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Sirén, Jouni
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1

Wheeler Maps:

, In: Lecture Notes in Computer Science; LATIN 2024: Theoretical Informatics,
Baláž, Andrej ; Gagie, Travis ; Goga, Adrián... - p. 178-192 , 2024
Link: https://doi.org/10.1007/..
 
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2

Haplotype-aware pantranscriptome analyses using spliced pan..:

Sibbesen, Jonas A. ; Eizenga, Jordan M. ; Novak, Adam M....
Nature Methods.  20 (2023)  2 - p. 239-247 , 2023
Link: https://doi.org/10.1038/..
 
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3

Computational graph pangenomics: a tutorial on data structu..:

Baaijens, Jasmijn A. ; Bonizzoni, Paola ; Boucher, Christina...
Natural Computing.  21 (2022)  1 - p. 81-108 , 2022
Link: https://doi.org/10.1007/..
 
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4

Pangenomics enables genotyping of known structural variants..:

Sirén, Jouni ; Monlong, Jean ; Chang, Xian...
Science.  374 (2021)  6574 - p. , 2021
Link: https://doi.org/10.1126/..
 
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5

Distance indexing and seed clustering in sequence graphs:

Chang, Xian ; Eizenga, Jordan ; Novak, Adam M..
Bioinformatics.  36 (2020)  Supplement_1 - p. i146-i153 , 2020
Link: https://doi.org/10.1093/..
 
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6

Genotyping structural variants in pangenome graphs using th..:

Hickey, Glenn ; Heller, David ; Monlong, Jean...
Genome Biology.  21 (2020)  1 - p. , 2020
Link: https://doi.org/10.1186/..
 
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7

Haplotype-aware graph indexes:

Sirén, Jouni ; Garrison, Erik ; Novak, Adam M...
Bioinformatics.  36 (2019)  2 - p. 400-407 , 2019
Link: https://doi.org/10.1093/..
 
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8

Variation graph toolkit improves read mapping by representi..:

Garrison, Erik ; Sirén, Jouni ; Novak, Adam M...
Nature Biotechnology.  36 (2018)  9 - p. 875-879 , 2018
Link: https://doi.org/10.1038/..
 
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9

Document retrieval on repetitive string collections:

Gagie, Travis ; Hartikainen, Aleksi ; Karhu, Kalle...
Information Retrieval Journal.  20 (2017)  3 - p. 253-291 , 2017
Link: https://doi.org/10.1007/..
 
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10

Wheeler graphs: A framework for BWT-based data structures:

Gagie, Travis ; Manzini, Giovanni ; Sirén, Jouni
Theoretical Computer Science.  698 (2017)  - p. 67-78 , 2017
Link: https://doi.org/10.1016/..
 
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11

Relative Suffix Trees:

Farruggia, Andrea ; Gagie, Travis ; Navarro, Gonzalo..
The Computer Journal.  61 (2017)  5 - p. 773-788 , 2017
Link: https://doi.org/10.1093/..
 
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12

Indexing graphs for path queries with applications in genom..:

Sirén, Jouni ; Välimäki, Niko ; Mäkinen, Veli
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB).  11 (2014)  2 - p. 375-388 , 2014
Link: https://dl.acm.org/doi/1..
 
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13

Distribution-Aware Compressed Full-Text Indexes:

Ferragina, Paolo ; Sirén, Jouni ; Venturini, Rossano
Algorithmica.  67 (2013)  4 - p. 529-546 , 2013
Link: https://doi.org/10.1007/..
 
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14

Fast in‐memory XPath search using compressed indexes:

Arroyuelo, Diego ; Claude, Francisco ; Maneth, Sebastian...
Software: Practice and Experience.  45 (2013)  3 - p. 399-434 , 2013
Link: https://doi.org/10.1002/..
 
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15

Personalized Pangenome References:

Sirén, Jouni ; Eskandar, Parsa ; Ungaro, Matteo Tommaso...
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10760139/.  , 2023
Link: http://www.ncbi.nlm.nih...
 
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