mäkinen, Veli; Navarro, Gonzalo
28
2005
Succinct suffix arrays based on run-length encoding. Zbl 1131.68431
Mäkinen, Veli; Navarro, Gonzalo
12
2005
Transposition invariant string matching. Zbl 1083.68030
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko
10
2005
Succinct suffix arrays based on run-length encoding. Zbl 1161.68402
Mäkinen, Veli; Navarro, Gonzalo
9
2005
An alphabet-friendly FM-index. Zbl 1111.68429
Ferragina, Paolo; Manzini, Giovanni; Mäkinen, Veli; Navarro, Gonzalo
9
2004
Rotation and lighting invariant template matching. Zbl 1196.68216
Fredriksson, Kimmo; Mäkinen, Veli; Navarro, Gonzalo
5
2004
Compressed compact suffix arrays. Zbl 1103.68481
Mäkinen, Veli; Navarro, Gonzalo
5
2004
Advantages of backward searching – efficient secondary memory and distributed implementation of compressed suffix arrays. Zbl 1116.68408
Mäkinen, Veli; Navarro, Gonzalo; Sadakane, Kunihiko
1
2004
Compact suffix array – a space-efficient full-text index. Zbl 1031.68053
Mäkinen, Veli
12
2003
Approximate matching of run-length compressed strings. Zbl 1045.68059
Mäkinen, Veli; Ukkonen, Esko; Navarro, Gonzalo
10
2003
Algorithms for transposition invariant string matching. Zbl 1035.68507
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko
4
2003
Sweepline the music! Zbl 1023.68687
Ukkonen, Esko; Lemström, Kjell; Mäkinen, Veli
3
2003
On minimizing pattern splitting in multi-track string matching. Zbl 1279.68370
Lemström, Kjell; Mäkinen, Veli
1
2003
Local similarity based point-pattern matching. Zbl 1077.68805
Mäkinen, Veli; Ukkonen, Esko
2
2002
Approximate matching of run-length compressed strings. Zbl 0990.68526
Mäkinen, Veli; Navarro, Gonzalo; Ukkonen, Esko
3
2001
Compact suffix array. Zbl 0964.68511
Mäkinen, Veli
8
2000
all top 5

Cited by 406 Authors

52 Navarro, Gonzalo
29 Thankachan, Sharma V.
21 Gagie, Travis
19 Mäkinen, Veli
18 Shah, Rahul
14 Manzini, Giovanni
13 Inenaga, Shunsuke
13 Kärkkäinen, Juha
13 Nekrich, Yakov
12 Munro, J. Ian
12 Sadakane, Kunihiko
11 Fischer, Johannes
11 Hon, Wing-Kai
10 Bannai, Hideo
10 Belazzougui, Djamal
10 Puglisi, Simon J.
9 Takeda, Masayuki
9 Tomescu, Alexandru Ioan
8 Bille, Philip
8 Iliopoulos, Costas S.
8 Kempa, Dominik
7 Crochemore, Maxime
7 Ganguly, Arnab
7 Gog, Simon
7 Gørtz, Inge Li
7 Louza, Felipe A.
7 Mouchard, Laurent
7 Pissis, Solon P.
7 Prezza, Nicola
7 Raman, Rajeev
7 Sciortino, Marinella
6 Arroyuelo, Diego
6 Cazaux, Bastien
6 Equi, Massimo
6 Ferragina, Paolo
6 Fici, Gabriele
6 Fredriksson, Kimmo
6 Gibney, Daniel
6 He, Meng
6 Köppl, Dominik
6 Léonard, Martine
6 Norri, Tuukka
6 Rosone, Giovanna
6 Salson, Mikaël
6 Satti, Srinivasa Rao
6 Vitter, Jeffrey Scott
5 Barbay, Jérémy
5 Cunial, Fabio
5 Egidi, Lavinia
5 I, Tomohiro
5 Kociumaka, Tomasz
5 Kucherov, Gregory
5 Lecroq, Thierry
5 Lipták, Zsuzsanna
5 Venturini, Rossano
4 Biswas, Sudip
4 Chen, Kuanyu
4 Claude, Francisco
4 Davoodi, Pooya
4 Gawrychowski, Paweł
4 Giancarlo, Raffaele
4 Grabowski, Szymon
4 Grossi, Roberto
4 Kosolobov, Dmitry
4 Landau, Gad M.
4 Ohlebusch, Enno
4 Östergård, Patric R. J.
4 Park, Kunsoo
4 Patil, Manish
4 Rahman, Mohammad Sohel
4 Restivo, Antonio
4 Sirén, Jouni
4 Telles, Guilherme P.
3 Beller, Timo
3 Boucher, Christina
3 Cáceres, Manuel Osvaldo
3 Chang, Jou-Ming
3 Chao, Kunmao
3 Charalampopoulos, Panagiotis
3 Díaz-Domínguez, Diego
3 Ferrada, Héctor
3 Fuentes-Sepúlveda, José
3 Goto, Keisuke
3 Héliou, Alice
3 Kurpicz, Florian
3 Lewenstein, Moshe
3 Mauri, Giancarlo
3 Mieno, Takuya
3 Nakashima, Yuto
3 Piątkowski, Marcin
3 Policriti, Alberto
3 Radoszewski, Jakub
3 Rao, Satti Srinivasa
3 Rizzo, Nicola
3 Sung, Wing-Kin
3 Takabatake, Yoshimasa
3 Tischler, German
3 Waleń, Tomasz
3 Wu, Ro-Yu
2 Akagi, Tooru
...and 306 more Authors

Citations by Year